cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7937270.v2
title: Exosomes mediate Zika virus transmission through SMPD3 neutral Sphingomyelinase in cortical neurons

description: The harmful effects of ZIKA virus (ZIKV) infection are reflected by severe neurological manifestations such as microcephaly in neonates and other complications associated with Guillain-Barré syndrome in adults. The transmission dynamics of ZIKV in or between neurons, or within the developing brains of the foetuses are not fully understood. Using primary cultures of murine cortical neurons, we show that ZIKV uses exosomes as mediators of viral transmission between neurons. Cryo-electron microscopy showed heterogeneous population of neuronal exosomes with a size range of 30–200 nm. Increased production of exosomes from neuronal cells was noted upon ZIKV infection. Neuronal exosomes contained both ZIKV viral RNA and protein(s) that were highly infectious to naïve cells. RNaseA and neutralizing antibodies treatment studies suggest the presence of viral RNA/proteins inside exosomes. Exosomes derived from time- and dose-dependent incubations showed increasing viral loads suggesting higher packaging and delivery of ZIKV RNA and proteins. Furthermore, we noted that ZIKV induced both activity and gene expression of neutral Sphingomyelinase (nSMase)-2/SMPD3, an important molecule that regulates production and release of exosomes. Silencing of SMPD3 in neurons resulted in reduced viral burden and transmission through exosomes. Treatment with SMPD3 specific inhibitor GW4869, significantly reduced ZIKV loads in both cortical neurons and in exosomes derived from these neuronal cells. Taken together, our results suggest that ZIKV modulates SMPD3 activity in cortical neurons for its infection and transmission through exosomes perhaps leading to severe neuronal death that may result in neurological manifestations such as microcephaly in the developing embryonic brains.
DOI: 10.6084/m9.figshare.8019968.v1
title: Evaluation of rodent control to fight Lassa fever based on field data and mathematical modelling

description: The Natal multimammate mouse (<i>Mastomys natalensis</i>) is the reservoir host of Lassa virus, an arenavirus that causes Lassa haemorrhagic fever in humans in West Africa. Because no vaccine exists and therapeutic options are limited, preventing infection through rodent control and human behavioural measures is currently considered to be the only option. In order to assess the efficacy of rodent control, we performed a 4-year field experiment in rural Upper Guinea and developed a mathematical model to simulate different control strategies (annual density control, continuous density control, and rodent vaccination). For the field study, rodenticide baits were placed each year in three rural villages, while three other villages were used as controls. Rodents were trapped before and after every treatment and their antibody status and age were determined. Data from the field study were used to parameterize the mathematical model. In the field study, we found a significant negative effect of rodent control on seroprevalence, but this effect was small especially given the effort. Furthermore, the rodent populations recovered rapidly after rodenticide application, leading us to conclude that an annual control strategy is unlikely to significantly reduce Lassa virus spillover to humans. In agreement with this finding, the mathematical model suggests that the use of continuous control or rodent vaccination is the only strategy that could lead to Lassa virus elimination. These field and model results can serve as a guide for determining how long and frequent rodent control should be done in order to eliminate Lassa virus in rural villages.
DOI: 10.6084/m9.figshare.7937375.v1
title: Genomic epidemiology of erythromycin-resistant <i>Bordetella pertussis</i> in China

