scholarly journals Transcriptional Analysis of Biofilm Formation Processes in the Anaerobic, Hyperthermophilic Bacterium Thermotoga maritima

2004 ◽  
Vol 70 (10) ◽  
pp. 6098-6112 ◽  
Author(s):  
Marybeth A. Pysz ◽  
Shannon B. Conners ◽  
Clemente I. Montero ◽  
Keith R. Shockley ◽  
Matthew R. Johnson ◽  
...  
Keyword(s):  
Differential Expression ◽  
Biofilm Formation ◽  
Mixed Model ◽  
Thermotoga Maritima ◽  
Expression Patterns ◽  
Transcriptional Analysis ◽  
Formation Processes ◽  
Cluster Assembly ◽  
Chemostat Cultivation ◽  
Hyperthermophilic Bacterium

ABSTRACT Thermotoga maritima, a fermentative, anaerobic, hyperthermophilic bacterium, was found to attach to bioreactor glass walls, nylon mesh, and polycarbonate filters during chemostat cultivation on maltose-based media at 80°C. A whole-genome cDNA microarray was used to examine differential expression patterns between biofilm and planktonic populations. Mixed-model statistical analysis revealed differential expression (twofold or more) of 114 open reading frames in sessile cells (6% of the genome), over a third of which were initially annotated as hypothetical proteins in the T. maritima genome. Among the previously annotated genes in the T. maritima genome, which showed expression changes during biofilm growth, were several that corresponded to biofilm formation genes identified in mesophilic bacteria (i.e., Pseudomonas species, Escherichia coli, and Staphylococcus epidermidis). Most notably, T. maritima biofilm-bound cells exhibited increased transcription of genes involved in iron and sulfur transport, as well as in biosynthesis of cysteine, thiamine, NAD, and isoprenoid side chains of quinones. These findings were all consistent with the up-regulation of iron-sulfur cluster assembly and repair functions in biofilm cells. Significant up-regulation of several β-specific glycosidases was also noted in biofilm cells, despite the fact that maltose was the primary carbon source fed to the chemostat. The reasons for increased β-glycosidase levels are unclear but are likely related to the processing of biofilm-based polysaccharides. In addition to revealing insights into the phenotype of sessile T. maritima communities, the methodology developed here can be extended to study other anaerobic biofilm formation processes as well as to examine aspects of microbial ecology in hydrothermal environments.

Transcriptional analysis of dynamic heat-shock response by the hyperthermophilic bacterium Thermotoga maritima

Extremophiles ◽  
2004 ◽  
Vol 8 (3) ◽  
pp. 209-217 ◽  
Author(s):  
Marybeth A. Pysz ◽  
Keith R. Shockley ◽  
Clemente I. Montero ◽  
Shannon B. Conners ◽  
Matthew R. Johnson ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Shock Response ◽  
Thermotoga Maritima ◽  
Transcriptional Analysis ◽  
Hyperthermophilic Bacterium ◽  
Shock Response

scholarly journals An Expression-Driven Approach to the Prediction of Carbohydrate Transport and Utilization Regulons in theHyperthermophilic Bacterium Thermotoga maritima

2005 ◽  
Vol 187 (21) ◽  
pp. 7267-7282 ◽  
Author(s):  
Shannon B. Conners ◽  
Clemente I. Montero ◽  
Donald A. Comfort ◽  
Keith R. Shockley ◽  
Matthew R. Johnson ◽  
...  
Keyword(s):  
Abc Transporters ◽  
Mixed Model ◽  
Thermotoga Maritima ◽  
Expression Patterns ◽  
Pentose Phosphate ◽  
Transport Systems ◽  
Upstream Sequence ◽  
Mixed Model Analysis ◽  
Microarray Expression Data ◽  
Genome Wide

