cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16611534.v1
title: A clubroot pathogen effector targets cruciferous cysteine proteases to suppress plant immunity

description: Plant pathogen effector proteins are key to pathogen virulence. In susceptible host Brassicas, the clubroot pathogen, <i>Plasmodiophora brassicae</i>, induces the production of nutrient-sink root galls, at the site of infection. Among a list of 32 <i>P. brassiae</i> effector candidates previously reported by our group, we identified SSPbP53 as a putative apoplastic cystatin-like protein highly expressed during the secondary infection. Here we found that SSPbP53 encoding gene is conserved among several <i>P. brassicae</i> pathotypes and that SSPbP53 is an apoplastic protein able to directly interact with and inhibit cruciferous papain-like cysteine proteases (PLCPs), specifically Arabidopsis XYLEM CYSTEINE PEPTIDASE 1 (<i>At</i>XCP1). The severity of clubroot disease is greatly reduced in the Arabidopsis <i>xcp1</i> null mutant (<i>At</i>Δ<i>xcp1</i>) after infection with <i>P. brassicae</i> resting spores, indicating that the interaction of <i>P. brassicae</i> SSPbP53 with XCP1 is important to clubroot susceptibility. SSPbP53 is the first cystatin-like effector identified and characterized for a plant pathogenic protist.
DOI: 10.6084/m9.figshare.14276999
title: PE_PGRS3 ensures provision of the vital phospholipids cardiolipin and phosphatidylinositols by promoting the interaction between <i>M. tuberculosis</i> and host cells

description: PE_PGRS proteins of <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) constitute a large family of complex modular proteins whose role is still unclear. Among those, we have previously shown, using the heterologous expression in <i>Mycobacterium smegmatis</i>, that PE_PGRS3 containing a unique arginine-rich C-terminal domain, promotes adhesion to host cells. In this study, we investigate the role of PE_PGRS3 and its C-terminal domain directly in <i>Mtb</i> using functional deletion mutants. The results obtained here show that PE_PGRS3 is localized on the mycobacterial cell wall and its arginine-rich C-terminal region protrudes from the mycobacterial membrane and mediates <i>Mtb</i> entry into epithelial cells. Most importantly, this positively charged helical domain specifically binds phosphorylated phosphatidylinositols and cardiolipin, whereas it is unable to bind other phospholipids. Interestingly, administration of cardiolipin and phosphatidylinositol but no other phospholipids was able to turn-off expression of <i>pe_pgrs</i>3 activated by phosphate starvation conditions. These findings suggest that PE_PGRS3 has the key role to serve as a bridge between mycobacteria and host cells by interacting with specific host phospholipids and extracting them from host cells, for their direct integration or as a source of phosphate, during phases of TB pathogenesis when <i>Mtb</i> is short of phosphate supply.
DOI: 10.6084/m9.figshare.14994546
title: Koi sleepy disease as a pathophysiological and immunological consequence of a branchial infection of common carp with carp edema virus

description: Gills of fish are involved in respiration, excretion and osmoregulation. Due to numerous interactions between these processes, branchial diseases have serious implications on fish health. Here, “koi sleepy disease” (KSD), caused by carp edema virus (CEV) infection was used to study physiological, immunological and metabolic consequences of a gill disease in fish. A metabolome analysis shows that the moderately hypoxic-tolerant carp can compensate the respiratory compromise related to this infection by various adaptations in their metabolism. Instead, the disease is accompanied by a massive disturbance of the osmotic balance with hyponatremia as low as 71.65 mmol L<sup>−1</sup>, and an accumulation of ammonia in circulatory blood causing a hyperammonemia as high as 1123.24 µmol L<sup>−1</sup>. At water conditions with increased ambient salt, the hydro-mineral balance and the ammonia excretion were restored. Importantly, both hyponatremia and hyperammonemia in KSD-affected carp can be linked to an immunosuppression leading to a four-fold drop in the number of white blood cells, and significant downregulation of <i>cd4, tcr a2</i> and <i>igm</i> expression in gills, which can be evaded by increasing the ion concentration in water. This shows that the complex host-pathogen interactions within the gills can have immunosuppressive consequences, which have not previously been addressed in fish. Furthermore, it makes the CEV infection of carp a powerful model for studying interdependent pathological and immunological effects of a branchial disease in fish.
DOI: 10.6084/m9.figshare.14994546.v1
title: Koi sleepy disease as a pathophysiological and immunological consequence of a branchial infection of common carp with carp edema virus

