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University of Edinburgh
1.
Waibel, Thomas.
Transcriptional regulation of taxol™ biosynthesis in Taxus cuspidate procambium cells.
Degree: PhD, 2011, University of Edinburgh
URL: http://hdl.handle.net/1842/5681
► This thesis presents an investigation into the transcriptional regulation of TaxolTM biosynthsis in Taxus cuspidata cell suspension cultures. The potent anticancer drug TaxolTM has been…
(more)
▼ This thesis presents an investigation into the transcriptional regulation of TaxolTM biosynthsis in Taxus cuspidata cell suspension cultures. The potent anticancer drug TaxolTM has been shown to be successful in the treatment of breast, lung and ovarian cancer and the acquired immunodeficiency syndrome (AIDS) related Kaposi’s sarcoma. Produced by all species of yew, TaxolTM belongs to the class of taxane diterpenoids and is of huge pharmaceutical importance. The plant material utilised in this thesis is a cell suspension culture initiated from isolated procambium cells of T. cuspidata. The latter is a meristematic tissue giving rise to the conductive tissue of plants. This un-differentiated cell suspension culture exhibits an increased and stable production of TaxolTM in response to the plant hormone elicitor methyljasmonate, limited cell aggregation and fast growth when compared to a cell suspension culture initiated from differentiated cells (somatic) of T. cuspidata. In order to assess the stem cell characteristics of the employed procambium cell suspension culture, the transcriptome of T. cuspidata was sequenced utilising Roche/ 454 and Illumina/ Solexa NlaIII tag sequencing technoloxiv gies. Statistical analysis uncovered differential expression profiles of 563 genes present within the procambium cell derived transcriptome by comparison with the somatic cell derived transcriptome. Gene ontology analysis of the latter identified that genes associated with response to stress and defence response were upregulated in the differentially expressed portion within the procambium cell suspension culture. This is consistent with the characteristics of animal stem cells which exhibit robust defence strategies to environmental stress. Furthermore PHLOEM INTERCALATED WITH XYLEM (PXY ) and TRACHEARY ELEMENT DIFFERENTIATION 2 (TED2), which are essential for ordered procambium cell division and differentiation into trachaery elements respectively in A. thaliana and Z. elegans, are up-regulated in the T. cuspidata procambium cell suspension culture. Further T. cuspidata homologues of the jasmonate signalling components JASMONATE ZINC FINGER LIKE ZIM DOMAIN 2 (JAZ2) and JAZ3 were identified among up-regulated transcripts in response to jasmonate treatment in both the procambium and the somatic cell line. Blast analysis identified 211 transcription factors within the APETELA 2 (AP2), BASIC-HELIX-LOOPHELIX (bHLH), WRKY, MYB and BASIC-LEUCIN-ZIPPER (bZIP) families. Further characterisation established 21 transcription factors which are significantly up-regulated in response to jasmonate treatment and show a higher expression level in procambium cells. These provide promising targets for further functional characterisation to elucidate their involvement within TaxolTM biosynthesis. In order to investigate transcriptional regulation of the TaxolTM structural genes, a 513 bp fragment corresponding to the TAXADIENE SYNTHASE (TASY ) promoter was cloned by genome walking. In-silico analysis of the TASY and 3’-N-DEBENZOYLTAXOL…
Subjects/Keywords: 616.994; taxol; taxus; 454; solexa; sequencing
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APA (6th Edition):
Waibel, T. (2011). Transcriptional regulation of taxol™ biosynthesis in Taxus cuspidate procambium cells. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/5681
Chicago Manual of Style (16th Edition):
Waibel, Thomas. “Transcriptional regulation of taxol™ biosynthesis in Taxus cuspidate procambium cells.” 2011. Doctoral Dissertation, University of Edinburgh. Accessed April 16, 2021.
http://hdl.handle.net/1842/5681.
MLA Handbook (7th Edition):
Waibel, Thomas. “Transcriptional regulation of taxol™ biosynthesis in Taxus cuspidate procambium cells.” 2011. Web. 16 Apr 2021.
Vancouver:
Waibel T. Transcriptional regulation of taxol™ biosynthesis in Taxus cuspidate procambium cells. [Internet] [Doctoral dissertation]. University of Edinburgh; 2011. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/1842/5681.
Council of Science Editors:
Waibel T. Transcriptional regulation of taxol™ biosynthesis in Taxus cuspidate procambium cells. [Doctoral Dissertation]. University of Edinburgh; 2011. Available from: http://hdl.handle.net/1842/5681

North Carolina State University
2.
Wheeler, Benjamin Matthew.
Automating the annotation and discovery of MicroRNA in multi-species high-throughput 454 Sequencing.
Degree: MS, Computer Science, 2008, North Carolina State University
URL: http://www.lib.ncsu.edu/resolver/1840.16/2025
Subjects/Keywords: MicroRNA; miRNA; 454 Sequencing; 454; high-throughput sequencing
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APA (6th Edition):
Wheeler, B. M. (2008). Automating the annotation and discovery of MicroRNA in multi-species high-throughput 454 Sequencing. (Thesis). North Carolina State University. Retrieved from http://www.lib.ncsu.edu/resolver/1840.16/2025
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Wheeler, Benjamin Matthew. “Automating the annotation and discovery of MicroRNA in multi-species high-throughput 454 Sequencing.” 2008. Thesis, North Carolina State University. Accessed April 16, 2021.
http://www.lib.ncsu.edu/resolver/1840.16/2025.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Wheeler, Benjamin Matthew. “Automating the annotation and discovery of MicroRNA in multi-species high-throughput 454 Sequencing.” 2008. Web. 16 Apr 2021.
Vancouver:
Wheeler BM. Automating the annotation and discovery of MicroRNA in multi-species high-throughput 454 Sequencing. [Internet] [Thesis]. North Carolina State University; 2008. [cited 2021 Apr 16].
Available from: http://www.lib.ncsu.edu/resolver/1840.16/2025.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Wheeler BM. Automating the annotation and discovery of MicroRNA in multi-species high-throughput 454 Sequencing. [Thesis]. North Carolina State University; 2008. Available from: http://www.lib.ncsu.edu/resolver/1840.16/2025
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
3.
Georges, Clément.
Les communautés de protistes au sein d'un bloom phytoplanctonique dans la région naturellement fertilisée en fer des îles de Kerguelen (Océan Australe) : Protistan communities in a phytoplankton bloom within a naturally iron-fertilized region of the Kerguelen Islands (Southern Ocean).
Degree: Docteur es, Géologie, Ecologie, Paléontologie, Océanologie, 2015, Littoral
URL: http://www.theses.fr/2015DUNK0415
► Depuis les années 90, les études portant sur les différentes zones HNLC ont permis d'étudier les effets biologiques et biogéochimiques qu'entrainaient les enrichissements artificiels ou…
(more)
▼ Depuis les années 90, les études portant sur les différentes zones HNLC ont permis d'étudier les effets biologiques et biogéochimiques qu'entrainaient les enrichissements artificiels ou naturels en fer. Il est maintenant bien documenté que l'enrichissement en fer induit des blooms phytoplanctoniques et notamment des blooms de diatomées. En dehors des diatomées, très peu d'informations sont disponibles concernant les autres groupes de protistes et en particulier les protistes hétérotrophes consommateur du phytoplancton. Ce travail a été effectué dans un contexte de fertilisation naturelle en fer, dans la région des îles de Kerguélen (Océan Australe) pendant la campagne KEOPS 2 (Kerguelen Ocean and Plateau compared Study 2) lors de l'initiation du bloom phytoplanctonique et s'est focalisé en particulier sur les protistes hétérotrophes. Des approches moléculaires (tag-pyroséquençages 454) et morphologiques (microscopie) ont été utilisées afin de caractériser la structure des communautés de protistes dans la zone de référence HNLC et dans les différents blooms phytoplanctoniques. l'approche moléculaire a permis (i) de caractériser les communautés de protistes présentes (ii) de mettre en évidence des différences notables entre les structures de protistes dans la région HNLC et la région naturellement enrichie en fer, mais également entre les différents blooms. Les observations microscopiques ont révélé des tendances similaires entre les différentes régions mais aussi des liens significatifs entre les communautés microzooplanctoniques et leurs proies phytoplanctoniques. Les observations microscopiques ont également fournis des valeurs de biomasses des différents compatiments qui ont permis d'estimer le potentiel du microzooplancton en tant que consommateur du phytoplancton ou en tant que source nutritive pour le mésozooplancton. Ce travail représente la première étude caractérisant la communauté des protistes planctoniques dans son ensemble dans un contexte de fertilisation naturelle en fer.
Since the 90s, studies on different HNLC areas allowed to investigated the biological and biogeochemical effects due to artificial or natural iron-enrichment. It is now well documented that iron enrichment induced phytoplankton blooms and more specifically diatom blooms. With the exception of diatoms, very few information is available concerning other protists groups e. g. heterotrophic protists which are consumers of phytoplankton.This work was performed is a natural iron-fertilization context in the Kerguelen Island area (Southern Ocean) during the KEOPS 2 (Kerguelen Ocean and Plateau compared Study 2) cruise at the beginning of the phytoplankton bloom and focused specifically on heterotrophic protists. Molecular (tag-pyrosequencing 454) and morphological (microscopy) approaches were used to characterize the structure of protist communities in the HNLC reference area and in the phytoplankton blooms. The molecular approach allowed (i) to provide a complete picture of the protist communities (ii) to evidence significant differences…
Advisors/Committee Members: Christaki, Urania (thesis director), Monchy, Sébastien (thesis director).
Subjects/Keywords: Zones HNLC; Protistes; Fertilisation en fer; Tag-pyrosequençage 454; HNLC areas; Protists; Iron-fertilization; Tag-pyrosequencing 454
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
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APA (6th Edition):
Georges, C. (2015). Les communautés de protistes au sein d'un bloom phytoplanctonique dans la région naturellement fertilisée en fer des îles de Kerguelen (Océan Australe) : Protistan communities in a phytoplankton bloom within a naturally iron-fertilized region of the Kerguelen Islands (Southern Ocean). (Doctoral Dissertation). Littoral. Retrieved from http://www.theses.fr/2015DUNK0415
Chicago Manual of Style (16th Edition):
Georges, Clément. “Les communautés de protistes au sein d'un bloom phytoplanctonique dans la région naturellement fertilisée en fer des îles de Kerguelen (Océan Australe) : Protistan communities in a phytoplankton bloom within a naturally iron-fertilized region of the Kerguelen Islands (Southern Ocean).” 2015. Doctoral Dissertation, Littoral. Accessed April 16, 2021.
http://www.theses.fr/2015DUNK0415.
MLA Handbook (7th Edition):
Georges, Clément. “Les communautés de protistes au sein d'un bloom phytoplanctonique dans la région naturellement fertilisée en fer des îles de Kerguelen (Océan Australe) : Protistan communities in a phytoplankton bloom within a naturally iron-fertilized region of the Kerguelen Islands (Southern Ocean).” 2015. Web. 16 Apr 2021.
Vancouver:
Georges C. Les communautés de protistes au sein d'un bloom phytoplanctonique dans la région naturellement fertilisée en fer des îles de Kerguelen (Océan Australe) : Protistan communities in a phytoplankton bloom within a naturally iron-fertilized region of the Kerguelen Islands (Southern Ocean). [Internet] [Doctoral dissertation]. Littoral; 2015. [cited 2021 Apr 16].
Available from: http://www.theses.fr/2015DUNK0415.
Council of Science Editors:
Georges C. Les communautés de protistes au sein d'un bloom phytoplanctonique dans la région naturellement fertilisée en fer des îles de Kerguelen (Océan Australe) : Protistan communities in a phytoplankton bloom within a naturally iron-fertilized region of the Kerguelen Islands (Southern Ocean). [Doctoral Dissertation]. Littoral; 2015. Available from: http://www.theses.fr/2015DUNK0415
4.
El-Shami , Ibtihal Fawzi.
Shielding effectiveness of mesh wire for 50hz magnetic field.
Degree: Fakulti Kejuruteraan Elektrik dan Elektronik, 2011, Universiti Tun Hussein Onn Malaysia
URL: http://eprints.uthm.edu.my/id/eprint/1732/
► A wire mesh shield composed of thin conductive wires will influence the behaviour of electromagnetic fields within it. Many researchers have investigated electromagnetic field behaviour…
(more)
▼ A wire mesh shield composed of thin conductive wires will influence the behaviour of electromagnetic fields within it. Many researchers have investigated electromagnetic field behaviour in solid metal, but little of this work has probed into the effects of a wire mesh. The primary goal of this work is to design wire mesh shielding under overhead power lines to investigate the electromagnetic energy transmitted to the ground and possibly can exposed people under certain risk.
The electromagnetic shielding of wire-mesh screens is discussed in the frequency range where the individual meshes are electrically small)1.0(λ<L. The screen, whose meshes are assumed to be square, its applicability to the measurement of mesh properties is described. The low-frequency magnetic shielding afforded by mesh enclosures is considered. Because of the reactive character of the mesh surface, the near field source shielding effectiveness decreases with increasing frequency. The enclosure magnetic-field shielding effectiveness increases with increasing frequency, but saturates at a maximum value that depends on the geometry of the mesh size, and the mesh wire radius. The enclosure electrostatic-field shielding effectiveness depends only on the enclosure and mesh geometries.
Experimentally, shielding effectiveness measurements have been performed. The wire mesh Shields designed in different sizes to find the relation between mesh size and shielding effectiveness.
Subjects/Keywords: TK452-454 Electric apparatus and materials. Electric circuits. Electric networks
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
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APA (6th Edition):
El-Shami , I. F. (2011). Shielding effectiveness of mesh wire for 50hz magnetic field. (Masters Thesis). Universiti Tun Hussein Onn Malaysia. Retrieved from http://eprints.uthm.edu.my/id/eprint/1732/
Chicago Manual of Style (16th Edition):
El-Shami , Ibtihal Fawzi. “Shielding effectiveness of mesh wire for 50hz magnetic field.” 2011. Masters Thesis, Universiti Tun Hussein Onn Malaysia. Accessed April 16, 2021.
http://eprints.uthm.edu.my/id/eprint/1732/.
MLA Handbook (7th Edition):
El-Shami , Ibtihal Fawzi. “Shielding effectiveness of mesh wire for 50hz magnetic field.” 2011. Web. 16 Apr 2021.
Vancouver:
El-Shami IF. Shielding effectiveness of mesh wire for 50hz magnetic field. [Internet] [Masters thesis]. Universiti Tun Hussein Onn Malaysia; 2011. [cited 2021 Apr 16].
Available from: http://eprints.uthm.edu.my/id/eprint/1732/.
Council of Science Editors:
El-Shami IF. Shielding effectiveness of mesh wire for 50hz magnetic field. [Masters Thesis]. Universiti Tun Hussein Onn Malaysia; 2011. Available from: http://eprints.uthm.edu.my/id/eprint/1732/

