bluuebunny/crossref_metadata_2025 huggingface dataset:
Methylation of Imprinted Genes in Sperm DNA Correlated to Urinary Polycyclic Aromatic Hydrocarbons (PAHs) Exposure Levels in Reproductive-Aged Men and the Birth Outcomes of the Offspring
Authors: Yang Jia , Lu Zhaoxu , Liu Zhichao , Wang Li , Qiang Mei
Published: January 2021

Polycyclic aromatic hydrocarbons (PAHs) are known environmental pollutants. Studies are very limited regarding the impacts of paternal PAHs exposure on birth outcomes as well as the underpinning mechanisms in human. In this study, 302 reproductive-aged males (22–46 years old) were enrolled and demographic informatics data were obtained by questionnaires. The levels of urinary hydroxylated PAHs (OH-PAHs) were assessed by ultra-high performance liquid chromatography-tandem mass spectrometry; and methylation levels of the imprinting genes H19, Meg3, and Peg3 of sperm DNA were evaluated via bisulfite pyrosequencing. The analysis of the correlation between OH-PAHs levels and methylation levels of imprinting genes showed that OH-PAHs are correlated with some CpG sites in H19, Peg3, and Meg3. To further investigate an association of urinary OH-PAHs with birth outcomes, follow-up study of wives of these subjects has been performed for 1–3 years. As the result, a total of 157 babies were born. The birth outcomes parameters including birth weight (BW), length (BL), and ponderal index (PI) were recorded. The further analysis of generalized estimating equation indicated a negative correlation between urinary total OH-PAHs levels and newborn BW (β = −0.081, p = 0.020); but this association has not been found for BL and PI. Furthermore, a logistic regression analysis was employed for examining associations of the methylation of imprinting genes with birth outcomes parameters, which indicated a negative correlation between BW and H19, namely, each unit percent (%) elevation in methylation of H19 (but not Peg3 and Meg3) was significantly associated with a 0.135 g reduction of BW (β = −0.135; 95% CI 0.781–0.978). Putting together, these results show that paternal non-occupational environmental exposure to PAHs is associated with newborn BW. And imprinting gene H19 methylation may be involved in the underlying mechanisms. This study in human population adds a support for previous animal study and implies that environmental impact on the offspring through paternal pathway.
Genome-Wide Investigation of the Phospholipase C Gene Family in Zea mays
Authors: Zhu Jiantang , Zhou Yuanyuan , Li Jiale , Li Hui
Published: January 2021

Phospholipase C (PLC) is one of the main hydrolytic enzymes in the metabolism of phosphoinositide and plays an important role in a variety of signal transduction processes responding to plant growth, development, and stress. Although the characteristics of many plant PLCs have been studied, PLC genes of maize have not been comprehensively identified. According to the study, five phosphatidylinositol-specific PLC (PI-PLC) and six non-specific PLC (NPC) genes were identified in maize. The PI-PLC and NPC genes of maize are conserved compared with homologous genes in other plants, especially in evolutionary relationship, protein sequences, conserved motifs, and gene structures. Transient expression of ZmPLC-GFP fusion protein in Arabidopsis protoplast cells showed that ZmPLCs are multi-localization. Analyses of transcription levels showed that ZmPLCs were significantly different under various different tissues and abiotic stresses. Association analysis shown that some ZmPLCs significantly associated with agronomic traits in 508 maize inbred lines. These results contribute to study the function of ZmPLCs and to provide good candidate targets for the yield and quality of superior maize cultivars.
An Immune Gene-Related Five-lncRNA Signature for to Predict Glioma Prognosis
Authors: Wang Xinzhuang , Gao Ming , Ye Junyi , Jiang Qiuyi , Yang Quan , Zhang Cheng , Wang Shengtao , Zhang Jian , Wang Ligang , Wu Jianing , Zhan Hua , Hou Xu , Han Dayong , Zhao Shiguang
Published: January 2021

Background

The tumor immune microenvironment is closely related to the malignant progression and treatment resistance of glioma. Long non-coding RNA (lncRNA) plays a regulatory role in this process. We investigated the pathological mechanisms within the glioma microenvironment and potential immunotherapy resistance related to lncRNAs.

Method

We downloaded datasets derived from glioma patients and analyzed them by hierarchical clustering. Next, we analyzed the immune microenvironment of glioma, related gene expression, and patient survival. Coexpressed lncRNAs were analyzed to generate a model of lncRNAs and immune-related genes. We analyzed the model using survival and Cox regression. Then, univariate, multivariate, receiver operating characteristic (ROC), and principle component analysis (PCA) methods were used to verify the accuracy of the model. Finally, GSEA was used to evaluate which functions and pathways were associated with the differential genes.

Results

Normal brain tissue maintains a low-medium immune state, and gliomas are clearly divided into three groups (low to high immunity). The stromal, immune, and estimate scores increased along with immunity, while tumor purity decreased. Further, human leukocyte antigen (HLA), programmed cell death-1 (PDL1), T cell immunoglobulin and mucin domain 3 (TIM-3), B7-H3, and cytotoxic T lymphocyte-associated antigen-4 (CTLA4) expression increases concomitantly with immune state, and the patient prognosis worsens. Five immune gene-related lncRNAs (AP001007.1, LBX-AS1, MIR155HG, MAPT-AS1, and LINC00515) were screened to construct risk models. We found that risk scores are related to patient prognosis and clinical characteristics, and are positively correlated with PDL1, TIM-3, and B7-H3 expression. These lncRNAs may regulate the tumor immune microenvironment through cytokine–cytokine receptor interactions, complement, and coagulation cascades, and may promote CD8 + T cell, regulatory T cell, M1 macrophage, and infiltrating neutrophils activity in the high-immunity group. In vitro, the abnormal expression of immune-related lncRNAs and the relationship between risk scores and immune-related indicators (PDL1, CTLA4, CD3, CD8, iNOS) were verified by q-PCR and immunohistochemistry (IHC).