description: Macrolides such as erythromycin are the empirical treatment of <i>Bordetella pertussis</i> infections. China has experienced an increase in erythromycin-resistant <i>B. pertussis</i> isolates since they were first reported in 2013. Here, we undertook a genomic study on Chinese <i>B. pertussis</i> isolates from 2012 to 2015 to elucidate the origins and phylogenetic relationships of erythromycin-resistant <i>B. pertussis</i> isolates in China. A total of 167 Chinese <i>B. pertussis</i> isolates were used for antibiotic sensitivity testing and multiple locus variable-number tandem repeat (VNTR) analysis (MLVA). All except four isolates were erythromycin-resistant and of the four erythromycin-sensitive isolates, three were <i>non-ptxP1</i>. MLVA types (MT), MT55, MT104 and MT195 were the predominant types. Fifty of those isolates were used for whole genome sequencing and phylogenetic analysis. Genome sequencing and phylogenetic analysis revealed three independent erythromycin-resistant lineages and all resistant isolates carried a mutation in the 23S rRNA gene. A novel <i>fhaB3</i> allele was found uniquely in Chinese <i>ptxP1</i> isolates and these Chinese <i>ptxP1-ptxA1-fhaB3</i> had a 5-fold higher mutation rate than the global <i>ptxP1-ptxA1 B. pertussis</i> population. Our results suggest that the evolution of Chinese <i>B. pertussis</i> is likely to be driven by selection pressure from both vaccination and antibiotics. The emergence of the new non-vaccine <i>fhaB3</i> allele in Chinese <i>B. pertussis</i> population may be a result of selection from vaccination, whereas the expansion of <i>ptxP1-fhaB3</i> lineages was most likely to be the result of selection pressure from antibiotics. Further monitoring of <i>B. pertussis</i> in China is required to better understand the evolution of the pathogen.
DOI: 10.6084/m9.figshare.8798144.v1
title: Zika virus differentially infects human neural progenitor cells according to their state of differentiation and dysregulates neurogenesis through the Notch pathway

description: Zika virus (ZIKV) is a mosquito-borne Flavivirus that causes Zika disease with particular neurological complications, including Guillain-Barré Syndrome and congenital microcephaly. Although ZIKV has been shown to directly infect human neural progenitor cells (hNPCs), thereby decreasing their viability and growth, it is as yet unknown which of the cellular pathways involved in the disruption of neurogenesis are affected following ZIKV infection. By comparing the effect of two ZIKV strains <i>in vitro</i> on hNPCs, the differentiation process of the latter cells was found to lead to a decreased susceptibility to infection and cell death induced by each of the ZIKV strains, which was associated with an earlier and stronger antiviral innate immune response in infected, differentiated hNPCs, as compared to undifferentiated cells. Moreover, ZIKV modulated, both in hNPCs and <i>in vivo</i> in fetal brain in an experimental mouse model, the expression of the Notch pathway which is involved in cellular proliferation, apoptosis and differentiation during neurogenesis. These results show that the differentiation state of hNPCs is a significant factor contributing to the outcome of ZIKV infection and furthermore suggest that ZIKV infection might initiate early activation of the Notch pathway resulting in an abnormal differentiation process, implicated in ZIKV-induced brain injury.
DOI: 10.5281/zenodo.5536254
title: Persistent Scatter data from Brande, Denmark

description: .KML files of Line-Of-Sight velocities of Persistent Scatters from StaMPS export over Brande, Denmark.
DOI: 10.6084/m9.figshare.9252428.v2
title: Combining sequencing approaches to fully resolve a carbapenemase-encoding megaplasmid in a <i>Pseudomonas shirazica</i> clinical strain

description: Horizontal transfer of plasmids plays a pivotal role in dissemination of antibiotic resistance genes and emergence of multidrug-resistant bacteria. Plasmid sequencing is thus paramount for accurate epidemiological tracking in hospitals and routine surveillance. Combining Nanopore and Illumina sequencing allowed full assembly of a carbapenemase-encoding megaplasmid carried by multidrug-resistant clinical isolate FFUP_PS_41. Average nucleotide identity analyses revealed that FFUP_PS_41 belongs to the recently proposed new species Pseudomonas shirazica, related to the P. putida phylogenetic group. FFUP_PS_41 harbours a 498,516-bp megaplasmid (pJBCL41) with limited similarity to publicly-available plasmids. pJBCL41 contains genes predicted to encode replication, conjugation, partitioning and maintenance functions and heavy metal resistance. The |aacA7|blaVIM-2|aacA4| cassette array (resistance to carbapenems and aminoglycosides) is located within a class 1 integron that is a defective Tn402 derivative. This transposon lies within a 50,273-bp region bound by Tn3-family 38-bp inverted repeats and flanked by 5-bp direct repeats (DR) that composes additional transposon fragments, five insertion sequences and a Tn3-Derived Inverted-Repeat Miniature Element. The hybrid Nanopore/Illumina approach allowed full resolution of a carbapenemase-encoding megaplasmid from P. shirazica. Identification of novel megaplasmids sheds new light on the evolutionary effects of gene transfer and the selective forces driving antibiotic resistance.
DOI: 10.5281/zenodo.5536253
title: Persistent Scatter data from Brande, Denmark