University of Bradford
5.
Ramli, Khairun Nidzam.
Modeling and analysis of complex electromagnetic problems using FDTD subgridding in hybrid computational methods.
Degree: phd, School of Engineering, Design and Technology, 2011, University of Bradford
URL: http://eprints.uthm.edu.my/id/eprint/2693/
► The main objective of this research is to model and analyse complex electromagnetic problems by means of a new hybridised computational technique combining the frequency…
(more)
▼ The main objective of this research is to model and analyse complex electromagnetic problems
by means of a new hybridised computational technique combining the frequency domain
Method of Moments (MoM), Finite-Difference Time-Domain (FDTD) method and a subgridded
Finite-Difference Time-Domain (SGFDTD) method. This facilitates a significant advance in the
ability to predict electromagnetic absorption in inhomogeneous, anisotropic and lossy dielectric
materials irradiated by geometrically intricate sources. The Method of Moments modelling
employed a two-dimensional electric surface patch integral formulation solved by independent
linear basis function methods in the circumferential and axial directions of the antenna wires. A
similar orthogonal basis function is used on the end surface and appropriate attachments with
the wire surface are employed to satisfy the requirements of current continuity. The surface
current distributions on structures which may include closely spaced parallel wires, such as
dipoles, loops and helical antennas are computed. The results are found to be stable and showed
good agreement with less comprehensive earlier work by others.
The work also investigated the interaction between overhead high voltage transmission lines and
underground utility pipelines using the FDTD technique for the whole structure, combined with
a subgridding method at points of interest, particularly the pipeline. The induced fields above
the pipeline are investigated and analysed.
FDTD is based on the solution of Maxwell�s equations in differential form. It is very useful for
modelling complex, inhomogeneous structures. Problems arise when open-region geometries
are modelled. However, the Perfectly Matched Layer (PML) concept has been employed to
circumvent this difficulty. The establishment of edge elements has greatly improved the
performance of this method and the computational burden due to huge numbers of time steps, in
the order of tens of millions, has been eased to tens of thousands by employing quasi-static
methods.
This thesis also illustrates the principle of the equivalent surface boundary employed close to
the antenna for MoM-FDTD-SGFDTD hybridisation. It depicts the advantage of using hybrid
techniques due to their ability to analyse a system of multiple discrete regions by employing the
principle of equivalent sources to excite the coupling surfaces. The method has been applied for
modelling human body interaction with a short range RFID antenna to investigate and analyse
the near field and far field radiation pattern for which the cumulative distribution function of
antenna radiation efficiency is presented. The field distributions of the simulated structures
show reasonable and stable results at 900 MHz. This method facilitates deeper investigation of
the phenomena in the interaction between electromagnetic fields and human tissues.P
Subjects/Keywords: TK452-454 Electric apparatus and materials. Electric circuits. Electric networks
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Ramli, K. N. (2011). Modeling and analysis of complex electromagnetic problems using FDTD subgridding in hybrid computational methods. (Doctoral Dissertation). University of Bradford. Retrieved from http://eprints.uthm.edu.my/id/eprint/2693/
Chicago Manual of Style (16th Edition):
Ramli, Khairun Nidzam. “Modeling and analysis of complex electromagnetic problems using FDTD subgridding in hybrid computational methods.” 2011. Doctoral Dissertation, University of Bradford. Accessed April 16, 2021.
http://eprints.uthm.edu.my/id/eprint/2693/.
MLA Handbook (7th Edition):
Ramli, Khairun Nidzam. “Modeling and analysis of complex electromagnetic problems using FDTD subgridding in hybrid computational methods.” 2011. Web. 16 Apr 2021.
Vancouver:
Ramli KN. Modeling and analysis of complex electromagnetic problems using FDTD subgridding in hybrid computational methods. [Internet] [Doctoral dissertation]. University of Bradford; 2011. [cited 2021 Apr 16].
Available from: http://eprints.uthm.edu.my/id/eprint/2693/.
Council of Science Editors:
Ramli KN. Modeling and analysis of complex electromagnetic problems using FDTD subgridding in hybrid computational methods. [Doctoral Dissertation]. University of Bradford; 2011. Available from: http://eprints.uthm.edu.my/id/eprint/2693/

Texas A&M University
6.
Pechal, Jennifer.
The Importance of Microbial and Primary Colonizer Interactions on an Ephemeral Resource.
Degree: PhD, Entomology, 2012, Texas A&M University
URL: http://hdl.handle.net/1969.1/ETD-TAMU-2012-05-11016
► Carrion decomposition is an essential ecosystem function as it is an important component of nutrient cycling. Carrion decomposition has primarily been attributed to insect consumption,…
(more)
▼ Carrion decomposition is an essential ecosystem function as it is an important component of nutrient cycling. Carrion decomposition has primarily been attributed to insect consumption, with little attention given to microbial communities or their potential interactions with insects. The first objective was to use passive insect-trapping methods to assess primary colonizer communities on swine carcasses between two treatments: 1) carrion with access to insects and 2) carrion excluded from insect access for five days using exclusion cages. Despite similarities between succession patterns within each treatment, carcasses initially exposed to insects had significantly fewer insect taxa. Therefore, collections of adult insect communities associated with carrion are promising as an indication of whether or not there has been a delay in insect colonization of a resource.
There has yet to be a study documenting bacterial communities during carrion decomposition. The second objective was to describe bacterial community succession and composition during decomposition in the presence and absence of naturally occurring insects. Total genomic DNA was used to identify bacterial community composition via a modified bacterial tagged encoded FLX amplicon pyrosequencing. I obtained 378,904 sequences and documented distinct bacterial community successional trajectories associated with insect access and exclusion carcasses. By the fifth day of decomposition, Proteus was the dominant (72%) bacterial genus on exclusion carcasses while Psychrobacillus (58%) and Ignatzschineria (18%) were dominant bacterial genera on insect carcasses. These data are the first to document bacterial community composition and succession on carrion.
My final objective was to assess microbial community function in response to carrion insect colonization using metabolic profiling. I characterized microbial community metabolic function in the presence and absence of the primary necrophagous insects. I documented significant microbial community metabolic profile changes during active decomposition of carcasses. Mean carcass microbial community metabolic function with insect access continuously decreased over decomposition during both field seasons. Thus demonstrating microbial metabolic activity may have discriminatory power to differentiate early and late stages of decomposition.
Overall, my data contributes to an understudied area of microbial research important to organic matter decomposition, forensic entomology, and microbial-insect ecological interactions.
Advisors/Committee Members: Tomberlin, Jeffery K. (advisor), Tarone, Aaron M. (committee member), Eubanks, Micky D. (committee member), Crippen, Tawni L. (committee member), Benbow, Mark E. (committee member).
Subjects/Keywords: decomposition ecology; carrion; forensic entomology; microbial communities; Biolog ECOplates; 454-pyrosequencing
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
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APA (6th Edition):
Pechal, J. (2012). The Importance of Microbial and Primary Colonizer Interactions on an Ephemeral Resource. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-2012-05-11016
Chicago Manual of Style (16th Edition):
Pechal, Jennifer. “The Importance of Microbial and Primary Colonizer Interactions on an Ephemeral Resource.” 2012. Doctoral Dissertation, Texas A&M University. Accessed April 16, 2021.
http://hdl.handle.net/1969.1/ETD-TAMU-2012-05-11016.
MLA Handbook (7th Edition):
Pechal, Jennifer. “The Importance of Microbial and Primary Colonizer Interactions on an Ephemeral Resource.” 2012. Web. 16 Apr 2021.
Vancouver:
Pechal J. The Importance of Microbial and Primary Colonizer Interactions on an Ephemeral Resource. [Internet] [Doctoral dissertation]. Texas A&M University; 2012. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2012-05-11016.
Council of Science Editors:
Pechal J. The Importance of Microbial and Primary Colonizer Interactions on an Ephemeral Resource. [Doctoral Dissertation]. Texas A&M University; 2012. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-2012-05-11016

Brigham Young University
7.
Soliai, Marcus Makina.
De novo Genome Assembly and SNP Marker Development of Pyrenophora semeniperda.
Degree: MS, 2011, Brigham Young University
URL: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3959&context=etd
► Pyrenophora semeniperda (anamorph Drechslera campulata) is a necrotrophic fungal seed pathogen of a variety of grass genra and species, including Bromus tectorum, an exotic…
(more)
▼ Pyrenophora semeniperda (anamorph Drechslera campulata) is a necrotrophic fungal seed pathogen of a variety of grass genra and species, including Bromus tectorum, an exotic grass that has invaded many natural ecosystems of the U.S. Intermountain West. As a natural seed pathogen of B. tectorum, P. semeniperda has potential as a biocontrol agent due to its effectiveness at killing dormant B. tectorum seeds; however, few genetic resources exist for this fungus. Here, the genome assembly of a P. semeniperda isolate using 454 GS-FLX genomic and paired-end pyrosequencing techniques is presented. The total assembly is 32.5 Mb and contains 11,453 gene models greater than 24 amino acids. The assembly contains a variety of predicted genes that are involved in pathogenic pathways typically found in necrotrophic fungi. In addition, 454 sequence reads were used to identify single nucleotide polymorphisms between two isolates of P. semeniperda. In total, 20 SNP markers were developed for the purposes of recombination assesment of 600 individual P. semeniperda isolates representing 36 populations from throughout the U.S. Intermountain West. Although 17 of the fungal populations were fixed at all SNP loci, linkage disequilibrium was determined in the remaining 18 populations. This research demonstrates the effectiveness of the 454 GS-FLX sequencing technology, for de novo assembly and marker development of filamentous fungal genomes. Many features of the assembly match those of other Pyrenophora genomes including P. tritici-repentis and P. teres f. teres, which lend validity to our assembly. These findings present a significant resource for examining and furthering our understanding of P. semeniperda biology.
Subjects/Keywords: 454 sequencing; genome assembly; SNPs; linkage disequilibrium; Animal Sciences
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
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APA (6th Edition):
Soliai, M. M. (2011). De novo Genome Assembly and SNP Marker Development of Pyrenophora semeniperda. (Masters Thesis). Brigham Young University. Retrieved from https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3959&context=etd
Chicago Manual of Style (16th Edition):
Soliai, Marcus Makina. “De novo Genome Assembly and SNP Marker Development of Pyrenophora semeniperda.” 2011. Masters Thesis, Brigham Young University. Accessed April 16, 2021.
https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3959&context=etd.
MLA Handbook (7th Edition):
Soliai, Marcus Makina. “De novo Genome Assembly and SNP Marker Development of Pyrenophora semeniperda.” 2011. Web. 16 Apr 2021.
Vancouver:
Soliai MM. De novo Genome Assembly and SNP Marker Development of Pyrenophora semeniperda. [Internet] [Masters thesis]. Brigham Young University; 2011. [cited 2021 Apr 16].
Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3959&context=etd.
Council of Science Editors:
Soliai MM. De novo Genome Assembly and SNP Marker Development of Pyrenophora semeniperda. [Masters Thesis]. Brigham Young University; 2011. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3959&context=etd

