cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16847587.v1
title: Sequence variations in the ETEC CS6 operon affect transcript and protein expression

description: Enterotoxigenic <i>Escherichia coli</i> (ETEC) is a leading cause of diarrheal disease in developing nations where it accounts for a significant disease burden in children between the ages of 0 to 59 months. It is also the number one bacterial causative agent of traveler’s diarrhea. ETEC infects hosts through the fecal-oral route and utilizes colonization factors (CF) to adhere within the small intestine. Over 25 CFs have been identified; 7 are considered major CFs and a vaccine targeting these is predicted to provide protection against up to 66% of ETEC associated disease. Coli Surface Antigen 6 (CS6) is a major CF and is associated with disease-causing ETEC isolates. Analysis of the CS6 operon sequence led to the identification of two regions of variability among clinical isolates which we predicted exert effects on CS6 transcript and protein expression. A total of 7 recombinant <i>E. coli</i> strains were engineered to encode the CS6 operon in wild-type, hybrid, and mutant configurations. Western blot analysis and RT-qPCR provided evidence to support the importance of an intergenic hairpin structure on CS6 expression. Our results reveal the significance of CS6 sequence selection regarding ETEC vaccine development and present novel information regarding CS6 sequence variation in WT ETEC strains.
DOI: 10.6084/m9.figshare.13537064
title: Verapamil inhibits efflux pumps in <i>Candida albicans</i>, exhibits synergism with fluconazole, and increases survival of <i>Galleria mellonella</i>

description: The emergence of resistance requires alternative methods to treat <i>Candida albicans</i> infections. We evaluated efficacy of the efflux pump inhibitor (EPI) verapamil (VER) with fluconazole (FLC) against FLC-resistant (CaR) and -susceptible <i>C. albicans</i> (CaS). The susceptibility of both strains to VER and FLC was determined, as well as the synergism of VER with FLC. Experiments were performed <i>in vitro</i> for planktonic cultures and biofilms and <i>in vivo</i> using <i>Galleria mellonella</i>. Larval survival and fungal recovery were evaluated after treatment with VER and FLC. Data were analyzed by analysis of variance and Kaplan-Meier tests. The combination of VER with FLC at sub-lethal concentrations reduced fungal growth. VER inhibited the efflux of rhodamine 123 and showed synergism with FLC against CaR. For biofilms, FLC and VER alone reduced fungal viability. The combination of VER with FLC at sub-lethal concentrations also reduced biofilm viability. In the <i>in vivo</i> assays, VER and FLC used alone or in combination increased the survival of larvae infected with CaR. Reduction of fungal recovery was observed only for larvae infected with CaR and treated with VER with FLC. VER reverted the FLC-resistance of <i>C. albicans</i>. Based on the results obtained, VER reverted the FLC-resistance of <i>C. albicans</i> and showed synergism with FLC against CaR. VER also increased the survival of <i>G. mellonella</i> infected with CaR and reduced the fungal recovery.
DOI: 10.6084/m9.figshare.13537064.v1
title: Verapamil inhibits efflux pumps in <i>Candida albicans</i>, exhibits synergism with fluconazole, and increases survival of <i>Galleria mellonella</i>

description: The emergence of resistance requires alternative methods to treat <i>Candida albicans</i> infections. We evaluated efficacy of the efflux pump inhibitor (EPI) verapamil (VER) with fluconazole (FLC) against FLC-resistant (CaR) and -susceptible <i>C. albicans</i> (CaS). The susceptibility of both strains to VER and FLC was determined, as well as the synergism of VER with FLC. Experiments were performed <i>in vitro</i> for planktonic cultures and biofilms and <i>in vivo</i> using <i>Galleria mellonella</i>. Larval survival and fungal recovery were evaluated after treatment with VER and FLC. Data were analyzed by analysis of variance and Kaplan-Meier tests. The combination of VER with FLC at sub-lethal concentrations reduced fungal growth. VER inhibited the efflux of rhodamine 123 and showed synergism with FLC against CaR. For biofilms, FLC and VER alone reduced fungal viability. The combination of VER with FLC at sub-lethal concentrations also reduced biofilm viability. In the <i>in vivo</i> assays, VER and FLC used alone or in combination increased the survival of larvae infected with CaR. Reduction of fungal recovery was observed only for larvae infected with CaR and treated with VER with FLC. VER reverted the FLC-resistance of <i>C. albicans</i>. Based on the results obtained, VER reverted the FLC-resistance of <i>C. albicans</i> and showed synergism with FLC against CaR. VER also increased the survival of <i>G. mellonella</i> infected with CaR and reduced the fungal recovery.
DOI: 10.6084/m9.figshare.14222489
title: Catalase impairs <i>Leishmania mexicana</i> development and virulence

