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Search Results: 1 - 10 of 281 matches for " Garret Suen "
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Predicting Prokaryotic Ecological Niches Using Genome Sequence Analysis
Garret Suen, Barry S. Goldman, Roy D. Welch
PLOS ONE , 2007, DOI: 10.1371/journal.pone.0000743
Abstract: Automated DNA sequencing technology is so rapid that analysis has become the rate-limiting step. Hundreds of prokaryotic genome sequences are publicly available, with new genomes uploaded at the rate of approximately 20 per month. As a result, this growing body of genome sequences will include microorganisms not previously identified, isolated, or observed. We hypothesize that evolutionary pressure exerted by an ecological niche selects for a similar genetic repertoire in those prokaryotes that occupy the same niche, and that this is due to both vertical and horizontal transmission. To test this, we have developed a novel method to classify prokaryotes, by calculating their Pfam protein domain distributions and clustering them with all other sequenced prokaryotic species. Clusters of organisms are visualized in two dimensions as ‘mountains’ on a topological map. When compared to a phylogenetic map constructed using 16S rRNA, this map more accurately clusters prokaryotes according to functional and environmental attributes. We demonstrate the ability of this map, which we term a “niche map”, to cluster according to ecological niche both quantitatively and qualitatively, and propose that this method be used to associate uncharacterized prokaryotes with their ecological niche as a means of predicting their functional role directly from their genome sequence.
The Evolutionary Innovation of Nutritional Symbioses in Leaf-Cutter Ants
Frank O. Aylward,Cameron R. Currie,Garret Suen
Insects , 2012, DOI: 10.3390/insects3010041
Abstract: Fungus-growing ants gain access to nutrients stored in plant biomass through their association with a mutualistic fungus they grow for food. This 50 million-year-old obligate mutualism likely facilitated some of these species becoming dominant Neotropical herbivores that can achieve immense colony sizes. Recent culture-independent investigations have shed light on the conversion of plant biomass into nutrients within ant fungus gardens, revealing that this process involves both the fungal cultivar and a symbiotic community of bacteria including Enterobacter, Klebsiella, and Pantoea species. Moreover, the genome sequences of the leaf-cutter ants Atta cephalotes and Acromyrmex echinatior have provided key insights into how this symbiosis has shaped the evolution of these ants at a genetic level. Here we summarize the findings of recent research on the microbial community dynamics within fungus-growing ant fungus gardens and discuss their implications for this ancient symbiosis.
The genomic basis for the evolution of a novel form of cellular reproduction in the bacterium Epulopiscium
David A Miller, Garret Suen, Kendall D Clements, Esther R Angert
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-265
Abstract: To test this, we sequenced the genome of Epulopiscium sp. type B to draft quality. Comparative analysis with the complete genome of its close, endospore-forming relative, Cellulosilyticum lentocellum, identified homologs of well-known sporulation genes characterized in Bacillus subtilis. Of the 147 highly conserved B. subtilis sporulation genes used in this analysis, we found 57 homologs in the Epulopiscium genome and 87 homologs in the C. lentocellum genome.Genes coding for components of the central regulatory network which govern the expression of forespore and mother-cell-specific sporulation genes and the machinery used for engulfment appear best conserved. Low conservation of genes expressed late in endospore formation, particularly those that confer resistance properties and encode germinant receptors, suggest that Epulopiscium has lost the ability to form a mature spore. Our findings provide a framework for understanding the evolution of a novel form of cellular reproduction.
Microbial Community Structure of Leaf-Cutter Ant Fungus Gardens and Refuse Dumps
Jarrod J. Scott,Kevin J. Budsberg,Garret Suen,Devin L. Wixon,Teri C. Balser,Cameron R. Currie
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0009922
Abstract: Leaf-cutter ants use fresh plant material to grow a mutualistic fungus that serves as the ants' primary food source. Within fungus gardens, various plant compounds are metabolized and transformed into nutrients suitable for ant consumption. This symbiotic association produces a large amount of refuse consisting primarily of partly degraded plant material. A leaf-cutter ant colony is thus divided into two spatially and chemically distinct environments that together represent a plant biomass degradation gradient. Little is known about the microbial community structure in gardens and dumps or variation between lab and field colonies.