ABSTRACT Comprehensive analysis of genome-wide expression patterns during growth of the hyperthermophilic bacterium Thermotoga maritima on 14 monosaccharide and polysaccharide substrates was undertaken with the goal of proposing carbohydrate specificities for transport systems and putative transcriptional regulators. Saccharide-induced regulons were predicted through the complementary use of comparative genomics, mixed-model analysis of genome-wide microarray expression data, and examination of upstream sequence patterns. The results indicate that T. maritima relies extensively on ABC transporters for carbohydrate uptake, many of which are likely controlled by local regulators responsive to either the transport substrate or a key metabolic degradation product. Roles in uptake of specific carbohydrates were suggested for members of the expanded Opp/Dpp family of ABC transporters. In this family, phylogenetic relationships among transport systems revealed patterns of possible duplication and divergence as a strategy for the evolution of new uptake capabilities. The presence of GC-rich hairpin sequences between substrate-binding proteins and other components of Opp/Dpp family transporters offers a possible explanation for differential regulation of transporter subunit genes. Numerous improvements to T. maritima genome annotations were proposed, including the identification of ABC transport systems originally annotated as oligopeptide transporters as candidate transporters for rhamnose, xylose, β-xylan, andβ -glucans and identification of genes likely to encode proteins missing from current annotations of the pentose phosphate pathway. Beyond the information obtained for T. maritima, the present study illustrates how expression-based strategies can be used for improving genome annotation in other microorganisms, especially those for which genetic systems are unavailable.

scholarly journals NEBULA: a fast negative binomial mixed model for differential expression and co-expression analyses of large-scale multi-subject single-cell data

2020 ◽  
Author(s):  
Liang He ◽  
Alexander M. Kulminski
Keyword(s):  
Single Cell ◽  
Differential Expression ◽  
Large Scale ◽  
Mixed Model ◽  
Negative Binomial ◽  
Expression Patterns ◽  
Marker Genes ◽  
Data Set ◽  
Cell Data ◽  
Negative Binomial Mixed Model

AbstractThe growing availability of large-scale single-cell data revolutionizes our understanding of biological mechanisms at a finer resolution. In differential expression and co-expression analyses of multi-subject single-cell data, it is important to take into account both subject-level and cell-level overdispersions through negative binomial mixed models (NBMMs). However, the application of NBMMs to large-scale single-cell data is computationally demanding. In this work, we propose an efficient NEgative Binomial mixed model Using a Large-sample Approximation (NEBULA)), which analytically solves the high-dimensional integral in the marginal likelihood instead of using the Laplace approximation. Our benchmarks show that NEBULA dramatically reduces the running time by orders of magnitude compared to existing tools. We showed that NEBULA controlled false positives in identifying marker genes, while a simple negative binomial model produced spurious associations. Leveraging NEBULA, we decomposed between-subject and within-subject overdispersions of an snRNA-seq data set in the frontal cortex comprising ∼80,000 cells from a cohort of 48 individuals for Alzheimer’s diseases (AD). We observed that subpopulations and known subject-level covariates contributed substantially to the overdispersions. We carried out cell-type-specific transcriptome-wide within-subject co-expression analysis of APOE. The results revealed that APOE was most co-expressed with multiple AD-related genes, including CLU and CST3 in astrocytes, TREM2 and C1q genes in microglia, and ITM2B, an inhibitor of the amyloid-beta peptide aggregation, in both cell types. We found that the co-expression patterns were different in APOE2+ and APOE4+ cells in microglia, which suggest an isoform-dependent regulatory role in the immune system through the complement system in microglia. NEBULA opens up a new avenue for the broad application of NBMMs in the analysis of large-scale multi-subject single-cell data.

scholarly journals Regulation of Endo-Acting Glycosyl Hydrolases in the Hyperthermophilic Bacterium Thermotoga maritima Grown on Glucan- and Mannan-Based Polysaccharides