description: .KML files of Line-Of-Sight velocities of Persistent Scatters from StaMPS export over Brande, Denmark.
DOI: 10.6084/m9.figshare.9891728.v2
title: The cytochrome d oxidase complex regulated by fexA is an Achilles' heel in the <i>in vivo</i> survival of <i>Vibrio vulnificus</i>

description: <i>Vibrio vulnificus</i> is a halophilic estuarine bacterium causing severe opportunistic infections. To successfully establish an infection, <i>V. vulnificus</i> must adapt to redox fluctuations in vivo. In the present study, we show that deletion of <i>V. vulnificus</i> fexA gene caused hypersensitivity to acid and reactive oxygen species. The <i>ΔfexA</i> mutant exhibited severe in vivo survival defects. For deeper understanding the role of <i>fexA</i> gene on the successful <i>V. vulnificus</i> infection, we analyzed differentially expressed genes in <i>ΔfexA</i> mutant in comparison with wild type under aerobic, anaerobic or in vivo culture conditions by genome-scale DNA microarray analyses. Twenty-two genes were downregulated in the <i>ΔfexA</i> mutant under all three culture conditions. Among them, <i>cydAB</i> appeared to dominantly contribute to the defective phenotypes of the <i>ΔfexA</i> mutant. The <i>fexA</i> deletion induced compensatory point mutations in the <i>cydAB</i> promoter region over subcultures, suggesting essentiality. Those point mutations (P<sub>cyd</sub>SMs) restored bacterial growth, motility, cytotoxicity ATP production and mouse lethality in the <i>ΔfexA</i> mutant. These results indicate that the <i>cydAB</i> operon, being regulated by <i>FexA</i>, plays a crucial role in <i>V. vulnificus</i> survival under redox-fluctuating in vivo conditions. The FexA-CydAB axis should serve an Achilles heel in the development of therapeutic regimens against <i>V. vulnificus</i> infection.
DOI: 10.6084/m9.figshare.9198914.v2
title: Mapping histoplasmosis in South East Asia – implications for diagnosis in AIDS

description: Histoplasmosis caused by the fungus <i>Histoplasma capsulatum</i> is often lethal in patients with AIDS. Urine antigen testing is highly sensitive and much quicker for diagnosis than culture. Histoplasmosis has a patchy and incompletely appreciated distribution around the world especially in South East Asia. We conducted a systematic literature review of cases of all disease forms of histoplasmosis in SE Asia, not including the Indian sub-continent. We also reviewed all histoplasmin skin test mapping studies to determine localities of exposure. We found a total of 407 cases contracted or likely to have been contracted in SE Asia. Numbers of cases by country varied: Thailand (233), Malaysia (76), Indonesia (48) and Singapore (21), with few or no cases reported in other countries. Most cases (255 (63%)) were disseminated histoplasmosis and 177 (43%) cases were HIV associated. Areas of high histoplasmin skin test sensitivity prevalence were found in Myanmar, the Philippines, Indonesia, Thailand and Vietnam - 86.4%, 26.0%, 63.6%, 36.0% and 33.7%, respectively. We have drawn maps of these data. Further study is required to ascertain the extent of histoplasmosis within SE Asia. Diagnostic capability for patients with HIV infection is urgently required in SE Asia, to reduce mortality and mis-diagnosis as tuberculosis.
DOI: 10.6084/m9.figshare.8015642.v2
title: Avian influenza virus detection, temporality and co-infection in poultry in Cambodian border provinces, 2017–2018

description: Avian influenza virus detection, temporality and co-infection in poultry in Cambodian border provinces, 2017–2018
DOI: 10.5281/zenodo.5515257
title: METADATA: Marie Skłodowska-Curie Action, DADA2GT, Project Number: 841780

