bluuebunny/crossref_metadata_2025 huggingface dataset:
The (Lack of) DNA Double-Strand Break Repair Pathway Choice During V(D)J Recombination
Authors: Libri Alice , Marton Timea , Deriano Ludovic
Published: January 2022

DNA double-strand breaks (DSBs) are highly toxic lesions that can be mended via several DNA repair pathways. Multiple factors can influence the choice and the restrictiveness of repair towards a given pathway in order to warrant the maintenance of genome integrity. During V(D)J recombination, RAG-induced DSBs are (almost) exclusively repaired by the non-homologous end-joining (NHEJ) pathway for the benefit of antigen receptor gene diversity. Here, we review the various parameters that constrain repair of RAG-generated DSBs to NHEJ, including the peculiarity of DNA DSB ends generated by the RAG nuclease, the establishment and maintenance of a post-cleavage synaptic complex, and the protection of DNA ends against resection and (micro)homology-directed repair. In this physiological context, we highlight that certain DSBs have limited DNA repair pathway choice options.
A Murine Model of X-Linked Moesin-Associated Immunodeficiency (X-MAID) Reveals Defects in T Cell Homeostasis and Migration
Authors: Avery Lyndsay , Robertson Tanner F. , Wu Christine F. , Roy Nathan H. , Chauvin Samuel D. , Perkey Eric , Vanderbeck Ashley , Maillard Ivan , Burkhardt Janis K.
Published: January 2022

X-linked moesin associated immunodeficiency (X-MAID) is a primary immunodeficiency disease in which patients suffer from profound lymphopenia leading to recurrent infections. The disease is caused by a single point mutation leading to a R171W amino acid change in the protein moesin (moesinR171W). Moesin is a member of the ERM family of proteins, which reversibly link the cortical actin cytoskeleton to the plasma membrane. Here, we describe a novel mouse model with global expression of moesinR171W that recapitulates multiple facets of patient disease, including severe lymphopenia. Further analysis reveals that these mice have diminished numbers of thymocytes and bone marrow precursors. X-MAID mice also exhibit systemic inflammation that is ameliorated by elimination of mature lymphocytes through breeding to a Rag1-deficient background. The few T cells in the periphery of X-MAID mice are highly activated and have mostly lost moesinR171W expression. In contrast, single-positive (SP) thymocytes do not appear activated and retain high expression levels of moesinR171W. Analysis of ex vivo CD4 SP thymocytes reveals defects in chemotactic responses and reduced migration on integrin ligands. While chemokine signaling appears intact, CD4 SP thymocytes from X-MAID mice are unable to polarize and rearrange cytoskeletal elements. This mouse model will be a valuable tool for teasing apart the complexity of the immunodeficiency caused by moesinR171W, and will provide new insights into how the actin cortex regulates lymphocyte function.
β-Glucan-Induced Immuno-Modulation: A Role for the Intestinal Microbiota and Short-Chain Fatty Acids in Common Carp
Authors: Petit Jules , de Bruijn Irene , Goldman Mark R. G. , van den Brink Erik , Pellikaan Wilbert F. , Forlenza Maria , Wiegertjes Geert F.
Published: January 2022