2002 ◽  
Vol 68 (2) ◽  
pp. 545-554 ◽  
Author(s):  
Swapnil R. Chhabra ◽  
Keith R. Shockley ◽  
Donald E. Ward ◽  
Robert M. Kelly
Keyword(s):  
Carboxymethyl Cellulose ◽  
Thermotoga Maritima ◽  
Expression Patterns ◽  
Intracellular Localization ◽  
Konjac Glucomannan ◽  
Unexpected Result ◽  
Glycosyl Hydrolases ◽  
Biochemical Basis ◽  
Intracellular Enzyme ◽  
Hyperthermophilic Bacterium

ABSTRACT The genome sequence of the hyperthermophilic bacterium Thermotoga maritima encodes a number of glycosyl hydrolases. Many of these enzymes have been shown in vitro to degrade specific glycosides that presumably serve as carbon and energy sources for the organism. However, because of the broad substrate specificity of many glycosyl hydrolases, it is difficult to determine the physiological substrate preferences for specific enzymes from biochemical information. In this study, T. maritima was grown on a range of polysaccharides, including barley β-glucan, carboxymethyl cellulose, carob galactomannan, konjac glucomannan, and potato starch. In all cases, significant growth was observed, and cell densities reached 109 cells/ml. Northern blot analyses revealed different substrate-dependent expression patterns for genes encoding the various endo-acting β-glycosidases; these patterns ranged from strong expression to no expression under the conditions tested. For example, cel74 (TM0305), a gene encoding a putative β-specific endoglucananse, was strongly expressed on all substrates tested, including starch, while no evidence of expression was observed on any substrate for lam16 (TM0024), xyl10A (TM0061), xyl10B (TM0070), and cel12A (TM1524), which are genes that encode a laminarinase, two xylanases, and an endoglucanase, respectively. The cel12B (TM1525) gene, which encodes an endoglucanase, was expressed only on carboxymethyl cellulose. An extracellular mannanase encoded by man5 (TM1227) was expressed on carob galactomannan and konjac glucomannan and to a lesser extent on carboxymethyl cellulose. An unexpected result was the finding that the cel5A (TM1751) and cel5B (TM1752) genes, which encode putative intracellular, β-specific endoglucanases, were induced only when T. maritima was grown on konjac glucomannan. To investigate the biochemical basis of this finding, the recombinant forms of Man5 (M r, 76,900) and Cel5A (M r, 37,400) were expressed in Escherichia coli and characterized. Man5, a T. maritima extracellular enzyme, had a melting temperature of 99�C and an optimun temperature of 90�C, compared to 90 and 80�C, respectively, for the intracellular enzyme Cel5A. While Man5 hydrolyzed both galactomannan and glucomannan, no activity was detected on glucans or xylans. Cel5A, however, not only hydrolyzed barley β-glucan, carboxymethyl cellulose, xyloglucan, and lichenin but also had activity comparable to that of Man5 on galactomannan and higher activity than Man5 on glucomannan. The biochemical characteristics of Cel5A, the fact that Cel5A was induced only when T. maritima was grown on glucomannan, and the intracellular localization of Cel5A suggest that the physiological role of this enzyme includes hydrolysis of glucomannan oligosaccharides that are transported following initial hydrolysis by extracellular glycosidases, such as Man5.

Analysis of the Differential Expression Patterns of Sumoylation Enzymes E1, E2 and E3 in Ocular Cell Lines

2019 ◽  
Vol 18 (8) ◽  
pp. 509-515 ◽  
Author(s):  
Qian Nie ◽  
Jie Xie ◽  
Xiaodong Gong ◽  
Zhongwen Luo ◽  
Ling Wang ◽  
...  
Keyword(s):  
Differential Expression ◽  
Cell Lines ◽  
Expression Patterns

scholarly journals Differential expression and correlation analysis of miRNA–mRNA profiles in swine testicular cells infected with porcine epidemic diarrhea virus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xiaoqian Zhang ◽  
Chang Li ◽  
Bingzhou Zhang ◽  
Zhonghua Li ◽  
Wei Zeng ◽  
...  
Keyword(s):  
Differential Expression ◽  
Porcine Epidemic Diarrhea Virus ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Bacterial Invasion ◽  
Sequencing Data ◽  
Diarrhea Virus ◽  
Comparison Groups ◽  
Porcine Epidemic Diarrhea

