cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.vzstr8
title: Occurrence Download

description: A dataset containing 9446 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Colección de Mamíferos del Instituto de Investigación de Recursos Biológicos Alexander von Humboldt (IAvH-M)"
 ]
}

 The dataset includes 9446 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0076125-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.7937045
title: Lysine acetylation of DosR regulates the hypoxia response of <i>Mycobacterium tuberculosis</i>

description: Tuberculosis caused by <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) infection remains a large global public health problem. One striking characteristic of <i>Mtb</i> is its ability to adapt to hypoxia and trigger the ensuing transition to a dormant state for persistent infection, but how the hypoxia response of <i>Mtb</i> is regulated remains largely unknown. Here we performed a quantitative acetylome analysis to compare the acetylation profile of <i>Mtb</i> under aeration and hypoxia, and showed that 377 acetylation sites in 269 <i>Mtb</i> proteins were significantly changed under hypoxia. In particular, deacetylation of dormancy survival regulator (DosR) at K182 promoted the hypoxia response in <i>Mtb</i> and enhanced the transcription of DosR-targeted genes. Mechanistically, recombinant DosR<sup>K182R</sup> protein demonstrated enhanced DNA-binding activity in comparison with DosR<sup>K182Q</sup> protein. Moreover, Rv0998 was identified as an acetyltransferase that mediates the acetylation of DosR at K182. Deletion of Rv0998 also promoted the adaptation of <i>Mtb</i> to hypoxia and the transcription of DosR-targeted genes. Mice infected with an <i>Mtb</i> strain containing acetylation-defective DosR<sup>K182R</sup> had much lower bacterial counts and less severe histopathological impairments compared with those infected with the wild-type strain. Our findings suggest that hypoxia induces the deacetylation of DosR, which in turn increases its DNA-binding ability to promote the transcription of target genes, allowing <i>Mtb</i> to shift to dormancy under hypoxia.
DOI: 10.6084/m9.figshare.7937045.v1
title: Lysine acetylation of DosR regulates the hypoxia response of <i>Mycobacterium tuberculosis</i>

description: Tuberculosis caused by <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) infection remains a large global public health problem. One striking characteristic of <i>Mtb</i> is its ability to adapt to hypoxia and trigger the ensuing transition to a dormant state for persistent infection, but how the hypoxia response of <i>Mtb</i> is regulated remains largely unknown. Here we performed a quantitative acetylome analysis to compare the acetylation profile of <i>Mtb</i> under aeration and hypoxia, and showed that 377 acetylation sites in 269 <i>Mtb</i> proteins were significantly changed under hypoxia. In particular, deacetylation of dormancy survival regulator (DosR) at K182 promoted the hypoxia response in <i>Mtb</i> and enhanced the transcription of DosR-targeted genes. Mechanistically, recombinant DosR<sup>K182R</sup> protein demonstrated enhanced DNA-binding activity in comparison with DosR<sup>K182Q</sup> protein. Moreover, Rv0998 was identified as an acetyltransferase that mediates the acetylation of DosR at K182. Deletion of Rv0998 also promoted the adaptation of <i>Mtb</i> to hypoxia and the transcription of DosR-targeted genes. Mice infected with an <i>Mtb</i> strain containing acetylation-defective DosR<sup>K182R</sup> had much lower bacterial counts and less severe histopathological impairments compared with those infected with the wild-type strain. Our findings suggest that hypoxia induces the deacetylation of DosR, which in turn increases its DNA-binding ability to promote the transcription of target genes, allowing <i>Mtb</i> to shift to dormancy under hypoxia.
DOI: 10.6084/m9.figshare.7936955
title: The emerging novel avian leukosis virus with mutations in the <i>pol</i> gene shows competitive replication advantages both in vivo and in vitro