University of Guelph
8.
Spall, Jennifer.
Investigating the Utility of Next Generation Sequencing for Evaluating Biodiversity in Benthic Communities.
Degree: MS, Department of Integrative Biology, 2014, University of Guelph
URL: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8382
► This thesis is an investigation into the current state of two methods of DNA sequencing and their ability to assess the biodiversity of benthic samples…
(more)
▼ This thesis is an investigation into the current state of two methods of DNA sequencing and their ability to assess the biodiversity of benthic samples containing the taxa generally used in biomonitoring studies. Its goal was to evaluate the ability of DNA Barcoding through Sanger sequencing and Next Generation Sequencing through
454 pyrosequencing to provide biodiversity information that would prove useful to biomonitoring organisations such as the Toronto and Region Conservation Authority. The investigation was performed by collecting benthic samples at four locations in the Humber River and determining the biodiversity captured by each sequencing technique. Further analyses were performed to determine the extent to which the known drawbacks of
454 pyrosequencing affect its ability to be useful in this regard. It was found that in the absence of primer binding biases the two sequencing techniques are statistically equal in their ability to measure the biodiversity of benthic samples.
Advisors/Committee Members: Hajibabaei, Mehrdad (advisor).
Subjects/Keywords: Next Generation Sequencing; Roche 454 Pyrosequencing; DNA Barcoding; Benthic Biodiversity
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to Zotero / EndNote / Reference
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APA (6th Edition):
Spall, J. (2014). Investigating the Utility of Next Generation Sequencing for Evaluating Biodiversity in Benthic Communities. (Masters Thesis). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8382
Chicago Manual of Style (16th Edition):
Spall, Jennifer. “Investigating the Utility of Next Generation Sequencing for Evaluating Biodiversity in Benthic Communities.” 2014. Masters Thesis, University of Guelph. Accessed April 16, 2021.
https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8382.
MLA Handbook (7th Edition):
Spall, Jennifer. “Investigating the Utility of Next Generation Sequencing for Evaluating Biodiversity in Benthic Communities.” 2014. Web. 16 Apr 2021.
Vancouver:
Spall J. Investigating the Utility of Next Generation Sequencing for Evaluating Biodiversity in Benthic Communities. [Internet] [Masters thesis]. University of Guelph; 2014. [cited 2021 Apr 16].
Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8382.
Council of Science Editors:
Spall J. Investigating the Utility of Next Generation Sequencing for Evaluating Biodiversity in Benthic Communities. [Masters Thesis]. University of Guelph; 2014. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/8382
9.
Abd Aziz, Azizul Rahman; Mohamad, Mahmod Abd Hakim; Ismail, Suhairi.
Mesin kentang berputar (spring) elektrik.
Degree: Pusat Pengajian Diploma, 2015, Universiti Tun Hussein Onn Malaysia
URL: http://eprints.uthm.edu.my/id/eprint/7970/
► Projek ini adalah bertujuan untuk menghasilkan mesin pemutar kentang dengan menggunakan motor elektrik dan berfungsi secara automatik. Hasil penciptaan mesin pemutar kentang automatik ini boleh…
(more)
▼ Projek ini adalah bertujuan untuk menghasilkan mesin pemutar kentang dengan
menggunakan motor elektrik dan berfungsi secara automatik. Hasil penciptaan mesin
pemutar kentang automatik ini boleh memudahkan pengguna dalam kegunaan
industri dan kegunaan harian. Setelah kajian dilakukan, kami mendapati kaedah
secara manual lebih perlahan dan merbahaya kerana melibatkan penggunaan mata
alat yang tajam dm terdedah serta mempunyai risiko yang tinggi mencederakan
pengguna semasa proses pemotongan. Kaedah yang kami lakukan adalah mereka
bentuk model baru yang disamping melakukan penambahbaikan pada model yang
lama setelah kajian dianalisis. Penambahbaikan yang dilakukan adalah menukar
motor yang lebih sesuai, sistem pemotongan yang lebih lancar dengan mengunakan
actuator, penjana kuasa mesin addah mengunakan bateri yang boleh dicas semula
dan menukar kompenan yang lebih baik. Jangkaan hasil projek adalah dapat
dijadikan satu rujukan yang lengkap dalam aspek penggunaan , ketahanan,
keselamatan dan fungsi. Oleh itu, reka bentuk yang dihasilkan haruslah mencapai
objektif projek agar dapat menyelesaikan masalah yang dihadapi oleh pengguna dan
boleh diaplikasikan dalam sektor industi atau persendirian. Secara keseluruhannya
antara penambaikan yang dapat dilakukan adalah meningkatkan keselamatan
pengguna, meningkatkan kecekapan produk, mengurangkan tenaga kerja serta masa,
dan penggunaan mata alat yang sesuai pada reka bentuk.
Subjects/Keywords: TK452-454 Electric apparatus and materials. Electric circuits. Electric networks
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
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APA (6th Edition):
Abd Aziz, Azizul Rahman; Mohamad, Mahmod Abd Hakim; Ismail, S. (2015). Mesin kentang berputar (spring) elektrik. (Thesis). Universiti Tun Hussein Onn Malaysia. Retrieved from http://eprints.uthm.edu.my/id/eprint/7970/
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Abd Aziz, Azizul Rahman; Mohamad, Mahmod Abd Hakim; Ismail, Suhairi. “Mesin kentang berputar (spring) elektrik.” 2015. Thesis, Universiti Tun Hussein Onn Malaysia. Accessed April 16, 2021.
http://eprints.uthm.edu.my/id/eprint/7970/.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Abd Aziz, Azizul Rahman; Mohamad, Mahmod Abd Hakim; Ismail, Suhairi. “Mesin kentang berputar (spring) elektrik.” 2015. Web. 16 Apr 2021.
Vancouver:
Abd Aziz, Azizul Rahman; Mohamad, Mahmod Abd Hakim; Ismail S. Mesin kentang berputar (spring) elektrik. [Internet] [Thesis]. Universiti Tun Hussein Onn Malaysia; 2015. [cited 2021 Apr 16].
Available from: http://eprints.uthm.edu.my/id/eprint/7970/.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Abd Aziz, Azizul Rahman; Mohamad, Mahmod Abd Hakim; Ismail S. Mesin kentang berputar (spring) elektrik. [Thesis]. Universiti Tun Hussein Onn Malaysia; 2015. Available from: http://eprints.uthm.edu.my/id/eprint/7970/
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Duke University
10.
Procter, Andrew.
Effects of Past and Future CO2 on Grassland Soil Carbon and Microbial Ecology
.
Degree: 2013, Duke University
URL: http://hdl.handle.net/10161/5778
► Rising atmospheric CO2 concentration, currently about 390 ppm, causes climate change and is expected to reach 500 ppm or higher this century due to…
(more)
▼ Rising atmospheric CO2 concentration, currently about 390 ppm, causes climate change and is expected to reach 500 ppm or higher this century due to human activities. Soils are the largest terrestrial pool of carbon, and changes in soil carbon storage due to plant and microbial activities could affect atmospheric CO2 levels. This dissertation studies soil carbon and microbial responses to an experimental preindustrial-to-future CO2 gradient (250-515 ppm) in a grassland ecosystem. Two contrasting soil types are studied in the gradient, providing insight on how natural ecosystem variation modifies CO2 effects. Although total soil organic carbon (SOC) did not change with CO2 treatment after four growing seasons, fast-cycling SOC pools did respond to CO2, particularly in the black clay soil. Microbial biomass increased 18% and microbial activity increased 30% across the CO2 gradient in the black clay, but neither factor changed with CO2 in the sandy loam. Similarly a one-year laboratory soil incubation showed that a fast-cycling SOC pool increased 75% across the CO2 gradient in the black clay. Size fractionation of SOC showed that coarse POM-C, the youngest and most labile fraction, increased four-fold across the CO2 gradient in the black clay, while it increased 50% across the gradient in the sandy loam. CO2 enrichment in this grassland increased the fast-cycling soil organic carbon pool as in other elevated CO2 studies, but only in the black clay soil. CO2 also induced changes in microbial community composition, and we explored the functional consequences in a microcosm experiment. Soil collected in the third growing season of CO2 treatment was used to inoculate Indiangrass seedlings grown in the lab. The elevated CO2 soil inoculum had higher microbial biomass C/N (C/N = 21) than the subambient CO2 soil inoculum (C/N = 16), suggesting a difference in community composition. Mean plant height in elevated CO2 soil inoculum (475 ppm) was 57% greater than in subambient CO2 soil inoculum (300 ppm), but the difference was not statistically significant. Similarly, total leaf N from plants in elevated CO2 soil was 28% greater on average than in subambient CO2 soil, but not significantly different. CO2-induced microbial effects on plant growth were either negligible or occurred at finer microbial taxonomic levels, making them difficult to resolve at the whole-community level. Soil fungi decompose soil organic matter, and studying fungal community responses to CO2 could improve our understanding of soil carbon responses. We studied fungal communities in the CO2 gradient using Sanger sequencing and pyrosequencing of rDNA. As in our soil C study, fungal community responses to CO2 were mostly linear, and occurred mostly in the black clay soil. Fungal species richness increased linearly with CO2 treatment in the black clay. The relative abundance of Chytridiomycota (chytrids) increased linearly with CO2 in the black clay, while the relative abundance of Glomeromycota (arbuscular mycorrhizal fungi)…
Advisors/Committee Members: Jackson, Robert (advisor).
Subjects/Keywords: Ecology;
Biology;
Microbiology;
454 pyrosequencing;
Atmospheric CO2;
fungi;
grassland;
soil type
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Procter, A. (2013). Effects of Past and Future CO2 on Grassland Soil Carbon and Microbial Ecology
. (Thesis). Duke University. Retrieved from http://hdl.handle.net/10161/5778
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Procter, Andrew. “Effects of Past and Future CO2 on Grassland Soil Carbon and Microbial Ecology
.” 2013. Thesis, Duke University. Accessed April 16, 2021.
http://hdl.handle.net/10161/5778.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Procter, Andrew. “Effects of Past and Future CO2 on Grassland Soil Carbon and Microbial Ecology
.” 2013. Web. 16 Apr 2021.
Vancouver:
Procter A. Effects of Past and Future CO2 on Grassland Soil Carbon and Microbial Ecology
. [Internet] [Thesis]. Duke University; 2013. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/10161/5778.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Procter A. Effects of Past and Future CO2 on Grassland Soil Carbon and Microbial Ecology
. [Thesis]. Duke University; 2013. Available from: http://hdl.handle.net/10161/5778
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Tennessee – Knoxville
11.
Chen, Si.
Toward Understanding the Physiological Determinants of Microbial Competitiveness in Methanogenic Processes.
Degree: 2014, University of Tennessee – Knoxville
URL: https://trace.tennessee.edu/utk_graddiss/3191
► Methanogenesis is of great significance in both natural and engineered processes. Anaerobic digestion technology represents the engineering-scale implementation of methanogenesis in waste treatment processes. Despite…
(more)
▼ Methanogenesis is of great significance in both natural and engineered processes. Anaerobic digestion technology represents the engineering-scale implementation of methanogenesis in waste treatment processes. Despite the broad application of anaerobic digestion as a common waste treatment option, much remains to be learned on the anaerobic food web underlying methanogenesis for more effective process modeling and control.
Following an initial screening of various substrates, six continuous lab-scale anaerobic digesters were developed with animal waste as the substrate. The linkage between microbial community composition and process performance was studied by initiating process imbalance with organic overloading. As a result, accumulation of short chain fatty acids, particularly acetate, occurred in response to the onset of process imbalance. Populations related to Methanosaeta vastly outnumbered those of Methanosarcina as the dominant acetoclastic methanogen throughout the study period, even at elevated acetate concentrations during process imbalance, which is unexpected as it is considered that Methanosaeta can out-compete Methanosarcina only at low acetate concentrations, typical for balanced anaerobic food webs. Subsequent methanogenic batch cultures enriched with high concentrations of acetate further confirmed the dominance of Methanosaeta over Methanosarcina. Given the significance of acetoclastic methanogenesis in the anaerobic food web and global carbon cycling, it is evident that the interactions between Methanosaeta and Methanosarcina need to be better defined. Other novel microbial populations were also identified as abundant constituents of the microbial communities in the anaerobic digesters, including populations related to Crenarchaeota. It is critical to understand the roles these abundant but poorly-described populations play in the anaerobic food web.
Subjects/Keywords: Archaea; Methanogenesis; qPCR; 454 pyrosequencing; Crenarchaeota; Methanosaeta; Environmental Engineering
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Chen, S. (2014). Toward Understanding the Physiological Determinants of Microbial Competitiveness in Methanogenic Processes. (Doctoral Dissertation). University of Tennessee – Knoxville. Retrieved from https://trace.tennessee.edu/utk_graddiss/3191
Chicago Manual of Style (16th Edition):
Chen, Si. “Toward Understanding the Physiological Determinants of Microbial Competitiveness in Methanogenic Processes.” 2014. Doctoral Dissertation, University of Tennessee – Knoxville. Accessed April 16, 2021.
https://trace.tennessee.edu/utk_graddiss/3191.
MLA Handbook (7th Edition):
Chen, Si. “Toward Understanding the Physiological Determinants of Microbial Competitiveness in Methanogenic Processes.” 2014. Web. 16 Apr 2021.
Vancouver:
Chen S. Toward Understanding the Physiological Determinants of Microbial Competitiveness in Methanogenic Processes. [Internet] [Doctoral dissertation]. University of Tennessee – Knoxville; 2014. [cited 2021 Apr 16].
Available from: https://trace.tennessee.edu/utk_graddiss/3191.
Council of Science Editors:
Chen S. Toward Understanding the Physiological Determinants of Microbial Competitiveness in Methanogenic Processes. [Doctoral Dissertation]. University of Tennessee – Knoxville; 2014. Available from: https://trace.tennessee.edu/utk_graddiss/3191