description: Catalase is one of the most abundant enzymes on Earth. It decomposes hydrogen peroxide, thus protecting cells from dangerous reactive oxygen species. The catalase-encoding gene is conspicuously absent from the genome of most representatives of the family Trypanosomatidae. Here, we expressed this protein from the <i>Leishmania mexicana Β-TUBULIN</i> locus using a novel bicistronic expression system, which relies on the 2A peptide of <i>Teschovirus A</i>. We demonstrated that catalase-expressing parasites are severely compromised in their ability to develop in insects, to be transmitted and to infect mice, and to cause clinical manifestation in their mammalian host. Taken together, our data support the hypothesis that the presence of catalase is not compatible with the dixenous life cycle of <i>Leishmania</i>, resulting in loss of this gene from the genome during the evolution of these parasites.
DOI: 10.6084/m9.figshare.14931601.v4
title: Pneumococcal surface adhesion A protein (PsaA) interacts with human Annexin A2 on airway epithelial cells

description: <i>Streptococcus pneumoniae</i> (pneumococcus) is a normal colonizer of the human nasopharynx capable of causing serious invasive disease. Since colonization of the nasopharynx is a prerequisite for progression to invasive diseases, the development of future protein-based vaccines requires an understanding of the intimate interaction of bacterial adhesins with host receptors. In this study, we identified that pneumococcal surface adhesin A (PsaA), a highly conserved pneumococcal protein known to play an important role in colonization of pneumococcus, can interact with Annexin A2 (ANXA2) on Detroit 562 nasopharyngeal epithelial cells. Lentiviral expression of ANXA2 in HEK 293 T/17 cells, which normally express minimal ANXA2, significantly increased pneumococcal adhesion. Blocking of ANXA2 with recombinant PsaA negatively impacted pneumococcal adherence to ANXA2-transduced HEK cells. These results suggest that ANXA2 is an important host cellular receptor for pneumococcal colonization.
DOI: 10.6084/m9.figshare.14222489.v1
title: Catalase impairs <i>Leishmania mexicana</i> development and virulence

description: Catalase is one of the most abundant enzymes on Earth. It decomposes hydrogen peroxide, thus protecting cells from dangerous reactive oxygen species. The catalase-encoding gene is conspicuously absent from the genome of most representatives of the family Trypanosomatidae. Here, we expressed this protein from the <i>Leishmania mexicana Β-TUBULIN</i> locus using a novel bicistronic expression system, which relies on the 2A peptide of <i>Teschovirus A</i>. We demonstrated that catalase-expressing parasites are severely compromised in their ability to develop in insects, to be transmitted and to infect mice, and to cause clinical manifestation in their mammalian host. Taken together, our data support the hypothesis that the presence of catalase is not compatible with the dixenous life cycle of <i>Leishmania</i>, resulting in loss of this gene from the genome during the evolution of these parasites.
DOI: 10.6084/m9.figshare.16553511.v1
title: Transcriptional response of <i>Aspergillus fumigatus</i> to copper and the role of the Cu chaperones

description: <i>Aspergillus fumigatus</i> is the leading cause of life-threatening invasive mold infections in immunocompromised individuals. This ubiquitous saprophyte possesses several natural attributes allowing it to evade the immune system, including the ability to withstand high toxic Cu concentrations within the phagosomes of macrophages and neutrophils. We previously established that at high levels, Cu binds and activates the <i>A. fumigatus</i> transcription factor AceA, which upregulates the expression of the Cu exporter CrpA to expel excess Cu. Deletion of <i>aceA</i> or <i>crpA</i> result in extreme Cu sensitivity and attenuated virulence. To identify other elements participating in resistance to Cu, we performed a genome-wide analysis of the transcriptome by RNAseq to analyze the AceA-dependent response of <i>A. fumigatus</i> to excess Cu. We deleted key genes whose transcription was strongly upregulated by high Cu, including those encoding homologs of the three Cu chaperones <i>cox17, atx1</i> and <i>ccs1</i>. Detailed analysis of these genes indicates that in <i>A. fumigatus, cox17</i> is an essential gene with a possible role in respiration, the <i>atxA</i> gene product participates in reductive iron uptake and <i>ccsA</i> encodes the Cu chaperone activating <i>A. fumigatus</i> Sod1. Interestingly, although the <i>ccsA</i>-null strain was extremely sensitive to high Cu and oxidative stress, it was not attenuated in virulence in a mouse model of invasive pulmonary aspergillosis. Our work provides (i) a detailed view of the genome-wide transcriptional response of <i>A. fumigatus</i> to excess Cu, (ii) identification of the AceA-dependent transcriptome and (iii) analysis of the roles of the three Cu chaperones <i>cox17, atxA</i> and <i>ccsA.</i>
DOI: 10.6084/m9.figshare.16699075.v1
title: Comparison of three <i>Coxiella burnetii</i> infectious routes in mice