Dietary supplementation of fish with β-glucans has been commonly associated with immunomodulation and generally accepted as beneficial for fish health. However, to date the exact mechanisms of immunomodulation by β-glucan supplementation in fish have remained elusive. In mammals, a clear relation between high-fibre diets, such as those including β-glucans, and diet-induced immunomodulation via intestinal microbiota and associated metabolites has been observed. In this study, first we describe by 16S rRNA sequencing the active naive microbiota of common carp intestine. Based on the abundance of the genus Bacteroides, well known for their capacity to degrade and ferment carbohydrates, we hypothesize that common carp intestinal microbiota could ferment dietary β-glucans. Indeed, two different β-glucan preparations (curdlan and MacroGard®) were both fermented in vitro, albeit with distinct fermentation dynamics and distinct production of short-chain fatty acids (SCFA). Second, we describe the potential immunomodulatory effects of the three dominant SCFAs (acetate, butyrate, and propionate) on head kidney leukocytes, showing effects on both nitric oxide production and expression of several cytokines (il-1b, il-6, tnfα, and il-10) in vitro. Interestingly, we also observed a regulation of expression of several gpr40L genes, which were recently described as putative SCFA receptors. Third, we describe how a single in vivo oral gavage of carp with MacroGard® modulated simultaneously, the expression of several pro-inflammatory genes (il-1b, il-6, tnfα), type I IFN-associated genes (tlr3.1, mx3), and three specific gpr40L genes. The in vivo observations provide indirect support to our in vitro data and the possible role of SCFAs in β-glucan-induced immunomodulation. We discuss how β-glucan-induced immunomodulatory effects can be explained, at least in part, by fermentation of MacroGard® by specific bacteria, part of the naive microbiota of common carp intestine, and how a subsequent production of SFCAs could possibly explain immunomodulation by β-glucan via SCFA receptors present on leukocytes.
Multi-Omics Analysis of the Gut-Liver Axis Reveals the Mechanism of Liver Injury in Colitis Mice
Authors: Zhu Luoyi , Zong Xin , Xiao Xiao , Cheng Yuanzhi , Fu Jie , Lu Zeqing , Jin Mingliang , Wang Fengqin , Wang Yizhen
Published: January 2022

Liver injury is a common complication of inflammatory bowel disease (IBD). However, the mechanisms of liver injury development are not clear in IBD patients. Gut microbiota is thought to be engaged in IBD pathogenesis. Here, by an integrated analysis of host transcriptome and colonic microbiome, we have attempted to reveal the mechanism of liver injury in colitis mice. In this study, dextran sulfate sodium (DSS) -induced mice colitis model was constructed. Liver transcriptome showed significant up- and down-regulation of pathways linked to immune response and lipid metabolism, respectively. Whilst the colon transcriptome exhibited dramatic alterations in immune response and pathways associated with cell growth and death. The microbiota of DSS-treated mice underwent strong transitions. Correlation analyses identified genes associated with liver and colon injury, whose expression was associated with the abundance of liver and gut health-related bacteria. Collectively, the results indicate that the liver injury in colitis mice may be related to the intestinal dysbiosis and host-microbiota interactions. These findings may provide new insights for identifying potential targets for the treatment of IBD and its induced liver injury.
miR-18a-3p and Its Target Protein HuR May Regulate Myogenic Differentiation in Immune-Mediated Necrotizing Myopathy
Authors: Ye Lifang , Zuo Yu , Chen Fang , Peng Qinglin , Lu Xin , Wang Guochun , Shu Xiaoming
Published: January 2022

Immune-mediated necrotizing myopathy (IMNM) is characterized by manifestation of myonecrosis and regeneration of muscle fibers; however, the underlying pathogenesis remains unclear. This study aimed to investigate the role and mechanism of miR-18a-3p and its target RNA-binding protein HuR in IMNM. HuR and miR-18a-3p levels were detected in the skeletal muscles of 18 patients with IMNM using quantitative reverse-transcription real-time polymerase chain reaction (qRT-PCR) and western blotting analysis. Human myoblasts were transfected with small interfering RNA targeting HuR and miR-18a-3p mimic or inhibitor. Myogenic differentiation markers, myogenin and myosin heavy chain, were analyzed by qRT-PCR, western blotting analysis, and immunofluorescence staining. The results showed that miR-18a-3p was upregulated (p=0.0002), whereas HuR was downregulated (p=0.002) in the skeletal muscles of patients with IMNM. The expression of miR-18a-3p in patients with IMNM was negatively correlated with those of HuR (r = -0.512, p = 0.029). We also found that disease activity was positively correlated with HuR expression (r = 0.576, p = 0.012) but muscle activity was negatively correlated with miR-18a-3p expression (r = -0.550, p = 0.017). Besides, bioinformatics analysis and dual-luciferase reporter assays suggested that miR-18a-3p could directly target HuR. Cellular experiments showed that overexpression of miR-18a-3p inhibited myogenic differentiation by targeting HuR, whereas inhibition of miR-18a-3p led to opposite results. Therefore, miR-18a-3p and its target protein HuR may be responsible for modulating the myogenic process in IMNM and can thus be therapeutic targets for the same.
The Predictive Value of MAP2K1/2 Mutations on Efficiency of Immunotherapy in Melanoma
Authors: Ye Ting , Zhang Jie-Ying , Liu Xin-Yi , Zhou Yu-Han , Yuan Si-Yue , Yang Meng-Mei , Xie Wen-Zhuan , Gao Chan , Chen Yao-Xu , Huang Meng-Li , Ye Cheng-Zhi , Chen Jing
Published: January 2022