Conclusion

For the first time, we constructed immune gene-related lncRNA risk models. The risk score may be a new biomarker for tumor immune subtypes and provide molecular targets for glioma immunotherapy.
A Mineralocorticoid Receptor Deficiency in Myeloid Cells Reduces Liver Steatosis by Impairing Activation of CD8+ T Cells in a Nonalcoholic Steatohepatitis Mouse Model
Authors: Muñoz-Durango Natalia , Arrese Marco , Hernández Alejandra , Jara Evelyn , Kalergis Alexis M. , Cabrera Daniel
Published: January 2021

Background and Aims

The mineralocorticoid receptor (MR) and renin-angiotensin-aldosterone system (RAAS) are implicated in non-alcoholic liver fatty disease (NALFD). However, inflammatory mechanisms linking MR and RAAS with disease pathology remain unclear. Here we aimed to evaluate the contribution of myeloid MR to the inflammatory response in an animal model of non-alcoholic steatohepatitis (NASH), induced with a methionine-choline deficient diet (MCD).

Methods

Mice with a conditional deficiency of MR in myeloid cells (MyMRKO) and their counterpart floxed control mice (FC) were fed for 18 days with MCD or chow diet, respectively. Serum levels of aminotransferases and aldosterone levels were measured and hepatic steatosis, inflammation and fibrosis scored histologically. Hepatic triglyceride content (HTC) and hepatic mRNA levels of pro-inflammatory pro-fibrotic-associated genes were also assessed. Deep flow cytometric analysis was used to dissect the immune response during NASH development.

Results

MyMRKO mice fed with an MCD diet exhibited reduced hepatic inflammation and lower HTC than controls. Absolute number and percentage of liver inflammatory infiltrate cells (except for CD8+ T lymphocytes) were similar in both MyMRKO and control mice fed with an MCD diet but expression of the costimulatory molecule CD86 by dendritic cells and the CD25 activation marker in CD8+ T cells were significantly reduced in MyMRKO.

Conclusions

Proinflammatory cells are functionally suppressed in the absence of MR. We hypothesized that loss of MR in myeloid cells reduces lipid accumulation in the liver, in part through modulating the adaptive immune response, which is pivotal for the development of steatosis.
Integrated Analysis of Key Pathways and Drug Targets Associated With Vogt-Koyanagi-Harada Disease
Authors: Chen Zhijun , Zhong Zhenyu , Zhang Wanyun , Su Guannan , Yang Peizeng
Published: January 2021

Background

Vogt-Koyanagi-Harada (VKH) disease is a complex disease associated with multiple molecular immunological mechanisms. As the underlying mechanism for VKH disease is unclear, we hope to utilize an integrated analysis of key pathways and drug targets to develop novel therapeutic strategies.

Methods

Candidate genes and proteins involved in VKH disease were identified through text-mining in the PubMed database. The GO and KEGG pathway analyses were used to examine the biological functions of the involved pathways associated with this disease. Molecule-related drugs were predicted through Drug-Gene Interaction Database (DGIdb) analysis.

Results

A total of 48 genes and 54 proteins were associated with VKH disease. Forty-two significantly altered pathways were identified through pathway analysis and were mainly related to immune and inflammatory responses. The top five of significantly altered pathways were termed as “inflammatory bowel disease,” “cytokine-cytokine receptor interaction,” “allograft rejection,” “antigen processing,” and “presentation and Herpes simplex infection” in the KEGG database. IFN-γ and IL-6 were identified as the key genes through network analysis. The DGIdb analysis predicted 48 medicines as possible drugs for VKH disease, among which Interferon Alfa-2B was co-associated both with IFN-γ and IL-6.

Conclusions

In this study, systematic analyses were utilized to detect key pathways and drug targets in VKH disease via bioinformatics analysis. IFN-γ and IL-6 were identified as the key mediators and possible drug targets in VKH disease. Interferon Alfa-2B was predicted to be a potentially effective drug for VKH disease treatment by targeting IFN-γ and IL-6, which warrants further experimental and clinical investigations.
Case Series: Gene Expression Analysis in Canine Vogt-Koyanagi-Harada/Uveodermatologic Syndrome and Vitiligo Reveals Conserved Immunopathogenesis Pathways Between Dog and Human Autoimmune Pigmentary Disorders
Authors: Egbeto Ista A. , Garelli Colton J. , Piedra-Mora Cesar , Wong Neil B. , David Clement N. , Robinson Nicholas A. , Richmond Jillian M.
Published: January 2021