description: The avian leukosis virus subgroup K (ALV-K), a novel subgroup in Chinese indigenous chicken breeds, has been difficult to isolate in the past due to its poor replication ability. However, according to the latest monitoring data, the replication ability and isolation rate of ALV-K have clearly increased, and new strains with mutations in the <i>pol</i> gene have also been found. To determine the effects of such mutations on the biological characteristics of ALV-K, a pair of infectious clones were constructed and rescued. The first virus was an ALV-K Chinese isolate with mutations in its <i>pol</i> gene, named rSDAUAK-11. The second virus was a recuperative rSDAUAK-11 from which mutations in the <i>pol</i> gene were recovered according to the corresponding region of the ALV-K prototype virus JS11C1, named rRSDAUAK-11. In addition, two quantitative real-time polymerase chain reaction assays were developed to specifically detect these virus strains. Using such methods, we observed a marked improvement of the reverse transcriptase activity, replication ability and vertical transmission ability of rSDAUAK-11, which also revealed a formidable competitive advantage in mixed infection with rRSDAUAK-11 and corresponded to the differences between the wild strains SDAUAK-11 and JS11C1. Accordingly, our findings not only show that mutations in the <i>pol</i> gene are an important molecular mechanism contributing to corresponding changes in the biological characteristics of the newest ALV-K but also emphasize the potential future eradication of ALV.
DOI: 10.6084/m9.figshare.7936955.v1
title: The emerging novel avian leukosis virus with mutations in the <i>pol</i> gene shows competitive replication advantages both in vivo and in vitro

description: The avian leukosis virus subgroup K (ALV-K), a novel subgroup in Chinese indigenous chicken breeds, has been difficult to isolate in the past due to its poor replication ability. However, according to the latest monitoring data, the replication ability and isolation rate of ALV-K have clearly increased, and new strains with mutations in the <i>pol</i> gene have also been found. To determine the effects of such mutations on the biological characteristics of ALV-K, a pair of infectious clones were constructed and rescued. The first virus was an ALV-K Chinese isolate with mutations in its <i>pol</i> gene, named rSDAUAK-11. The second virus was a recuperative rSDAUAK-11 from which mutations in the <i>pol</i> gene were recovered according to the corresponding region of the ALV-K prototype virus JS11C1, named rRSDAUAK-11. In addition, two quantitative real-time polymerase chain reaction assays were developed to specifically detect these virus strains. Using such methods, we observed a marked improvement of the reverse transcriptase activity, replication ability and vertical transmission ability of rSDAUAK-11, which also revealed a formidable competitive advantage in mixed infection with rRSDAUAK-11 and corresponded to the differences between the wild strains SDAUAK-11 and JS11C1. Accordingly, our findings not only show that mutations in the <i>pol</i> gene are an important molecular mechanism contributing to corresponding changes in the biological characteristics of the newest ALV-K but also emphasize the potential future eradication of ALV.
DOI: 10.25549/pcra-c14-64210
title: Redemption tidings, vol. 44, nos. 1-52, 4 Jan. - 26 Dec. 1968

description: [description english/roman)] Issued weekly.
DOI: 10.6084/m9.figshare.7937819
title: Novel type of pilus associated with a Shiga-toxigenic <i>E. coli</i> hybrid pathovar conveys aggregative adherence and bacterial virulence

description: A large German outbreak in 2011 was caused by a locus of enterocyte effacement (LEE)-negative enterohemorrhagic <i>E. coli</i> (EHEC) strain of the serotype O104:H4. This strain harbors markers that are characteristic of both EHEC and enteroaggregative <i>E. coli</i> (EAEC), including aggregative adhesion fimbriae (AAF) genes. Such rare EHEC/EAEC hybrids are highly pathogenic due to their possession of a combination of genes promoting severe toxicity and aggregative adhesion. We previously identified novel EHEC/EAEC hybrids and observed that one strain exhibited aggregative adherence but had no AAF genes. In this study, a genome sequence analysis showed that this strain belongs to the genoserotype O23:H8, MLST ST26, and harbors a 5.2 Mb chromosome and three plasmids. One plasmid carries some EAEC marker genes, such as <i>aatA</i> and genes with limited protein homology (11–61%) to those encoding the bundle-forming pilus (BFP) of enteropathogenic <i>E. coli</i>. Due to significant protein homology distance to known pili, we designated these as aggregate-forming pili (AFP)-encoding genes and the respective plasmid as pAFP. The <i>afp</i> operon was arranged similarly to the operon of BFP genes but contained an additional gene, <i>afpA2</i>, which is homologous to <i>afpA</i>. The deletion of the <i>afp</i> operon, <i>afpA</i>, or a nearby gene (<i>afpR</i>) encoding an AraC-like regulator, but not <i>afpA2</i>, led to a loss of pilin production, piliation, bacterial autoaggregation, and importantly, a &gt;80% reduction in adhesion and cytotoxicity toward epithelial cells. Gene sets similar to the <i>afp</i> operon were identified in a variety of <i>aatA</i>-positive but AAF-negative intestinal pathogenic <i>E. coli</i>. In summary, we characterized widely distributed and novel fimbriae that are essential for aggregative adherence and cytotoxicity in a LEE-negative Shiga-toxigenic hybrid.
DOI: 10.6084/m9.figshare.7937819.v1
title: Novel type of pilus associated with a Shiga-toxigenic <i>E. coli</i> hybrid pathovar conveys aggregative adherence and bacterial virulence