description: This repository contains the data generated through the Marie Skłodowska-Curie Action DADA2GT (Project Number: 841780) entitled "Development of gene therapy and genome editing strategies to treat adenosine deaminase 2 deficiency." All the data are stored as .cvs files. The results of the Action have been included in the publication entitled "Lentiviral correction of enzymatic activity restrains macrophage inflammation in adenosine deaminase 2 deficiency" published in the open-access journal Blood Advances and available at https://doi.org/10.1182/bloodadvances.2020003811 and Zenodo.
DOI: 10.6084/m9.figshare.10007921.v1
title: The Nsp12-coding region of type 2 PRRSV is required for viral subgenomic mRNA synthesis

description: As one of many nonstructural proteins of porcine reproductive and respiratory syndrome virus (PRRSV), nonstructural protein 12 (Nsp12) has received relatively little attention, and its role in virus replication, if any, is essentially unknown. By the application of reverse genetic manipulation of an infectious PRRSV clone, the current study is the first to demonstrate that Nsp12 is a key component of PRRSV replication. In addition, the biochemical properties of Nsp12 were evaluated, revealing that Nsp12 forms dimers when exposed to oxidative conditions. Furthermore, we systemically analyzed the function of Nsp12 in PRRSV RNA synthesis using a strand-specific PCR method. To our surprise, Nsp12 was not found to be involved in minus-strand genomic RNA (-gRNA) synthesis; importantly, our results indicate that Nsp12 is involved in the synthesis of both plus- and minus-strand subgenomic mRNAs (+sgmRNA and -sgmRNA). Finally, we found that the combination of cysteine 35 and cysteine 79 in Nsp12 is required for sgmRNA synthesis. To our knowledge, we are the first to report the biological role of Nsp12 in the PRRSV lifecycle, and we conclude that Nsp12 is involved in the synthesis of both + sgRNA and -sgRNA.
DOI: 10.5281/zenodo.5515256
title: METADATA: Marie Skłodowska-Curie Action, DADA2GT, Project Number: 841780

description: This repository contains the data generated through the Marie Skłodowska-Curie Action DADA2GT (Project Number: 841780) entitled "Development of gene therapy and genome editing strategies to treat adenosine deaminase 2 deficiency." All the data are stored as .cvs files. The results of the Action have been included in the publication entitled "Lentiviral correction of enzymatic activity restrains macrophage inflammation in adenosine deaminase 2 deficiency" published in the open-access journal Blood Advances and available at https://doi.org/10.1182/bloodadvances.2020003811 and Zenodo.
DOI: 10.6084/m9.figshare.16699027
title: Supplementary Material for: Serum biomarker status with a distinctive pattern in prognosis of gastroenteropancreatic neuroendocrine carcinoma

description: Medicine
DOI: 10.6084/m9.figshare.16699027.v1
title: Supplementary Material for: Serum biomarker status with a distinctive pattern in prognosis of gastroenteropancreatic neuroendocrine carcinoma

description: Medicine
DOI: 10.6084/m9.figshare.10620929.v1
title: Dual activity of PNGM-1 pinpoints the evolutionary origin of subclass B3 metallo-<i>β</i>-lactamases: a molecular and evolutionary study

description: Resistance to <i>β</i>-lactams is one of the most serious problems associated with Gram-negative infections. <i>β</i>-Lactamases are able to hydrolyze <i>β</i>-lactams such as cephalosporins and/or carbapenems. Evolutionary origin of metallo-<i>β</i>-lactamases (MBLs), conferring critical antibiotic resistance threats, remains unknown. We discovered PNGM-1, the novel subclass B3 MBL, in deep-sea sediments that predate the antibiotic era. Here, our phylogenetic analysis suggests that PNGM-1 yields insights into the evolutionary origin of subclass B3 MBLs. We reveal the structural similarities between tRNase Zs and PNGM-1, and demonstrate that PNGM-1 has both MBL and tRNase Z activities, suggesting that PNGM-1 is thought to have evolved from a tRNase Z. We also show kinetic and structural comparisons between PNGM-1 and other proteins including subclass B3 MBLs and tRNase Zs. These comparisons revealed that the B3 MBL activity of PNGM-1 is a promiscuous activity and subclass B3 MBLs are thought to have evolved through PNGM-1 activity.
DOI: 10.6084/m9.figshare.8397356.v1
title: The native European <i>Aedes geniculatus</i> mosquito species can transmit chikungunya virus