Vogt-Koyanagi-Harada syndrome (VKH) and vitiligo are autoimmune diseases that target melanocytes. VKH affects several organs such as the skin, hair follicle, eyes, ears, and meninges, whereas vitiligo is often limited to the skin and mucosa. Many studies have identified immune genes, pathways and cells that drive the pathogeneses of VKH and vitiligo, including interleukins, chemokines, cytotoxic T-cells, and other leukocytes. Here, we present case studies of 2 canines with VKH and 1 with vitiligo, which occurred spontaneously in client-owned companion dogs. We performed comparative transcriptomics and immunohistochemistry studies on lesional skin biopsies from these cases in order to determine if the immunopathogenesis of autoimmune responses against melanocytes are conserved. In dogs, we found enrichment of T cell gene signatures, with upregulation of IFNG, TNF, PRF1, IL15, CTSW, CXCL10, and CCL5 in both VKH and vitiligo in dogs compared to healthy controls. Similar findings were reported in humans, suggesting that these genes play a role in the pathogenesis of spontaneous VKH and vitiligo. T cell-associated genes, including FOXP3 and TBX21, were enriched, while IGFBP5, FOXO1, and PECAM1 were decreased compared to healthy controls. Further, we identified TGFB3, SFRP2, and CXCL7 as additional potential drivers of autoimmune pigmentary disorders. Future studies exploring the immunopathogenesis of spontaneous autoimmunity will expand our understanding of these disorders, and will be useful in developing targeted therapies, repurposing drugs for veterinary and human medicine, and predicting disease prognosis and treatment response.
Vasculature-Associated Lymphoid Tissue: A Unique Tertiary Lymphoid Tissue Correlates With Renal Lesions in Lupus Nephritis Mouse Model
Authors: Masum Md. Abdul , Ichii Osamu , Elewa Yaser Hosny Ali , Otani Yuki , Namba Takashi , Kon Yasuhiro
Published: January 2021

Lupus nephritis (LN) is a common complication in young patients and the most predominant cause of glomerulonephritis. Infiltrating immune cells and presence of immunocomplexes in the kidney are hallmarks of LN, which is closely associated with renal lesions (RLs). However, their regulatory mechanism in the kidney remains unclear, which is valuable for prevention of RL development. Here, we show the development of vasculature-associated lymphoid tissue (VALT) in LN, which is related to renal inflammatory cytokines, indicating that VALT is a unique tertiary lymphoid tissue. Transcriptomic analysis revealed different chemokines and costimulatory molecules for VALT induction and organization. Vascular and perivascular structures showed lymphoid tissue organization through lymphorganogenic chemokine production. Transcriptional profile and intracellular interaction also demonstrated antigen presentation, lymphocyte activity, clonal expansion, follicular, and germinal center activity in VALT. Importantly, VALT size was correlated with infiltrating immune cells in kidney and RLs, indicating its direct correlation with the development of RLs. In addition, dexamethasone administration reduced VALT size. Therefore, inhibition of VALT formation would be a novel therapeutic strategy against LN.
Deep Sequencing of B Cell Receptor Repertoires From COVID-19 Patients Reveals Strong Convergent Immune Signatures
Authors: Galson Jacob D. , Schaetzle Sebastian , Bashford-Rogers Rachael J. M. , Raybould Matthew I. J. , Kovaltsuk Aleksandr , Kilpatrick Gavin J. , Minter Ralph , Finch Donna K. , Dias Jorge , James Louisa K. , Thomas Gavin , Lee Wing-Yiu Jason , Betley Jason , Cavlan Olivia , Leech Alex , Deane Charlotte M. , Seoane Joan , Caldas Carlos , Pennington Daniel J. , Pfeffer Paul , Osbourn Jane
Published: January 2021

Deep sequencing of B cell receptor (BCR) heavy chains from a cohort of 31 COVID-19 patients from the UK reveals a stereotypical naive immune response to SARS-CoV-2 which is consistent across patients. Clonal expansion of the B cell population is also observed and may be the result of memory bystander effects. There was a strong convergent sequence signature across patients, and we identified 1,254 clonotypes convergent between at least four of the COVID-19 patients, but not present in healthy controls or individuals following seasonal influenza vaccination. A subset of the convergent clonotypes were homologous to known SARS and SARS-CoV-2 spike protein neutralizing antibodies. Convergence was also demonstrated across wide geographies by comparison of data sets between patients from UK, USA, and China, further validating the disease association and consistency of the stereotypical immune response even at the sequence level. These convergent clonotypes provide a resource to identify potential therapeutic and prophylactic antibodies and demonstrate the potential of BCR profiling as a tool to help understand patient responses.
Different Innate and Adaptive Immune Responses to SARS-CoV-2 Infection of Asymptomatic, Mild, and Severe Cases
Authors: Carsetti Rita , Zaffina Salvatore , Piano Mortari Eva , Terreri Sara , Corrente Francesco , Capponi Claudia , Palomba Patrizia , Mirabella Mattia , Cascioli Simona , Palange Paolo , Cuccaro Ilaria , Milito Cinzia , Zumla Alimuddin , Maeurer Markus , Camisa Vincenzo , Vinci Maria Rosaria , Santoro Annapaola , Cimini Eleonora , Marchioni Luisa , Nicastri Emanuele , Palmieri Fabrizio , Agrati Chiara , Ippolito Giuseppe , Porzio Ottavia , Concato Carlo , Onetti Muda Andrea , Raponi Massimiliano , Quintarelli Concetta , Quinti Isabella , Locatelli Franco
Published: January 2021

SARS-CoV-2 is a novel coronavirus, not encountered before by humans. The wide spectrum of clinical expression of SARS-CoV-2 illness suggests that individual immune responses to SARS-CoV-2 play a crucial role in determining the clinical course after first infection. Immunological studies have focused on patients with moderate to severe disease, demonstrating excessive inflammation in tissues and organ damage. In order to understand the basis of the protective immune response in COVID-19, we performed a longitudinal follow-up, flow-cytometric and serological analysis of innate and adaptive immunity in 64 adults with a spectrum of clinical presentations: 28 healthy SARS-CoV-2-negative contacts of COVID-19 cases; 20 asymptomatic SARS-CoV-2-infected cases; eight patients with Mild COVID-19 disease and eight cases of Severe COVID-19 disease. Our data show that high frequency of NK cells and early and transient increase of specific IgA, IgM and, to a lower extent, IgG are associated with asymptomatic SARS-CoV-2 infection. By contrast, monocyte expansion and high and persistent levels of IgA and IgG, produced relatively late in the course of the infection, characterize severe disease. Modest increase of monocytes and different kinetics of antibodies are detected in mild COVID-19. The importance of innate NK cells and the short-lived antibody response of asymptomatic individuals and patients with mild disease suggest that only severe COVID-19 may result in protective memory established by the adaptive immune response.
How to Combine the Two Landmark Treatment Methods—Allogeneic Hematopoietic Stem Cell Transplantation and Chimeric Antigen Receptor T Cell Therapy Together to Cure High-Risk B Cell Acute Lymphoblastic Leukemia?
Authors: Zhang Mingming , Huang He
Published: January 2021