description: Evidence suggests that <i>Coxiella burnetii</i>, which is shed in the milk, urine, feces, and birth products of infected domestic ruminants, can lead to Q fever disease following consumption of unpasteurized dairy products; however, <i>C. burnetii</i> is not believed to be a major gastrointestinal pathogen. Most infections are associated with inhalation of aerosols generated from the excreta of domestic ruminants. We recently demonstrated that <i>C. burnetii</i> delivered by oral gavage (OG) resulted in dissemination and an immune response; however, it is unclear how infection via the oral route compares to other well-established routes. Therefore, we delivered three strains of <i>C. burnetii</i> (representing three pertinent sequence types in the United States, such as ST16, ST20, and ST8) to immunocompetent mice in four doses via aerosol challenge (AC), intraperitoneal injection (IP), or OG. Low dose (10^5) of ST16 by OG was insufficient to cause infection, yet doses 1,000- or 100-fold lower by IP or AC, respectively, induced a robust immune response and dissemination. Despite being able to induce an immune response in a dose-dependent manner, administration of <i>C. burnetii</i> via OG is the least efficient route tested. Not only were the immune responses and bacterial loads diminished in mice exposed by OG relative to AC or IP, the efficiency of transmission was also inferior. High doses (10^8) were not sufficient to ensure transmission to 100% of the ST20 or ST8 cohorts. These results may provide some basis for why ingestion of <i>C. burnetii</i> as a mode of Q fever transmission is not often reported.
DOI: 10.6084/m9.figshare.16699075.v2
title: Comparison of three <i>Coxiella burnetii</i> infectious routes in mice

description: Evidence suggests that <i>Coxiella burnetii</i>, which is shed in the milk, urine, feces, and birth products of infected domestic ruminants, can lead to Q fever disease following consumption of unpasteurized dairy products; however, <i>C. burnetii</i> is not believed to be a major gastrointestinal pathogen. Most infections are associated with inhalation of aerosols generated from the excreta of domestic ruminants. We recently demonstrated that <i>C. burnetii</i> delivered by oral gavage (OG) resulted in dissemination and an immune response; however, it is unclear how infection via the oral route compares to other well-established routes. Therefore, we delivered three strains of <i>C. burnetii</i> (representing three pertinent sequence types in the United States, such as ST16, ST20, and ST8) to immunocompetent mice in four doses via aerosol challenge (AC), intraperitoneal injection (IP), or OG. Low dose (10^5) of ST16 by OG was insufficient to cause infection, yet doses 1,000- or 100-fold lower by IP or AC, respectively, induced a robust immune response and dissemination. Despite being able to induce an immune response in a dose-dependent manner, administration of <i>C. burnetii</i> via OG is the least efficient route tested. Not only were the immune responses and bacterial loads diminished in mice exposed by OG relative to AC or IP, the efficiency of transmission was also inferior. High doses (10^8) were not sufficient to ensure transmission to 100% of the ST20 or ST8 cohorts. These results may provide some basis for why ingestion of <i>C. burnetii</i> as a mode of Q fever transmission is not often reported.
DOI: 10.6084/m9.figshare.13603295
title: The lipoprotein NlpD in <i>Cronobacter sakazakii</i> responds to acid stress and regulates macrophage resistance and virulence by maintaining membrane integrity

