cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12319646
title: Identification of conditionally essential genes for <i>Streptococcus suis</i> infection in pigs

description: <b>Streptococcus suis</b> is a Gram-positive bacterium and zoonotic pathogen that causes meningitis and sepsis in pigs and humans. The aim of this study was to identify genes required for <i>S. suis</i> infection. We created Tn-Seq libraries in a virulent <i>S. suis</i> strain 10, which was used to inoculate pigs in an intrathecal experimental infection. Comparative analysis of the relative abundance of mutants recovered from different sites of infection (blood, cerebrospinal fluid, and meninges of the brain) identified 361 conditionally essential genes, i.e. required for infection, which is about 18% of the genome. The conditionally essential genes were primarily involved in metabolic and transport processes, regulation, ribosomal structure and biogenesis, transcription, and cell wall membrane and envelope biogenesis, stress defenses, and immune evasion. Directed mutants were created in a set of 10 genes of different genetic ontologies and their role was determined in <i>ex vivo</i> models. Mutants showed different levels of sensitivity to survival in whole blood, serum, cerebrospinal fluid, thermic shock, and stress conditions, as compared to the wild type. Additionally, the role of three selected mutants was validated in co-infection experiments in which pigs were infected with both wild type and isogenic mutant strains. The genetic determinants of infection identified in this work contribute to novel insights in <i>S. suis</i> pathogenesis and could serve as targets for novel vaccines or antimicrobial drugs.
DOI: 10.6084/m9.figshare.12319646.v3
title: Identification of conditionally essential genes for <i>Streptococcus suis</i> infection in pigs

description: is a Gram-positive bacterium and zoonotic pathogen that causes meningitis and sepsis in pigs and humans. The aim of this study was to identify genes required for <i>S. suis</i> infection. We created Tn-Seq libraries in a virulent <i>S. suis</i> strain 10, which was used to inoculate pigs in an intrathecal experimental infection. Comparative analysis of the relative abundance of mutants recovered from different sites of infection (blood, cerebrospinal fluid, and meninges of the brain) identified 361 conditionally essential genes, i.e. required for infection, which is about 18% of the genome. The conditionally essential genes were primarily involved in metabolic and transport processes, regulation, ribosomal structure and biogenesis, transcription, and cell wall membrane and envelope biogenesis, stress defenses, and immune evasion. Directed mutants were created in a set of 10 genes of different genetic ontologies and their role was determined in <i>ex vivo</i> models. Mutants showed different levels of sensitivity to survival in whole blood, serum, cerebrospinal fluid, thermic shock, and stress conditions, as compared to the wild type. Additionally, the role of three selected mutants was validated in co-infection experiments in which pigs were infected with both wild type and isogenic mutant strains. The genetic determinants of infection identified in this work contribute to novel insights in <i>S. suis</i> pathogenesis and could serve as targets for novel vaccines or antimicrobial drugs.
DOI: 10.6084/m9.figshare.12851991
title: Phylogenetic and codon usage analysis of atypical porcine pestivirus (APPV)

description: Atypical porcine pestivirus (APPV) has been identified as the main causative agent for congenital tremor (CT) type A-II in piglets, which is threatening the health of the global swine herd. However, the evolution of APPV remains largely unknown. In this study, phylogenetic analysis showed that APPV could be divided into three phylogroups (I, II, and III). Phylogroups I and II included viral strains from China, while phylogroup III contained strains from Europe, North America, and Asia. Phylogroups I and II are tentatively thought to be of Chinese origin. Next, compositional property analysis revealed that a high frequency of nucleotide A and A-end codons was used in the APPV genome. Intriguingly, the analysis of preferred codons revealed that the AGA[Arg] and AGG[Arg] were overrepresented. Dinucleotide CC was found to be overrepresented, and dinucleotide CG was underrepresented. Furthermore, it was found that the weak codon usage bias of APPV was mainly dominated by selection pressures versus mutational forces. The codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses showed that the codon usage patterns of phylogroup II and III were more similar to the one of a pig than phylogroup I, suggesting that phylogroup II and III may be more adaptive to pigs. Overall, this study provides insights into APPV evolution through phylogeny and codon usage pattern analysis.
DOI: 10.6084/m9.figshare.12851991.v1
title: Phylogenetic and codon usage analysis of atypical porcine pestivirus (APPV)