Allogeneic hematopoietic stem cell transplantation (allo-HSCT) has made tremendous progress in the last few decades and is increasingly being used worldwide. The success of haploidentical HSCT has made it possible to have “a donor for everyone”. Patients who received transplantation in remission may have a favorable outcome, while those who were transplanted in advanced stages of disease have a poor prognosis. Although chimeric antigen receptor T (CAR-T) cell therapy is currently a milestone in the immunotherapy of relapsed or refractory (R/R) B cell acute lymphoblastic leukemia (B-ALL) and has demonstrated high remission rates in patients previously treated in multiple lines, the relatively high relapse rate remains a barrier to CAR-T cell therapy becoming an excellent cure option. Therefore, combining these two approaches (allo-HSCT and CAR-T cell therapy) is an attractive area of research to further improve the prognosis of R/R B-ALL. In this review, we will discuss the current clinical practices of combining allo-HSCT with CAR-T cell therapy based on available data, including CAR-T cells as a bridge to allo-HSCT for R/R B-ALL and CAR-T cell infusion for post-transplant relapse. We will further explore not only other possible ways to combine the two approaches, including CAR-T cell therapy to clear minimal residual disease peri-transplantation and incorporation of CAR technology to treat graft-versus-host disease, but also the potential of CAR-T cells as a part of allo-HSCT.
Identification of Pro-Fibrotic Macrophage Populations by Single-Cell Transcriptomic Analysis in West Highland White Terriers Affected With Canine Idiopathic Pulmonary Fibrosis
Authors: Fastrès Aline , Pirottin Dimitri , Fievez Laurence , Tutunaru Alexandru-Cosmin , Bolen Géraldine , Merveille Anne-Christine , Marichal Thomas , Desmet Christophe J. , Bureau Fabrice , Clercx Cécile
Published: January 2021

Canine idiopathic pulmonary fibrosis (CIPF) affects old dogs from the West Highland white terrier (WHWT) breed and mimics idiopathic pulmonary fibrosis (IPF) in human. The disease results from deposition of fibrotic tissue in the lung parenchyma causing respiratory failure. Recent studies in IPF using single-cell RNA sequencing (scRNA-seq) revealed the presence of profibrotic macrophage populations in the lung, which could be targeted for therapeutic purpose. In dogs, scRNA-seq was recently validated for the detection of cell populations in bronchoalveolar lavage fluid (BALF) from healthy dogs. Here we used the scRNA-seq to characterize disease-related heterogeneity within cell populations of macrophages/monocytes (Ma/Mo) in the BALF from five WHWTs affected with CIPF in comparison with three healthy WHWTs. Gene set enrichment analysis was also used to assess pro-fibrotic capacities of Ma/Mo populations. Five clusters of Ma/Mo were identified. Gene set enrichment analyses revealed the presence of pro-fibrotic monocytes in higher proportion in CIPF WHWTs than in healthy WHWTs. In addition, monocyte-derived macrophages enriched in pro-fibrotic genes in CIPF compared with healthy WHWTs were also identified. These results suggest the implication of Ma/Mo clusters in CIPF processes, although, further research is needed to understand their role in disease pathogenesis. Overexpressed molecules associated with pulmonary fibrosis processes were also identified that could be used as biomarkers and/or therapeutic targets in the future.
FcγRIIb Expression Is Decreased on Naive and Marginal Zone-Like B Cells From Females With Multiple Sclerosis
Authors: Trend Stephanie , Leffler Jonatan , Teige Ingrid , Frendéus Björn , Kermode Allan G. , French Martyn A. , Hart Prue H.
Published: January 2021

B cells are critical to the development of multiple sclerosis (MS), but the mechanisms by which they contribute to the disease are poorly defined. We hypothesised that the expression of CD32b (FcγRIIb), a receptor for the Fc region of IgG with inhibitory activities in B cells, is lower on B cell subsets from people with clinically isolated syndrome (CIS) or MS. CD32b expression was highest on post-naive IgM+ B cell subsets in healthy controls. For females with MS or CIS, significantly lower CD32b expression was identified on IgM+ B cell subsets, including naive and IgMhi MZ-like B cells, when compared with control females. Lower CD32b expression on these B cell subsets was associated with detectable anti-Epstein Barr Virus viral capsid antigen IgM antibodies, and higher serum levels of B cell activating factor. To investigate the effects of lower CD32b expression, B cells were polyclonally activated in the presence of IgG immune complexes, with or without a CD32b blocking antibody, and the expression of TNF and IL-10 in B cell subsets was assessed. The reduction of TNF but not IL-10 expression in controls mediated by IgG immune complexes was reversed by CD32b blockade in naive and IgMhi MZ-like B cells only. However, no consequence of lower CD32b expression on these cells from females with CIS or MS was detected. Our findings highlight a potential role for naive and marginal zone-like B cells in the immunopathogenesis of MS in females, which requires further investigation.
Using LBB Tools to Assess Miter Squid Stock in the Northeastern South China Sea
Authors: Wang Xuehui , He Yinglin , Du Feiyan , Liu Mengna , Bei Weilie , Cai Yancong , Qiu Yongsong
Published: January 2021

