d-Xylose Concentration-Dependent Hydrolase Expression Profiles and the Function of CreA and XlnR in Aspergillus niger

ABSTRACTAspergillus nigeris an important organism for the production of industrial enzymes such as hemicellulases and pectinases. The xylan-backbone monomer,d-xylose, is an inducing substance for the coordinate expression of a large number of polysaccharide-degrading enzymes. In this study, the responses of 22 genes to low (1 mM) and high (50 mM)d-xylose concentrations were investigated. These 22 genes encode enzymes that function as xylan backbone-degrading enzymes, accessory enzymes, cellulose-degrading enzymes, or enzymes involved in the pentose catabolic pathway inA. niger. Notably, genes encoding enzymes that have a similar function (e.g., xylan backbone degradation) respond in a similar manner to different concentrations ofd-xylose. Although lowd-xylose concentrations provoke the greatest change in transcript levels, in particular, for hemicellulase-encoding genes, transcript formation in the presence of high concentrations ofd-xylose was also observed. Interestingly, a highd-xylose concentration is favorable for certain groups of genes. Furthermore, the repressing influence of CreA on the transcription and transcript levels of a subset of these genes was observed regardless of whether a low or high concentration ofd-xylose was used. Interestingly, the decrease in transcript levels of certain genes on highd-xylose concentrations is not reflected by the transcript level of their activator, XlnR. Regardless of thed-xylose concentration applied and whether CreA was functional,xlnRwas constitutively expressed at a low level.

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Basal Body Structures Differentially Affect Transcription of RpoN- and FliA-Dependent Flagellar Genes in Helicobacter pylori

Journal of Bacteriology ◽

10.1128/jb.02533-14 ◽

2015 ◽

Vol 197 (11) ◽

pp. 1921-1930 ◽

Cited By ~ 5

Author(s):

Jennifer Tsang ◽

Timothy R. Hoover

Keyword(s):

Helicobacter Pylori ◽

Basal Body ◽

Protein Interactions ◽

Transcript Levels ◽

Content Type ◽

Genes Encoding ◽

H Pylori ◽

Flagellar Biogenesis ◽

Flagellar Genes

ABSTRACTFlagellar biogenesis inHelicobacter pyloriis regulated by a transcriptional hierarchy governed by three sigma factors, RpoD (σ80), RpoN (σ54), and FliA (σ28), that temporally coordinates gene expression with the assembly of the flagellum. Previous studies showed that loss of flagellar protein export apparatus components inhibits transcription of flagellar genes. The FlgS/FlgR two-component system activates transcription of RpoN-dependent genes though an unknown mechanism. To understand better the extent to which flagellar gene regulation is coupled to flagellar assembly, we disrupted flagellar biogenesis at various points and determined how these mutations affected transcription of RpoN-dependent (flaBandflgE) and FliA-dependent (flaA) genes. The MS ring (encoded byfliF) is one of the earliest flagellar structures assembled. Deletion offliFresulted in the elimination of RpoN-dependent transcripts and an ∼4-fold decrease inflaAtranscript levels. FliH is a cytoplasmic protein that functions with the C ring protein FliN to shuttle substrates to the export apparatus. Deletions offliHand genes encoding C ring components (fliMandfliY) decreased transcript levels offlaBandflgEbut had little or no effect on transcript levels offlaA. Transcript levels offlaBandflgEwere elevated in mutants where genes encoding rod proteins (fliEandflgBC) were deleted, while transcript levels offlaAwas reduced ∼2-fold in both mutants. We propose that FlgS responds to an assembly checkpoint associated with the export apparatus and that FliH and one or more C ring component assist FlgS in engaging this flagellar structure.IMPORTANCEThe mechanisms used by bacteria to couple transcription of flagellar genes with assembly of the flagellum are poorly understood. The results from this study identified components of theH. pyloriflagellar basal body that either positively or negatively affect expression of RpoN-dependent flagellar genes. Some of these basal body proteins may interact directly with regulatory proteins that control transcription of theH. pyloriRpoN regulon, a hypothesis that can be tested by examining protein-protein interactionsin vitro.