description: Atypical porcine pestivirus (APPV) has been identified as the main causative agent for congenital tremor (CT) type A-II in piglets, which is threatening the health of the global swine herd. However, the evolution of APPV remains largely unknown. In this study, phylogenetic analysis showed that APPV could be divided into three phylogroups (I, II, and III). Phylogroups I and II included viral strains from China, while phylogroup III contained strains from Europe, North America, and Asia. Phylogroups I and II are tentatively thought to be of Chinese origin. Next, compositional property analysis revealed that a high frequency of nucleotide A and A-end codons was used in the APPV genome. Intriguingly, the analysis of preferred codons revealed that the AGA[Arg] and AGG[Arg] were overrepresented. Dinucleotide CC was found to be overrepresented, and dinucleotide CG was underrepresented. Furthermore, it was found that the weak codon usage bias of APPV was mainly dominated by selection pressures versus mutational forces. The codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses showed that the codon usage patterns of phylogroup II and III were more similar to the one of a pig than phylogroup I, suggesting that phylogroup II and III may be more adaptive to pigs. Overall, this study provides insights into APPV evolution through phylogeny and codon usage pattern analysis.
DOI: 10.6084/m9.figshare.13134275
title: Respiratory ß-2-Microglobulin exerts pH dependent antimicrobial activity

description: The respiratory tract is a major entry site for microbial pathogens. To combat bacterial infections, the immune system has various defense mechanisms at its disposal, including antimicrobial peptides (AMPs). To search for novel AMPs from the respiratory tract, a peptide library from human broncho-alveolar-lavage (BAL) fluid was screened for antimicrobial activity by radial diffusion assays allowing the efficient detection of antibacterial activity within a small sample size. After repeated testing-cycles and subsequent purification, we identified ß-2-microglobulin (B2M) in antibacterially active fractions. B2M belongs to the MHC-1 receptor complex present at the surface of nucleated cells. It is known to inhibit the growth of <i>Listeria monocytogenes</i> and <i>Escherichia coli</i> and to facilitate phagocytosis of <i>Staphylococcus aureus</i>. Using commercially available B2M we confirmed a dose-dependent inhibition of <i>Pseudomonas aeruginosa</i> and <i>L. monocytogenes</i>. To characterize AMP activity within the B2M sequence, peptide fragments of the molecule were tested for antimicrobial activity. Activity could be localized to the C-terminal part of B2M. Investigating pH dependency of the antimicrobial activity of B2M demonstrated an increased activity at pH values of 5.5 and below, a hallmark of infection and inflammation. Sytox green uptake into bacterial cells following the exposure to B2M was determined and revealed a pH-dependent loss of bacterial membrane integrity. TEM analysis showed areas of disrupted bacterial membranes in <i>L. monocytogenes</i> incubated with B2M and high amounts of lysed bacterial cells. In conclusion, B2M as part of a ubiquitous cell surface complex may represent a potent antimicrobial agent by interfering with bacterial membrane integrity.
DOI: 10.6084/m9.figshare.12852042.v3
title: PE_PGRS proteins of <i>Mycobacterium tuberculosis</i>: A specialized molecular task force at the forefront of host–pathogen interaction

description: To the PE_PGRS protein subfamily belongs a group of surface-exposed mycobacterial antigens that in <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) H37Rv accounts to more than 65 genes, 51 of which are thought to express a functional protein. PE_PGRS proteins share a conserved structural architecture with three main domains: the N-terminal PE domain; the PGRS domain, that can vary in sequence and size and is characterized by the presence of multiple GGA-GGX amino acid repeats; the highly conserved sequence containing the GRPLI motif that links the PE and PGRS domains; the unique C-terminus end that can vary in size from few to up to ≈ 300 amino acids. <i>pe_pgrs</i> genes emerged in slow-growing mycobacteria and expanded and diversified in MTBC and few other pathogenic mycobacteria. Interestingly, despite sequence homology and apparent redundancy, PE_PGRS proteins seem to have evolved a peculiar function. In this review, we summarize the actual knowledge on this elusive protein family in terms of evolution, structure, and function, focusing on the role of PE_PGRS in TB pathogenesis. We provide an original hypothesis on the role of the PE domain and propose a structural model for the polymorphic PGRS domain that might explain how so similar proteins can have different physiological functions.
DOI: 10.5281/zenodo.6957540
title: Summary Statistics from "Meta-GWAS of PCSK9 levels detects two novel loci at APOB and TM6SF2"