Based on length frequency data of miter squid (Uroteuthis chinensis) collected in the northeastern South China Sea in 1975–1977, 1997–1999, and 2018–2019, asymptotic length, optimal length at first capture, relative mortality, and relative biomass of the stock were estimated using length-based Bayesian biomass estimation (LBB). The LBB-estimated asymptotic length for 2018–2019 was smaller. Optimal lengths at first capture for the later far exceeded average lengths in catches because of a major increase in fishing intensity. Between 1975 and 1977, relative total mortality (Z/K) was low, but it increased in the latter two periods, while relative natural mortality (M/K) showed a downward trend. Relative biomasses (B/B0 and B/Bmsy) indicated that the stock was close to unexploited between 1975 and 1977, but they declined to the levels of 6% and 4% in the later periods, which correspond to growth in fishing horsepower. Indeed, by 2018, fishing horsepower increased by nearly four times the optimal level. The analysis suggests that the stock of miter squid has been overfished since the mid-1980s and is now under heavy fishing pressure. To recover the stock, it is imperative to reduce fishing intensity and enforce size-at-first-capture regulations.
Three-Dimensional Imaging Lidar for Characterizing Particle Fields and Organisms in the Mesopelagic Zone
Authors: McKenzie Trevor , Twardowski Michael , Briggs Nathan , Nayak Aditya R. , Boswell Kevin M. , Dalgleish Fraser
Published: January 2021

The ocean’s mesopelagic zone is largely uncharacterized despite its vital role in sustaining ocean ecosystems. The composition, cycling, and fate of particle fields in the mesopelagic lacks an integrative multi-scale understanding of organism migration patterns, distribution, and diversity. This problem is addressed by combining complementary technologies with overlapping size spectra, including profiler mounted optical scattering sensors, profiler, and ship mounted acoustic devices, and a custom Unobtrusive Multi-Static Lidar Imager (UMSLI). This unique sensor suite can observe distributions of particles including organisms over a six order of magnitude dynamic size range, from microns to meters. Overlapping size ranges between different methods allows for cross-validation. This work focuses on the lidar imaging measurements and optical backscattering and attenuation, covering a combined particle size range of 0.1 mm to several cm. Particles at the small end of this range are sized using an existing backscattering time series inversion method after Briggs et al. (2013). Larger particles are resolved with UMSLI over an expanding volume using three-dimensional photo-realistic laser serial imaging. UMSLI’s image rectifying ability over time allows for derivation of particle concentration, size, and spatial distribution. Technical details on the development and post-processing methods for the novel UMSLI system are provided. Image resolved particle size distributions (PSDs) revealed a size shift from smaller to larger particles (>0.5 mm) as indicated by flatter slopes from dawn (slope = 2.6) to dusk (slope = 3.0). PSD trends are supported by an optical backscatter and transmissometer time series inversion analysis. Size shifts in the particle field are largely attributed to aggregation effects. Images support evidence of temporal variation between dusk and dawn stations through statistical analysis of particle concentrations for particle sizes 0.50–5.41 mm. Spatial analysis of the particle field revealed a dominantly uniform distributed marine snow background. The importance and potential of integrated approaches to studying particle and organism dynamics in ocean environments are discussed.
Calcifying Phytoplankton Demonstrate an Enhanced Role in Greenhouse Atmospheric CO2 Regulation
Authors: Kvale Karin , Koeve Wolfgang , Mengis Nadine
Published: January 2021

The impact of calcifying phytoplankton on atmospheric CO2 concentration is determined by a number of factors, including their degree of ecological success as well as the buffering capacity of the ocean/marine sediment system. The relative importance of these factors has changed over Earth's history and this has implications for atmospheric CO2 and climate regulation. We explore some of these implications with four “Strangelove” experiments: two in which soft-tissue production and calcification is stopped, and two in which only calcite production is forced to stop, in idealized icehouse and greenhouse climates. We find that in the icehouse climate the loss of calcifiers compensates the atmospheric CO2 impact of the loss of all phytoplankton by roughly one-sixth. But in the greenhouse climate the loss of calcifiers compensates the loss of all phytoplankton by about half. This increased impact on atmospheric CO2 concentration is due to the combination of higher rates of pelagic calcification due to warmer temperatures and weaker buffering due to widespread acidification in the greenhouse ocean. However, the greenhouse atmospheric temperature response per unit of CO2 change to removing ocean soft-tissue production and calcification is only one-fourth that in an icehouse climate, owing to the logarithmic radiative forcing dependency on atmospheric CO2 thereby reducing the climate feedback of mass extinction. This decoupling of carbon cycle and temperature sensitivities offers a mechanism to explain the dichotomy of both enhanced climate stability and destabilization of the carbonate compensation depth in greenhouse climates.
Salmonella spvC Gene Inhibits Pyroptosis and Intestinal Inflammation to Aggravate Systemic Infection in Mice
Authors: Zuo Lingli , Zhou Liting , Wu Chaoyi , Wang Yanlin , Li Yuanyuan , Huang Rui , Wu Shuyan
Published: January 2021