Background

MAP2K1/2 genes are mutated in approximately 8% of melanoma patients; however, the impact of MAP2K1/2 gene alterations on the efficiency of immunotherapy has not been clarified. This study focused on the correlation between MAP2K1/2 gene mutations and the treatment response.

Methods

Six metastatic melanoma clinical cohorts treated with immune checkpoint inhibitors [anti-cytotoxic T lymphocyte antigen-4 (CTLA-4) or anti-programmed cell death-1 (PD-1)] were recruited in this study. RNA expression profiling results from each of these six cohorts and the Cancer Genome Atlas (TCGA) melanoma cohort were analysed to explore the mechanism related to immune activation.

Results

Compared to patients with wild-type MAP2K1/2, those with MAP2K1/2 mutations in an independent anti-CTLA-4-treated cohort had higher objective response rates, longer progression-free survival, and longer overall survival (OS). These findings were further validated in a pooled anti-CTLA-4-treated cohort in terms of the OS. However, there was no correlation between MAP2K1/2 mutations and OS in the anti-PD-1-treated cohort. Subgroup Cox regression analysis suggested that patients with MAP2K1/2 mutations received fewer benefits from anti-PD-1 monotherapy than from anti-CTLA-4 treatment. Furthermore, transcriptome profiling analysis revealed that melanoma tumours with MAP2K mutation was enriched in CD8+ T cells, B cells, and neutrophil cells, also expressed high levels of CD33 and IL10, implying a potential mechanism underlying the benefit of melanoma patients with MAP2K1/2 mutations from anti-CTLA-4 treatment.

Conclusions

MAP2K1/2 mutations were identified as an independent predictive factor for anti-CTLA-4 therapy in melanoma patients. Anti-CTLA-4 treatment might be more effective than anti-PD-1 therapy for patients with MAP2K1/2-mutated melanoma.
Optimization of Single-Dose VSV-Based COVID-19 Vaccination in Hamsters
Authors: O’Donnell Kyle L. , Clancy Chad S. , Griffin Amanda J. , Shifflett Kyle , Gourdine Tylisha , Thomas Tina , Long Carrie M. , Furuyama Wakako , Marzi Andrea
Published: January 2022

The ongoing COVID-19 pandemic has resulted in global effects on human health, economic stability, and social norms. The emergence of viral variants raises concerns about the efficacy of existing vaccines and highlights the continued need for the development of efficient, fast-acting, and cost-effective vaccines. Here, we demonstrate the immunogenicity and protective efficacy of two vesicular stomatitis virus (VSV)-based vaccines encoding the SARS-CoV-2 spike protein either alone (VSV-SARS2) or in combination with the Ebola virus glycoprotein (VSV-SARS2-EBOV). Intranasally vaccinated hamsters showed an early CD8+ T cell response in the lungs and a greater antigen-specific IgG response, while intramuscularly vaccinated hamsters had an early CD4+ T cell and NK cell response. Intranasal vaccination resulted in protection within 10 days with hamsters not showing clinical signs of pneumonia when challenged with three different SARS-CoV-2 variants. This data demonstrates that VSV-based vaccines are viable single-dose, fast-acting vaccine candidates that are protective from COVID-19.
Applications and Immunological Effects of Quantum Dots on Respiratory System
Authors: Ren Laibin , Wang Lingwei , Rehberg Markus , Stoeger Tobias , Zhang Jianglin , Chen Shanze
Published: January 2022