AbstractThe variant virulent porcine epidemic diarrhea virus (PEDV) strain (YN15) can cause severe porcine epidemic diarrhea (PED); however, the attenuated vaccine-like PEDV strain (YN144) can induce immunity in piglets. To investigate the differences in pathogenesis and epigenetic mechanisms between the two strains, differential expression and correlation analyses of the microRNA (miRNA) and mRNA in swine testicular (ST) cells infected with YN15, YN144, and mock were performed on three comparison groups (YN15 vs Control, YN144 vs Control, and YN15 vs YN144). The mRNA and miRNA expression profiles were obtained using next-generation sequencing (NGS), and the differentially expressed (DE) (p-value < 0.05) mRNA and miRNA were obtained using DESeq R package. mRNAs targeted by DE miRNAs were predicted using the miRanda algortithm. 8039, 8631 and 3310 DE mRNAs, and 36, 36, and 22 DE miRNAs were identified in the three comparison groups, respectively. 14,140, 15,367 and 3771 DE miRNA–mRNA (targeted by DE miRNAs) interaction pairs with negatively correlated expression patterns were identified, and interaction networks were constructed using Cytoscape. Six DE miRNAs and six DE mRNAs were randomly selected to verify the sequencing data by real-time relative quantitative reverse transcription polymerase chain reaction (qRT-PCR). Based on bioinformatics analysis, we discovered the differences were mostly involved in host immune responses and viral pathogenicity, including NF-κB signaling pathway and bacterial invasion of epithelial cells, etc. This is the first comprehensive comparison of DE miRNA–mRNA pairs in YN15 and YN144 infection in vitro, which could provide novel strategies for the prevention and control of PED.

scholarly journals Signalling pathways and mechanistic cues highlighted by transcriptomic analysis of primordial, primary, and secondary ovarian follicles in domestic cat

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shauna Kehoe ◽  
Katarina Jewgenow ◽  
Paul R. Johnston ◽  
Susan Mbedi ◽  
Beate C. Braun
Keyword(s):  
Gene Expression ◽  
Transforming Growth Factor ◽  
Ovarian Follicle ◽  
Mammalian Species ◽  
Expression Patterns ◽  
Ovarian Follicles ◽  
Domestic Cat ◽  
Transcriptional Analysis ◽  
Ovarian Folliculogenesis

AbstractIn vitro growth (IVG) of dormant primordial ovarian follicles aims to produce mature competent oocytes for assisted reproduction. Success is dependent on optimal in vitro conditions complemented with an understanding of oocyte and ovarian follicle development in vivo. Complete IVG has not been achieved in any other mammalian species besides mice. Furthermore, ovarian folliculogenesis remains sparsely understood overall. Here, gene expression patterns were characterised by RNA-sequencing in primordial (PrF), primary (PF), and secondary (SF) ovarian follicles from Felis catus (domestic cat) ovaries. Two major transitions were investigated: PrF-PF and PF-SF. Transcriptional analysis revealed a higher proportion in gene expression changes during the PrF-PF transition. Key influencing factors during this transition included the interaction between the extracellular matrix (ECM) and matrix metalloproteinase (MMPs) along with nuclear components such as, histone HIST1H1T (H1.6). Conserved signalling factors and expression patterns previously described during mammalian ovarian folliculogenesis were observed. Species-specific features during domestic cat ovarian folliculogenesis were also found. The signalling pathway terms “PI3K-Akt”, “transforming growth factor-β receptor”, “ErbB”, and “HIF-1” from the functional annotation analysis were studied. Some results highlighted mechanistic cues potentially involved in PrF development in the domestic cat. Overall, this study provides an insight into regulatory factors and pathways during preantral ovarian folliculogenesis in domestic cat.

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