Oklahoma State University
12.
Ding, Tao.
Analysis of the Diversity and Distribution of Leaf Endophytic Bacterial Communities.
Degree: Department of Microbiology and Molecular Genetics, 2012, Oklahoma State University
URL: http://hdl.handle.net/11244/6837
► This research project aimed to reveal the basic composition of leaf endophytic bacterial communities, to detect the dominant and significant bacterial groups and to study…
(more)
▼ This research project aimed to reveal the basic composition of leaf endophytic bacterial communities, to detect the dominant and significant bacterial groups and to study the environmental influences on the structure of leaf endophytic bacterial communities; specifically, to see the relationship between host plants and endophytic bacteria and to track the dynamics of the endophytic bacteria during the host plant growing season. This research employed cultivation-independent methods to analyze bacterial communities, including total DNA extraction, polymerase chain reaction (PCR), terminal restriction fragment length polymorphism (T-RFLP) and tagged
454 pyrosequencing. Research data was analyzed using statistical software including R, SAS and CANOCO. Sequencing data was analyzed using Mothur and quantitative insight into microbial ecology (QIIME). T-RFLP has helped to study the environmental influences on the leaf endophytic bacterial communities quantitatively. Three major environmental factors, including host plant species, sampling date and collecting locations, were all tested significant using the profiles of the proportion of terminal restriction fragments (T-RF) by partial Canonical Correlation Analysis (pCCA). Dominant T-RFs were detected and host-specific T-RFs were also defined. Tagged
454 pyrosequencing allowed revealing the leaf endophytic bacterial communities at a deeper level. Sequences (64,591) of the 16S rDNA fragments were obtained, and after alignment and distance calculation were categorized into 3,291 Operational Taxonomic Units (OTUs) at 97% similarity level. Bacteria species from 16 phyla were detected with the dominant group, from Proteobacteria, represented by 1982 OTUs, followed by Bacteriodetes and Actinobacteria. Environmental influences were also evaluated. Host-specific OTUs were recognized. Three main types of trends of the OTU dynamics during the host plant growing season were observed. Alphaproteobacteria was significantly more abundant in Asclepias viridis among the five host plant species, and also expanded greatly in July in the whole leaf endophytic bacterial community. Pyrosequencing data were also used to identify the dominant T-RFs, showing that the result of T-RFLP is consistent with pyrosequencing.
Advisors/Committee Members: Melcher, Ulrich K. (advisor), DeSilva, Udaya (committee member), Mahalingam, Ramamurthy (committee member), Elshahed, Mostafa (committee member).
Subjects/Keywords: 454 pyrosequencing; leaf endophytic bacteria; pcca; proteobacteria; t-rflp
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Ding, T. (2012). Analysis of the Diversity and Distribution of Leaf Endophytic Bacterial Communities. (Thesis). Oklahoma State University. Retrieved from http://hdl.handle.net/11244/6837
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Ding, Tao. “Analysis of the Diversity and Distribution of Leaf Endophytic Bacterial Communities.” 2012. Thesis, Oklahoma State University. Accessed April 16, 2021.
http://hdl.handle.net/11244/6837.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Ding, Tao. “Analysis of the Diversity and Distribution of Leaf Endophytic Bacterial Communities.” 2012. Web. 16 Apr 2021.
Vancouver:
Ding T. Analysis of the Diversity and Distribution of Leaf Endophytic Bacterial Communities. [Internet] [Thesis]. Oklahoma State University; 2012. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/11244/6837.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Ding T. Analysis of the Diversity and Distribution of Leaf Endophytic Bacterial Communities. [Thesis]. Oklahoma State University; 2012. Available from: http://hdl.handle.net/11244/6837
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Oulu
13.
Huusko, K. (Karoliina).
Dynamics of root-associated fungal communities in relation to disturbance in boreal and subarctic forests.
Degree: 2018, University of Oulu
URL: http://urn.fi/urn:isbn:9789526218038
► Abstract Disturbance may shift microbial communities from one state to another. However, species differ in their ecological characteristics and their abilities to withstand disturbance. No…
(more)
▼ Abstract
Disturbance may shift microbial communities from one state to another. However, species differ in their ecological characteristics and their abilities to withstand disturbance. No single species or individuals of a species exist alone, but they are parts of complex interaction networks including species above- and belowground. In boreal and subarctic forests, almost all plants and a high number of fungi form mycorrhizas at the plant roots. In mycorrhiza, the fungal partner harvests nutrients for the host plant and, in return, gains carbon from the plant. In general, these common associations benefit both partners, but as heterotrophs, fungi are dependent on carbon photosynthesized by plants, whereas plants can survive alone as autotrophs. In addition to mycorrhizal fungi, also other fungi, such as endophytes, saprotrophs and pathogens, live in and on plant roots.
This thesis concerns the impacts of disturbance on fungi living in plant roots and in soil near the roots. I hypothesized that i) root-associated fungal (RAF) and soil fungal communities and colonization types change after disturbance, that ii) the observed shifts relate to disturbance intensity and that iii) they co-occur with changes in soil conditions and vegetation. Changes in RAF were studied as changes in root fungal colonization, or in fungal community composition. The latter were detected with next-generation sequencing methods.
The responses of RAF to disturbance seemed to be context dependent and related to sources of fungal communities (e.g. soil, RAF networks), environmental conditions (e.g. soil pH and nutrients) and host performance. It seems that abundances of those RAF species, which are present in the roots first (priority effect), may be increased by disturbance. Research produced new information related to ecological roles of the genera Phialocephala and Meliniomyces. Altogether, the results indicate connections between both abiotic and biotic environments and RAF, and host species viability and RAF.
Tiivistelmä
Häiriöt voivat siirtää eliöyhteisön tilasta toiseen. Lajien ominaisuudet ja häiriönsietokyvyt eroavat toisistaan. Mikään laji tai yksilö ei elä yksin, vaan lajit ovat osa maan ylä- ja alapuolelle ulottuvia monimutkaisia vuorovaikutusverkostoja. Boreaalisissa ja subarktisissa metsissä lähes kaikki kasvit ja useat sienet muodostavat sienijuuren eli mykorritsan. Mykorritsassa sieniosakas hankkii isäntäkasville ravinteita ja saa vastavuoroisesti kasvilta hiiltä. Tavallisesti nämä vuorovaikutussuhteet hyödyttävät molempia sienijuuren osakkaita, mutta toisenvaraisina (heterotrofeina) sienet ovat riippuvaisia kasvien yhteyttämästä hiilestä, kun taas tuottajina (autotrofeina) kasvit voivat elää itsenäisesti. Mykorritsasienten lisäksi kasvien juurissa elää yleisesti myös muita sieniä kuten endofyyttejä, saprotrofeja ja patogeeneja.
Tämä väitöskirja käsittelee häiriön vaikutuksia sieniin, jotka elävät kasvien juurissa ja juuria ympäröivässä maassa. Hypoteesieni mukaan i) juurissa ja maassa elävien sienten yhteisöt ja…
Advisors/Committee Members: Markkola, A. (Annamari), Ruotsalainen, A. (Anna Liisa), Saravesi, K. (Karita).
Subjects/Keywords: 454-pyrosequencing; Deschampsia flexuosa; Ion Torrent sequencing; diversity; succession; 454-pyrosekvensointi; Deschampsia flexuosa; Ion Torrent -sekvensointi; diversiteetti; sukkessio; Betula pubescens ssp. czerepanovii; Picea abies
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Huusko, K. (. (2018). Dynamics of root-associated fungal communities in relation to disturbance in boreal and subarctic forests. (Doctoral Dissertation). University of Oulu. Retrieved from http://urn.fi/urn:isbn:9789526218038
Chicago Manual of Style (16th Edition):
Huusko, K (Karoliina). “Dynamics of root-associated fungal communities in relation to disturbance in boreal and subarctic forests.” 2018. Doctoral Dissertation, University of Oulu. Accessed April 16, 2021.
http://urn.fi/urn:isbn:9789526218038.
MLA Handbook (7th Edition):
Huusko, K (Karoliina). “Dynamics of root-associated fungal communities in relation to disturbance in boreal and subarctic forests.” 2018. Web. 16 Apr 2021.
Vancouver:
Huusko K(. Dynamics of root-associated fungal communities in relation to disturbance in boreal and subarctic forests. [Internet] [Doctoral dissertation]. University of Oulu; 2018. [cited 2021 Apr 16].
Available from: http://urn.fi/urn:isbn:9789526218038.
Council of Science Editors:
Huusko K(. Dynamics of root-associated fungal communities in relation to disturbance in boreal and subarctic forests. [Doctoral Dissertation]. University of Oulu; 2018. Available from: http://urn.fi/urn:isbn:9789526218038
14.
Kurata, Naoko.
Sea Surface Microlayer Microbial Observation System.
Degree: 2012, Nova Southeastern University
URL: http://nsuworks.nova.edu/occ_stuetd/188
► Chapter 2 The sea surface microlayer is a biogenic thin layer, comprising less than one millimeter of the ocean surface. This surface layer has gained…
(more)
▼ Chapter 2
The sea surface microlayer is a biogenic thin layer, comprising less than one millimeter of the ocean surface. This surface layer has gained much attention due to its dampening effect on ocean capillary ripples. The chemistry of the air-sea interface has been studied for decades; however, the structure and function of the marine bacterial community within the sea surface microlayer are still understudied. Although various sea surface microlayer sampling techniques were developed over the past decades, aseptic bacterial sampling in the open ocean is a rather challenging task. In this study, a new approach is presented. It is designed for bacterial sampling of the sea surface microlayer, which intends to reduce sampling contamination from the vessel, subsurface water and the investigators. A 47mm polycarbonate membrane was utilized at each sampling site. In addition, the metagenomic approach using the new generation 454 high-throughput DNA sequencing system was employed to compensate for the small sample size. Two sample sets were collected in summer 2010 and fall 2011 from the sea surface microlayer and underlying water (20 cm deep). A contamination assessment was carried out to determine that contamination might have been caused during the use of the sampling techniques. A total of 14,120 bacterial 16S rRNA gene sequences with an average length of 437.8 bp were obtained. A total of 1,254 Operational Taxonomic Units (OTUs) were constructed and 268 genera were identified. The results indicated that the bacterial compositions of the sea surface microlayer samples were distinct from those of the underlying water samples. This experiment demonstrated that the new generation sequencing platform and microbial metagenomics analysis software together served as powerful tools to gain a deeper understanding of microbial communities within the sea surface microlayer. Furthermore, it is suggested that the newly employed sampling methods could be used to obtain a snapshot of bacterial community structure as well as environmental conditions.
Chapter 3
Synthetic aperture radar (SAR) remote sensing captures various fine-scale features on the ocean surface such as coastal discharge, oil pollution, vessel traffic, algal blooms and sea slicks. Although numerous factors potentially affect the SAR imaging process, the influence of biogenic and anthropogenic surfactants has been suggested as one of the primary parameters, especially under relatively low wind conditions. Surfactants have a tendency to dampen the short gravity-capillary ocean waves causing the sea surface to smoothen, thus allowing the radar to detect areas of surfactants. Surfactants are found in sea slicks, which are the accumulation of organic material shaped as elongated bands on the ocean’s surface. Sea slicks are often observable with the naked eye due to their glassy appearance and can also be seen on SAR images as dark scars. While the sources of surfactants can vary, some are known to be associated with marine bacteria. Countless numbers of marine bacteria…
Subjects/Keywords: bacteria; ocean surface; 16S rRNA; 454 GS FLX sequencing; bacteria; sea slicks; synthetic aperture radar; 16S rRNA; 454 GS FLX sequencing; Marine Biology; Oceanography and Atmospheric Sciences and Meteorology
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Kurata, N. (2012). Sea Surface Microlayer Microbial Observation System. (Thesis). Nova Southeastern University. Retrieved from http://nsuworks.nova.edu/occ_stuetd/188
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Kurata, Naoko. “Sea Surface Microlayer Microbial Observation System.” 2012. Thesis, Nova Southeastern University. Accessed April 16, 2021.
http://nsuworks.nova.edu/occ_stuetd/188.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Kurata, Naoko. “Sea Surface Microlayer Microbial Observation System.” 2012. Web. 16 Apr 2021.
Vancouver:
Kurata N. Sea Surface Microlayer Microbial Observation System. [Internet] [Thesis]. Nova Southeastern University; 2012. [cited 2021 Apr 16].
Available from: http://nsuworks.nova.edu/occ_stuetd/188.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Kurata N. Sea Surface Microlayer Microbial Observation System. [Thesis]. Nova Southeastern University; 2012. Available from: http://nsuworks.nova.edu/occ_stuetd/188
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
15.
Fernanda Alves de Freitas Guedes.
Pirossequenciamento do transcriptoma de folha de Lippia alba por meio da plataforma 454 GS FLX (Roche).
Degree: 2011, Universidade Federal de Juiz de Fora
URL: http://www.bdtd.ufjf.br/tde_busca/arquivo.php?codArquivo=1108
► Lippia alba, popularly known as erva cidreira, is widely distributed throughout the Americas and can be found through almost whole Brazil. This species is largely…
(more)
▼ Lippia alba, popularly known as erva cidreira, is widely distributed throughout the Americas and can be found through almost whole Brazil. This species is largely used in folk medicine to treat gastrointestinal and respiratory problems, especially leaves, which produce an essential oil rich in terpenes, mainly mono-and sesquiterpenes. These compounds are not only of pharmacological interest, as well as industrial. Composition of essencial oil can vary depending on the developmental stage, the plant part and other abiotic factors. However, genotypic variations also contribute to oil composition variation. Given the complexity of terpenes synthesis, including diversity of enzymes involved in these metabolic pathways, the purpose of this work was a L. alba leaf transcriptome characterization, in addition to identifying some enzymes probably involved in terpene synthesis. For that, it was made a transcriptome sequencing using 454 platform (Roche) followed by a de novo assembly. This platform, along with other NGS technologies, has been increasingly used for transcriptome sequencing in an approach known as RNA-Seq. Sequencing of a library prepared from total RNA in 1/8 plate generated 104,631 reads with average length of 184.48 bp and a total of 19,302,161 bases. Read assemblies were made using two different assemblers in order to compare them. While Newbler 2.5, proprietary software platform, assembled 2686 contigs with average length of 349bp, SeqMan2.2 generated 13,448 contigs with an average of 284bp. Then, functional annotation was performed with Blast2GO for all contigs from both assemblies; 51.49% and 30.88% of contigs, respectively, from Newbler and SeqMan were annotated. Finally, analysis of annotated sequences revealed some enzymes potentially involved in terpene synthesis. Results obtained from this pioneering study on the species show that NGS technology can be a very efficient tool for transcriptome sequencing and they will serve as reference for preparation of other more specific libraries. New sequencings should contribute to a better coverage of this transcriptome, allowing discovery of even rare transcripts
Lippia alba, também conhecida popularmente como erva cidreira, é uma espécie amplamente distribuída pelas Américas podendo ser encontrada por praticamente todo o Brasil. Muito usada pela medicina popular para o tratamento de problemas gastrointestinais e respiratórios, a folha desta espécie produz um óleo essencial rico em terpenos, principalmente mono e sesquiterpenos. Estes compostos não são apenas de interesse farmacológico, como também industrial. A composição deste óleo pode variar em função de fatores abióticos e também de variações genotípicas. Diante da complexidade da síntese destes compostos a proposta deste trabalho foi uma ampla caracterização do transcriptoma de folha de Lippia alba, além da identificação de prováveis enzimas envolvidas na síntese de terpenos. Para isso, foi feito um sequenciamento deste transcriptoma usando a plataforma 454 (Roche) seguido de uma montagem de novo. Esta…
Advisors/Committee Members: Lyderson Facio Viccini, Marisa Fabiana Nicolás, Marcelo de Oliveira Santos.
Subjects/Keywords: GENETICA; Lippia alba; terpenos; transcriptoma; sequenciamento; plataformas NGS; 454; contig; anotação funcional; Lippia alba; terpenes; transcriptome; sequencing; NGS plataforms; 454; contig; functional annotation
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APA (6th Edition):
Guedes, F. A. d. F. (2011). Pirossequenciamento do transcriptoma de folha de Lippia alba por meio da plataforma 454 GS FLX (Roche). (Thesis). Universidade Federal de Juiz de Fora. Retrieved from http://www.bdtd.ufjf.br/tde_busca/arquivo.php?codArquivo=1108
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Guedes, Fernanda Alves de Freitas. “Pirossequenciamento do transcriptoma de folha de Lippia alba por meio da plataforma 454 GS FLX (Roche).” 2011. Thesis, Universidade Federal de Juiz de Fora. Accessed April 16, 2021.
http://www.bdtd.ufjf.br/tde_busca/arquivo.php?codArquivo=1108.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Guedes, Fernanda Alves de Freitas. “Pirossequenciamento do transcriptoma de folha de Lippia alba por meio da plataforma 454 GS FLX (Roche).” 2011. Web. 16 Apr 2021.
Vancouver:
Guedes FAdF. Pirossequenciamento do transcriptoma de folha de Lippia alba por meio da plataforma 454 GS FLX (Roche). [Internet] [Thesis]. Universidade Federal de Juiz de Fora; 2011. [cited 2021 Apr 16].
Available from: http://www.bdtd.ufjf.br/tde_busca/arquivo.php?codArquivo=1108.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Guedes FAdF. Pirossequenciamento do transcriptoma de folha de Lippia alba por meio da plataforma 454 GS FLX (Roche). [Thesis]. Universidade Federal de Juiz de Fora; 2011. Available from: http://www.bdtd.ufjf.br/tde_busca/arquivo.php?codArquivo=1108
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
16.
Chevignon, Germain.
Impact moléculaire et physiologique de la guêpe parasitoïde Cotesia congregata et de son polydnavirus sur l'insecte hôte Manduca sexta : Molecular and physiological impact of the parasitoid wasp Cotesia congregata and its polydnavirus on the insect host Manduca sexta.
Degree: Docteur es, Biologie des interactions, 2014, Université François-Rabelais de Tours
URL: http://www.theses.fr/2014TOUR4025
► Cotesia congregata est une guêpe parasitoïde qui se développe à l’intérieur de la larve du Lépidoptère, Manduca sexta. Ce parasitoïde a développé une stratégie de…
(more)
▼ Cotesia congregata est une guêpe parasitoïde qui se développe à l’intérieur de la larve du Lépidoptère, Manduca sexta. Ce parasitoïde a développé une stratégie de virulence qui utilise un symbionte viral de la famille des Polydnavirus nommé Cotesia congregata bracovirus. Mon travail de thèse a permis de caractériser le dialogue moléculaire au cours de l’interaction par des approches de transcriptomique à haut débit et de physiologie. Ces travaux ont permis d’établir la première carte fonctionnelle du génome viral et de visualiser l’ensemble des gènes de M. sexta régulés au cours du parasitisme. La régulation des gènes de l’immunité a révélé que le parasitisme n’empêche pas l’induction de peptides antimicrobiens, mais entraine la sous-expression de gènes impliqués dans la réponse cellulaire. De plus j’ai pu mettre en évidence une réduction du nombre de cellules adhérentes au cours de l’interaction et décrire l’induction d’un phénotype de type apoptose d’une catégorie de cellules immunitaires. Ces résultats permettent d’identifier des gènes acteurs de l’interaction et apportent de nouvelles connaissances relatives aux interactions hôtes-parasitoïdes.
Cotesia congregata is a parasitoid wasp that develops inside the lepidopteran larvae, Manduca sexta. This parasitoid wasp has evolved virulence strategies using an obligate viral symbiont from the Polydnavirus family named Cotesia congregata bracovirus. My thesis work has allowed us to characterize the molecular dialogue during the interaction by physiological and high-throughput transcriptomic approaches. This work allowed to obtain the first functional map of the viral genome and to identify all M. sexta genes regulated during parasitism. Regulation of immune genes revealed that parasitism does not prevent induction of antimicrobial peptides, but leads to the down-regulation of genes involved in the cellular response. Moreover, I was able to demonstrate a reduction in the number of adherent cells during the interaction and to describe this induction as an apoptosis-like phenotype targeting a specific population of immune cells. These findings open the way to the identification of candidate genes involved in this particular interaction and provide new insights into host-parasitoid interactions in general.
Advisors/Committee Members: Huguet, Élisabeth (thesis director), Moreau, Sébastien (thesis director).
Subjects/Keywords: Polydnavirus; Guêpe parasitoïde; Transcriptome; 454; Mort cellulaire; Cotesia congregata; Manduca sexta; Polydnavirus; Parsitoid wasp; Transcriptome; 454; Cell death; Cotesia congregata; Manduca sexta
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
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APA (6th Edition):
Chevignon, G. (2014). Impact moléculaire et physiologique de la guêpe parasitoïde Cotesia congregata et de son polydnavirus sur l'insecte hôte Manduca sexta : Molecular and physiological impact of the parasitoid wasp Cotesia congregata and its polydnavirus on the insect host Manduca sexta. (Doctoral Dissertation). Université François-Rabelais de Tours. Retrieved from http://www.theses.fr/2014TOUR4025
Chicago Manual of Style (16th Edition):
Chevignon, Germain. “Impact moléculaire et physiologique de la guêpe parasitoïde Cotesia congregata et de son polydnavirus sur l'insecte hôte Manduca sexta : Molecular and physiological impact of the parasitoid wasp Cotesia congregata and its polydnavirus on the insect host Manduca sexta.” 2014. Doctoral Dissertation, Université François-Rabelais de Tours. Accessed April 16, 2021.
http://www.theses.fr/2014TOUR4025.
MLA Handbook (7th Edition):
Chevignon, Germain. “Impact moléculaire et physiologique de la guêpe parasitoïde Cotesia congregata et de son polydnavirus sur l'insecte hôte Manduca sexta : Molecular and physiological impact of the parasitoid wasp Cotesia congregata and its polydnavirus on the insect host Manduca sexta.” 2014. Web. 16 Apr 2021.
Vancouver:
Chevignon G. Impact moléculaire et physiologique de la guêpe parasitoïde Cotesia congregata et de son polydnavirus sur l'insecte hôte Manduca sexta : Molecular and physiological impact of the parasitoid wasp Cotesia congregata and its polydnavirus on the insect host Manduca sexta. [Internet] [Doctoral dissertation]. Université François-Rabelais de Tours; 2014. [cited 2021 Apr 16].
Available from: http://www.theses.fr/2014TOUR4025.
Council of Science Editors:
Chevignon G. Impact moléculaire et physiologique de la guêpe parasitoïde Cotesia congregata et de son polydnavirus sur l'insecte hôte Manduca sexta : Molecular and physiological impact of the parasitoid wasp Cotesia congregata and its polydnavirus on the insect host Manduca sexta. [Doctoral Dissertation]. Université François-Rabelais de Tours; 2014. Available from: http://www.theses.fr/2014TOUR4025

