cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19153871.v1
title: From environmental adaptation to host survival: Attributes that mediate pathogenicity of <i>Candida auris</i>

description: <i>Candida</i> species are a major cause of invasive fungal infections. While <i>Candida albicans, C. glabrata, C. parapsilosis</i>, and <i>C. tropicalis</i> are the most dominant species causing life-threatening candidiasis, <i>C. auris</i> recently emerged as a new species causing invasive infections with high rates of clinical treatment failures. To mimic initial phases of systemic <i>Candida</i> infections with dissemination <i>via</i> the bloodstream and to elucidate the pathogenic potential of <i>C. auris</i>, we used an <i>ex vivo</i> whole blood infection model. Similar to other clinically relevant <i>Candida</i> spp., <i>C. auris</i> is efficiently killed in human blood, but showed characteristic patterns of immune cell association, survival rates, and cytokine induction. Dual-species transcriptional profiling of <i>C. auris</i>-infected blood revealed a unique <i>C. auris</i> gene expression program during infection, while the host response proofed similar and conserved compared to other <i>Candida</i> species. <i>C. auris</i>-specific responses included adaptation and survival strategies, such as counteracting oxidative burst of immune cells, but also expression of potential virulence factors, (drug) transporters, and cell surface-associated genes. Despite comparable pathogenicity to other <i>Candida</i> species in our model, <i>C. auris</i>-specific transcriptional adaptations as well as its increased stress resistance and long-term environmental survival, likely contribute to the high risk of contamination and distribution in a nosocomial setting. Moreover, infections of neutrophils with pre-starved <i>C. auris</i> cells suggest that environmental preconditioning can have modulatory effects on the early host interaction. In summary, we present novel insights into <i>C. auris</i> pathogenicity, revealing adaptations to human blood and environmental niches distinctive from other <i>Candida</i> species.
DOI: 10.6084/m9.figshare.19093256
title: Complement evasion factor (CEF), a novel immune evasion factor of <i>Streptococcus pyogenes</i>

description: <i>Streptococcus pyogenes</i>, a leading human pathogen, is responsible for a wide range of diseases, including skin and soft tissue infections and severe invasive diseases. <i>S. pyogenes</i> produces a large arsenal of virulence factors, including several immune evasion factors. We have identified an open reading frame (<i>spy0136</i>) in the <i>S. pyogenes</i> SF370 genome encoding a protein of unknown function. Using recombinant Spy0136 in a pull-down assay with human plasma and ELISA, we have identified four complement proteins (C1r, C1s, C3, and C5) as binding partners. Treatment of the complement proteins with PNGase F abrogated binding to C1s, C3, and C5, indicating glycan-dependent interactions. rSpy0136 inhibited complement-mediated hemolysis and interfered with all three complement pathways in a Wieslab complement assay. Furthermore, rSpy0136 inhibited deposition of the C3b opsonin and the membrane attack complex (MAC) on the surface of <i>S. pyogenes</i>. We therefore named the previously unknown protein ‘complement evasion factor’ (CEF). An <i>S. pyogenes Δspy0136/cef</i> deletion mutant showed decreased virulence in an <i>in-vitro</i> whole blood killing assay and a <i>Galleria mellonella</i> (wax moth) infection model. Furthermore, an <i>L. lactis spy0136/cef</i> gain-of-function mutant showed increased survival during growth in whole human blood. Analysis of serum samples from patients with invasive <i>S. pyogenes</i> revealed Spy0136/CEF sero-conversion indicating expression during disease. In summary, we have identified a novel <i>S. pyogenes</i> immune evasion factor that binds to several complement proteins to interfere with complement function. This is the first example of a <i>S. pyogenes</i> virulence factor binding to several different target proteins via glycan-dependent interactions.
DOI: 10.6084/m9.figshare.19093256.v1
title: Complement evasion factor (CEF), a novel immune evasion factor of <i>Streptococcus pyogenes</i>