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Regulation of Major Cellulosomal Endoglucanases of Clostridium thermocellum Differs from That of a Prominent Cellulosomal Xylanase

Journal of Bacteriology ◽

10.1128/jb.187.7.2261-2266.2005 ◽

2005 ◽

Vol 187 (7) ◽

pp. 2261-2266 ◽

Cited By ~ 37

Author(s):

Tali W. Dror ◽

Adi Rolider ◽

Edward A. Bayer ◽

Raphael Lamed ◽

Yuval Shoham

Keyword(s):

Growth Rate ◽

Clostridium Thermocellum ◽

Transcript Level ◽

Clear Correlation ◽

Transcript Levels ◽

Batch Cultures ◽

Processive Endoglucanase ◽

The Family ◽

Genes Encoding ◽

Family 10 Xylanase

ABSTRACT The expression of scaffoldin-anchoring genes and one of the major processive endoglucanases (CelS) from the cellulosome of Clostridium thermocellum has been shown to be dependent on the growth rate. For the present work, we studied the gene regulation of selected cellulosomal endoglucanases and a major xylanase in order to examine the previously observed substrate-linked alterations in cellulosome composition. For this purpose, the transcript levels of genes encoding endoglucanases CelB, CelG, and CelD and the family 10 xylanase XynC were determined in batch cultures, grown on either cellobiose or cellulose, and in carbon-limited continuous cultures at different dilution rates. Under all conditions tested, the transcript levels of celB and celG were at least 10-fold higher than that of celD. Like the major processive endoglucanase CelS, the transcript levels of these endoglucanase genes were also dependent on the growth rate. Thus, at a rate of 0.04 h−1, the levels of celB, celG, and celD were threefold higher than those obtained in cultures grown at maximal rates (0.35 h−1) on cellobiose. In contrast, no clear correlation was observed between the transcript level of xynC and the growth rate—the levels remained relatively high, fluctuating between 30 and 50 transcripts per cell. The results suggest that the regulation of C. thermocellum endoglucanases is similar to that of the processive endoglucanase celS but differs from that of a major cellulosomal xylanase in that expression of the latter enzyme is independent of the growth rate.

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Comparative RNA-seq-Based Transcriptome Analysis of the Virulence Characteristics of Methicillin-Resistant and -Susceptible Staphylococcus pseudintermedius Strains Isolated from Small Animals

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01907-15 ◽

2015 ◽

Vol 60 (2) ◽

pp. 962-967 ◽

Cited By ~ 15

Author(s):

Natacha Couto ◽

Adriana Belas ◽

Manuela Oliveira ◽

Paulo Almeida ◽

Carla Clemente ◽

...

Keyword(s):

Virulence Genes ◽

Expression Profiles ◽

Brain Heart Infusion ◽

Surface Proteins ◽

Rna Seq ◽

Staphylococcus Pseudintermedius ◽

Methicillin Resistant ◽

Content Type ◽

Genes Encoding

ABSTRACTStaphylococcus pseudintermediusis often associated with pyoderma, which can turn into a life-threatening disease. The dissemination of highly resistant isolates has occurred in the last 10 years and has challenged antimicrobial treatment of these infections considerably. We have compared the carriage of virulence genes and biofilm formation between methicillin-resistant and methicillin-susceptibleS. pseudintermedius(MRSP and MSSP, respectively) isolates and theirin vitrogene expression profiles by transcriptome sequencing (RNA-seq). Isolates were relatively unevenly distributed among the fouragrgroups, andagrtype III predominated in MRSP. Five virulence genes were detected in all isolates. Only thespsOgene was significantly associated with MSSP isolates (P= 0.04). All isolates produced biofilm in brain heart infusion broth (BHIB)–4% NaCl. MSSP isolates produced more biofilm on BHIB and BHIB–1% glucose media than MRSP isolates (P= 0.03 andP= 0.02, respectively). Virulence genes encoding surface proteins and toxins (spsA,spsB,spsD,spsK,spsL,spsN,nucC,coa, andluk-I) and also prophage genes (encoding phage capsid protein, phage infection protein, two phage portal proteins, and a phage-like protein) were highly expressed in the MRSP isolate (compared with the MSSP isolate), suggesting they may play a role in the rapid and widespread dissemination of MRSP. This study indicates that MRSP may upregulate surface proteins, which may increase the adherence of MRSP isolates (especially sequence type 71 [ST71]) to corneocytes. MSSP isolates may have an increased ability to form biofilm under acidic circumstances, through upregulation of the entirearcoperon. Complete understanding ofS. pseudintermediuspathogenesis and host-pathogen signal interaction during infections is critical for the treatment and prevention ofS. pseudintermediusinfections.