Université de Bordeaux I
17.
Cordier, Tristan.
Structure des assemblages fongiques de la phyllosphère des arbres forestiers et effet potentiel du changement climatique : Novel multiscale methods for nonlinear speech analysis.
Degree: Docteur es, Ecologie évolutive, fonctionnelle et des communautés, 2012, Université de Bordeaux I
URL: http://www.theses.fr/2012BOR14511
► La phyllosphère est l’habitat fourni par la partie foliaire des plantes. De nombreuses espèces microbiennes - pathogènes, saprophytes ou mutualistes des plantes - peuplent cet…
(more)
▼ La phyllosphère est l’habitat fourni par la partie foliaire des plantes. De nombreuses espèces microbiennes - pathogènes, saprophytes ou mutualistes des plantes - peuplent cet environnement. Ce compartiment microbien influence donc la dynamique et la structure des communautés végétales. L’objectif principal de cette thèse était d’étudier les effets potentiels du changement climatique sur la structure des assemblages fongiques de la phyllosphère des arbres forestiers, et sur la niche écologique des espèces fongiques pathogènes des arbres forestiers. Nous avons pour cela utilisé deux approches, i) l’étude de gradients altitudinaux et ii) la construction de modèles de niche bioclimatique.Les assemblages fongiques de la phyllosphère des arbres forestiers étant encore peu connus, nous avons dans un premier temps décrit leur diversité et quantifié leur variabilité spatiale à l’échelle d’une parcelle forestière.Nos résultats montrent que la phyllosphère d’un arbre forestier abrite quelques centaines d’espèces fongiques, avec quelques espèces dominantes et beaucoup d’espèces rares. Les facteurs structurant ces assemblages incluent à la fois des facteurs abiotiques et biotiques : la température apparaît comme la variable climatique la plus explicative le long d’un gradient altitudinal ; à l’échelle d’une parcelle, la proximité génétique entre arbres est plus déterminante que leur distance géographique.L’analyse des modèles de niche des champignons pathogènes forestiers à l’échelle de la France met en évidence des limitations climatiques, les pluies estivales étant une variable explicative importante.Toutefois, plusieurs espèces introduites occupent déjà la plus grande part de la distribution de leur hôte,sans limitation apparente par le climat. Les effets du changement climatique sur la plupart des pathogènes s’exerceront d’abord indirectement par des effets dépressifs très importants sur l’abondance de leurs arbres-hôtes. Seuls les pathogènes adaptés au biotope méditerranéen verraient leur impact s’accroitre.
Phyllosphere is the habitat provided by the leaves of living plants. Many microbial species -pathogens, saprophytes or mutualists of plants - inhabit this environment. These microbes therefore influence the dynamics and structure of plant communities. The main objective was to study the potential effects of climate change on the structure of phyllosphere fungal assemblages, and on the ecological niche of pathogenic fungal species of forest trees. We used two approaches, i) the study of altitudinal gradients and ii) the construction of bioclimatic niche models. Since phyllosphere fungal assemblages of forest trees are still poorly known, we first described their diversity and quantified their spatial variability at the scale of a forest stand.Our results show that the phyllosphere of a forest tree houses hundreds of fungal species, with few dominant species and many rare species. Factors structuring these assemblages include both abiotic and biotic factors: the temperature appears as the most explanatory variable…
Advisors/Committee Members: Desprez-Loustau, Marie-Laure (thesis director), Robin, Cécile (thesis director), Vacher, Corinne (thesis director).
Subjects/Keywords: Phyllosphère; Champignons; Fagus sylvatica; Changement climatique; Gradient altitudinal; Pyroséquençage 454; Modèle de niche; Santé des forêts; Phyllosphere; Fungi; Fagus sylvatica; Change climate; Elevation gradient; 454 pyrosequencing; Niche model; Forest health
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Cordier, T. (2012). Structure des assemblages fongiques de la phyllosphère des arbres forestiers et effet potentiel du changement climatique : Novel multiscale methods for nonlinear speech analysis. (Doctoral Dissertation). Université de Bordeaux I. Retrieved from http://www.theses.fr/2012BOR14511
Chicago Manual of Style (16th Edition):
Cordier, Tristan. “Structure des assemblages fongiques de la phyllosphère des arbres forestiers et effet potentiel du changement climatique : Novel multiscale methods for nonlinear speech analysis.” 2012. Doctoral Dissertation, Université de Bordeaux I. Accessed April 16, 2021.
http://www.theses.fr/2012BOR14511.
MLA Handbook (7th Edition):
Cordier, Tristan. “Structure des assemblages fongiques de la phyllosphère des arbres forestiers et effet potentiel du changement climatique : Novel multiscale methods for nonlinear speech analysis.” 2012. Web. 16 Apr 2021.
Vancouver:
Cordier T. Structure des assemblages fongiques de la phyllosphère des arbres forestiers et effet potentiel du changement climatique : Novel multiscale methods for nonlinear speech analysis. [Internet] [Doctoral dissertation]. Université de Bordeaux I; 2012. [cited 2021 Apr 16].
Available from: http://www.theses.fr/2012BOR14511.
Council of Science Editors:
Cordier T. Structure des assemblages fongiques de la phyllosphère des arbres forestiers et effet potentiel du changement climatique : Novel multiscale methods for nonlinear speech analysis. [Doctoral Dissertation]. Université de Bordeaux I; 2012. Available from: http://www.theses.fr/2012BOR14511

INP Toulouse
18.
Yapi, Yapo Magloire.
Physiologie digestive de l'aulacode (Thryonomys swinderianus) en croissance et impact des teneurs en fibres et céréales de la ration sur la santé et les performances zootechniques : Digestive physiology of the growing cane rat (Thryonomys swinderianus) and impact of fibre and cereal content of the diet on health and zootechnical performance.
Degree: Docteur es, Pathologie, Toxicologie, Génétique et Nutrition, 2013, INP Toulouse
URL: http://www.theses.fr/2013INPT0019
► L’aulacode (Thryonomys swinderianus) est un rongeur herbivore récemment domestiqué en Afrique pour la production de viande. Quelques études antérieures ont portés sur l’alimentation de cet…
(more)
▼ L’aulacode (Thryonomys swinderianus) est un rongeur herbivore récemment domestiqué en Afrique pour la production de viande. Quelques études antérieures ont portés sur l’alimentation de cet animal, dans le but d’améliorer la productivité des élevages. A ce jour, nos connaissances sur la digestion et les besoins nutritionnels de cet animal sont encore très parcellaires. Le premier objectif de notre étude était d’améliorer nos connaissances sur la physiologie digestive de l’aulacode en croissance, en particulier en relation avec les apports de fibres alimentaires, avec pour finalité de proposer des recommandations nutritionnelles en fibres pour optimiser la croissance et la santé digestive de cet animal. Notre second objectif était d’analyser les effets d’une diminution du ratio protéines digestibles / énergie digestible parallèlement à une hausse des apports d’amidon, sur la digestion et les performances. La finalité était d’analyser les possibilités de formuler un aliment complet moins onéreux pour les éleveurs et qui respecte les besoins de l’aulacode en croissance. Notre étude a permis de savoir que le caecum est le compartiment digestif le plus important du jeune aulacode entre 1 et 3 mois d’âge, avec plus de 40% du contenu digestif total. L’activité microbienne caecale (100 mM d’acides gras volatils totaux (AGVt) par gramme de contenu frais) est élevée, et similaire à celle des ruminants ou d’autres herbivores monogastriques. Le profil fermentaire est caractérisé par une prédominance de l’acétate (75 % des AGVt) et un ratio propionate / butyrate supérieur à 1. Le pyroséquençage 454 de l’ADN16S bactérien a permis de caractériser le microbiote caecal. Au sevrage, nous observons une prédominance du phylum des Bacteroidetes, avec 51 % d’abondance relative, alors que le phylum des Firmicutes devient majoritaire (50%) à 3 mois d’âge. Le microbiote caecal est caractérisé par la présence de genres souvent identifiés dans d’autres écosystèmes digestifs d’herbivores, tels que : RC9 (2 à 8%), Parabacteroides (1 à 8%), Prevotella (3 à 6%) et Xylanibacter (1%), Erysipelotrichaceae Turicibacter (1 à 7%), Lachnospiraceae Incertae_Sedis (4 à 5%), Ruminococcaceae Incertae_Sedis (1 à 2%) et Ruminococcus (1 à 3%). D’autres genres, absents chez des espèces voisines comme le lapin et le cobaye, semblent plus spécifiques de l’aulacode, tels que Termite_Treponema_cluster (1.7 à 2.2%) et Treponema (7 à 13%), du phylum des Spirochaetes. L’analyse des performances zootechniques indique qu’un taux de fibres compris entre 17 et 21 % d’ADF représenterait un bon compromis entre santé digestive et croissance de l’aulacode après son sevrage. Descendre au dessous de 6 g de protéines digestibles par MJ d’énergie digestible, via une hausse importante des apports d’amidon et une baisse importante du taux de protéines brutes (en dessous de 11 %) et de fibres, est préjudiciable à la croissance des animaux.
The cane rat or grasscutter (Thryonomys swinderianus) is a rodent herbivore recently domesticated in Africa for meat production. Some previous…
Advisors/Committee Members: Enjalbert, Francis (thesis director), Gidenne, Thierry (thesis director).
Subjects/Keywords: Aulacode; Thryonomys swinderianus; Physiologie digestive; Pyroséquençage 454; Communautés bactériennes; Fibres alimentaires; Croissance; Santé digestive; Cane rat; Thryonomys swinderianus; Digestive physiology; 454 pyrosequencing; Bacterial communities; Dietary fibre; Growth; Digestive health
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Yapi, Y. M. (2013). Physiologie digestive de l'aulacode (Thryonomys swinderianus) en croissance et impact des teneurs en fibres et céréales de la ration sur la santé et les performances zootechniques : Digestive physiology of the growing cane rat (Thryonomys swinderianus) and impact of fibre and cereal content of the diet on health and zootechnical performance. (Doctoral Dissertation). INP Toulouse. Retrieved from http://www.theses.fr/2013INPT0019
Chicago Manual of Style (16th Edition):
Yapi, Yapo Magloire. “Physiologie digestive de l'aulacode (Thryonomys swinderianus) en croissance et impact des teneurs en fibres et céréales de la ration sur la santé et les performances zootechniques : Digestive physiology of the growing cane rat (Thryonomys swinderianus) and impact of fibre and cereal content of the diet on health and zootechnical performance.” 2013. Doctoral Dissertation, INP Toulouse. Accessed April 16, 2021.
http://www.theses.fr/2013INPT0019.
MLA Handbook (7th Edition):
Yapi, Yapo Magloire. “Physiologie digestive de l'aulacode (Thryonomys swinderianus) en croissance et impact des teneurs en fibres et céréales de la ration sur la santé et les performances zootechniques : Digestive physiology of the growing cane rat (Thryonomys swinderianus) and impact of fibre and cereal content of the diet on health and zootechnical performance.” 2013. Web. 16 Apr 2021.
Vancouver:
Yapi YM. Physiologie digestive de l'aulacode (Thryonomys swinderianus) en croissance et impact des teneurs en fibres et céréales de la ration sur la santé et les performances zootechniques : Digestive physiology of the growing cane rat (Thryonomys swinderianus) and impact of fibre and cereal content of the diet on health and zootechnical performance. [Internet] [Doctoral dissertation]. INP Toulouse; 2013. [cited 2021 Apr 16].
Available from: http://www.theses.fr/2013INPT0019.
Council of Science Editors:
Yapi YM. Physiologie digestive de l'aulacode (Thryonomys swinderianus) en croissance et impact des teneurs en fibres et céréales de la ration sur la santé et les performances zootechniques : Digestive physiology of the growing cane rat (Thryonomys swinderianus) and impact of fibre and cereal content of the diet on health and zootechnical performance. [Doctoral Dissertation]. INP Toulouse; 2013. Available from: http://www.theses.fr/2013INPT0019

INP Toulouse
19.
Rey, Mickael.
Implantation du microbiote et mise en place des fonction du rumen chez le veau de race laitière et effet de la supplémentation en levures vivantes. : Establishment of ruminal microbiota and function in the dairy calf and the effect of live yeasts supplementation.
Degree: Docteur es, Pathologie, Toxicologie, Génétique et Nutrition, 2012, INP Toulouse
URL: http://www.theses.fr/2012INPT0086
► Le veau nouveau-né possède un rumen peu développé et non fonctionnel. Au cours des premiers mois, les fonctions digestives s’établissent, avec l’implantation du microbiote composé…
(more)
▼ Le veau nouveau-né possède un rumen peu développé et non fonctionnel. Au cours des premiers mois, les fonctions digestives s’établissent, avec l’implantation du microbiote composé majoritairement de bactéries, archées et protozoaires. Les objectifs de ce travail étaient doubles : i) caractériser et comprendre la séquence d’implantation taxonomique des microorganismes du rumen chez le veau par des techniques de biologie moléculaire et de dénombrement, ainsi que la séquence de mise en place des paramètres fermentaires (AGV et ammoniac) et des activités principales enzymatiques chez le veau en périodes pré- et post-sevrage, ii) étudier l’effet de l’addition de levures vivantes sur la mise en place de cet écosystème ruminal en périodes pré- et post-sevrage. D’une part, nos travaux ont permis de confirmer qu’à la naissance, le rumen chez le veau, est dépourvu de micro-organismes, d’AGV, d’activité xylanasique et amylasique, avec un pH proche de la neutralité et un Eh fortement positif. La colonisation du rumen se fait dès la naissance, pendant les 15 premiers jours de la vie de l’animal par un microbiote complexe prédominé par les bactéries (phyla Proteobacteria et Bacteroidetes) et comprenant aussi des archées (majoritairement Methanobrevibacter). En même temps, le Eh devient fortement négatif. Ces communautés entraînent la production de produits fermentaires grâce à leurs activités enzymatiques. Entre 15 jours et le sevrage, avec l’ingestion d’aliments solides, la composition du microbiote du rumen évolue pour se rapprocher de celle de ruminants adultes, sans atteindre pour autant la maturité en termes de densités et abondances relatives. A cette période, le phylum Bacteroidetes est majoritaire, avec le genre Prevotella. Après le sevrage de légers changements apparaissent sur certains paramètres fermentaires comme les AGV sans doute en raison d’une évolution du microbiote qui devient moins diversifié et plus adapté à la dégradation d’aliments solides. L’apparition, à partir de 90 jours, des protozoaires ciliés dans le rumen semble conditionnée par la présence d’animaux adultes à proximité. A 4 mois d’âge, l’écosystème ruminal tend à devenir proche de celui observé chez les animaux adultes en matière de paramètres fermentaires, activités enzymatiques et composition taxonomique du microbiote. D’autre part, nos travaux ont permis de conclure que, avant sevrage, une supplémentation en levures vivantes (Saccharomyces cerevisiae) diminue l’ingestion de concentrés, conduit à une apparition plus précoce de la communauté des protozoaires et une plus grande densité d’archées, mais a peu d'effets sur la densité et la diversité de la communauté bactérienne, à l'exception de variations d’abondances de quelques taxa mineurs. L’apport de levures entraîne une diminution de la protéolyse, une augmentation de la proportion d'acétate ruminal et une diminution de la proportion de propionate. Au cours de la période post-sevrage, les veaux supplémentés en levures consomment plus de foin et la densité en archées est plus importante alors…
Advisors/Committee Members: Enjalbert, Francis (thesis director), Monteils, Valérie (thesis director).
Subjects/Keywords: Implantation; Microbiote; Pyroséquençage 454; Rumen; Veaux; Agv; Ammoniac; Xylanase; Amylase; Protéase; Establishment; Microbiota; 454 pyrosequencing; Rumen; Calves; Vfa; Ammonia; Xylanase; Amylase; Protease
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
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Manager
APA (6th Edition):
Rey, M. (2012). Implantation du microbiote et mise en place des fonction du rumen chez le veau de race laitière et effet de la supplémentation en levures vivantes. : Establishment of ruminal microbiota and function in the dairy calf and the effect of live yeasts supplementation. (Doctoral Dissertation). INP Toulouse. Retrieved from http://www.theses.fr/2012INPT0086
Chicago Manual of Style (16th Edition):
Rey, Mickael. “Implantation du microbiote et mise en place des fonction du rumen chez le veau de race laitière et effet de la supplémentation en levures vivantes. : Establishment of ruminal microbiota and function in the dairy calf and the effect of live yeasts supplementation.” 2012. Doctoral Dissertation, INP Toulouse. Accessed April 16, 2021.
http://www.theses.fr/2012INPT0086.
MLA Handbook (7th Edition):
Rey, Mickael. “Implantation du microbiote et mise en place des fonction du rumen chez le veau de race laitière et effet de la supplémentation en levures vivantes. : Establishment of ruminal microbiota and function in the dairy calf and the effect of live yeasts supplementation.” 2012. Web. 16 Apr 2021.
Vancouver:
Rey M. Implantation du microbiote et mise en place des fonction du rumen chez le veau de race laitière et effet de la supplémentation en levures vivantes. : Establishment of ruminal microbiota and function in the dairy calf and the effect of live yeasts supplementation. [Internet] [Doctoral dissertation]. INP Toulouse; 2012. [cited 2021 Apr 16].
Available from: http://www.theses.fr/2012INPT0086.
Council of Science Editors:
Rey M. Implantation du microbiote et mise en place des fonction du rumen chez le veau de race laitière et effet de la supplémentation en levures vivantes. : Establishment of ruminal microbiota and function in the dairy calf and the effect of live yeasts supplementation. [Doctoral Dissertation]. INP Toulouse; 2012. Available from: http://www.theses.fr/2012INPT0086