Salmonella enterica serovar Typhimurium (S). Typhimurium is a primary foodborne pathogen infecting both humans and animals. Salmonella plasmid virulence C (spvC) gene is closely related to S. Typhimurium dissemination in mice, while the mechanisms remain to be fully elucidated. Pyroptosis, a gasdermin-mediated inflammatory cell death, plays a role in host defense against bacterial infection, whereas the effect of spvC on pyroptosis and its function in inflammatory injury induced by S. Typhimurium are rather limited. In our study, C57BL/6 mice and J774A.1 cells infected with S. Typhimurium wild-type strain SL1344, spvC deletion mutant, spvC K136A site-directed mutant, and complemented strain were used to investigate potential pathogenesis of spvC. We verity that SpvC attenuates intestinal inflammation, suppresses pyroptosis through phosphothreonine lyase activity, and reduces pyroptosis in the ceca. Moreover, the reduction of inflammation via spvC results in systemic infection. These findings demonstrate that spvC inhibits pyroptosis and intestinal inflammation to promote bacterial dissemination, which provide new strategies for controlling systemic infection caused by Salmonella and novel insights for the treatment of other corresponding diseases.
Evaluation of MALDI–TOF Mass Spectrometry in Diagnostic and Environmental Surveillance of Legionella Species: A Comparison With Culture and Mip-Gene Sequencing Technique
Authors: Pascale Maria Rosaria , Mazzotta Marta , Salaris Silvano , Girolamini Luna , Grottola Antonella , Simone Maria Luisa , Cordovana Miriam , Bisognin Francesco , Dal Monte Paola , Bucci Sabattini Maria Antonietta , Viggiani Mariagabriella , Cristino Sandra
Published: January 2021

Legionella spp. are widespread bacteria in aquatic environments with a growing impact on human health. Between the 61 species, Legionella pneumophila is the most prevalent in human diseases; on the contrary, Legionella non-pneumophila species are less detected in clinical diagnosis or during environmental surveillance due to their slow growth in culture and the absence of specific and rapid diagnostic/analytical tools. Reliable and rapid isolate identification is essential to estimate the source of infection, to undertake containment measures, and to determine clinical treatment. Matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI–TOF MS), since its introduction into the routine diagnostics of laboratories, represents a widely accepted method for the identification of different bacteria species, described in a few studies on the Legionella clinical and environmental surveillance. The focus of this study was the improvement of MALDI–TOF MS on Legionella non-pneumophila species collected during Legionella nosocomial and community surveillance. Comparative analysis with cultural and mip-gene sequencing results was performed. Moreover, a phylogenetic analysis was carried out to estimate the correlations amongst isolates. MALDI–TOF MS achieved correct species-level identification for 45.0% of the isolates belonging to the Legionella anisa, Legionella rubrilucens, Legionella feeleii, and Legionella jordanis species, displaying a high concordance with the mip-gene sequencing results. In contrast, less reliable identification was found for the remaining 55.0% of the isolates, corresponding to the samples belonging to species not yet included in the database. The phylogenetic analysis showed relevant differences inside the species, regruped in three main clades; among the Legionella anisa clade, a subclade with a divergence of 3.3% from the main clade was observed. Moreover, one isolate, identified as Legionella quinlivanii, displayed a divergence of 3.8% from the corresponding reference strain. However, these findings require supplementary investigation. The results encourage the implementation of MALDI–TOF MS in routine diagnostics and environmental Legionella surveillance, as it displays a reliable and faster identification at the species level, as well as the potential to identify species that are not yet included in the database. Moreover, phylogenetic analysis is a relevant approach to correlate the isolates and to track their spread, especially in unconventional reservoirs, where Legionella prevention is still underestimated.
Skin and Gut Microbiome in Psoriasis: Gaining Insight Into the Pathophysiology of It and Finding Novel Therapeutic Strategies
Authors: Chen Lihui , Li Jie , Zhu Wu , Kuang Yehong , Liu Tao , Zhang Wei , Chen Xiang , Peng Cong
Published: January 2021

Psoriasis affects the health of myriad populations around the world. The pathogenesis is multifactorial, and the exact driving factor remains unclear. This condition arises from the interaction between hyperproliferative keratinocytes and infiltrating immune cells, with poor prognosis and high recurrence. Better clinical treatments remain to be explored. There is much evidence that alterations in the skin and intestinal microbiome play an important role in the pathogenesis of psoriasis, and restoration of the microbiome is a promising preventive and therapeutic strategy for psoriasis. Herein, we have reviewed recent studies on the psoriasis-related microbiome in an attempt to confidently identify the “core” microbiome of psoriasis patients, understand the role of microbiome in the pathogenesis of psoriasis, and explore new therapeutic strategies for psoriasis through microbial intervention.
Over-Expression of Hypochlorite Inducible Major Facilitator Superfamily (MFS) Pumps Reduces Antimicrobial Drug Susceptibility by Increasing the Production of MexXY Mediated by ArmZ in Pseudomonas aeruginosa
Authors: Dulyayangkul Punyawee , Satapoomin Naphat , Avison Matthew B. , Charoenlap Nisanart , Vattanaviboon Paiboon , Mongkolsuk Skorn
Published: January 2021

Pseudomonas aeruginosa, a well-known cause of nosocomial infection, is frequently antibiotic resistant and this complicates treatment. Links between oxidative stress responses inducing antibiotic resistance through over-production of RND-type efflux pumps have been reported in P. aeruginosa, but this has not previously been associated with MFS-type efflux pumps. Two MFS efflux pumps encoded by mfs1 and mfs2 were selected for study because they were found to be sodium hypochlorite (NaOCl) inducible. Antibiotic susceptibility testing was used to define the importance of these MFS pumps in antibiotic resistance and proteomics was used to characterize the resistance mechanisms involved. The results revealed that mfs1 is NaOCl inducible whereas mfs2 is NaOCl, N-Ethylmaleimide and t-butyl hydroperoxide inducible. Deletion of mfs1 or mfs2 did not affect antibiotic or paraquat susceptibility. However, over-production of Mfs1 and Mfs2 reduced susceptibility to aminoglycosides, quinolones, and paraquat. Proteomics, gene expression analysis and targeted mutagenesis showed that over-production of the MexXY RND-type efflux pump in a manner dependent upon armZ, but not amgRS, is the cause of reduced antibiotic susceptibility upon over-production of Mfs1 and Mfs2. mexXY operon expression analysis in strains carrying various lengths of mfs1 and mfs2 revealed that at least three transmembrane domains are necessary for mexXY over-expression and decreased antibiotic susceptibility. Over-expression of the MFS-type efflux pump gene tetA(C) did not give the same effect. Changes in paraquat susceptibility were independent of mexXY and armZ suggesting that it is a substrate of Mfs1 and Mfs2. Altogether, this is the first evidence of cascade effects where the over-production of an MFS pump causes over-production of an RND pump, in this case MexXY via increased armZ expression.
Microbial Flow Within an Air-Phyllosphere-Soil Continuum
Authors: Zhou Shu-Yi-Dan , Li Hu , Giles Madeline , Neilson Roy , Yang Xiao-ru , Su Jian-qiang
Published: January 2021