description: GWAMA summary statistics of PCSK9 levels using fixed-effect model. Genome-wide data is given for Europeans with statin adjustment and Europeans without statin treatment only (subset of the population). In addition, locus-wide data of the PCSK9 gene locus for African-Americans without statin treatment is listed. When using this data, please cite: Pott J, Gadin J, Theusch E, et al.. Meta-GWAS of PCSK9 levels detects two novel loci at APOB and TM6SF2. Hum Mol Genet. 2021 Sep 30:ddab279. doi: 10.1093/hmg/ddab279. PMID: 34590679 All txt files contain the following columns: markername chr bp_hg19 (base position according to hg19) ea (effect allele) oa (other allele) eaf (effect allele frequency) info (minimal info score across all used studies) nSamples (sample size per SNP) nStudies (number of studies) beta (effect estimate) se (standard error) p (p-value) I2 (SNP heterogeneity across studies) phenotype (phenotyp setting)
description: Update: we added the sex-stratified summary statistics for the four genome-wide significant loci.
description: {"references": ["Pott J, Gadin J, Theusch E, Kleber ME, Delgado GE, Kirsten H, Hauck SM, Burkhardt R, Scharnagl H, Krauss RM, Loeffler M, M\u00e4rz W, Thiery J, Silveira A, Vant Hooft FM, Scholz M. Meta-GWAS of PCSK9 levels detects two novel loci at APOB and TM6SF2. Hum Mol Genet. 2021 Sep 30:ddab279. doi: 10.1093/hmg/ddab279"]}
DOI: 10.6084/m9.figshare.13134275.v2
title: Respiratory ß-2-Microglobulin exerts pH dependent antimicrobial activity

description: The respiratory tract is a major entry site for microbial pathogens. To combat bacterial infections, the immune system has various defense mechanisms at its disposal, including antimicrobial peptides (AMPs). To search for novel AMPs from the respiratory tract, a peptide library from human broncho-alveolar-lavage (BAL) fluid was screened for antimicrobial activity by radial diffusion assays allowing the efficient detection of antibacterial activity within a small sample size. After repeated testing-cycles and subsequent purification, we identified ß-2-microglobulin (B2M) in antibacterially active fractions. B2M belongs to the MHC-1 receptor complex present at the surface of nucleated cells. It is known to inhibit the growth of <i>Listeria monocytogenes</i> and <i>Escherichia coli</i> and to facilitate phagocytosis of <i>Staphylococcus aureus</i>. Using commercially available B2M we confirmed a dose-dependent inhibition of <i>Pseudomonas aeruginosa</i> and <i>L. monocytogenes</i>. To characterize AMP activity within the B2M sequence, peptide fragments of the molecule were tested for antimicrobial activity. Activity could be localized to the C-terminal part of B2M. Investigating pH dependency of the antimicrobial activity of B2M demonstrated an increased activity at pH values of 5.5 and below, a hallmark of infection and inflammation. Sytox green uptake into bacterial cells following the exposure to B2M was determined and revealed a pH-dependent loss of bacterial membrane integrity. TEM analysis showed areas of disrupted bacterial membranes in <i>L. monocytogenes</i> incubated with B2M and high amounts of lysed bacterial cells. In conclusion, B2M as part of a ubiquitous cell surface complex may represent a potent antimicrobial agent by interfering with bacterial membrane integrity.
DOI: 10.6084/m9.figshare.12072120
title: Characterization of Schu S4 <i>aro</i> mutants as live attenuated tularemia vaccine candidates