INP Toulouse
20.
Zened, Asma.
Particularités du microbiote et son activité lors de la déviation de la biohydrogénation ruminale de l'acide linoléique de la voie trans-11 à la voie trans-10 : Features of the rumen microbiota and its activity associated with the shift of linoleic acid biohydrogenation from trans-11 to trans-10 pathway.
Degree: Docteur es, Pathologie, Toxicologie, Génétique et Nutrition, 2011, INP Toulouse
URL: http://www.theses.fr/2011INPT0083
► La biohydrogénation (BH) ruminale des acides gras polyinsaturés (AGPI) est à l'origine de la production d'intermédiaires trans retrouvés dans les productions de ruminants (essentiellement le…
(more)
▼ La biohydrogénation (BH) ruminale des acides gras polyinsaturés (AGPI) est à l'origine de la production d'intermédiaires trans retrouvés dans les productions de ruminants (essentiellement le lait). Il existe deux voies de BH produisant des acides gras (AG) trans qui auraient des propriétés différentes : les isomères t11 auraient des effets bénéfiques pour la santé des consommateurs et les isomères t10 seraient responsables d'une forte diminution du taux butyreux du lait, représentant une contrainte majeure pour les éleveurs. Dans des conditions physiologiques normales, la voie t11 est fortement majoritaire, par contre avec des rations à base d'ensilage de maïs, riches en concentrés et surtout si elles comprennent des suppléments lipidiques riches en AGPI, une déviation de la voie t11 à la voie t10 peut se produire avec une augmentation significative des isomères t10 au détriment des isomères t11. L'objectif de cette thèse est d'expliquer les modalités de cette déviation, afin de mieux la maîtriser en élevage. Nos travaux permettent de conclure que les facteurs alimentaires de maîtrise de la déviation de la voie t11 vers la voie t10, sont la teneur en amidon rapidement fermentescible et la teneur en c9,c12-C18:2. Lorsque la quantité de c9,c12-C18:2 présente dans le rumen est faible, même avec une ration riche en amidon et un pH bas dans le rumen, la déviation n'a pas lieu, la voie t11 suffisant à assurer l'hydrogénation des AGPI puisque dans ces conditions, la ∆9 isomérisation est elle aussi peu efficace à pH bas. En revanche, lorsqu'en plus de l'amidon, du c9,c12-C18:2 est ajouté dans la ration, la voie t11 devient insuffisante et c'est la voie t10 qui prend le relais. Le pyroséquençage 454 couplé à une régression multiple SPLS nous ont permis d'établir des corrélations entre les taxons identifiés et la proportion d'AG (t10 ou t11) dans le rumen. Il s'avère que les genres bactériens corrélés fortement et positivement aux AG t10 sont plus ou moins impliqués dans le métabolisme ruminal du lactate ainsi qu'au faible pH ruminal. Cependant, l'identification des taxons les plus corrélés aux AG t11 était moins précise, elle s'arrête à l'ordre des Clostridiales. Enfin, dans des conditions de déviation de la voie t11 à la voie t10, l'addition de vitamine E dans la ration des vaches n'a pas permis de restaurer un ratio déjà élevé. Ces résultats ont abouti à une meilleure compréhension de cette déviation et orientent vers une meilleure maîtrise en élevage.
Rumen biohydrogenation (BH) of polyunsaturated fatty acids (PUFA) is responsible of the production of trans intermediates found in ruminant products (mainly milk). There are two BH pathways leading to trans fatty acids (FA) with different biological properties: t11 isomers have beneficial effects for consumer's health and t10 isomers result in low milk fat content, representing a major constraint for farmers. In most conditions, t11 FA are the major trans FA, but in some conditions, especially with diets based on corn silage and including lipid supplements rich in PUFA, a…
Advisors/Committee Members: Enjalbert, Francis (thesis director), Najar, Taha (thesis director).
Subjects/Keywords: Biohydrogénation; Rumen; Amidon; Acide linoléique; Alimentation; Ratio trans10 / trans11; Pyroséquençage 454; Microbiote; Biohydrogenation; Rumen; Starch; Linoleic acid; Diet; Trans10 / trans11 ratio; 454 pyrosequencing; Microbiota
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APA (6th Edition):
Zened, A. (2011). Particularités du microbiote et son activité lors de la déviation de la biohydrogénation ruminale de l'acide linoléique de la voie trans-11 à la voie trans-10 : Features of the rumen microbiota and its activity associated with the shift of linoleic acid biohydrogenation from trans-11 to trans-10 pathway. (Doctoral Dissertation). INP Toulouse. Retrieved from http://www.theses.fr/2011INPT0083
Chicago Manual of Style (16th Edition):
Zened, Asma. “Particularités du microbiote et son activité lors de la déviation de la biohydrogénation ruminale de l'acide linoléique de la voie trans-11 à la voie trans-10 : Features of the rumen microbiota and its activity associated with the shift of linoleic acid biohydrogenation from trans-11 to trans-10 pathway.” 2011. Doctoral Dissertation, INP Toulouse. Accessed April 16, 2021.
http://www.theses.fr/2011INPT0083.
MLA Handbook (7th Edition):
Zened, Asma. “Particularités du microbiote et son activité lors de la déviation de la biohydrogénation ruminale de l'acide linoléique de la voie trans-11 à la voie trans-10 : Features of the rumen microbiota and its activity associated with the shift of linoleic acid biohydrogenation from trans-11 to trans-10 pathway.” 2011. Web. 16 Apr 2021.
Vancouver:
Zened A. Particularités du microbiote et son activité lors de la déviation de la biohydrogénation ruminale de l'acide linoléique de la voie trans-11 à la voie trans-10 : Features of the rumen microbiota and its activity associated with the shift of linoleic acid biohydrogenation from trans-11 to trans-10 pathway. [Internet] [Doctoral dissertation]. INP Toulouse; 2011. [cited 2021 Apr 16].
Available from: http://www.theses.fr/2011INPT0083.
Council of Science Editors:
Zened A. Particularités du microbiote et son activité lors de la déviation de la biohydrogénation ruminale de l'acide linoléique de la voie trans-11 à la voie trans-10 : Features of the rumen microbiota and its activity associated with the shift of linoleic acid biohydrogenation from trans-11 to trans-10 pathway. [Doctoral Dissertation]. INP Toulouse; 2011. Available from: http://www.theses.fr/2011INPT0083
21.
Gustavo Rocha Garcia.
Estudo do proteoma e imunoproteoma salivar do carrapato de bovinos, Rhipicephalus (Boophilus) microplus, para identificação e caracterização de antígenos silenciosos.
Degree: 2013, University of São Paulo
URL: http://www.teses.usp.br/teses/disponiveis/17/17147/tde-27052013-085600/
► Infestações com Rhipicephalus microplus, o carrapato dos bovinos, causam enormes prejuízos econômicos para a pecuária. Os carrapatos estão desenvolvendo resistência aos carrapaticidas que, além dessa…
(more)
▼ Infestações com Rhipicephalus microplus, o carrapato dos bovinos, causam enormes prejuízos econômicos para a pecuária. Os carrapatos estão desenvolvendo resistência aos carrapaticidas que, além dessa desvantagem, deixam resíduos em carne e leite. Vacinas anticarrapato representam uma alternativa sustentável de controle de infestações, mas as atualmente disponíveis têm efeitos parciais e transitórios. Surge, assim, a necessidade de identificar novos antígenos vacinais. Para alcançar esse objetivo este trabalho explora o fato de que bovinos apresentam fenótipos contrastantes e herdáveis de infestações que são específicos de certas raças. Além disso, o nível de imunidade do hospedeiro afeta a transcrição de genes de glândulas salivares do carrapato, órgão que produz proteínas que medeiam o parasitismo. A hipótese de trabalho é a que os diferentes níveis da imunidade anticarrapato do hospedeiro afetam, também, a composição salivar do parasita. Assim,
em carrapatos alimentando-se em hospedeiros resistentes as proteínas que são cruciais ao parasitismo poderão estar ausentes ou deficientes na sua saliva e por isso os carrapatos não terminam sua refeição de sangue. A neutralização dessas mesmas proteínas pela imunidade humoral pode ter o mesmo efeito e por isso, essas proteínas constituem bons antígenos vacinais. Assim, o objetivo do trabalho foi identificar novos antígenos vacinais em saliva de fêmeas e glândulas salivares de ninfas, machos e fêmeas de carrapatos alimentados em hospedeiros resistentes e suscetíveis, bem como em larvas não alimentadas oriundas de ovos de fêmeas alimentadas nestes mesmos hospedeiros. Para isso, foram empregadas abordagens de sequenciamento de nova geração \"RNA-Seq(̈
454) e abordagens proteômicas, como análise diferencial em gel (DIGE) e Western Blots (imunoproteoma) seguido de sequenciamento de massa, além da tecnologia de identificação de proteínas multidimensionais (ou Multidimensional Protein
Identification Technology, MudPIT) para descrever o proteoma das glândulas salivares e da saliva de fêmeas. A análise transcriptômica resultou no sequencimanto de 1.999.086 reads que permitiu identificar e classificar 11.676 sequências codificadoras (CDS), muitas das quais (3.600 CDS) contêm peptídeo sinal que é indicativo de secreção, portanto podendo estar presente na saliva e Resumo Gustavo Rocha Garcia apresentar função importante na hematofagia. Por meio de MudPIT, identificamos 321 proteínas salivares diferentes, além de 126 proteínas no DIGE e 266 proteínas nos imunoproteomas. Muitas dessas proteínas podem ser consideradas antígenos potenciais por estarem associadas com a hematofagia/parasitismo, tais como proteases, nucleases, inibidores de proteases, peptídeos antimicrobianos, proteínas de fixação, entre outros, inclusive proteínas ainda não caracterizadas. A maioria dos genes codificantes dessas proteínas está mais expressa em carrapatos alimentados em hospedeiros
suscetíveis, principalmente em carrapatos machos. Além disso, muitas dessas proteínas não são reconhecidas por soros bovinos,…
Advisors/Committee Members: Isabel Kinney Ferreira de Miranda Santos, Angela Kaysel Cruz, Fábio Cesar Gozzo, Wilson Araújo da Silva Junior, Russolina Benedeta Zingali.
Subjects/Keywords: carrapato Rhipicephalus microplus; imunoproteoma; MudPIT e DIGE; proteomas salivares do carrapato; sialotranscriptoma - 454 sequencing technology; immunoproteome; MudPIT and DIGE.; Rhipicephalus microplus tick; sialotranscriptome - 454 sequencing technology; tick salivary proteomes
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
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APA (6th Edition):
Garcia, G. R. (2013). Estudo do proteoma e imunoproteoma salivar do carrapato de bovinos, Rhipicephalus (Boophilus) microplus, para identificação e caracterização de antígenos silenciosos. (Doctoral Dissertation). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/17/17147/tde-27052013-085600/
Chicago Manual of Style (16th Edition):
Garcia, Gustavo Rocha. “Estudo do proteoma e imunoproteoma salivar do carrapato de bovinos, Rhipicephalus (Boophilus) microplus, para identificação e caracterização de antígenos silenciosos.” 2013. Doctoral Dissertation, University of São Paulo. Accessed April 16, 2021.
http://www.teses.usp.br/teses/disponiveis/17/17147/tde-27052013-085600/.
MLA Handbook (7th Edition):
Garcia, Gustavo Rocha. “Estudo do proteoma e imunoproteoma salivar do carrapato de bovinos, Rhipicephalus (Boophilus) microplus, para identificação e caracterização de antígenos silenciosos.” 2013. Web. 16 Apr 2021.
Vancouver:
Garcia GR. Estudo do proteoma e imunoproteoma salivar do carrapato de bovinos, Rhipicephalus (Boophilus) microplus, para identificação e caracterização de antígenos silenciosos. [Internet] [Doctoral dissertation]. University of São Paulo; 2013. [cited 2021 Apr 16].
Available from: http://www.teses.usp.br/teses/disponiveis/17/17147/tde-27052013-085600/.
Council of Science Editors:
Garcia GR. Estudo do proteoma e imunoproteoma salivar do carrapato de bovinos, Rhipicephalus (Boophilus) microplus, para identificação e caracterização de antígenos silenciosos. [Doctoral Dissertation]. University of São Paulo; 2013. Available from: http://www.teses.usp.br/teses/disponiveis/17/17147/tde-27052013-085600/