description: Gills of fish are involved in respiration, excretion and osmoregulation. Due to numerous interactions between these processes, branchial diseases have serious implications on fish health. Here, “koi sleepy disease” (KSD), caused by carp edema virus (CEV) infection was used to study physiological, immunological and metabolic consequences of a gill disease in fish. A metabolome analysis shows that the moderately hypoxic-tolerant carp can compensate the respiratory compromise related to this infection by various adaptations in their metabolism. Instead, the disease is accompanied by a massive disturbance of the osmotic balance with hyponatremia as low as 71.65 mmol L<sup>−1</sup>, and an accumulation of ammonia in circulatory blood causing a hyperammonemia as high as 1123.24 µmol L<sup>−1</sup>. At water conditions with increased ambient salt, the hydro-mineral balance and the ammonia excretion were restored. Importantly, both hyponatremia and hyperammonemia in KSD-affected carp can be linked to an immunosuppression leading to a four-fold drop in the number of white blood cells, and significant downregulation of <i>cd4, tcr a2</i> and <i>igm</i> expression in gills, which can be evaded by increasing the ion concentration in water. This shows that the complex host-pathogen interactions within the gills can have immunosuppressive consequences, which have not previously been addressed in fish. Furthermore, it makes the CEV infection of carp a powerful model for studying interdependent pathological and immunological effects of a branchial disease in fish.
DOI: 10.6084/m9.figshare.13713068
title: The transcription factor Ndt80 is a repressor of <i>Candida parapsilosis</i> virulence attributes

description: <i>Candida parapsilosis</i> is an emergent opportunistic yeast among hospital settings that affects mainly neonates and immunocompromised patients. Its most remarkable virulence traits are the ability to adhere to prosthetic materials, as well as the formation of biofilm on abiotic surfaces. The Ndt80 transcription factor was identified as one of the regulators of biofilm formation by <i>C. parapsilosis</i>; however, its function in this process was not yet clarified. By knocking out <i>NDT80</i> (<i>CPAR2-213640</i>) gene, or even just one single copy of the gene, we observed substantial alterations of virulence attributes, including morphogenetic changes, adhesion and biofilm growth profiles. Both <i>ndt80Δ</i> and <i>ndt80ΔΔ</i> mutants changed colony and cell morphologies from smooth, yeast-shaped to crepe and pseudohyphal elongated forms, exhibiting promoted adherence to polystyrene microspheres and notably, forming a higher amount of biofilm compared to wild-type strain. Interestingly, we identified transcription factors Ume6, Cph2, Cwh41, Ace2, Bcr1, protein kinase Mkc1 and adhesin Als7 to be under Ndt80 negative regulation, partially explaining the phenotypes displayed by the <i>ndt80ΔΔ</i> mutant. Furthermore, <i>ndt80ΔΔ</i> pseudohyphae adhered more rapidly and were more resistant to murine macrophage attack, becoming deleterious to such cells after phagocytosis. Unexpectedly, our findings provide the first evidence for a direct role of Ndt80 as a repressor of <i>C. parapsilosis</i> virulence attributes. This finding shows that <i>C. parapsilosis</i> Ndt80 functionally diverges from its homolog in the close related fungal pathogen <i>C. albicans</i>.
DOI: 10.6084/m9.figshare.13662206
title: A glycoengineered antigen exploiting a conserved protein O-glycosylation pathway in the Burkholderia genus for detection of glanders infections