description: A large German outbreak in 2011 was caused by a locus of enterocyte effacement (LEE)-negative enterohemorrhagic <i>E. coli</i> (EHEC) strain of the serotype O104:H4. This strain harbors markers that are characteristic of both EHEC and enteroaggregative <i>E. coli</i> (EAEC), including aggregative adhesion fimbriae (AAF) genes. Such rare EHEC/EAEC hybrids are highly pathogenic due to their possession of a combination of genes promoting severe toxicity and aggregative adhesion. We previously identified novel EHEC/EAEC hybrids and observed that one strain exhibited aggregative adherence but had no AAF genes. In this study, a genome sequence analysis showed that this strain belongs to the genoserotype O23:H8, MLST ST26, and harbors a 5.2 Mb chromosome and three plasmids. One plasmid carries some EAEC marker genes, such as <i>aatA</i> and genes with limited protein homology (11–61%) to those encoding the bundle-forming pilus (BFP) of enteropathogenic <i>E. coli</i>. Due to significant protein homology distance to known pili, we designated these as aggregate-forming pili (AFP)-encoding genes and the respective plasmid as pAFP. The <i>afp</i> operon was arranged similarly to the operon of BFP genes but contained an additional gene, <i>afpA2</i>, which is homologous to <i>afpA</i>. The deletion of the <i>afp</i> operon, <i>afpA</i>, or a nearby gene (<i>afpR</i>) encoding an AraC-like regulator, but not <i>afpA2</i>, led to a loss of pilin production, piliation, bacterial autoaggregation, and importantly, a &gt;80% reduction in adhesion and cytotoxicity toward epithelial cells. Gene sets similar to the <i>afp</i> operon were identified in a variety of <i>aatA</i>-positive but AAF-negative intestinal pathogenic <i>E. coli</i>. In summary, we characterized widely distributed and novel fimbriae that are essential for aggregative adherence and cytotoxicity in a LEE-negative Shiga-toxigenic hybrid.
DOI: 10.6084/m9.figshare.7936790.v1
title: Detection of <i>Coccidioides posadasii</i> from xerophytic environments in Venezuela reveals risk of naturally acquired coccidioidomycosis infections

description: A wide range of mammals are susceptible to infection by the fungal species <i>Coccidioides immitis</i> and <i>C. posadasii</i>. In humans, 60% of infections are asymptomatic; however, certain patients may develop a severe and deep systemic mycosis called coccidioidomycosis. Genetic analysis suggests that the majority of clinical isolates recovered from South America are <i>C. posadasii</i>; however, little is known about the prevalence, species distribution, and ecological factors that favor the occurrence of this pathogen in those areas. By using a combined quantitative polymerase chain reaction (qPCR)-based approach and mycobiome amplicon sequencing, we provide evidence that at least two genotypes of <i>C. posadasii</i> are found in the xerophytic environment in Venezuela. We detected a 3806-fold range in the amount of <i>Coccidioides</i> DNA when comparing among the sampled locations, which indicates that human exposure risk is variable, and is one critical factor for disease manifestation. We identified fungal communities that are correlated with a higher prevalence of <i>C. posadasii</i>, suggesting that a combination of specific microbes and a xeric microenvironment may favor the growth of <i>Coccidioides</i> in certain locations. Moreover, we discuss the use of a combinatorial approach, using both qPCR and deep-sequencing methods to assess and monitor fungal pathogen burden at outbreak sources.
DOI: 10.6084/m9.figshare.7936934
title: Swine influenza viruses in Northern Vietnam in 2013–2014