Penn State University
22.
Lin, Yishan.
Evaluation of microbial communities and their relationships with chemical performance in passive acid mine drainage treatment systems amended with crab shell.
Degree: 2013, Penn State University
URL: https://submit-etda.libraries.psu.edu/catalog/19891
► Acid mine drainage (AMD), a common environmental problem caused by mining activities, adversely impacts receiving watersheds, wildlife, and even public health due to its low…
(more)
▼ Acid mine drainage (AMD), a common environmental problem caused by mining activities, adversely impacts receiving watersheds, wildlife, and even public health due to its low pH and high concentration of toxic metals. The choice of organic substrates utilized in low-cost, low-maintenance, passive treatment systems for AMD is crucial to maintain a diverse microbial community for successful remediation. Recent studies by our research team have shown that crab shell (CS) amendments improve the longevity and performance of traditional AMD treatment systems containing spent mushroom compost (SMC). However, the microbial contribution to this has not been thoroughly explained. In this research, both chemical and biological techniques were used to comprehensively evaluate microbial communities and their relationship with chemical performance under varying environmental conditions in passive AMD treatment systems amended with CS. This might shed light on future design and operation strategies for AMD bioremediation systems.
Previous performance data of five sulfate-reducing columns treating AMD suggested that columns amended with higher fractions of CS supported more efficient and stable performance in terms of alkalinity generation, sulfate reduction, and metal removal, as compared to columns with traditional SMC and limestone substrates. Accordingly, microbial analyses conducted on packing materials of the five columns in this study revealed significant advantages of CS amendment in sustaining the growth of functionally more diverse microbial groups including cellulose degraders, chitin degraders, fermenters, and sulfur or sulfate reducers. Remarkably, the 100% CS column supported the growth of sulfate-reducing bacteria (SRB) from eight different genera—key players in AMD treatment systems. PCoA and phylogenetic ARB trees showed that bacterial communities in 50% CS and 100% CS columns were more likely to cluster together. Archaea predominantly identified as methanogens and fungi capable of polysaccharide degradation were only detected in columns containing SMC. In the 100% CS column, copy numbers of the functional genes representing fermenters, sulfate reducers, and chitin degraders were approximately 2.4, 3.9, and 3.2 times higher than those in SMC column, respectively.
In a field study, four pilot-scale vertical flow pond (VFP) systems featuring different substrate combinations of CS and SMC and different underdrain materials were constructed and operated for 633 days at the Klondike-1 site in Cambria County, PA. Analyses of chemical performance data,
454 sequencing, and quantitative PCR (qPCR) data suggested that under changing environmental conditions at the Klondike-1 site, the VFPs containing CS sustained more efficient and reliable treatment of AMD coupled with functionally more diverse and stable microbial communities. Influent pH rapidly increased from < 3.0 to above 6.0 and was maintained circum-neutral by all VFPs. As compared to a control reactor containing SMC, the reactors containing CS sustained higher…
Advisors/Committee Members: Rachel Alice Brennan, Dissertation Advisor/Co-Advisor, Rachel Alice Brennan, Committee Chair/Co-Chair, John Michael Regan, Committee Member, William D Burgos, Committee Member, Maryann Victoria Bruns, Committee Member.
Subjects/Keywords: acid mine drainage; chitin; bioremediation; cloning; qPCR; 454 sequencing; sulfate-reducing bacteria; Manganese removal
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Lin, Y. (2013). Evaluation of microbial communities and their relationships with chemical performance in passive acid mine drainage treatment systems amended with crab shell. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/19891
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Lin, Yishan. “Evaluation of microbial communities and their relationships with chemical performance in passive acid mine drainage treatment systems amended with crab shell.” 2013. Thesis, Penn State University. Accessed April 16, 2021.
https://submit-etda.libraries.psu.edu/catalog/19891.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Lin, Yishan. “Evaluation of microbial communities and their relationships with chemical performance in passive acid mine drainage treatment systems amended with crab shell.” 2013. Web. 16 Apr 2021.
Vancouver:
Lin Y. Evaluation of microbial communities and their relationships with chemical performance in passive acid mine drainage treatment systems amended with crab shell. [Internet] [Thesis]. Penn State University; 2013. [cited 2021 Apr 16].
Available from: https://submit-etda.libraries.psu.edu/catalog/19891.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Lin Y. Evaluation of microbial communities and their relationships with chemical performance in passive acid mine drainage treatment systems amended with crab shell. [Thesis]. Penn State University; 2013. Available from: https://submit-etda.libraries.psu.edu/catalog/19891
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Saskatchewan
23.
Li, Minghui.
Assessment of arbuscular mycorrhizal fungi in flax production.
Degree: 2015, University of Saskatchewan
URL: http://hdl.handle.net/10388/ETD-2015-10-2394
► Arbuscular mycorrhizal fungi (AMF) play an important role in nutrient cycling and growth of flax (Linum usitatissimum L.). However, limited information is available regarding the…
(more)
▼ Arbuscular mycorrhizal fungi (AMF) play an important role in nutrient cycling and growth of flax (Linum usitatissimum L.). However, limited information is available regarding the symbiotic association between flax and AMF in field environments. A study was conducted to survey AMF communities colonizing flax grown in Saskatchewan. Additionally, field and growth chamber studies investigated the impact of AMF inoculation on nutrient uptake and growth of flax. Eighteen commercial flax fields were surveyed to assess mycorrhizal colonization of flax and to assess the impact of agricultural practices and soil abiotic factors on AMF activity. The flax root-associated AMF communities were explored using a
454 sequencing method, together with microscopic-based measurements of root AMF colonization and soil spore density. High levels of root colonization were detected in most flax fields. Of the 222 AMF operational taxonomic units (OTUs) identified in flax roots, 181 OTUs clustered as Funneliformis-Rhizophagus, 19 as Claroideoglomus, 14 as Paraglomus, six as Diversisporales and two as Archaeospora. Results suggest that tillage influenced the composition of AMF communities colonizing flax, and reduced relative AMF abundance and species richness. Additionally, AMF community characteristics were related to soil abiotic factors such as pH, EC, available phosphorus and nitrogen. Field experiments were conducted over two years (two sites per year) using a commercial AMF inoculant applied at three rates (0, 1X, and 2X the recommended rate) with or without P fertilizer (16.8 kg ha-1). The response of flax cultivars to AMF inoculation was examined in a growth chamber experiment. In addition,
454 sequencing was employed to examine the impact of AMF inoculation on root-associated AMF communities. Under field conditions, only one site showed increased root colonization with AMF inoculation. Flax responded to AMF inoculation differently under different field conditions. At the two sites with intermediate initial soil P level, evidence of increased above-ground biomass and plant nutrient uptake with AMF inoculation was observed. However, such an effect was not detected when P fertilizer was combined with the inoculation. At a low P site and an irrigated site, P application accounted for all of the increases in plant nutrient uptake and biomass of flax, whereas no responses to AMF inoculation were detected. The
454 sequencing revealed different inoculation-induced changes in the diversity and composition of root-associated AMF communities between sites, which was possibly related to different field environments and native AMF communities. In the growth chamber, AMF inoculation resulted in general increases of plant nutrient uptake among cultivars, but only one cultivar showed enhanced biomass with inoculation. The diversity of AMF communities colonizing different flax cultivars was generally reduced by AMF inoculation. Community composition shifted under AMF inoculation, and the shifts appeared to be cultivar specific. These results suggested…
Advisors/Committee Members: Walley, Fran, Germida, Jim, Schoenau, Jeff, Knight, Diane.
Subjects/Keywords: arbuscular mycorrhizal fungi; flax growth; flax nutrient uptake; 454 sequencing; community assembly
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Li, M. (2015). Assessment of arbuscular mycorrhizal fungi in flax production. (Thesis). University of Saskatchewan. Retrieved from http://hdl.handle.net/10388/ETD-2015-10-2394
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Li, Minghui. “Assessment of arbuscular mycorrhizal fungi in flax production.” 2015. Thesis, University of Saskatchewan. Accessed April 16, 2021.
http://hdl.handle.net/10388/ETD-2015-10-2394.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Li, Minghui. “Assessment of arbuscular mycorrhizal fungi in flax production.” 2015. Web. 16 Apr 2021.
Vancouver:
Li M. Assessment of arbuscular mycorrhizal fungi in flax production. [Internet] [Thesis]. University of Saskatchewan; 2015. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/10388/ETD-2015-10-2394.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Li M. Assessment of arbuscular mycorrhizal fungi in flax production. [Thesis]. University of Saskatchewan; 2015. Available from: http://hdl.handle.net/10388/ETD-2015-10-2394
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
24.
Tisserant, Emilie.
Analyse bioinformatique du transcriptome des champignons mycorhiziens Tuber melanosporum et Glomus intraradices : Bioinformatic analysis of the transcriptome of mycorrhizal fungi Tuber melanosporum and Glomus intraradices.
Degree: Docteur es, Biologie végétale et forestière, 2011, Université Henri Poincaré – Nancy I
URL: http://www.theses.fr/2011NAN10105
► La symbiose mycorhizienne est une interaction mutualiste formée entre les racines des plantes terrestres et des champignons du sol. Les changements morphoanatomiques associés au développement…
(more)
▼ La symbiose mycorhizienne est une interaction mutualiste formée entre les racines des plantes terrestres et des champignons du sol. Les changements morphoanatomiques associés au développement de cette symbiose sont accompagnés de modifications dans la régulation de l'expression génique. L'étude des profils transcriptomiques est donc fondamentale afin de caractériser les mécanismes moléculaires gouvernant la symbiose mycorhizienne. Le développement récent des approches de transcriptomique à haut débit offre de nouvelles perspectives pour la compréhension de ces mécanismes. Le travail entrepris dans le cadre de ce projet de thèse visait à caractériser in silico le transcriptome symbiotique du champignon ectomycorhizien Tuber melanosporum et du champignon endomycorhizien Glomus intraradices. Il s'agissait de mettre en place les outils et les protocoles bioinformatiques permettant l'exploitation des données transcriptomiques issues des nouvelles technologies de séquençage, afin de caractériser les transcrits exprimés par les symbiotes et d'identifier les gènes régulés au cours de la symbiose. Ce travail original a permis de souligner l'existence de traits communs aux profils d'expression des champignons mycorhiziens. De plus, la caractérisation du transcriptome de G. intraradices a permis d'établir le premier répertoire de gènes à l'échelle du génome pour un champignon endomycorhizien. Cette étude de génomique contribue à l'amélioration des connaissances sur les processus moléculaires qui sous-tendent la symbiose mycorhizienne et constitue une ressource unique pour de futures recherches sur les réseaux de gènes contrôlant la symbiose
Mycorrhizal symbiosis is a mutualistic interaction involving roots of terrestrial plants and soil fungi. Morphological changes associated with the development of this symbiosis are accompanied by changes in gene expression. The study of transcriptomic profiles is thus essential to characterize the molecular mechanisms that govern the mycorrhizal symbiosis. The recent development of high-throughput transcriptomic approaches provides new insights for the understanding of these mechanisms. The work undertaken during this thesis aimed to characterize in silico the transcriptome of the ectomycorrhizal fungus Tuber melanosporum and the endomycorrhizal fungus Glomus intraradices. In order to characterize transcripts expressed by the symbionts and to identify genes regulated during symbiosis, bioinformatic tools and protocols were implemented to process transcriptomic data derived from new sequencing technologies. This work has allowed to highlight common features in the expression profiles of mycorrhizal fungi. In addition, characterization of the G. intraradices transcriptome has allowed to establish the first genome-wide repertoire of genes for an endomycorrhizal fungus. The study helps to improve knowledge about the molecular processes underlying the mycorrhizal symbiosis and provides a unique resource for future research on the gene networks controlling symbiosis
Advisors/Committee Members: Martin, Francis (thesis director).
Subjects/Keywords: Symbiose; Champignons; Mycorhize; Transcriptomique; Bioinformatique; 454; RNA-Seq; 572.802 85; 579.617 85
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❌
APA ·
Chicago ·
MLA ·
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CSE |
Export
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Manager
APA (6th Edition):
Tisserant, E. (2011). Analyse bioinformatique du transcriptome des champignons mycorhiziens Tuber melanosporum et Glomus intraradices : Bioinformatic analysis of the transcriptome of mycorrhizal fungi Tuber melanosporum and Glomus intraradices. (Doctoral Dissertation). Université Henri Poincaré – Nancy I. Retrieved from http://www.theses.fr/2011NAN10105
Chicago Manual of Style (16th Edition):
Tisserant, Emilie. “Analyse bioinformatique du transcriptome des champignons mycorhiziens Tuber melanosporum et Glomus intraradices : Bioinformatic analysis of the transcriptome of mycorrhizal fungi Tuber melanosporum and Glomus intraradices.” 2011. Doctoral Dissertation, Université Henri Poincaré – Nancy I. Accessed April 16, 2021.
http://www.theses.fr/2011NAN10105.
MLA Handbook (7th Edition):
Tisserant, Emilie. “Analyse bioinformatique du transcriptome des champignons mycorhiziens Tuber melanosporum et Glomus intraradices : Bioinformatic analysis of the transcriptome of mycorrhizal fungi Tuber melanosporum and Glomus intraradices.” 2011. Web. 16 Apr 2021.
Vancouver:
Tisserant E. Analyse bioinformatique du transcriptome des champignons mycorhiziens Tuber melanosporum et Glomus intraradices : Bioinformatic analysis of the transcriptome of mycorrhizal fungi Tuber melanosporum and Glomus intraradices. [Internet] [Doctoral dissertation]. Université Henri Poincaré – Nancy I; 2011. [cited 2021 Apr 16].
Available from: http://www.theses.fr/2011NAN10105.
Council of Science Editors:
Tisserant E. Analyse bioinformatique du transcriptome des champignons mycorhiziens Tuber melanosporum et Glomus intraradices : Bioinformatic analysis of the transcriptome of mycorrhizal fungi Tuber melanosporum and Glomus intraradices. [Doctoral Dissertation]. Université Henri Poincaré – Nancy I; 2011. Available from: http://www.theses.fr/2011NAN10105

University of Arizona
25.
Ortiz-Ortiz, Marianyoly.
Kartchner Caverns: Habitat Scale Community Diversity and Function in a Carbonate Cave
.
Degree: 2012, University of Arizona
URL: http://hdl.handle.net/10150/265356
► This dissertation examines the microbial and functional diversity in Kartchner Caverns, a limestone cave in Arizona, USA. Kartchner is highly oligotrophic due to the lack…
(more)
▼ This dissertation examines the microbial and functional diversity in Kartchner Caverns, a limestone cave in Arizona, USA. Kartchner is highly oligotrophic due to the lack of photosynthesis and the limited inputs of organic material from the surface. This characteristic poses a challenge for microbial life in the cave. The first objective of this work was to evaluate the bacterial richness, diversity and taxonomic composition of speleothems surfaces within Kartchner Caverns in order to gain insight into the distribution patterns associated with these communities. Secondly, the metabolic strategies used by cave communities to survive harsh cave conditions were investigated based on phylogenetic associations and metagenomics. Both objectives were directed toward answering the questions "who are there?" and "what are they doing?". The
454-pyrotag analysis of the V6 region of the 16S rRNA gene revealed an unexpectedly high bacterial diversity with each speleothem supporting a unique bacterial community profile. A focused study on one room of the cave revealed three community types: Type 1 was dominated by the phylum Proteobacteria; Type 2 by Actinobacteria; and Type 3 by Acidobacteria. Phylogenetic associations of the sequences generated by the
454 sequencing and by a Sanger clone library suggested cave microbial communities are supported by chemoautotrophic activities such as nitrite and iron oxidation. Results from the phylogenetic associations guided the metagenomic analysis which supports the presence of chemoautotrophic activities in the cave. Genes for two complete CO2 fixation mechanisms, the Calvin-Benson-Bashan and the rTCA cycles were identified in the cave metagenome, as well as genes for ammonia and nitrite oxidation. These genes are associated with both Bacteria and Archaea suggesting members of both domains are acting as primary producers in the cave ecosystem. Comparative analysis of cave samples to other environments suggests an overabundance of DNA repair mechanisms which could be potentially used by cave communities to overcome the toxicity due to high concentrations of calcium on the speleothem surfaces. This work provides the first comprehensive analysis of the microbial diversity and potential strategies used by microbial communities to survive under the extreme conditions found in a semi-arid limestone cave environment.
Advisors/Committee Members: Curry, Joan (advisor), Rich, Virginia (committeemember), Vedantam, Gayatri (committeemember), Curry, Joan (committeemember), Maier, Raina M. (committeemember).
Subjects/Keywords: limestone cave;
metagenomic;
oligotrophy;
pyrosequencing;
Soil, Water & Environmental Science;
16S rRNA gene;
454-pyrotag
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
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APA (6th Edition):
Ortiz-Ortiz, M. (2012). Kartchner Caverns: Habitat Scale Community Diversity and Function in a Carbonate Cave
. (Doctoral Dissertation). University of Arizona. Retrieved from http://hdl.handle.net/10150/265356
Chicago Manual of Style (16th Edition):
Ortiz-Ortiz, Marianyoly. “Kartchner Caverns: Habitat Scale Community Diversity and Function in a Carbonate Cave
.” 2012. Doctoral Dissertation, University of Arizona. Accessed April 16, 2021.
http://hdl.handle.net/10150/265356.
MLA Handbook (7th Edition):
Ortiz-Ortiz, Marianyoly. “Kartchner Caverns: Habitat Scale Community Diversity and Function in a Carbonate Cave
.” 2012. Web. 16 Apr 2021.
Vancouver:
Ortiz-Ortiz M. Kartchner Caverns: Habitat Scale Community Diversity and Function in a Carbonate Cave
. [Internet] [Doctoral dissertation]. University of Arizona; 2012. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/10150/265356.
Council of Science Editors:
Ortiz-Ortiz M. Kartchner Caverns: Habitat Scale Community Diversity and Function in a Carbonate Cave
. [Doctoral Dissertation]. University of Arizona; 2012. Available from: http://hdl.handle.net/10150/265356

Brigham Young University
26.
Vert, Joshua Christopher.
Hypersaline Lake Environments Exhibit Reduced Microbial Dormancy.
Degree: MS, 2013, Brigham Young University
URL: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=5049&context=etd
► From acid seeps and deep-sea thermal vents to glacial ice and hypersaline lakes, extreme environments contain relatively simplified communities consisting of extremophiles that have evolved…
(more)
▼ From acid seeps and deep-sea thermal vents to glacial ice and hypersaline lakes, extreme environments contain relatively simplified communities consisting of extremophiles that have evolved to survive and thrive under adverse abiotic conditions. In more neutral environments, microorganisms use dormancy as a common life history strategy to weather temporal fluctuations of resources or stresses until more 'optimal' conditions are present. It is unclear if dormancy is an essential survival mechanism for microorganisms in extreme environments; however, recent studies suggest that extreme environments may create stable conditions for extremophiles to the extent that dormancy is of less ecological importance. Using lake salinity levels as measurements of "extreme," we evaluated the dormancy of bacterial and archaeal phyla and lake chemistry in five hypersaline and five freshwater lakes across the western United States. Dormancy was calculated using targeted metagenomics to analyze 16S rDNA and rRNA tag sequences. It was hypothesized that bacteria and archaea in hypersaline lake communities would exhibit lower levels dormancy than bacterial and archaeal communities in geologically similar freshwater lake controls. It was also hypothesized that microbial dormancy would decrease as the dominant extreme environmental variable increased in the lakes. As hypothesized, overall dormancy decreased at least 2-fold in hypersaline compared to freshwater lakes for both bacteria and archaea. Of the predominant phyla and subclasses, Firmicutes, Bacteroidetes, and Gammaproteobacteria each demonstrated at least a seven-fold decrease in dormancy in hypersaline lakes compared to freshwater lakes. Specifically, species within the genus Clostridium were responsible for 85% of the dormancy observed in the phylum Firmicutes. Also as hypothesized, microbial dormancy decreased as salinity increased in the lakes. Lower dormancy in hypersaline lakes correlated with increasing salinity while lower dormancy in freshwater lakes correlated with increasing total phosphorus levels. These results suggest that dormancy is a less common life history strategy for microorganisms in extreme environments; it is proposed that this is due to the relatively stable environment in hypersaline lakes and the reduced number of available microbial niches. These results also suggest that the dominant extreme stress (i.e., salinity) may override other driving factors in an environment to ultimately determine microbial community composition, diversity and richness.
Subjects/Keywords: niche differentiation; archaea; bacteria; 454 pyrosequencing; 16S; targeted metagenomics; phosphorus; extremophiles; Microbiology
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Vert, J. C. (2013). Hypersaline Lake Environments Exhibit Reduced Microbial Dormancy. (Masters Thesis). Brigham Young University. Retrieved from https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=5049&context=etd
Chicago Manual of Style (16th Edition):
Vert, Joshua Christopher. “Hypersaline Lake Environments Exhibit Reduced Microbial Dormancy.” 2013. Masters Thesis, Brigham Young University. Accessed April 16, 2021.
https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=5049&context=etd.
MLA Handbook (7th Edition):
Vert, Joshua Christopher. “Hypersaline Lake Environments Exhibit Reduced Microbial Dormancy.” 2013. Web. 16 Apr 2021.
Vancouver:
Vert JC. Hypersaline Lake Environments Exhibit Reduced Microbial Dormancy. [Internet] [Masters thesis]. Brigham Young University; 2013. [cited 2021 Apr 16].
Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=5049&context=etd.
Council of Science Editors:
Vert JC. Hypersaline Lake Environments Exhibit Reduced Microbial Dormancy. [Masters Thesis]. Brigham Young University; 2013. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=5049&context=etd