description: We recently described a protein <i>O</i>-glycosylation pathway conserved in all species of the <i>Burkholderia</i> genus that results in the synthesis and incorporation of a trisaccharide glycan to membrane-exported proteins. Here, we exploited this system to construct and evaluate a diagnostic tool for glanders. <i>Burkholderia mallei</i>, the causative agent of glanders, is a highly infectious and fatal zoonotic pathogen that infects horses, mules, donkeys, and occasionally humans. A highly sensitive and specific diagnostic tool is crucial for the control, elimination, and eradication of <i>B. mallei</i> infections. We constructed plasmids carrying synthetic genes encoding a modified, previously unannotated <i>Burkholderia</i> glycoprotein containing three glycosylation sequons fused to the cholera toxin B-subunit. The resulting proteins were glycosylated in the <i>B. cenocepacia</i> K56-2 parental strain, but not in glycosylation-deficient mutants, as determined by SDS-PAGE and fluorescent lectin blots. One of these glycoproteins was used as an antigen in ELISA and western blots to screen a panel of serum samples collected from glanders-infected and healthy horses, which were previously investigated by complement fixation test and indirect ELISA based on a semi-purified fraction of <i>B. mallei</i>. We show that ELISA and western blot assays based on our glycoprotein antigen provide 100% specificity, with a sensitivity greater than 88%. The glycoprotein antigen was recognized by serum samples collected from patients infected with <i>B. pseudomallei, B. mallei, B. multivorans,</i> and <i>B. cenocepacia</i>. Our results indicate that protein <i>O</i>-glycosylation in <i>Burkholderia</i> can be exploited as a biomarker for diagnosis of <i>Burkholderia</i>-associated infections.
DOI: 10.6084/m9.figshare.13662206.v1
title: A glycoengineered antigen exploiting a conserved protein O-glycosylation pathway in the Burkholderia genus for detection of glanders infections

description: We recently described a protein <i>O</i>-glycosylation pathway conserved in all species of the <i>Burkholderia</i> genus that results in the synthesis and incorporation of a trisaccharide glycan to membrane-exported proteins. Here, we exploited this system to construct and evaluate a diagnostic tool for glanders. <i>Burkholderia mallei</i>, the causative agent of glanders, is a highly infectious and fatal zoonotic pathogen that infects horses, mules, donkeys, and occasionally humans. A highly sensitive and specific diagnostic tool is crucial for the control, elimination, and eradication of <i>B. mallei</i> infections. We constructed plasmids carrying synthetic genes encoding a modified, previously unannotated <i>Burkholderia</i> glycoprotein containing three glycosylation sequons fused to the cholera toxin B-subunit. The resulting proteins were glycosylated in the <i>B. cenocepacia</i> K56-2 parental strain, but not in glycosylation-deficient mutants, as determined by SDS-PAGE and fluorescent lectin blots. One of these glycoproteins was used as an antigen in ELISA and western blots to screen a panel of serum samples collected from glanders-infected and healthy horses, which were previously investigated by complement fixation test and indirect ELISA based on a semi-purified fraction of <i>B. mallei</i>. We show that ELISA and western blot assays based on our glycoprotein antigen provide 100% specificity, with a sensitivity greater than 88%. The glycoprotein antigen was recognized by serum samples collected from patients infected with <i>B. pseudomallei, B. mallei, B. multivorans,</i> and <i>B. cenocepacia</i>. Our results indicate that protein <i>O</i>-glycosylation in <i>Burkholderia</i> can be exploited as a biomarker for diagnosis of <i>Burkholderia</i>-associated infections.
DOI: 10.6084/m9.figshare.14401735
title: Tribolium castaneum defensin 1 kills Moraxella catarrhalis in an in vitro infection model but does not harm commensal bacteria

description: <i>Moraxella catarrhalis</i> is a bacterial pathogen that causes respiratory tract infections in humans. The increasing prevalence of antibiotic-resistant <i>M. catarrhalis</i> strains has created a demand for alternative treatment options. We therefore tested 23 insect antimicrobial peptides (AMPs) for their activity against <i>M. catarrhalis</i> in a human <i>in vitro</i> infection model with primary macrophages, and against commensal bacteria. Effects on bacterial growth were determined by colony counting and growth curve analysis. The inflammatory macrophage response was characterized by qPCR and multiplex ELISA. Eleven of the AMPs were active against <i>M. catarrhalis</i>. Defensin 1 from the red flour beetle <i>Tribolium castaneum</i> significantly inhibited bacterial growth and reduced the number of colony forming units. This AMP also showed antibacterial activity in the <i>in vitro</i> infection model, reducing cytokine expression and release by macrophages. Defensin 1 had no effect on the commensal bacteria <i>Escherichia coli</i> and <i>Enterococcus faecalis</i>. However, sarcotoxin 1 C from the green bottle fly <i>Lucilia sericata</i> was active against <i>M. catarrhalis</i> and <i>E. coli</i>, but not against <i>E. faecalis</i>. The ability of <i>T. castaneum</i> defensin 1 to inhibit <i>M. catarrhalis</i> but not selected commensal bacteria, and the absence of cytotoxic or inflammatory effects against human blood-derived macrophages, suggests this AMP may be suitable for development as a new therapeutic lead against antibiotic-resistant <i>M. catarrhalis</i>.
DOI: 10.6084/m9.figshare.14672298
title: Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis

description: New SARS-CoV-2 mutants have been continuously indentified with enhanced transmission ever since its outbreak in early 2020. As an RNA virus, SARS-CoV-2 has a high mutation rate due to the low fidelity of RNA polymerase. To study the single nucleotide polymorphisms (SNPs) dynamics of SARS-CoV-2, 158 SNPs with high confidence were identified by deep meta-transcriptomic sequencing, and the most common SNP type was C &gt; T. Analyses of intra-host population diversity revealed that intra-host quasispecies’ composition varies with time during the early onset of symptoms, which implicates viral evolution during infection. Network analysis of co-occurring SNPs revealed the most abundant non-synonymous SNP 22,638 in the S glycoprotein RBD region and 28,144 in the ORF8 region. Furthermore, SARS-CoV-2 variations differ in an individual’s respiratory tissue (nose, throat, BALF, or sputum), suggesting independent compartmentalization of SARS-CoV-2 populations in patients. The positive selection analysis of the SARS-CoV-2 genome uncovered the positive selected amino acid G251V on ORF3a. Alternative allele frequency spectrum (AAFS) of all variants revealed that ORF8 could bear alternate alleles with high frequency. Overall, the results show the quasispecies’ profile of SARS-CoV-2 in the respiratory tract in the first two months after the outbreak.
DOI: 10.6084/m9.figshare.16571390
title: Cleavage of E-cadherin by porcine respiratory bacterial pathogens facilitates airway epithelial barrier disruption and bacterial paracellular transmigration

description: Airway epithelial cells are the first line of defense against respiratory pathogens. Porcine bacterial pathogens, such as <i>Bordetella bronchiseptica, Actinobacillus pleuropneumoniae, Glaesserella</i> (<i>Haemophilus</i>) <i>parasuis</i>, and <i>Pasteurella multocida</i>, breach this barrier to lead to local or systematic infections. Here, we demonstrated that respiratory bacterial pathogen infection disrupted the airway epithelial intercellular junction protein, E-cadherin, thus contributing to impaired epithelial cell integrity. E-cadherin knocking-out in newborn pig tracheal cells via CRISPR/Cas9 editing technology confirmed that E-cadherin was sufficient to suppress the paracellular transmigration of these porcine respiratory bacterial pathogens, including <i>G. parasuis, A. pleuropneumoniae, P. multocida</i>, and <i>B. bronchiseptica</i>. The E-cadherin ectodomain cleavage by these pathogens was probably attributed to bacterial HtrA/DegQ protease, but not host HtrA1, MMP7 and ADAM10, and the prominent proteolytic activity was further confirmed by a serine-to-alanine substitution mutation in the active center of HtrA/DegQ protein. Moreover, deletion of the <i>htrA</i> gene in <i>G. parasuis</i> led to severe defects in E-cadherin ectodomain cleavage, cell adherence and paracellular transmigration <i>in vitro</i>, as well as bacterial breaking through the tracheal epithelial cells, systemic invasion and dissemination <i>in vivo</i>. This common pathogenic mechanism shared by other porcine respiratory bacterial pathogens explains how these bacterial pathogens destroy the airway epithelial cell barriers and proliferate in respiratory mucosal surface or other systemic tissues.
DOI: 10.6084/m9.figshare.14672298.v1
title: Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis

description: New SARS-CoV-2 mutants have been continuously indentified with enhanced transmission ever since its outbreak in early 2020. As an RNA virus, SARS-CoV-2 has a high mutation rate due to the low fidelity of RNA polymerase. To study the single nucleotide polymorphisms (SNPs) dynamics of SARS-CoV-2, 158 SNPs with high confidence were identified by deep meta-transcriptomic sequencing, and the most common SNP type was C &gt; T. Analyses of intra-host population diversity revealed that intra-host quasispecies’ composition varies with time during the early onset of symptoms, which implicates viral evolution during infection. Network analysis of co-occurring SNPs revealed the most abundant non-synonymous SNP 22,638 in the S glycoprotein RBD region and 28,144 in the ORF8 region. Furthermore, SARS-CoV-2 variations differ in an individual’s respiratory tissue (nose, throat, BALF, or sputum), suggesting independent compartmentalization of SARS-CoV-2 populations in patients. The positive selection analysis of the SARS-CoV-2 genome uncovered the positive selected amino acid G251V on ORF3a. Alternative allele frequency spectrum (AAFS) of all variants revealed that ORF8 could bear alternate alleles with high frequency. Overall, the results show the quasispecies’ profile of SARS-CoV-2 in the respiratory tract in the first two months after the outbreak.
DOI: 10.6084/m9.figshare.16653244
title: Early oseltamivir reduces risk for influenza-associated aspergillosis in a double-hit murine model