description: Europe is the world’s leading tourism destination and is receiving every year travellers from areas with active arbovirus transmission. There is thus a threat of mosquito-borne virus emergence in Europe due to the presence of the invasive mosquito vector <i>Aedes albopictus</i>. Little attention has been paid about the possible role of indigenous mosquito species as vectors of emerging arboviruses. Here, we assessed the vector competence dynamic of <i>Aedes geniculatus</i>, a European anthropophilic mosquito species, for chikungunya virus (CHIKV) in comparison with an European population of <i>Ae. albopictus</i>. We revealed that <i>Ae. geniculatus</i> is highly susceptible to CHIKV infection and could transmit the virus. By specifically exploring the vector competence dynamic in both mosquito species, we revealed that the cumulative distribution of CHIKV incubation period in <i>Ae. geniculatus</i> was delayed by several days as compared to <i>Ae. albopictus</i>. Our results strengthen the importance of considering indigenous species as potential vectors for emerging arboviruses. They also revealed the importance of considering variation in arbovirus dissemination or transmission dynamics in mosquitoes when performing vector competence assays. We will discuss the implications of our results on a CHIKV outbreak dynamic in a theoretical framework.
DOI: 10.5281/zenodo.5534941
title: SARS-CoV-2–host proteome interactions for antiviral drug discovery

description: Images and datasets used in Fig 6 and corresponding supplementary material Image analysis was performed with Harmony 4.9 software (PerkinElmer) with feature extraction and linear classification of N-protein positive cells from the total population as presented in the PlateResults file. Prism files (GraphPad Software) include the calculations for curve fits of drug testing data (4PL logistic regression) as well as area under the curve (AUC) of the fitted curves..
DOI: 10.5281/zenodo.5534940
title: SARS-CoV-2–host proteome interactions for antiviral drug discovery

description: Images and datasets used in Fig 6 and corresponding supplementary material Image analysis was performed with Harmony 4.9 software (PerkinElmer) with feature extraction and linear classification of N-protein positive cells from the total population as presented in the PlateResults file. Prism files (GraphPad Software) include the calculations for curve fits of drug testing data (4PL logistic regression) as well as area under the curve (AUC) of the fitted curves..
DOI: 10.5517/ccdc.csd.cc250rrq
title: CCDC 1996733: Experimental Crystal Structure Determination

description: Related Article: Jiuling Li, Bin Li, Juan Chen, Xinyu Jia, Min Wang, Chengjun Hao, Xinhua Zheng, Hongmei Dai, Wenhao Hu|2021|Org.Biomol.Chem.|19|8030|doi:10.1039/D1OB01422F
DOI: 10.5517/ccdc.csd.cc2697nf
title: CCDC 2034674: Experimental Crystal Structure Determination

description: Related Article: Rashmi Singh, Vishal Prasad Sharma, Priyanka Yadav, Priyanka Sonker, Radhey Mohan Singh, Ashish Kumar Tewari|2021|Org.Biomol.Chem.|19|8108|doi:10.1039/D1OB01085A
DOI: 10.5517/ccdc.csd.cc269lvz
title: CCDC 2035021: Experimental Crystal Structure Determination

description: Related Article: Rashmi Singh, Vishal Prasad Sharma, Priyanka Yadav, Priyanka Sonker, Radhey Mohan Singh, Ashish Kumar Tewari|2021|Org.Biomol.Chem.|19|8108|doi:10.1039/D1OB01085A
DOI: 10.5517/ccdc.csd.cc26cb86
title: CCDC 2036677: Experimental Crystal Structure Determination

description: Related Article: Atena B. Solea, Sining Wang, Xiao-Song Xue, Aurelien Crochet, Katharina M. Fromm, Kendall N. Houk, Olimpia Mamula, Christophe Allemann|2021|Org.Biomol.Chem.|19|8025|doi:10.1039/D1OB01343B
DOI: 10.5517/ccdc.csd.cc26cb97
title: CCDC 2036678: Experimental Crystal Structure Determination

description: Related Article: Atena B. Solea, Sining Wang, Xiao-Song Xue, Aurelien Crochet, Katharina M. Fromm, Kendall N. Houk, Olimpia Mamula, Christophe Allemann|2021|Org.Biomol.Chem.|19|8025|doi:10.1039/D1OB01343B
DOI: 10.5517/ccdc.csd.cc26cbb8
title: CCDC 2036679: Experimental Crystal Structure Determination