description: <i>Cronobacter sakazakii</i>, an emerging opportunistic pathogen, is implicated in severe foodborne outbreak infections in premature and full-term infants. Generally, acid tolerance is vital for the pathogenesis of foodborne pathogens; however, its role in <i>C. sakazakii</i> virulence remains largely unknown. To screen out acid-tolerance determinants from transposon mutants, anovel counterselection method using gentamicin and acid was developed. Using the counterselection method and growth assay, we screened several acid-sensitive mutants and found that <i>nlpD</i> encodes an acid-resistance factor in <i>C. sakazakii</i>.  Compared to the wild-type strain, the <i>nlpD</i> mutant exhibited attenuated virulence in a rat model. Using macrophage THP-1 cells and a pH probe, we verified that <i>nlpD</i> enables bacteria to resist macrophages by resisting acidification. Finally, we confirmed that <i>nlpD</i> maintains <i>C. sakazakii</i> membrane integrity in acid using propidium iodide permeabilization assays via flow cytometry. Our results confirm that <i>nlpD</i> is a novel virulence factor that permits <i>C. sakazakii</i> to survive under acid stress conditions. Considering that NlpD is a conserved lipoprotein located in the bacterial outer membrane, NlpD could be used as a target for drug development.
DOI: 10.6084/m9.figshare.16870745
title: Set1-mediated H3K4 methylation is required for <i>Candida albicans</i> virulence by regulating intracellular level of reactive oxygen species

description: <i>Candida albicans</i> is an opportunistic human fungal pathogen that exists in normal flora but can cause infection in immunocompromised individuals. The transition to pathogenic <i>C. albicans</i> requires a change of various gene expressions. Because histone-modifying enzymes can regulate gene expression, they are thought to control the virulence of <i>C. albicans</i>. Indeed, the absence of H3 lysine 4 (H3K4) methyltransferase Set1 has been shown to reduce the virulence of <i>C. albicans</i>; however, Set1-regulated genes responsible for this attenuated virulence phenotype remain unknown. Here, we demonstrated that Set1 positively regulates the expression of mitochondrial protein genes by methylating H3K4. In particular, levels of cellular mitochondrial reactive oxygen species (ROS) were higher in <i>Δset1</i> than in the wild-type due to the defect of those genes’ expression. Set1 deletion also increases H<sub>2</sub>O<sub>2</sub> sensitivity and prevents proper colony formation when interacting with macrophage <i>in vitro</i>, consistent with its attenuated virulence <i>in vivo</i>. Together, these findings suggest that Set1 is required to regulate proper cellular ROS production by positively regulating the expression of mitochondrial protein genes and subsequently sustaining mitochondrial membrane integrity. Consequently, <i>C. albicans</i> maintains proper ROS levels via Set1-mediated transcriptional regulation, thus establishing a rapid defense against external ROS generated by the host.
DOI: 10.6084/m9.figshare.16870745.v7
title: Set1-mediated H3K4 methylation is required for <i>Candida albicans</i> virulence by regulating intracellular level of reactive oxygen species

description: <i>Candida albicans</i> is an opportunistic human fungal pathogen that exists in normal flora but can cause infection in immunocompromised individuals. The transition to pathogenic <i>C. albicans</i> requires a change of various gene expressions. Because histone-modifying enzymes can regulate gene expression, they are thought to control the virulence of <i>C. albicans</i>. Indeed, the absence of H3 lysine 4 (H3K4) methyltransferase Set1 has been shown to reduce the virulence of <i>C. albicans</i>; however, Set1-regulated genes responsible for this attenuated virulence phenotype remain unknown. Here, we demonstrated that Set1 positively regulates the expression of mitochondrial protein genes by methylating H3K4. In particular, levels of cellular mitochondrial reactive oxygen species (ROS) were higher in <i>Δset1</i> than in the wild-type due to the defect of those genes’ expression. Set1 deletion also increases H<sub>2</sub>O<sub>2</sub> sensitivity and prevents proper colony formation when interacting with macrophage <i>in vitro</i>, consistent with its attenuated virulence <i>in vivo</i>. Together, these findings suggest that Set1 is required to regulate proper cellular ROS production by positively regulating the expression of mitochondrial protein genes and subsequently sustaining mitochondrial membrane integrity. Consequently, <i>C. albicans</i> maintains proper ROS levels via Set1-mediated transcriptional regulation, thus establishing a rapid defense against external ROS generated by the host.
DOI: 10.6084/m9.figshare.13603295.v1
title: The lipoprotein NlpD in <i>Cronobacter sakazakii</i> responds to acid stress and regulates macrophage resistance and virulence by maintaining membrane integrity