description: Invasive pulmonary aspergillosis (IPA) is a life-threatening fungal infection occurring mainly in immunocompromised patients. We recently identified IPA as an emerging co-infection with high mortality in critically ill, but otherwise immunocompetent influenza patients. The neuraminidase inhibitor oseltamivir is the current standard-of-care treatment in hospitalized influenza patients; however, its efficacy in influenza-associated pulmonary aspergillosis (IAPA) is not known. Therefore, we have established an imaging-supported double-hit mouse model to investigate the therapeutic effect of oseltamivir on the development of IAPA. Immunocompetent mice received intranasal instillation influenza A or PBS followed by orotracheal inoculation with <i>Aspergillus fumigatus</i> 4 days later. Oseltamivir treatment or placebo was started at day 0, day 2, or day 4. Daily monitoring included micro-computed tomography and bioluminescence imaging of pneumonia and fungal burden. Non-invasive biomarkers were complemented with imaging, molecular, immunological, and pathological analysis. Influenza virus-infected immunocompetent mice developed proven airway IPA upon co-infection with <i>Aspergillus fumigatus</i>, whereas non-influenza-infected mice fully cleared <i>Aspergillus</i>, confirming influenza as a risk factor for developing IPA. Longitudinal micro-CT showed pulmonary lesions after influenza infection worsening after <i>Aspergillus</i> co-infection, congruent with bioluminescence imaging and histology confirming <i>Aspergillus</i> pneumonia. Early oseltamivir treatment prevented severe influenza pneumonia and mitigated the development of IPA and associated mortality. A time-dependent treatment effect was consistently observed with imaging, molecular, and pathological analyses. Hence, our findings underscore the importance of initiating oseltamivir as soon as possible, to suppress influenza infection and mitigate the risk of potentially lethal IAPA disease.
DOI: 10.6084/m9.figshare.13498995
title: A systematic review of the epidemiology of Hepatitis E virus infection in South – Eastern Asia

description: Hepatitis E virus (HEV) infection is an emerging zoonotic viral disease, with an increasingly international public health challenge. Despite the concerns that the global disease burden may be underestimated. Therefore, evaluation of the disease epidemiology in South – eastern Asia through a systematic review will assist in unraveling the burden of the disease in the subregion. A priori protocol was prepared for the systematic review and followed by a literature search involving five electronic databases. Identified publications were screened for high quality studies and the elimination of bias and relevant data extracted. A total of 4157 citations were captured, and only 35 were included in the review. A wide range of HEV seroprevalence was recorded from 2% (urban blood donors in Malaysia) to 77.7% (lowland communities in Lao PDR). Sporadic HEV infection and epidemics were also detected in the subregion. Indicating hyperendemicity of the disease in South – eastern Asia.
DOI: 10.6084/m9.figshare.13498995.v1
title: A systematic review of the epidemiology of Hepatitis E virus infection in South – Eastern Asia

description: Hepatitis E virus (HEV) infection is an emerging zoonotic viral disease, with an increasingly international public health challenge. Despite the concerns that the global disease burden may be underestimated. Therefore, evaluation of the disease epidemiology in South – eastern Asia through a systematic review will assist in unraveling the burden of the disease in the subregion. A priori protocol was prepared for the systematic review and followed by a literature search involving five electronic databases. Identified publications were screened for high quality studies and the elimination of bias and relevant data extracted. A total of 4157 citations were captured, and only 35 were included in the review. A wide range of HEV seroprevalence was recorded from 2% (urban blood donors in Malaysia) to 77.7% (lowland communities in Lao PDR). Sporadic HEV infection and epidemics were also detected in the subregion. Indicating hyperendemicity of the disease in South – eastern Asia.