description: <i>Streptococcus pyogenes</i>, a leading human pathogen, is responsible for a wide range of diseases, including skin and soft tissue infections and severe invasive diseases. <i>S. pyogenes</i> produces a large arsenal of virulence factors, including several immune evasion factors. We have identified an open reading frame (<i>spy0136</i>) in the <i>S. pyogenes</i> SF370 genome encoding a protein of unknown function. Using recombinant Spy0136 in a pull-down assay with human plasma and ELISA, we have identified four complement proteins (C1r, C1s, C3, and C5) as binding partners. Treatment of the complement proteins with PNGase F abrogated binding to C1s, C3, and C5, indicating glycan-dependent interactions. rSpy0136 inhibited complement-mediated hemolysis and interfered with all three complement pathways in a Wieslab complement assay. Furthermore, rSpy0136 inhibited deposition of the C3b opsonin and the membrane attack complex (MAC) on the surface of <i>S. pyogenes</i>. We therefore named the previously unknown protein ‘complement evasion factor’ (CEF). An <i>S. pyogenes Δspy0136/cef</i> deletion mutant showed decreased virulence in an <i>in-vitro</i> whole blood killing assay and a <i>Galleria mellonella</i> (wax moth) infection model. Furthermore, an <i>L. lactis spy0136/cef</i> gain-of-function mutant showed increased survival during growth in whole human blood. Analysis of serum samples from patients with invasive <i>S. pyogenes</i> revealed Spy0136/CEF sero-conversion indicating expression during disease. In summary, we have identified a novel <i>S. pyogenes</i> immune evasion factor that binds to several complement proteins to interfere with complement function. This is the first example of a <i>S. pyogenes</i> virulence factor binding to several different target proteins via glycan-dependent interactions.
DOI: 10.6084/m9.figshare.20712880
title: The spectrum of clinical biomarkers in severe malaria and new avenues for exploration

description: Globally, malaria is a public health concern, with severe malaria (SM) contributing a major share of the disease burden in malaria endemic countries. In this context, identification and validation of SM biomarkers are essential in clinical practice. Some biomarkers (C-reactive protein, angiopoietin 2, angiopoietin-2/1 ratio, platelet count, histidine-rich protein 2) have yielded interesting results in the prognosis of <i>Plasmodium falciparum</i> severe malaria, but for severe <i>P. vivax</i> and <i>P. knowlesi</i> malaria, similar evidence is missing. The validation of these biomarkers is hindered by several factors such as low sample size, paucity of evidence-evaluating studies, suboptimal values of sensitivity/specificity, poor clinical practicality of measurement methods, mixed <i>Plasmodium</i> infections, and good clinical value of the biomarkers for concurrent infections (pneumonia and current COVID-19 pandemic). Most of these biomarkers are non-specific to pathogens as they are related to host response and hence should be regarded as prognostic/predictive biomarkers that complement but do not replace pathogen biomarkers for clinical evaluation of SM patients. This review highlights the importance of research on diagnostic/predictive/therapeutic biomarkers, neglected malaria species, and clinical practicality of measurement methods in future studies. Finally, the importance of omics technologies for faster identification/validation of SM biomarkers is also included.
DOI: 10.6084/m9.figshare.20712880.v1
title: The spectrum of clinical biomarkers in severe malaria and new avenues for exploration

description: Globally, malaria is a public health concern, with severe malaria (SM) contributing a major share of the disease burden in malaria endemic countries. In this context, identification and validation of SM biomarkers are essential in clinical practice. Some biomarkers (C-reactive protein, angiopoietin 2, angiopoietin-2/1 ratio, platelet count, histidine-rich protein 2) have yielded interesting results in the prognosis of <i>Plasmodium falciparum</i> severe malaria, but for severe <i>P. vivax</i> and <i>P. knowlesi</i> malaria, similar evidence is missing. The validation of these biomarkers is hindered by several factors such as low sample size, paucity of evidence-evaluating studies, suboptimal values of sensitivity/specificity, poor clinical practicality of measurement methods, mixed <i>Plasmodium</i> infections, and good clinical value of the biomarkers for concurrent infections (pneumonia and current COVID-19 pandemic). Most of these biomarkers are non-specific to pathogens as they are related to host response and hence should be regarded as prognostic/predictive biomarkers that complement but do not replace pathogen biomarkers for clinical evaluation of SM patients. This review highlights the importance of research on diagnostic/predictive/therapeutic biomarkers, neglected malaria species, and clinical practicality of measurement methods in future studies. Finally, the importance of omics technologies for faster identification/validation of SM biomarkers is also included.
DOI: 10.6084/m9.figshare.19732230
title: Guanylate-Binding protein 2b regulates the AMPK/mTOR/ULK1 signalling pathway to induce autophagy during <i>Mycobacterium bovis</i> infection