description: <i>Cronobacter sakazakii</i>, an emerging opportunistic pathogen, is implicated in severe foodborne outbreak infections in premature and full-term infants. Generally, acid tolerance is vital for the pathogenesis of foodborne pathogens; however, its role in <i>C. sakazakii</i> virulence remains largely unknown. To screen out acid-tolerance determinants from transposon mutants, anovel counterselection method using gentamicin and acid was developed. Using the counterselection method and growth assay, we screened several acid-sensitive mutants and found that <i>nlpD</i> encodes an acid-resistance factor in <i>C. sakazakii</i>.  Compared to the wild-type strain, the <i>nlpD</i> mutant exhibited attenuated virulence in a rat model. Using macrophage THP-1 cells and a pH probe, we verified that <i>nlpD</i> enables bacteria to resist macrophages by resisting acidification. Finally, we confirmed that <i>nlpD</i> maintains <i>C. sakazakii</i> membrane integrity in acid using propidium iodide permeabilization assays via flow cytometry. Our results confirm that <i>nlpD</i> is a novel virulence factor that permits <i>C. sakazakii</i> to survive under acid stress conditions. Considering that NlpD is a conserved lipoprotein located in the bacterial outer membrane, NlpD could be used as a target for drug development.
DOI: 10.6084/m9.figshare.16870745.v6
title: Set1-mediated H3K4 methylation is required for <i>Candida albicans</i> virulence by regulating intracellular level of reactive oxygen species

description: <i>Candida albicans</i> is an opportunistic human fungal pathogen that exists in normal flora but can cause infection in immunocompromised individuals. The transition to pathogenic <i>C. albicans</i> requires a change of various gene expressions. Because histone-modifying enzymes can regulate gene expression, they are thought to control the virulence of <i>C. albicans</i>. Indeed, the absence of H3 lysine 4 (H3K4) methyltransferase Set1 has been shown to reduce the virulence of <i>C. albicans</i>; however, Set1-regulated genes responsible for this attenuated virulence phenotype remain unknown. Here, we demonstrated that Set1 positively regulates the expression of mitochondrial protein genes by methylating H3K4. In particular, levels of cellular mitochondrial reactive oxygen species (ROS) were higher in <i>Δset1</i> than in the wild-type due to the defect of those genes’ expression. Set1 deletion also increases H<sub>2</sub>O<sub>2</sub> sensitivity and prevents proper colony formation when interacting with macrophage <i>in vitro</i>, consistent with its attenuated virulence <i>in vivo</i>. Together, these findings suggest that Set1 is required to regulate proper cellular ROS production by positively regulating the expression of mitochondrial protein genes and subsequently sustaining mitochondrial membrane integrity. Consequently, <i>C. albicans</i> maintains proper ROS levels via Set1-mediated transcriptional regulation, thus establishing a rapid defense against external ROS generated by the host.
DOI: 10.6084/m9.figshare.14494907
title: Genomic population structure of <i>Helicobacter pylori</i> Shanghai isolates and identification of genomic features uniquely linked with pathogenicity

description: Severe <i>Helicobacter pylori</i>-linked gastric disorders are especially prevalent in the East Asia region. The ability of <i>H. pylori</i> to cause different clinical outcomes is thought to be associated with unique sets of its genetic features. However, only few genetic features have been definitively linked to specific gastrointestinal pathologies. Genome heterogeneity of clinical <i>H. pylori</i> strains from patients with four different gastric disorders was studied to explore the population structure and molecular genomic features and their association with pathogenicity. Population analysis showed that 92.9% of the Shanghai <i>H. pylori</i> isolates were clustered in the East Asia group. Among 2,866 genes detected in all genomes, 1,146 genes formed the core genome, whereas 209 unique genes were detected in individual disease groups. The unique genes of peptic ulcer and gastric cancer groups represented the inorganic ion transport and metabolism function gene clusters. Sixteen virulence genes were detected with statistically different detection rates among the four disease groups. Furthermore, 127 clustered regularly interspaced short palindromic repeats were found with significantly different rates in the four disease groups. A total of 337 putative genomic islands were identified, and three genomic islands were individually found in more than 10% of strains. The genomic islands included several metabolism-associated genes and many genes with unknown function. In total, 88 sequence types were detected among the 112 Shanghai <i>H. pylori</i> isolates. Our study provides an essential milestone in the mapping of specific genomic features and their functions to identify factors needed to induce specific gastric disorders in <i>H. pylori.</i>