Brigham Young University
27.
Bajgain, Prabin.
Transcriptome Characterization and Polymorphism Detection in Subspecies of Big Sagebrush (Artemisia tridentata).
Degree: MS, 2011, Brigham Young University
URL: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3654&context=etd
► Big sagebrush (Artemisia tridentata) is one of the ecologically most important shrub species in western North America. The species serves as a major source…
(more)
▼ Big sagebrush (Artemisia tridentata) is one of the ecologically most important shrub species in western North America. The species serves as a major source of food and habitat for the near-threatened sage grouse and various other fauna. Habitat loss due to a combination of disturbances followed by establishment of invasive plant species is considered as a serious threat to sustainability of the big sagebrush ecosystem. Because of its importance, restoration of this species is very crucial to those dependent on big sagebrush community. However, restoration of big sagebrush carried out by using diverse seed source can lead to imbalance and degradation in the native ecosystem. Therefore, restoration works aided by understanding of adaptive traits of big sagebrush using molecular markers will aid successful restoration. The major objective of this research was to create a substantial resource of nuclear sequence data and identify markers that can be used in future studies in big sagebrush. We report the development and annotation of the first expressed sequence tag (EST) collection for big sagebrush based on 454 sequencing of leaf tissue. Expressed genes of subspecies tridentata and vaseyana were sequenced using the 454 GS-FLX titanium platform, which produced 823,392 reads with an average read length of 404 bp and 702,001 reads with an average read length of 333 bp for sspp. tridentata and vaseyana, respectively. Assembly of the reads resulted in 212,102 consensus sequences in ssp. tridentata and 199,439 in ssp. vaseyana. A combined assembly of both subspecies sequences generated 29,541 contigs with an average length of 796 bp and 275,866 singletons with an average length of 370 bp. A BLASTx search against the non-redundant (NR) protein database using the contigs obtained from a combined assembly resulted in 21,436 sequences with significant blast alignments (≤ 1e-15). Gene Ontology (GO) IDs were assigned to 18,397 sequences. A total of 20,952 SNPs were detected between the two subspecies and 1,182 SNPs were confirmed in tetraploid ssp. wyomingensis. In addition, 1,003 and 507 SSRs were detected in ssp. tridentata contigs and ssp. vaseyana contigs, respectively.
Subjects/Keywords: Artemisia tridentata; EST assembly; 454 sequencing; SNPs; SSRs; Ka; Ks; Animal Sciences
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Bajgain, P. (2011). Transcriptome Characterization and Polymorphism Detection in Subspecies of Big Sagebrush (Artemisia tridentata). (Masters Thesis). Brigham Young University. Retrieved from https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3654&context=etd
Chicago Manual of Style (16th Edition):
Bajgain, Prabin. “Transcriptome Characterization and Polymorphism Detection in Subspecies of Big Sagebrush (Artemisia tridentata).” 2011. Masters Thesis, Brigham Young University. Accessed April 16, 2021.
https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3654&context=etd.
MLA Handbook (7th Edition):
Bajgain, Prabin. “Transcriptome Characterization and Polymorphism Detection in Subspecies of Big Sagebrush (Artemisia tridentata).” 2011. Web. 16 Apr 2021.
Vancouver:
Bajgain P. Transcriptome Characterization and Polymorphism Detection in Subspecies of Big Sagebrush (Artemisia tridentata). [Internet] [Masters thesis]. Brigham Young University; 2011. [cited 2021 Apr 16].
Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3654&context=etd.
Council of Science Editors:
Bajgain P. Transcriptome Characterization and Polymorphism Detection in Subspecies of Big Sagebrush (Artemisia tridentata). [Masters Thesis]. Brigham Young University; 2011. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3654&context=etd

North-West University
28.
Jordaan, Karen.
Molecular profiling of microbial population dynamics in environmental water / Karen Jordaan
.
Degree: 2015, North-West University
URL: http://hdl.handle.net/10394/15308
► Increasing socio-economic growth and development of South Africa’s freshwater systems require continuous augmentation of water sources to meet the growing water requirements of communities and…
(more)
▼ Increasing socio-economic growth and development of South Africa’s freshwater systems require continuous augmentation of water sources to meet the growing water requirements of communities and industries. Anthropogenic disturbances have caused the water quality of many freshwater systems to drastically deteriorate due to constant disposal of domestic, industrial, and agricultural waste into surface waters. Government agencies make use of biomonitoring programmes to effectively manage the countries’ freshwater resources. These programmes use a variety of biological indicators (e.g., macroinvertebrates, fish, diatoms and algal species) and physico-chemical variables to determine the state of the environment. However, attempts to use microbial community structures as bioindicators of anthropogenic perturbations are greatly neglected. This study used molecular techniques (PCR-DGGE and 454-pyrosequencing) and multivariate analysis to develop a robust monitoring technique to determine the impacts of environmental disturbances on bacterial community compositions in river systems in the North West Province. Significant contributions made by this project included the establishment of a bacterial diversity framework for South African freshwater systems that are impacted by a variety of anthropogenic activities (e.g., urban and informal settlements, agriculture and mining). Furthermore, case studies demonstrated the prevalence of specific taxa at polluted sites, as well as positive and negative associations between taxa and environmental variables and pollutants. Finally, biogeochemical cycles could be partially matched to bacterial community structures in river systems. The first part of the project included a pilot study that investigated bacterial structures in a segment of the Vaal River in response to environmental parameters using molecular techniques and multivariate analysis. The most important observations made during this study included the generation of a larger bacterial diversity dataset by pyrosequencing compared to PCR-DGGE. In addition, metagenomic and multivariate analyses provided clues about potential biogeochemical roles of different taxa. The second and third part of the project included two case studies that investigated bacterial communities in the Mooi River and Wonderfonteinspruit in response to environmental activities. Both these systems are impacted by a variety of external sources such as urban and informal settlements, agriculture, and mining. The results demonstrated that perturbations nearby the Mooi River and Wonderfonteinspruit caused the overall water quality to deteriorate which in
turn had a profound impact on bacterial community composition. Bacterial community structures at reference/control sites (Muiskraal and Turffontein dolomitic eye) had overall high species diversity (richness and evenness), whereas polluted sites showed lower species diversity and were dominated by the Beta- and Gammaproteobacteria, Bacteroidetes, and Verrucomicrobia. In addition, various potential pathogens (e.g.…
Subjects/Keywords: Freshwater;
Physico-chemical parameters;
Bacterial community composition;
PCR-DGGE;
454-pyrosequencing;
Multivariate analysis
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Jordaan, K. (2015). Molecular profiling of microbial population dynamics in environmental water / Karen Jordaan
. (Thesis). North-West University. Retrieved from http://hdl.handle.net/10394/15308
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Jordaan, Karen. “Molecular profiling of microbial population dynamics in environmental water / Karen Jordaan
.” 2015. Thesis, North-West University. Accessed April 16, 2021.
http://hdl.handle.net/10394/15308.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Jordaan, Karen. “Molecular profiling of microbial population dynamics in environmental water / Karen Jordaan
.” 2015. Web. 16 Apr 2021.
Vancouver:
Jordaan K. Molecular profiling of microbial population dynamics in environmental water / Karen Jordaan
. [Internet] [Thesis]. North-West University; 2015. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/10394/15308.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Jordaan K. Molecular profiling of microbial population dynamics in environmental water / Karen Jordaan
. [Thesis]. North-West University; 2015. Available from: http://hdl.handle.net/10394/15308
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Manitoba
29.
Liang, Binhua.
Examination of HIV-1 diversity and evolution by a bioinformatics approach.
Degree: Medical Microbiology, 2010, University of Manitoba
URL: http://hdl.handle.net/1993/3932
► HIV-1 genetic diversity is a major obstacle for developing an effective vaccine. My hypothesis is that HIV-1 genetic diversity can be characterized and that cross-clade…
(more)
▼ HIV-1 genetic diversity is a major obstacle for developing an effective vaccine. My hypothesis is that HIV-1 genetic diversity can be characterized and that cross-clade immunogens can be predicted at the population level. I systematically investigated positive selection (PS) pressures on HIV-1 Env and Gag proteins based on the analysis of the sequences collected from the Los Alamos Sequence Database. I identified PS sites, investigated PS patterns, correlated PS with the known functional sites of the two proteins, calculated frequencies of HLA alleles targeting CTL epitopes, and compared PS patterns among major subtypes. The results showed that PS pressure was widely dispersed across the entire regions of both HIV-1 Env and Gag proteins, suggesting the conserved regions are under host immune response pressure. The neutralizing antibody, non-neutralizing antibody, and CTL responses were found to be the major forces driving genetic diversity of HIV-1 env and gag genes at population level. However, PS pressures on both Env and Gag proteins remain stable over time, suggesting genetic diversity of HIV-1 driven by host immune responses changed very little over the last 29 years. Furthermore, the results also demonstrated that up to 70% PS sites were shared among the major HIV-1 clades, implying the existence of cross-clade immunogenicity. A number of potential cross-clades immunogens were predicted to elicit CTL or neutralizing antibody responses from Env and Gag proteins. I also detected a significant correlation between HLA allele frequencies and host CTL responses elicited by Accessory/Regulator’s proteins at population level. Moreover, I detected an association between the frequency of HLA-B7 supertype and the number of identified optimal CTL epitopes. The results suggest HLA class I allele frequencies in a population influence the evolution of HIV-1. I also systematically evaluated the utility of ultra-deep pyrosequencing to characterize genetic diversity of HIV-1 gag genes within quasispecies. The results showed that ultra-deep pyrosequencing of amplified HIV genes is a better method than the traditional Sanger-clone-based method in the comprehensive characterization of genetic diversity of HIV-1 quasispecies, especially in detecting low frequency variations. In conclusion, my thesis provides important information for rational design of an effective HIV-1 vaccine.
Advisors/Committee Members: Plummer, Francis A. (Medical Microbiology) Jones, Steven J.M. (Medical Microbiology) (supervisor), Yang, Xi (Medical Microbiology) Ball, Blake T. (Medical Microbiology) Fristensky, Brian W. (Plant Science)Van Domselaar, Gary (Pharmacy).
Subjects/Keywords: HIV-1; Bioinformatics; Evolution; Envelope; Gag; 454; Positive selection; Host immune response; CTL
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Liang, B. (2010). Examination of HIV-1 diversity and evolution by a bioinformatics approach. (Thesis). University of Manitoba. Retrieved from http://hdl.handle.net/1993/3932
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Liang, Binhua. “Examination of HIV-1 diversity and evolution by a bioinformatics approach.” 2010. Thesis, University of Manitoba. Accessed April 16, 2021.
http://hdl.handle.net/1993/3932.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Liang, Binhua. “Examination of HIV-1 diversity and evolution by a bioinformatics approach.” 2010. Web. 16 Apr 2021.
Vancouver:
Liang B. Examination of HIV-1 diversity and evolution by a bioinformatics approach. [Internet] [Thesis]. University of Manitoba; 2010. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/1993/3932.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Liang B. Examination of HIV-1 diversity and evolution by a bioinformatics approach. [Thesis]. University of Manitoba; 2010. Available from: http://hdl.handle.net/1993/3932
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of New Mexico
30.
Preut, Meghan.
COMMUNITY ANALYSIS OF A UNIQUE FULL-SCALE WASTEWATER TREATMENT PLANT AS REVEALED BY 454-PYROSEQUENCING.
Degree: Civil Engineering, 2014, University of New Mexico
URL: http://hdl.handle.net/1928/24508
► Activated sludge is one of the most commonly applied biological treatment processes for wastewater treatment. The microorganisms grown in activated sludge systems are responsible for…
(more)
▼ Activated sludge is one of the most commonly applied biological treatment processes for wastewater treatment. The microorganisms grown in activated sludge systems are responsible for the removal and transformation of wastewater contaminants. These bacterial populations are sensitive to wastewater characteristics, plant design and operational parameters. Because the effectiveness of activated sludge relies on microbial activity, a better understanding of the microbial communities and how they respond to constraints may be useful for improving plant performance. Environmental conditions in the activated sludge process are complex and the identification and classification of the communities present has proven a challenge for engineers as well as microbiologists and ecologists. Many bacteria in activated sludge cannot be cultured and conventional culture dependent techniques are not adequate in defining these populations in depth. Recent molecular methods have advanced the understanding of this complicated ecosystem, yet much remains unclear due to plant specific dynamics that influence community structure. Sequencing techniques are a novel approach to the identification of the microbial populations of activated sludge. This new technology allows researchers to ask exploratory questions about specific and distinct wastewater treatment processes that could not be efficiently completed with other methods. One such unique wastewater treatment plant that may benefit from the use of pyrosequencing techniques is the Los Alamos National Laboratory Sanitary Wastewater System (LANL SWWS) located in Los Alamos, New Mexico. This plant experiences highly variable flow and utilizes glycerin as a supplemental carbon source due to low-strength carbon influent. In addition, the plant experienced an upset in 2012 with respect to excessive tardigrade growth. In response introduced sludge from another wastewater treatment plant (seed event) to help improve the microbial populations.
454-pyrosequencing was used as a method to identify and analyze the microbial populations of this glycerin enriched activated sludge wastewater treatment plant. The objectives of this research were to 1) determine the differences between LANL SWWS activated sludge population and that in other plants, 2) identify and evaluate the effects of glycerin as a supplemental carbon source on the microbial population, 3) identify any adaptive characteristics or population changes due to the seeding event, 4) determine if there were certain operational conditions or environmental factors that influence specific microbial populations. In order to accomplish these objectives, samples were taken from LANL SWWS and other nearby wastewater treatment plants. These samples were pyrosequenced and the results were analyzed with various bioinformatics tools. The microbial communities were compared between LANL SWWS and other plants that did not utilize an external carbon source. Analysis of the activated sludge population before and after the seed event was…
Advisors/Committee Members: Schuler, Andrew, Thomson, Bruce, Takacs-Vesbach, Cristina, Wingo, Robert.
Subjects/Keywords: Wastewater; Microbial populations; 454-pyrosequencing; supplemental carbon source; Glycerin; Los Alamos National Laboratory
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Preut, M. (2014). COMMUNITY ANALYSIS OF A UNIQUE FULL-SCALE WASTEWATER TREATMENT PLANT AS REVEALED BY 454-PYROSEQUENCING. (Masters Thesis). University of New Mexico. Retrieved from http://hdl.handle.net/1928/24508
Chicago Manual of Style (16th Edition):
Preut, Meghan. “COMMUNITY ANALYSIS OF A UNIQUE FULL-SCALE WASTEWATER TREATMENT PLANT AS REVEALED BY 454-PYROSEQUENCING.” 2014. Masters Thesis, University of New Mexico. Accessed April 16, 2021.
http://hdl.handle.net/1928/24508.
MLA Handbook (7th Edition):
Preut, Meghan. “COMMUNITY ANALYSIS OF A UNIQUE FULL-SCALE WASTEWATER TREATMENT PLANT AS REVEALED BY 454-PYROSEQUENCING.” 2014. Web. 16 Apr 2021.
Vancouver:
Preut M. COMMUNITY ANALYSIS OF A UNIQUE FULL-SCALE WASTEWATER TREATMENT PLANT AS REVEALED BY 454-PYROSEQUENCING. [Internet] [Masters thesis]. University of New Mexico; 2014. [cited 2021 Apr 16].
Available from: http://hdl.handle.net/1928/24508.
Council of Science Editors:
Preut M. COMMUNITY ANALYSIS OF A UNIQUE FULL-SCALE WASTEWATER TREATMENT PLANT AS REVEALED BY 454-PYROSEQUENCING. [Masters Thesis]. University of New Mexico; 2014. Available from: http://hdl.handle.net/1928/24508
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