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The Severity of Plasmodium falciparum Infection Is Associated with Transcript Levels of var Genes Encoding Endothelial Protein C Receptor-Binding P. falciparum Erythrocyte Membrane Protein 1

Infection and Immunity ◽

10.1128/iai.00841-16 ◽

2017 ◽

Vol 85 (4) ◽

Cited By ~ 39

Author(s):

Sixbert I. Mkumbaye ◽

Christian W. Wang ◽

Eric Lyimo ◽

Jakob S. Jespersen ◽

Alphaxard Manjurano ◽

...

Keyword(s):

Plasmodium Falciparum ◽

Membrane Protein ◽

Severe Malaria ◽

Erythrocyte Membrane ◽

Protein C ◽

Transcript Level ◽

Endothelial Protein C Receptor ◽

Transcript Levels ◽

Content Type ◽

Erythrocyte Membrane Protein

ABSTRACT By attaching infected erythrocytes to the vascular lining, Plasmodium falciparum parasites leave blood circulation and avoid splenic clearance. This sequestration is central to pathogenesis. Severe malaria is associated with parasites expressing an antigenically distinct P. falciparum erythrocyte membrane protein 1 (PfEMP1) subset mediating binding to endothelial receptors. Previous studies indicate that PfEMP1 adhesins with so-called CIDRα1 domains capable of binding endothelial protein C receptor (EPCR) constitute the PfEMP1 subset associated with severe pediatric malaria. To analyze the relative importance of different subtypes of CIDRα1 domains, we compared Pfemp1 transcript levels in children with severe malaria (including 9 fatal and 114 surviving cases), children hospitalized with uncomplicated malaria (n = 42), children with mild malaria not requiring hospitalization (n = 10), and children with parasitemia and no ongoing fever (n = 12). High levels of transcripts encoding EPCR-binding PfEMP1 were found in patients with symptomatic infections, and the abundance of these transcripts increased with disease severity. The compositions of CIDRα1 subtype transcripts varied markedly between patients, and none of the subtypes were dominant. Transcript-level analyses targeting other domain types indicated that subtypes of DBLβ or DBLζ domains might mediate binding phenomena that, in conjunction with EPCR binding, could contribute to pathogenesis. These observations strengthen the rationale for targeting the PfEMP1-EPCR interaction by vaccines and adjunctive therapies. Interventions should target EPCR binding of all CIDRα1 subtypes.

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Joint Effects of Host Genetic Background and Mycobacterial Pathogen on Susceptibility to Infection

Infection and Immunity ◽

10.1128/iai.00985-10 ◽

2011 ◽

Vol 79 (6) ◽

pp. 2372-2378 ◽

Cited By ~ 10

Author(s):

Tania Di Pietrantonio ◽

José A. Correa ◽

Marianna Orlova ◽

Marcel A. Behr ◽

Erwin Schurr

Keyword(s):

Genetic Background ◽

Expression Profiles ◽

Transcript Levels ◽

Content Type ◽

Joint Effects ◽

Susceptibility To Infection ◽

Interaction Terms ◽

Pathogen Variability ◽

Host Genetic ◽

The Individual

ABSTRACTThe present study examined the differential contribution of host genetic background and mycobacterial pathogen variability to biological and mechanistic phenotypes of infection. For this purpose, A/J and C57BL/6J mice were infected intravenously with a low dose ofMycobacterium tuberculosisH37Rv or the Russia, Japan, and Pasteur substrains ofMycobacterium bovisbacille Calmette-Guérin (BCG). The pulmonary bacterial counts (number of CFU) and transcript levels of select cytokines (e.g.,Ifng,Il12b, andIl4) at 1, 3, and 6 weeks postinfection were measured as biological and mechanistic phenotypes, respectively. The individual and combined impact of the host and mycobacteria on these phenotypes was assessed using three-way analysis of variance (ANOVA), which partitions phenotypic variation into host, pathogen, time, and interaction effects. All phenotypes, except pulmonaryIl4transcript levels, displayed evidence for host-mycobacterium specificity by means of significant interaction terms. Pulmonary expression profiles of 34 chemokines and chemokine-related genes were compared across the hosts and mycobacteria. The differences in induction of these immune messenger genes between A/J and C57BL/6J mice were modest and generally failed to reach significance. In contrast, the mycobacteria induced significant variance in a subset of the immune messenger genes, which was more evident in A/J mice relative to that in C57BL/6J mice. Overall, the results demonstrated the importance of considering the joint effects of the mycobacterial and host genetic backgrounds on susceptibility to mycobacterial infections.