The Genome Sequences of Cellulomonas fimi and “Cellvibrio gilvus” Reveal the Cellulolytic Strategies of Two Facultative Anaerobes, Transfer of “Cellvibrio gilvus” to the Genus Cellulomonas, and Proposal of Cellulomonas gilvus sp. nov
Melissa R. Christopherson, Garret Suen, Shanti Bramhacharya, Kelsea A. Jewell, Frank O. Aylward, David Mead, Phillip J. Brumm
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0053954
Abstract: Actinobacteria in the genus Cellulomonas are the only known and reported cellulolytic facultative anaerobes. To better understand the cellulolytic strategy employed by these bacteria, we sequenced the genome of the Cellulomonas fimi ATCC 484T. For comparative purposes, we also sequenced the genome of the aerobic cellulolytic “Cellvibrio gilvus” ATCC 13127T. An initial analysis of these genomes using phylogenetic and whole-genome comparison revealed that “Cellvibrio gilvus” belongs to the genus Cellulomonas. We thus propose to assign “Cellvibrio gilvus” to the genus Cellulomonas. A comparative genomics analysis between these two Cellulomonas genome sequences and the recently completed genome for Cellulomonas flavigena ATCC 482T showed that these cellulomonads do not encode cellulosomes but appear to degrade cellulose by secreting multi-domain glycoside hydrolases. Despite the minimal number of carbohydrate-active enzymes encoded by these genomes, as compared to other known cellulolytic organisms, these bacteria were found to be proficient at degrading and utilizing a diverse set of carbohydrates, including crystalline cellulose. Moreover, they also encode for proteins required for the fermentation of hexose and xylose sugars into products such as ethanol. Finally, we found relatively few significant differences between the predicted carbohydrate-active enzymes encoded by these Cellulomonas genomes, in contrast to previous studies reporting differences in physiological approaches for carbohydrate degradation. Our sequencing and analysis of these genomes sheds light onto the mechanism through which these facultative anaerobes degrade cellulose, suggesting that the sequenced cellulomonads use secreted, multidomain enzymes to degrade cellulose in a way that is distinct from known anaerobic cellulolytic strategies.
Sparse Additive Gaussian Process with Soft Interactions  [PDF]
Garret Vo, Debdeep Pati
Open Journal of Statistics (OJS) , 2017, DOI: 10.4236/ojs.2017.74039
Abstract: This paper presents a novel variable selection method in additive nonparametric regression model. This work is motivated by the need to select the number of nonparametric components and number of variables within each nonparametric component. The proposed method uses a combination of hard and soft shrinkages to separately control the number of additive components and the variables within each component. An efficient algorithm is developed to select the importance of variables and estimate the interaction network. Excellent performance is obtained in simulated and real data examples.
Computer Model for Evaluating Multi-Target Tracking Algorithms  [PDF]
Garret Vo, Chiwoo Park
Open Journal of Modelling and Simulation (OJMSi) , 2019, DOI: 10.4236/ojmsi.2019.71001
Abstract: Public benchmark datasets have been widely used to evaluate multi-target tracking algorithms. Ideally, the benchmark datasets should include the video scenes of all scenarios that need to be tested. However, a limited amount of the currently available benchmark datasets does not comprehensively cover all necessary test scenarios. This limits the evaluation of multitarget tracking algorithms with various test scenarios. This paper introduced a computer simulation model that generates benchmark datasets for evaluating multi-target tracking algorithms with the complexity of multitarget tracking scenarios directly controlled by simulation inputs such as target birth and death rates, target movement, the rates of target merges and splits, target appearances, and image noise types and levels. The simulation model generated a simulated video and also provides the ground-truth target tracking for the simulated video, so the evaluation of multitarget tracking algorithms can be easily performed without any manual video annotation process. We demonstrated the use of the proposed simulation model for evaluating tracking-by-detection algorithms and filtering-based tracking algorithms.