description: Related Article: Atena B. Solea, Sining Wang, Xiao-Song Xue, Aurelien Crochet, Katharina M. Fromm, Kendall N. Houk, Olimpia Mamula, Christophe Allemann|2021|Org.Biomol.Chem.|19|8025|doi:10.1039/D1OB01343B
DOI: 10.5517/ccdc.csd.cc26ql9v
title: CCDC 2047497: Experimental Crystal Structure Determination

description: Related Article: Wenzhong Li, Yu Wang, Huijing Qi, Ran Shi, Jiazhu Li, Si Chen, Xin-Ming Xu, Wei-Li Wang|2021|Org.Biomol.Chem.|19|8086|doi:10.1039/D1OB01206A
DOI: 10.5517/ccdc.csd.cc26rf8p
title: CCDC 2048302: Experimental Crystal Structure Determination

description: Related Article: Wenzhong Li, Yu Wang, Huijing Qi, Ran Shi, Jiazhu Li, Si Chen, Xin-Ming Xu, Wei-Li Wang|2021|Org.Biomol.Chem.|19|8086|doi:10.1039/D1OB01206A
DOI: 10.5517/ccdc.csd.cc27fxrc
title: CCDC 2068963: Experimental Crystal Structure Determination

description: Related Article: Tomáš Landovský, Martin Babor, Jan Čejka, Václav Eigner, Hana Dvořáková, Martin Krupička, Pavel Lhoták|2021|Org.Biomol.Chem.|19|8075|doi:10.1039/D1OB01487K
DOI: 10.5517/ccdc.csd.cc27g686
title: CCDC 2069227: Experimental Crystal Structure Determination

description: Related Article: Tomáš Landovský, Martin Babor, Jan Čejka, Václav Eigner, Hana Dvořáková, Martin Krupička, Pavel Lhoták|2021|Org.Biomol.Chem.|19|8075|doi:10.1039/D1OB01487K
DOI: 10.5517/ccdc.csd.cc27gbvx
title: CCDC 2069369: Experimental Crystal Structure Determination

description: Related Article: Tomáš Landovský, Martin Babor, Jan Čejka, Václav Eigner, Hana Dvořáková, Martin Krupička, Pavel Lhoták|2021|Org.Biomol.Chem.|19|8075|doi:10.1039/D1OB01487K
DOI: 10.5517/ccdc.csd.cc27gy7x
title: CCDC 2069939: Experimental Crystal Structure Determination

description: Related Article: Tomáš Landovský, Martin Babor, Jan Čejka, Václav Eigner, Hana Dvořáková, Martin Krupička, Pavel Lhoták|2021|Org.Biomol.Chem.|19|8075|doi:10.1039/D1OB01487K
DOI: 10.5517/ccdc.csd.cc27gy8y
title: CCDC 2069940: Experimental Crystal Structure Determination

description: Related Article: Tomáš Landovský, Martin Babor, Jan Čejka, Václav Eigner, Hana Dvořáková, Martin Krupička, Pavel Lhoták|2021|Org.Biomol.Chem.|19|8075|doi:10.1039/D1OB01487K
DOI: 10.5517/ccdc.csd.cc27llyd
title: CCDC 2073464: Experimental Crystal Structure Determination

description: Related Article: Kai Yang, Shi-He Luo, Si-Hong Chen, Xi-Ying Cao, Yong-Jun Zhou, Yan-Lan Lin, Yan-Ping Huo, Zhao-Yang Wang|2021|Org.Biomol.Chem.|19|8133|doi:10.1039/D1OB01424B
DOI: 10.5517/ccdc.csd.cc27llzf
title: CCDC 2073465: Experimental Crystal Structure Determination

description: Related Article: Kai Yang, Shi-He Luo, Si-Hong Chen, Xi-Ying Cao, Yong-Jun Zhou, Yan-Lan Lin, Yan-Ping Huo, Zhao-Yang Wang|2021|Org.Biomol.Chem.|19|8133|doi:10.1039/D1OB01424B