description: Autophagic isolation and degradation of intracellular pathogens are employed by host cells as primary innate immune defense mechanisms to control intercellular <i>M. bovis</i> infection. In this study, RNA-Seq technology was used to obtain the total mRNA from bone marrow-derived macrophages (BMDMs) infected with <i>M. bovis</i> at 6 and 24 h after infection. One of the differential genes, GBP2b, was also investigated. Analysis of the significant pathway involved in GBP2b-coexpressed mRNA demonstrated that GBP2b was associated with autophagy and autophagy-related mammalian target of rapamycin (mTOR) signaling and AMP-activated protein kinase (AMPK) signaling. The results of in vivo and in vitro experiments showed significant up-regulation of GBP2b during <i>M. bovis</i> infection. For in vitro validation, small interfering RNA-GBP2b plasmids were transfected into BMDMs and RAW264.7 cells lines to down-regulate the expression of GBP2b. The results showed that the down-regulation of GBP2b impaired autophagy via the AMPK/mTOR/ULK1 pathway, thereby promoting the intracellular survival of <i>M. bovis</i>. Further studies revealed that the activation of AMPK signaling was essential for the regulation of autophagy during <i>M. bovis</i> infection. These findings expand the understanding of how GBP2b regulates autophagy and suggest that GBP2b may be a potential target for the treatment of diseases caused by <i>M. bovis</i>.
DOI: 10.6084/m9.figshare.19732230.v2
title: Guanylate-Binding protein 2b regulates the AMPK/mTOR/ULK1 signalling pathway to induce autophagy during <i>Mycobacterium bovis</i> infection

description: Autophagic isolation and degradation of intracellular pathogens are employed by host cells as primary innate immune defense mechanisms to control intercellular <i>M. bovis</i> infection. In this study, RNA-Seq technology was used to obtain the total mRNA from bone marrow-derived macrophages (BMDMs) infected with <i>M. bovis</i> at 6 and 24 h after infection. One of the differential genes, GBP2b, was also investigated. Analysis of the significant pathway involved in GBP2b-coexpressed mRNA demonstrated that GBP2b was associated with autophagy and autophagy-related mammalian target of rapamycin (mTOR) signaling and AMP-activated protein kinase (AMPK) signaling. The results of in vivo and in vitro experiments showed significant up-regulation of GBP2b during <i>M. bovis</i> infection. For in vitro validation, small interfering RNA-GBP2b plasmids were transfected into BMDMs and RAW264.7 cells lines to down-regulate the expression of GBP2b. The results showed that the down-regulation of GBP2b impaired autophagy via the AMPK/mTOR/ULK1 pathway, thereby promoting the intracellular survival of <i>M. bovis</i>. Further studies revealed that the activation of AMPK signaling was essential for the regulation of autophagy during <i>M. bovis</i> infection. These findings expand the understanding of how GBP2b regulates autophagy and suggest that GBP2b may be a potential target for the treatment of diseases caused by <i>M. bovis</i>.
DOI: 10.6084/m9.figshare.14229847.v1
title: Enhancing the chemical transformation of <i>Candida parapsilosis</i>

description: <i>Candida parapsilosis</i> is a leading cause of invasive mycoses and the major cause of nosocomial fungaemia amongst low and very low birth weight neonates. However, the molecular and physiological characteristics of this fungus remain understudied. To advance our knowledge about the pathobiology of this pathogen, we sought to develop and validate an effective method for chemical transformation of <i>C. parapsilosis</i>. Chemical transformation is the primary procedure for introducing foreign DNA into <i>Candida</i> yeast as it requires no special equipment, although its performance efficacy drops rapidly when the size of the transforming DNA increases. To define optimal conditions for chemical transformation in <i>C. parapsilosis</i>, we selected a leucine auxotroph laboratory strain. We identified optimal cell density for transformation, incubation times, inclusion of specific enhancing chemicals, and size and amounts of DNA fragments that resulted in maximized transformation efficiency. We determined that the inclusion of dimethyl sulfoxide was beneficial, but dithiothreitol pretreatment reduced colony recovery. As a result, the modified protocol led to a 20–55-fold increase in transformation efficiency, depending on the size of the transforming fragment. We validated the modified methodology with prototrophic isolates and demonstrated that the new approach resulted in the recovery of significantly more transformants in 5 of 6 isolates. Additionally, we identified a medium in which transformation competent yeast cells could safely be maintained at −80°C for up to 6 weeks that reduces laboratory work and shortens the overall procedure. These modifications will significantly aid further investigations into the genetic basis for virulence in <i>C. parapsilosis.</i>
DOI: 10.6084/m9.figshare.19130001
title: MERS-CoV nsp1 impairs the cellular metabolic processes by selectively downregulating mRNAs in a novel granules