description: There is a need for development of an effective vaccine against <i>Francisella tularensis</i>, as this potential bioweapon has a high mortality rate and low infectious dose when delivered via the aerosol route. Moreover, this Tier 1 agent has a history of weaponization. We engineered targeted mutations in the Type A strain <i>F. tularensis</i> subspecies <i>tularensis</i> Schu S4 in <i>aro</i> genes encoding critical enzymes in aromatic amino acid biosynthesis. <i>F. tularensis</i> Schu S4<i>ΔaroC</i>, Schu S4Δ<i>aroD</i>, and Schu S4Δ<i>aroC</i>Δ<i>aroD</i> mutant strains were attenuated for intracellular growth <i>in vitro</i> and for virulence <i>in vivo</i> and, conferred protection against pulmonary wild-type (WT) <i>F. tularensis</i> Schu S4 challenge in the C57BL/6 mouse model. <i>F. tularensis</i> Schu S4Δ<i>aroD</i> was identified as the most promising vaccine candidate, demonstrating protection against high-dose intranasal challenge; it protected against 1,000 CFU Schu S4, the highest level of protection tested to date. It also provided complete protection against challenge with 92 CFU of a <i>F. tularensis</i> subspecies <i>holarctica</i> strain (Type B). Mice responded to vaccination with Schu S4Δ<i>aroD</i> with systemic IgM and IgG2c, as well as the production of a functional T cell response as measured in the splenocyte-macrophage co-culture assay. This vaccine was further characterized for dissemination, histopathology, and cytokine/chemokine gene induction at defined time points following intranasal vaccination which confirmed its attenuation compared to WT Schu S4. Cytokine, chemokine, and antibody induction patterns compared to wild-type Schu S4 distinguish protective <i>vs</i>. pathogenic responses to <i>F. tularensis</i> and elucidate correlates of protection associated with vaccination against this agent.
DOI: 10.6084/m9.figshare.12852042
title: PE_PGRS proteins of <i>Mycobacterium tuberculosis</i>: A specialized molecular task force at the forefront of host–pathogen interaction

description: To the PE_PGRS protein subfamily belongs a group of surface-exposed mycobacterial antigens that in <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) H37Rv accounts to more than 65 genes, 51 of which are thought to express a functional protein. PE_PGRS proteins share a conserved structural architecture with three main domains: the N-terminal PE domain; the PGRS domain, that can vary in sequence and size and is characterized by the presence of multiple GGA-GGX amino acid repeats; the highly conserved sequence containing the GRPLI motif that links the PE and PGRS domains; the unique C-terminus end that can vary in size from few to up to ≈ 300 amino acids. <i>pe_pgrs</i> genes emerged in slow-growing mycobacteria and expanded and diversified in MTBC and few other pathogenic mycobacteria. Interestingly, despite sequence homology and apparent redundancy, PE_PGRS proteins seem to have evolved a peculiar function. In this review, we summarize the actual knowledge on this elusive protein family in terms of evolution, structure, and function, focusing on the role of PE_PGRS in TB pathogenesis. We provide an original hypothesis on the role of the PE domain and propose a structural model for the polymorphic PGRS domain that might explain how so similar proteins can have different physiological functions.
DOI: 10.6084/m9.figshare.12072120.v1
title: Characterization of Schu S4 <i>aro</i> mutants as live attenuated tularemia vaccine candidates

description: There is a need for development of an effective vaccine against <i>Francisella tularensis</i>, as this potential bioweapon has a high mortality rate and low infectious dose when delivered via the aerosol route. Moreover, this Tier 1 agent has a history of weaponization. We engineered targeted mutations in the Type A strain <i>F. tularensis</i> subspecies <i>tularensis</i> Schu S4 in <i>aro</i> genes encoding critical enzymes in aromatic amino acid biosynthesis. <i>F. tularensis</i> Schu S4<i>ΔaroC</i>, Schu S4Δ<i>aroD</i>, and Schu S4Δ<i>aroC</i>Δ<i>aroD</i> mutant strains were attenuated for intracellular growth <i>in vitro</i> and for virulence <i>in vivo</i> and, conferred protection against pulmonary wild-type (WT) <i>F. tularensis</i> Schu S4 challenge in the C57BL/6 mouse model. <i>F. tularensis</i> Schu S4Δ<i>aroD</i> was identified as the most promising vaccine candidate, demonstrating protection against high-dose intranasal challenge; it protected against 1,000 CFU Schu S4, the highest level of protection tested to date. It also provided complete protection against challenge with 92 CFU of a <i>F. tularensis</i> subspecies <i>holarctica</i> strain (Type B). Mice responded to vaccination with Schu S4Δ<i>aroD</i> with systemic IgM and IgG2c, as well as the production of a functional T cell response as measured in the splenocyte-macrophage co-culture assay. This vaccine was further characterized for dissemination, histopathology, and cytokine/chemokine gene induction at defined time points following intranasal vaccination which confirmed its attenuation compared to WT Schu S4. Cytokine, chemokine, and antibody induction patterns compared to wild-type Schu S4 distinguish protective <i>vs</i>. pathogenic responses to <i>F. tularensis</i> and elucidate correlates of protection associated with vaccination against this agent.
DOI: 10.6084/m9.figshare.12851982
title: A novel biosafety level 2 compliant tuberculosis infection model using a Δ<i>leuD</i>Δ<i>panCD</i> double auxotroph of <i>Mycobacterium tuberculosis</i> H37Rv and <i>Galleria mellonella</i>