SREB, a GATA Transcription Factor That Directs Disparate Fates in Blastomyces dermatitidis Including Morphogenesis and Siderophore Biosynthesis
Gregory M. Gauthier ,Thomas D. Sullivan,Sergio S. Gallardo,T. Tristan Brandhorst,Amber J. Vanden Wymelenberg,Christina A. Cuomo,Garret Suen,Cameron R. Currie,Bruce S. Klein
PLOS Pathogens , 2010, DOI: 10.1371/journal.ppat.1000846
Abstract: Blastomyces dermatitidis belongs to a group of human pathogenic fungi that exhibit thermal dimorphism. At 22°C, these fungi grow as mold that produce conidia or infectious particles, whereas at 37°C they convert to budding yeast. The ability to switch between these forms is essential for virulence in mammals and may enable these organisms to survive in the soil. To identify genes that regulate this phase transition, we used Agrobacterium tumefaciens to mutagenize B. dermatitidis conidia and screened transformants for defects in morphogenesis. We found that the GATA transcription factor SREB governs multiple fates in B. dermatitidis: phase transition from yeast to mold, cell growth at 22°C, and biosynthesis of siderophores under iron-replete conditions. Insertional and null mutants fail to convert to mold, do not accumulate significant biomass at 22°C, and are unable to suppress siderophore biosynthesis under iron-replete conditions. The defect in morphogenesis in the SREB mutant was independent of exogenous iron concentration, suggesting that SREB promotes the phase transition by altering the expression of genes that are unrelated to siderophore biosynthesis. Using bioinformatic and gene expression analyses, we identified candidate genes with upstream GATA sites whose expression is altered in the null mutant that may be direct or indirect targets of SREB and promote the phase transition. We conclude that SREB functions as a transcription factor that promotes morphogenesis and regulates siderophore biosynthesis. To our knowledge, this is the first gene identified that promotes the conversion from yeast to mold in the dimorphic fungi, and may shed light on environmental persistence of these pathogens.
On a Grouping Method for Constructing Mixed Orthogonal Arrays  [PDF]
Chung-Yi Suen
Open Journal of Statistics (OJS) , 2012, DOI: 10.4236/ojs.2012.22022
Abstract: Mixed orthogonal arrays of strength two and size smn are constructed by grouping points in the finite projective geometry PG(mn-1, s). PG(mn-1, s) can be partitioned into [(smn-1)/(sn-1)](n-1)-flats such that each (n-1)-flat is associated with a point in PG(m-1, sn). An orthogonal array Lsmn((sn)(smn-)(sn-1) can be constructed by using (smn-1)/( sn-1) points in PG(m-1, sn). A set of (st-1)/(s-1) points in PG(m-1, sn) is called a (t-1)-flat over GF(s) if it is isomorphic to PG(t-1, s). If there exists a (t-1)-flat over GF(s) in PG(m-1, sn), then we can replace the corresponding [(st-1)/(s-1)] sn-level columns in Lsmn((sn)(smn-)(sn-1) by (smn-1)/( sn-1) st -level columns and obtain a mixed orthogonal array. Many new mixed orthogonal arrays can be obtained by this procedure. In this paper, we study methods for finding disjoint (t-1)-flats over GF(s) in PG(m-1, sn) in order to construct more mixed orthogonal arrays of strength two. In particular, if m and n are relatively prime then we can construct an Lsmn((sm)smn-1/sm-1-i(sn-1)/ (s-1)( sn) i(sm-1)/ s-1) for any 0<i<(smn-1)(s-1)/( sm-1)( sn-1) New orthogonal arrays of sizes 256, 512, and 1024 are obtained by using PG(7,2), PG(8,2), and PG(9,2) respectively.
Geometry of moving planes
Garret Sobczyk
Physics , 2007,
Abstract: The concept of number and its generalization has played a central role in the development of mathematics over many centuries and many civilizations. Noteworthy milestones in this long and arduous process were the developments of the real and complex numbers which have achieved universal acceptance. Serious attempts have been made at further extensions, such as Hamiltons quaternions, Grassmann's exterior algebra and Clifford's geometric algebra. By examining the geometry of moving planes, we show how new mathematics is within reach, if the will to learn these powerful methods can be found.
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