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Complex Regulation Pathways of AmpC-Mediated β-Lactam Resistance in Enterobacter cloacae Complex

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01729-15 ◽

2015 ◽

Vol 59 (12) ◽

pp. 7753-7761 ◽

Cited By ~ 34

Author(s):

François Guérin ◽

Christophe Isnard ◽

Vincent Cattoir ◽

Jean Christophe Giard

Keyword(s):

Drug Targets ◽

Genetic Regulation ◽

Enterobacter Cloacae ◽

Opportunistic Pathogen ◽

Regulation Mechanism ◽

Content Type ◽

Genes Encoding ◽

High Concentrations ◽

High Level

ABSTRACTEnterobacter cloacaecomplex (ECC), an opportunistic pathogen causing numerous infections in hospitalized patients worldwide, is able to resist β-lactams mainly by producing the AmpC β-lactamase enzyme. AmpC expression is highly inducible in the presence of some β-lactams, but the underlying genetic regulation, which is intricately linked to peptidoglycan recycling, is still poorly understood. In this study, we constructed different mutant strains that were affected in genes encoding enzymes suspected to be involved in this pathway. As expected, the inactivation ofampC,ampR(which encodes the regulator protein ofampC), andampG(encoding a permease) abolished β-lactam resistance. Reverse transcription-quantitative PCR (qRT-PCR) experiments combined with phenotypic studies showed that cefotaxime (at high concentrations) and cefoxitin induced the expression ofampCin different ways: one involving NagZ (aN-acetyl-β-d-glucosaminidase) and another independent of NagZ. Unlike the model established forPseudomonas aeruginosa, inactivation of DacB (also known as PBP4) was not responsible for a constitutiveampCoverexpression in ECC, whereas it caused AmpC-mediated high-level β-lactam resistance, suggesting a post-transcriptional regulation mechanism. Global transcriptomic analysis by transcriptome sequencing (RNA-seq) of adacBdeletion mutant confirmed these results. Lastly, analysis of 37 ECC clinical isolates showed that amino acid changes in the AmpD sequence were likely the most crucial event involved in the development of high-level β-lactam resistancein vivoas opposed toP. aeruginosawheredacBmutations have been commonly found. These findings bring new elements for a better understanding of β-lactam resistance in ECC, which is essential for the identification of novel potential drug targets.

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Challenges in recruiting hard-to-reach populations focusing on Latin American recent immigrants

International Journal of Human Rights in Healthcare ◽

10.1108/ijhrh-01-2014-0002 ◽

2015 ◽

Vol 8 (1) ◽

pp. 36-44 ◽

Cited By ~ 3

Author(s):

Mandana Vahabi ◽

Sandra Isaacs ◽

Mustafa Koc ◽

Cynthia Damba

Keyword(s):

Latin American ◽

Census Data ◽

Sampling Strategy ◽

Recruitment Strategy ◽

High Concentration ◽

Community Members ◽

Content Type ◽

Recent Immigrants ◽

Hard To Reach Populations ◽

High Concentrations

Purpose – Recruiting immigrant populations, particularly recent arrivals, is challenging due to lack of sampling frames and other factors. The purpose of this paper is to report the feasibility of using a quasi-random sampling strategy for recruiting recent Latin American (LA) immigrants. Design/methodology/approach – The initial recruitment strategy included random selection of two census tracts (CTs) with high concentrations and numbers of recent LAs in Toronto, and door-to-door recruitment. Based on challenges encountered this strategy was modified by consulting trusted community members and recruiting participants residing in selected CTs using cultural venues. Findings – Door-to-door recruitment of the target group is difficult. Challenges included accessing individuals living in apartment buildings, lack of trust and fear of deportation, transitory residency, and difficulty recruiting very recent arrivals. The modified strategy was more efficient and yielded higher recruitment rates, and was more acceptable to participants. Research limitations/implications – The limited timeframe of the study and lack of timely census data may have prevented full exploration of study methodologies. Originality/value – The study demonstrated that recruitment rates of recent immigrants and refugees can be improved by randomly selecting CTs with high concentrations and numbers of recent immigrants and using culturally appropriate recruitment strategies. These groups may not be homogeneously distributed in selected geographic areas (e.g. CTs); it may be necessary to focus on pockets of high concentration as identified by community members who are familiar with the area.