description: MERS-CoV infection can damage the cellular metabolic processes, but the underlying mechanisms are largely unknown. Through screening, we found non-structural protein 1 (nsp1) of MERS-CoV could inhibit cell viability, cell cycle, and cell migration through its endonuclease activity. Transcriptome sequencing revealed that MERS-CoV nsp1 specifically downregulated the mRNAs of ribosomal protein genes, oxidative phosphorylation protein genes, and antigen presentation genes, but upregulated the mRNAs of transcriptional regulatory genes. Further analysis shown nsp1 existed in a novel ribonucleosome complex formed via liquid-liquid phase separation, which did not co-localize with mitochondria, lysosomes, P-bodies, or stress granules. Interestingly, the nsp1-located granules specifically contained mRNAs of ribosomal protein genes and oxidative phosphorylation genes, which may explain why MERS-CoV nsp1 selectively degraded these mRNAs in cells. Finally, MERS-CoV nsp1 transgenic mice showed significant loss of body weight and an increased sensitivity to poly(I:C)-induced inflammatory death. These findings demonstrate a new mechanism by which MERS-CoV impairs cell viability, which serves as a potential novel target for preventing MERS-CoV infection-induced pathological damage. <b>Abbreviations:</b> (Middle East respiratory syndrome coronavirus (MERS-CoV), Actinomycin D (Act D), liquid-liquid phase separation (LLPS), stress granules (SGs), Mass spectrometry (IP-MS), RNA Binding Protein Immunoprecipitation (RIP))
DOI: 10.6084/m9.figshare.19130001.v1
title: MERS-CoV nsp1 impairs the cellular metabolic processes by selectively downregulating mRNAs in a novel granules

description: MERS-CoV infection can damage the cellular metabolic processes, but the underlying mechanisms are largely unknown. Through screening, we found non-structural protein 1 (nsp1) of MERS-CoV could inhibit cell viability, cell cycle, and cell migration through its endonuclease activity. Transcriptome sequencing revealed that MERS-CoV nsp1 specifically downregulated the mRNAs of ribosomal protein genes, oxidative phosphorylation protein genes, and antigen presentation genes, but upregulated the mRNAs of transcriptional regulatory genes. Further analysis shown nsp1 existed in a novel ribonucleosome complex formed via liquid-liquid phase separation, which did not co-localize with mitochondria, lysosomes, P-bodies, or stress granules. Interestingly, the nsp1-located granules specifically contained mRNAs of ribosomal protein genes and oxidative phosphorylation genes, which may explain why MERS-CoV nsp1 selectively degraded these mRNAs in cells. Finally, MERS-CoV nsp1 transgenic mice showed significant loss of body weight and an increased sensitivity to poly(I:C)-induced inflammatory death. These findings demonstrate a new mechanism by which MERS-CoV impairs cell viability, which serves as a potential novel target for preventing MERS-CoV infection-induced pathological damage. <b>Abbreviations:</b> (Middle East respiratory syndrome coronavirus (MERS-CoV), Actinomycin D (Act D), liquid-liquid phase separation (LLPS), stress granules (SGs), Mass spectrometry (IP-MS), RNA Binding Protein Immunoprecipitation (RIP))
DOI: 10.6084/m9.figshare.19732230.v1
title: Guanylate-binding protein 2b regulates the AMPK/mTOR/ULK1 signalling pathway to induce autophagy during <i>Mycobacterium bovis</i> infection