description: Mammalian infection models have contributed significantly to our understanding of the host-mycobacterial interaction, revealing potential mechanisms and targets for novel antimycobacterial therapeutics. However, the use of conventional mammalian models such as mice, are typically expensive, high maintenance, require specialized animal housing, and are ethically regulated. Furthermore, research using <i>Mycobacterium tuberculosis</i> (MTB), is inherently difficult as work needs to be carried out at biosafety level 3 (BSL3). The insect larvae of <i>Galleria mellonella</i> (greater wax moth), have become increasingly popular as an infection model, and we previously demonstrated its potential as a mycobacterial infection model using <i>Mycobacterium bovis</i> BCG. Here we present a novel BSL2 complaint MTB infection model using <i>G. mellonella</i> in combination with a bioluminescent <i>ΔleuDΔpanCD</i> double auxotrophic mutant of MTB H37Rv (SAMTB <i>lux</i>) which offers safety and practical advantages over working with wild type MTB. Our results show a SAMTB <i>lux</i> dose dependent survival of <i>G. mellonella</i> larvae and demonstrate proliferation and persistence of SAMTB <i>lux</i> bioluminescence over a 1 week infection time course. Histopathological analysis of <i>G. mellonella</i>, highlight the formation of early granuloma-like structures which matured over time. We additionally demonstrate the drug efficacy of first (isoniazid, rifampicin, and ethambutol) and second line (moxifloxacin) antimycobacterial drugs. Our findings demonstrate the broad potential of this insect model to study MTB infection under BSL2 conditions. We anticipate that the successful adaptation and implementation of this model will remove the inherent limitations of MTB research at BSL3 and increase tuberculosis research output.
DOI: 10.6084/m9.figshare.12851982.v1
title: A novel biosafety level 2 compliant tuberculosis infection model using a Δ<i>leuD</i>Δ<i>panCD</i> double auxotroph of <i>Mycobacterium tuberculosis</i> H37Rv and <i>Galleria mellonella</i>

description: Mammalian infection models have contributed significantly to our understanding of the host-mycobacterial interaction, revealing potential mechanisms and targets for novel antimycobacterial therapeutics. However, the use of conventional mammalian models such as mice, are typically expensive, high maintenance, require specialized animal housing, and are ethically regulated. Furthermore, research using <i>Mycobacterium tuberculosis</i> (MTB), is inherently difficult as work needs to be carried out at biosafety level 3 (BSL3). The insect larvae of <i>Galleria mellonella</i> (greater wax moth), have become increasingly popular as an infection model, and we previously demonstrated its potential as a mycobacterial infection model using <i>Mycobacterium bovis</i> BCG. Here we present a novel BSL2 complaint MTB infection model using <i>G. mellonella</i> in combination with a bioluminescent <i>ΔleuDΔpanCD</i> double auxotrophic mutant of MTB H37Rv (SAMTB <i>lux</i>) which offers safety and practical advantages over working with wild type MTB. Our results show a SAMTB <i>lux</i> dose dependent survival of <i>G. mellonella</i> larvae and demonstrate proliferation and persistence of SAMTB <i>lux</i> bioluminescence over a 1 week infection time course. Histopathological analysis of <i>G. mellonella</i>, highlight the formation of early granuloma-like structures which matured over time. We additionally demonstrate the drug efficacy of first (isoniazid, rifampicin, and ethambutol) and second line (moxifloxacin) antimycobacterial drugs. Our findings demonstrate the broad potential of this insect model to study MTB infection under BSL2 conditions. We anticipate that the successful adaptation and implementation of this model will remove the inherent limitations of MTB research at BSL3 and increase tuberculosis research output.