description: Swine are an important intermediate host for emergence of pandemic influenza. Vietnam is the largest swine producer in South East Asia. Systematic virological and serological surveillance of swine influenza viruses was carried out in Northern Vietnam from May 2013 to June 2014 with monthly sampling of pigs in local and large collective slaughterhouses and in a live pig market. Influenza A seroprevalence in the local slaughterhouses and in the large collective slaughterhouse was 48.7% and 29.1%, respectively. Seventy-seven influenza A viruses were isolated, all from the large collective slaughterhouse. Genetic analysis revealed six virus genotypes including H1N1 2009 pandemic (H1N1pdm09) viruses, H1N2 with H1 of human origin, H3N2 and H1N1pdm09 reassortants, and triple-reassortant H3N2 viruses. Phylogenetic analysis of swine and human H1N1pdm09 viruses showed evidence of repeated spill-over from humans to swine rather than the establishment of H1N1pdm09 as long-term distinct lineage in swine. Surveillance at the large collective slaughterhouse proved to be the most efficient, cost-effective, and sustainable method of surveillance for swine influenza viruses in Vietnam.
DOI: 10.6084/m9.figshare.7936934.v3
title: Swine influenza viruses in Northern Vietnam in 2013–2014

description: Swine are an important intermediate host for emergence of pandemic influenza. Vietnam is the largest swine producer in South East Asia. Systematic virological and serological surveillance of swine influenza viruses was carried out in Northern Vietnam from May 2013 to June 2014 with monthly sampling of pigs in local and large collective slaughterhouses and in a live pig market. Influenza A seroprevalence in the local slaughterhouses and in the large collective slaughterhouse was 48.7% and 29.1%, respectively. Seventy-seven influenza A viruses were isolated, all from the large collective slaughterhouse. Genetic analysis revealed six virus genotypes including H1N1 2009 pandemic (H1N1pdm09) viruses, H1N2 with H1 of human origin, H3N2 and H1N1pdm09 reassortants, and triple-reassortant H3N2 viruses. Phylogenetic analysis of swine and human H1N1pdm09 viruses showed evidence of repeated spill-over from humans to swine rather than the establishment of H1N1pdm09 as long-term distinct lineage in swine. Surveillance at the large collective slaughterhouse proved to be the most efficient, cost-effective, and sustainable method of surveillance for swine influenza viruses in Vietnam.
DOI: 10.6084/m9.figshare.7936790
title: Detection of <i>Coccidioides posadasii</i> from xerophytic environments in Venezuela reveals risk of naturally acquired coccidioidomycosis infections

description: A wide range of mammals are susceptible to infection by the fungal species <i>Coccidioides immitis</i> and <i>C. posadasii</i>. In humans, 60% of infections are asymptomatic; however, certain patients may develop a severe and deep systemic mycosis called coccidioidomycosis. Genetic analysis suggests that the majority of clinical isolates recovered from South America are <i>C. posadasii</i>; however, little is known about the prevalence, species distribution, and ecological factors that favor the occurrence of this pathogen in those areas. By using a combined quantitative polymerase chain reaction (qPCR)-based approach and mycobiome amplicon sequencing, we provide evidence that at least two genotypes of <i>C. posadasii</i> are found in the xerophytic environment in Venezuela. We detected a 3806-fold range in the amount of <i>Coccidioides</i> DNA when comparing among the sampled locations, which indicates that human exposure risk is variable, and is one critical factor for disease manifestation. We identified fungal communities that are correlated with a higher prevalence of <i>C. posadasii</i>, suggesting that a combination of specific microbes and a xeric microenvironment may favor the growth of <i>Coccidioides</i> in certain locations. Moreover, we discuss the use of a combinatorial approach, using both qPCR and deep-sequencing methods to assess and monitor fungal pathogen burden at outbreak sources.
DOI: 10.6084/m9.figshare.7936934.v2
title: Swine influenza viruses in Northern Vietnam in 2013–2014