description: <i>Mycobacterium bovis</i> is a major cause of animal tuberculosis that is also highly dangerous to human health. Autophagic isolation and degradation of intracellular pathogens are employed by host cells as primary innate immune defence mechanisms to control intercellular <i>M. bovis</i> infection. In this study, RNA-Seq technology was used to obtain the total mRNA from bone marrow-derived macrophages (BMDMs) infected with <i>M. bovis</i> at 6 and 24 h after infection. One of the differential genes, GBP2b, was also investigated. Analysis of the significant pathway involved in GBP2b-coexpressed mRNA demonstrated that GBP2b was associated with autophagy and autophagy-related mammalian target of rapamycin (mTOR) signalling and AMP-activated protein kinase (AMPK) signalling. The results of in vivo and in vitro experiments showed significant up-regulation of GBP2b during <i>M. bovis</i> infection. For in vitro validation, small interfering RNA-GBP2b plasmids were transfected into BMDMs and RAW264.7 cells lines to down-regulate the expression of GBP2b. The results showed that the down-regulation of GBP2b impaired autophagy via the AMPK/mTOR/ULK1 pathway. Further studies revealed that the activation of AMPK signalling was essential for the regulation of autophagy during <i>M. bovis</i> infection, and the down-regulation of GBP2b promoted the intracellular survival of <i>M. bovis</i>. These findings were validated on two types of macrophages, which extended the knowledge about the involvement of GBP2b in the autophagic process. Based on these observations, GBP2b should be developed as a promising molecular target for intervening on host–pathogen interactions to develop novel therapeutic strategies to control <i>M. bovis</i> infections in humans and animals.
DOI: 10.6084/m9.figshare.21154901
title: Novel mycoplasma nucleomodulin MbovP475 decreased cell viability by regulating expression of CRYAB and MCF2L2

description: Nucleomodulins are secreted bacterial proteins whose molecular targets are located in host cell nuclei. They are gaining attention as critical virulence factors that either modify the epigenetics of host cells or directly regulate host gene expression. <i>Mycoplasma bovis</i> is a major veterinary pathogen that secretes several potential virulence factors. The aim of this study was to determine whether any of their secreted proteins might function as nucleomodulins. After an initial <i>in silico</i> screening, the nuclear localization of the secreted putative lipoprotein MbovP475 of <i>M. bovis</i> was demonstrated in bovine macrophage cell line (BoMac) experimentally infected with <i>M. bovis</i>. Through combined application of ChIP-seq, Electrophoretic mobility shift assay (EMSA) and surface plasmon resonance (SPR) analysis, MbovP475 was determined to bind the promoter regions of the cell cycle central regulatory genes <i>CRYAB</i> and <i>MCF2L2</i>. MbovP475 has similar secondary structures with the transcription activator-like effectors (TALEs). Screening of various mutants affecting the potential DNA binding sites indicated that the residues <sup>242</sup>NI<sup>243</sup> within MbovP475 loop region of the helix-loop-helix domain were essential to its DNA binding activity, thereby contributing to decrease in BoMac cell viability. In conclusion, this is the first report to confirm <i>M. bovis</i> secretes a conserved TALE-like nucleomodulin that binds the promoters of <i>CRYAB</i> and <i>MCF2L2</i> genes, and subsequently down-regulates their expression and decreases BoMac cell viability. Therefore, this study offers a new understanding of mycoplasma pathogenesis.
DOI: 10.6084/m9.figshare.21154901.v1
title: Novel mycoplasma nucleomodulin MbovP475 decreased cell viability by regulating expression of CRYAB and MCF2L2

description: Nucleomodulins are secreted bacterial proteins whose molecular targets are located in host cell nuclei. They are gaining attention as critical virulence factors that either modify the epigenetics of host cells or directly regulate host gene expression. <i>Mycoplasma bovis</i> is a major veterinary pathogen that secretes several potential virulence factors. The aim of this study was to determine whether any of their secreted proteins might function as nucleomodulins. After an initial <i>in silico</i> screening, the nuclear localization of the secreted putative lipoprotein MbovP475 of <i>M. bovis</i> was demonstrated in bovine macrophage cell line (BoMac) experimentally infected with <i>M. bovis</i>. Through combined application of ChIP-seq, Electrophoretic mobility shift assay (EMSA) and surface plasmon resonance (SPR) analysis, MbovP475 was determined to bind the promoter regions of the cell cycle central regulatory genes <i>CRYAB</i> and <i>MCF2L2</i>. MbovP475 has similar secondary structures with the transcription activator-like effectors (TALEs). Screening of various mutants affecting the potential DNA binding sites indicated that the residues <sup>242</sup>NI<sup>243</sup> within MbovP475 loop region of the helix-loop-helix domain were essential to its DNA binding activity, thereby contributing to decrease in BoMac cell viability. In conclusion, this is the first report to confirm <i>M. bovis</i> secretes a conserved TALE-like nucleomodulin that binds the promoters of <i>CRYAB</i> and <i>MCF2L2</i> genes, and subsequently down-regulates their expression and decreases BoMac cell viability. Therefore, this study offers a new understanding of mycoplasma pathogenesis.