The phyllosphere is populated by numerous microorganisms. Microbes from the wider environment, i.e., air and soil, are considered key contributors to phyllosphere microbial communities, but their contribution is unclear. This study seeks to address this knowledge gap by controlling the movement of microbes along the air-phyllosphere-soil continuum. Customized equipment with dual chambers was constructed that permitted airflow to enter the first chamber while the second chamber recruited filtered microbe-free air from the initial chamber. Allium schoenoprasum (chive) and Sonchus oleraceus (sow thistle) were cultivated in both chambers, and the microbial communities from air, phyllosphere, and soil samples were characterized. Shares of microbial OTUs in the equipment suggested a potential interconnection between the air, phyllosphere, and soil system. Fast expectation-maximization microbial source tracking (FEAST) suggested that soil was the major source of airborne microbial communities. In contrast, the contribution of airborne and soil microbes to phyllosphere microbial communities of either A. schoenoprasum or S. oleraceus was limited. Notably, the soilborne microbes were the only environmental sources to phyllosphere in the second chamber and could affect the composition of phyllosphere microbiota indirectly by air flow. The current study demonstrated the possible sources of phyllosphere microbes by controlling external airborne microbes in a designed microcosm system and provided a potential strategy for recruitment for phyllosphere recruitment.
Characterization of Three Calcium-Dependent Protein Kinases of Cryptosporidium parvum
Authors: Zhang Qiang , Shao Qian , Guo Yaqiong , Li Na , Li Yu , Su Jiayuan , Xu Rui , Zhang Ziding , Xiao Lihua , Feng Yaoyu
Published: January 2021

In Cryptosporidium spp., calcium-dependent protein kinases (CDPKs) are considered promising targets for the development of pharmaceutical interventions. Whole-genome sequencing has revealed the presence of 11 CDPKs in Cryptosporidium parvum (CpCDPKs). In this study, we expressed recombinant CpCDPK4, CpCDPK5, and CpCDPK6 in Escherichia coli. The biological characteristics and functions of these CpCDPKs were examined by using quantitative reverse transcription PCR (qRT-PCR), immunofluorescence microscopy, and an in vitro neutralization assay. The expression of the CpCDPK4 gene peaked at 12 h post-infection, the CpCDPK5 gene peaked at 12 and 48 h, and the CpCDPK6 gene peaked at 2–6 h. CpCDPK4 protein was located in the anterior and mid-anterior regions of sporozoites, and CpCDPK5 protein was located over the entire sporozoites, while CpCDPK6 protein was expressed in a spotty pattern. Immune sera of CpCDPK4 and CpCDPK6 exhibited significant inhibitory effects on host cell invasion, while the immune sera of CpCDPK5 had no effects. These differences in protein localization, gene expressions, and neutralizing capacities indicated that the CpCDPK proteins may have different roles during the lifecycle of Cryptosporidium spp.
African Swine Fever Virus Ubiquitin-Conjugating Enzyme Interacts With Host Translation Machinery to Regulate the Host Protein Synthesis
Authors: Barrado-Gil Lucía , Del Puerto Ana , Muñoz-Moreno Raquel , Galindo Inmaculada , Cuesta-Geijo Miguel Ángel , Urquiza Jesús , Nistal-Villán Estanislao , Maluquer de Motes Carlos , Alonso Covadonga
Published: January 2021

African Swine Fever virus (ASFV) causes one of the most relevant emerging diseases affecting swine, now extended through three continents. The virus has a large coding capacity to deploy an arsenal of molecules antagonizing the host functions. In the present work, we have studied the only known E2 viral-conjugating enzyme, UBCv1 that is encoded by the I215L gene of ASFV. UBCv1 was expressed as an early expression protein that accumulates throughout the course of infection. This versatile protein, bound several types of polyubiquitin chains and its catalytic domain was required for enzymatic activity. High throughput mass spectrometry analysis in combination with a screening of an alveolar macrophage library was used to identify and characterize novel UBCv1-host interactors. The analysis revealed interaction with the 40S ribosomal protein RPS23, the cap-dependent translation machinery initiation factor eIF4E, and the E3 ubiquitin ligase Cullin 4B. Our data show that during ASFV infection, UBCv1 was able to bind to eIF4E, independent from the cap-dependent complex. Our results provide novel insights into the function of the viral UBCv1 in hijacking cellular components that impact the mTORC signaling pathway, the regulation of the host translation machinery, and the cellular protein expression during the ASFV lifecycle.
Susceptibility of Clinical Enterobacterales Isolates With Common and Rare Carbapenemases to Mecillinam
Authors: Fuchs Frieder , Ahmadzada Aysel , Plambeck Lars , Wille Thorsten , Hamprecht Axel
Published: January 2021

Purpose: To investigate the susceptibility of carbapenemase-producing Enterobacterales (CPE) to mecillinam based on the recently updated European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints for uncomplicated Urinary Tract Infection (uUTI).