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Effects of DMSO on gene expression in human and rat hepatocytes

Human & Experimental Toxicology ◽

10.1177/0960327111399325 ◽

2011 ◽

Vol 30 (10) ◽

pp. 1701-1709 ◽

Cited By ~ 31

Author(s):

Kayo Sumida ◽

Yoshinobu Igarashi ◽

Naoki Toritsuka ◽

Tomochika Matsushita ◽

Kaori Abe-Tomizawa ◽

...

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Rat Hepatocytes ◽

Cytotoxicity Test ◽

High Concentration ◽

Ldh Activity ◽

High Concentrations ◽

Microarray Analyses

Dimethyl sulfoxide (DMSO) is a very common organic solvent used for dissolving lipophilic substances, for example for in vitro cell-based assays. At the same time, DMSO is known to be cytotoxic at high concentrations. Therefore, it is important to define threshold concentrations of DMSO for cells but relevant data at the molecular level are very limited. We have focused on conducting microarray analyses of human and rat hepatocytes treated with more than 100 chemicals in attempts to identify candidate biomarker genes. In the present study, the effects of DMSO on gene expression and cytotoxicity were assessed in human cryopreserved hepatocytes and rat primary cultured hepatocytes. A cytotoxicity test with lactate dehydrogenase (LDH) activity demonstrated DMSO to be noncytotoxic up to a concentration of 2% (v/v) in both cases and there were only few effects on the gene expression profiles up to 0.5% (v/v). The observed differences from controls were considered to be of little toxicological importance, but still need to be taken into account in interpretation of findings when DMSO is used at high concentration.

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Gene expression profiling of adp-glucose pyrophosphorylase (AGPase) in sink and source organs of some cassava varieties with different starch contents in Vietnam

Vietnam Journal of Biotechnology ◽

10.15625/1811-4989/14/4/12300 ◽

2018 ◽

Vol 14 (4) ◽

pp. 673-682

Author(s):

Nguyen Thi Minh Hong ◽

Le Thu Ngoc ◽

Nguyen Mau Hung ◽

Pham Bich Ngoc ◽

Chu Hoang Ha

Keyword(s):

Expression Profiles ◽

Expression Patterns ◽

Transcript Level ◽

Starch Biosynthesis ◽

Storage Roots ◽

Genes Encoding ◽

Adp Glucose Pyrophosphorylase ◽

Level Analysis ◽

Starch Production ◽

Cassava Varieties

Starch is the most widespread and abundant storage carbohydrate in plants. We depend upon starch for our nutrition, exploit its unique properties in industry, and use it as a feedstock for bio-ethanol production. Starch is stored in the form of osmotically inactive, water-insoluble granules in amyloplasts (storage starch) and chloroplasts (transitory starch). The biosynthesis of starch involves not only the production of the composite glucans but also their arrangement into an organized form within the starch granule. Understanding the specific functions played by individual isoforms of enzymes involved in starch biosynthesis pathways will provide important basis for regulation of starch production in plant. A transcript-level analysis of the genes which encode starch-synthesis enzymes is fundamental for assessment of enzyme function and the regulatory mechanism for starch biosynthesis in source and sink organs. In this work, the expression level of the genes encoding ADP-glucose pyrophosphorylase (AGPase) in two local varieties Do Dia Phuong (Do DF) and Trang Hoa Binh (Trang HB) as well as two imported varieties KM94 (Rayong1 X Rayong 90) and KM140 (KM98-1 x KM36) with different starch contents were evaluated by quantitative real-time PCR method. The result of transcript level analysis made the expression profiles of cassava AGPS and AGPL genes (encoding AGPase small and large subunits) during three development periods, 90, 180 and 270 DAP (day after planting). The transcriptional activities of these genes exhibited tissue-specific expression patterns. In particular, AGPS2 and AGPL1 transcripts were predominant in leaves, whereas expression of AGPS1, AGPL2, and AGPL3 appeared to be mostly confined to storage roots. Despite of having disparities between development stages, expression patterns of both AGPS2 and AGPL1 in leaves did not show significant differences amongst investigated cassava varieties. In contrast, transcriptional activities of AGPS1 and AGPL3 in tubers had patterns directly related to the starch contents of the cultivars. These results indicated that AGPS1 and AGPL3 genes likely play an important role in the starch biosynthesis pathway and have potential for regulation of starch production in cassava.

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