description: Swine are an important intermediate host for emergence of pandemic influenza. Vietnam is the largest swine producer in South East Asia. Systematic virological and serological surveillance of swine influenza viruses was carried out in Northern Vietnam from May 2013 to June 2014 with monthly sampling of pigs in local and large collective slaughterhouses and in a live pig market. Influenza A seroprevalence in the local slaughterhouses and in the large collective slaughterhouse was 48.7% and 29.1%, respectively. Seventy-seven influenza A viruses were isolated, all from the large collective slaughterhouse. Genetic analysis revealed six virus genotypes including H1N1 2009 pandemic (H1N1pdm09) viruses, H1N2 with H1 of human origin, H3N2 and H1N1pdm09 reassortants, and triple-reassortant H3N2 viruses. Phylogenetic analysis of swine and human H1N1pdm09 viruses showed evidence of repeated spill-over from humans to swine rather than the establishment of H1N1pdm09 as long-term distinct lineage in swine. Surveillance at the large collective slaughterhouse proved to be the most efficient, cost-effective, and sustainable method of surveillance for swine influenza viruses in Vietnam.
DOI: 10.6084/m9.figshare.7937084
title: Comparison of the pathogenic potential of highly pathogenic avian influenza (HPAI) H5N6, and H5N8 viruses isolated in South Korea during the 2016–2017 winter season

description: Highly pathogenic avian influenza (HPAI) A(H5N6) and A(H5N8) virus infections resulted in the culling of more than 37 million poultry in the Republic of Korea during the 2016/17 winter season. Here we characterize two representative viruses, A/Environment/Korea/W541/2016 [Em/W541(H5N6)] and A/Common Teal/Korea/W555/2017 [CT/W555(H5N8)], and evaluate their zoonotic potential in various animal models. Both Em/W541(H5N6) and CT /W555(H5N8) are novel reassortants derived from various gene pools of wild bird viruses present in migratory waterfowl arising from eastern China. Despite strong preferential binding to avian virus–type receptors, the viruses were able to grow in human respiratory tract tissues. Em/W541(H5N6) was found to be highly pathogenic in both chickens and ducks, while CT/W555(H5N8) caused lethal infections in chickens but did not induce remarkable clinical illness in ducks. In mice, both viruses appeared to be moderately pathogenic and displayed limited tissue tropism relative to HPAI H5N1 viruses. Em/W541(H5N6) replicated to moderate levels in the upper respiratory tract of ferrets and was detected in the lungs, brain, spleen, liver, and colon. Unexpectedly, two of three ferrets in direct contact with Em/W541(H5N6)-infected animals shed virus and seroconverted at 14 dpi. CT/W555(H5N8) was less pathogenic than the H5N6 virus in ferrets and no transmission was detected. Given the co-circulation of different, phenotypically distinct, subtypes of HPAI H5Nx viruses for the first time in South Korea, detailed virologic investigations are imperative given the capacity of these viruses to evolve and cause human infections.
DOI: 10.6084/m9.figshare.7937084.v2
title: Comparison of the pathogenic potential of highly pathogenic avian influenza (HPAI) H5N6, and H5N8 viruses isolated in South Korea during the 2016–2017 winter season

description: Highly pathogenic avian influenza (HPAI) A(H5N6) and A(H5N8) virus infections resulted in the culling of more than 37 million poultry in the Republic of Korea during the 2016/17 winter season. Here we characterize two representative viruses, A/Environment/Korea/W541/2016 [Em/W541(H5N6)] and A/Common Teal/Korea/W555/2017 [CT/W555(H5N8)], and evaluate their zoonotic potential in various animal models. Both Em/W541(H5N6) and CT /W555(H5N8) are novel reassortants derived from various gene pools of wild bird viruses present in migratory waterfowl arising from eastern China. Despite strong preferential binding to avian virus–type receptors, the viruses were able to grow in human respiratory tract tissues. Em/W541(H5N6) was found to be highly pathogenic in both chickens and ducks, while CT/W555(H5N8) caused lethal infections in chickens but did not induce remarkable clinical illness in ducks. In mice, both viruses appeared to be moderately pathogenic and displayed limited tissue tropism relative to HPAI H5N1 viruses. Em/W541(H5N6) replicated to moderate levels in the upper respiratory tract of ferrets and was detected in the lungs, brain, spleen, liver, and colon. Unexpectedly, two of three ferrets in direct contact with Em/W541(H5N6)-infected animals shed virus and seroconverted at 14 dpi. CT/W555(H5N8) was less pathogenic than the H5N6 virus in ferrets and no transmission was detected. Given the co-circulation of different, phenotypically distinct, subtypes of HPAI H5Nx viruses for the first time in South Korea, detailed virologic investigations are imperative given the capacity of these viruses to evolve and cause human infections.