Methods: The challenge collection consisted of 105 molecularly characterized Enterobacterales [Klebsiella spp. (N = 49), Escherichia coli (N = 30), Enterobacter cloacae (n = 13), Citrobacter freundii (N = 9), Proteus mirabilis (N = 3), and Raoultella ornithinolytica (N = 1)]. Isolates produced OXA-48 (N = 18), OXA-48-like (N = 18), VIM (N = 22), NDM (N = 22), KPC (N = 12), IMI (N = 9), IMP (N = 6), GES (N = 1), OXA-58 (N = 2) or combinations thereof (N = 5). MICs of carbapenems were determined by agar gradient diffusion (AGD). MICs of mecillinam were assessed by agar dilution (reference method) and compared to disk diffusion (DD) and AGD.

Results: Overall 23/105 CPE (21.9%) were susceptible to mecillinam. Susceptibility was observed in E. coli (N = 12), E. cloacae (N = 7), and Klebsiella pneumoniae (N = 4) producing IMI, OXA-48, OXA-48-like, and NDM-1 carbapenemases. MIC50 for mecillinam in all isolates was 128 mg/L while MIC50 for meropenem was 8 mg/L. Lower MICs for mecillinam were found in IMI (MIC50 8 mg/L) and OXA-48-like (MIC50 16 mg/L) producers. The comparison of the different susceptibility methods showed very major errors of 12.2% with AGD and 8.5% with disk diffusion when compared to the reference method.

Conclusion: Mecillinam susceptibility was restricted to isolates producing IMI-, OXA-48-like, and NDM-1 carbapenemases and was documented despite high carbapenem MICs in some isolates. Mecillinam could be a promising oral antimicrobial in uUTI caused by E. coli and E. cloacae isolates carrying IMI- and OXA-48-like carbapenemases; however, susceptibility testing by AGD and disk diffusion remains problematic.
Spatial Correlations and Distribution of Competence Gene Expression in Biofilms of Streptococcus mutans
Authors: Ishkov Ivan P. , Kaspar Justin R. , Hagen Stephen J.
Published: January 2021

Streptococcus mutans is an important pathogen in the human oral biofilm. It expresses virulent behaviors that are linked to its genetic competence regulon, which is controlled by comX. Expression of comX is modulated by two diffusible signaling peptides, denoted CSP and XIP, and by other environmental cues such as pH and oxidative stress. The sensitivity of S. mutans competence to environmental inputs that may vary on microscopic length scales raises the question of whether the biofilm environment creates microniches where competence and related phenotypes are concentrated, leading to spatial clustering of S. mutans virulence behaviors. We have used two-photon microscopy to characterize the spatial distribution of comX expression among individual S. mutans cells in biofilms. By analyzing correlations in comX activity, we test for spatial clustering that may suggest localized competence microenvironments. Our data indicate that both competence-signaling peptides diffuse efficiently through the biofilm. XIP elicits a population-wide response. CSP triggers a Poisson-like, spatially random comX response from a subpopulation of cells that is homogeneously dispersed. Our data indicate that competence microenvironments if they exist are small enough that the phenotypes of individual cells are not clustered or correlated to any greater extent than occurs in planktonic cultures.
Characteristics of COVID-19 Patients Based on the Results of Nucleic Acid and Specific Antibodies and the Clinical Relevance of Antibody Levels
Authors: Chen Hao , Qin Rundong , Huang Zhifeng , He Li , Luo Wenting , Zheng Peiyan , Huang Huimin , Wang Hui , Sun Baoqing
Published: January 2021

Combination of nucleic acid and specific antibody testing is often required in the diagnosis of COVID-19, but whether patients with different nucleic acid and antibody results have different laboratory parameters, severities and clinical outcomes, has not yet been comprehensively investigated. Thus, according to different groups of nucleic acid and antibody results, we aimed to investigate the differences in demographic characteristics, and laboratory parameters among the different groups and predict their clinical outcomes. In our study, nasopharyngeal swab nucleic acids and antibodies were detected by reverse-transcription polymerase chain reaction and chemiluminescence, respectively. Patients with confirmed COVID-19 with different severities, were divided into the PCR+Ab+, PCR+Ab−, and PCR−Ab+ groups. Demographic characteristics, symptoms, comorbidities, laboratory parameters, and clinical outcomes were compared among the three groups. The correlation of antibodies with laboratory parameters and clinical outcomes was also explored, and antibodies were used to predict the timing of nucleic acid conversion. We found that a total of 364 COVID-19 patients were included in the final analysis. Of these, a total of 184, 37, and 143 patients were assigned to the PCR+Ab+, PCR+Ab−, and PCR−Ab+ groups, respectively. Compared to patients in the PCR+Ab− or PCR− Ab+ groups, patients in the PCR+Ab+ group presented worse symptoms, more comorbidities, more laboratory abnormalities, and worse clinical outcomes (P < 0.05). In addition, the levels of IgG, IgM, and IgA were all significantly correlated with the days of hospitalization, days of PCR turning negative, and multiple laboratory parameters (P < 0.05). Meanwhile, combined IgM, IgA, and IgG predicted the days of PCR turning negative within 1 week. The best performance was achieved when the cut-off values of IgM, IgG, and IgA were 3.2, 1.8 and 0.5, respectively, with a sensitivity of 73% and specificity of 82%. In conclusion, COVID-19 patients who were both positive for nucleic acids and antibodies presented with worse clinical features, laboratory abnormalities, and clinical outcomes. The three specific antibodies were positively correlated with clinical outcomes and most laboratory parameters. Furthermore, antibody levels can predict the time of nucleic acid conversion.