Quantum dots (QDs), are one kind of nanoscale semiconductor crystals with specific electronic and optical properties, offering near-infrared mission and chemically active surfaces. Increasing interest for QDs exists in developing theranostics platforms for bioapplications such as imaging, drug delivery and therapy. Here we summarized QDs’ biomedical applications, toxicity, and immunological effects on the respiratory system. Bioapplications of QDs in lung include biomedical imaging, drug delivery, bio-sensing or diagnosis and therapy. Generically, toxic effects of nanoparticles are related to the generation of oxidative stresses with subsequent DNA damage and decreased lung cells viability in vitro and in vivo because of release of toxic metal ions or the features of QDs like its surface charge. Lastly, pulmonary immunological effects of QDs mainly include proinflammatory cytokines release and recruiting innate leukocytes or adaptive T cells.
The Role of m6A Epigenetic Modification in the Treatment of Colorectal Cancer Immune Checkpoint Inhibitors
Authors: Tong Huan , Wei He , Smith Alhaji Osman , Huang Juan
Published: January 2022

Tumor immunotherapy, one of the efficient therapies in cancers, has been called to the scientific community’s increasing attention lately. Among them, immune checkpoint inhibitors, providing entirely new modalities to treat cancer by leveraging the patient’s immune system. They are first-line treatments for varieties of advanced malignancy, such as melanoma, gastrointestinal tumor, esophageal cancer. Although immune checkpoint inhibitors (ICIs) treatment has been successful in different cancers, drug resistance and relapses are common, such as in colorectal cancer. Therefore, it is necessary to improve the efficacy of immune checkpoint therapy for cancer patients who do not respond or lowly response to current treatments. N6-methyladenosine (m6A), as a critical regulator of transcript expression, is the most frequently internal modification of mRNA in the human body. Recently, it has been proposed that m6A epigenetic modification is a potential driver of tumor drug resistance. In this report, we will briefly outline the relevant mechanisms, general treatment status of immune checkpoint inhibitors in colorectal cancer, how m6A epigenetic modifications regulate the response of ICIs in CRC and provide new strategies for overcoming the resistance of ICIs in CRC.
PTRF/Cavin-1 as a Novel RNA-Binding Protein Expedites the NF-κB/PD-L1 Axis by Stabilizing lncRNA NEAT1, Contributing to Tumorigenesis and Immune Evasion in Glioblastoma
Authors: Yi Kaikai , Cui Xiaoteng , Liu Xing , Wang Yunfei , Zhao Jixing , Yang Shixue , Xu Can , Yang Eryan , Xiao Menglin , Hong Biao , Fang Chuan , Kang Chunsheng , Tan Yanli , Wang Qixue
Published: January 2022

Background

Immunotherapy, especially checkpoint inhibitors targeting PD-1 or PD-L1, has revolutionized cancer therapy. However, PD-1/PD-L1 inhibitors have not been investigated thoroughly in glioblastoma (GBM). Studies have shown that polymerase 1 and transcript release factor (PTRF/Cavin-1) has an immune-suppressive function in GBM. Thus, the relationship between PTRF and PD-L1 and their role in immune suppression requires further investigation in GBM.

Methods

We used public databases and bioinformatics analysis to investigate the relationship between PTRF and PD-L1. We next confirmed the predicted relationship between PTRF and PD-L1 in primary GBM cell lines by using different experimental approaches. RIP-Seq, RIP, ChIP, and qRT-PCR were conducted to explore the molecular mechanism of PTRF in immunosuppression.

Results

We found that PTRF stabilizes lncRNA NEAT1 to induce NF-κB and PD-L1 and promotes immune evasion in GBM. PTRF was found to correlate with immunosuppression in the public GBM databases. PTRF increased the level of PD-L1 in primary cell lines from GBM patients. We carried out RIP-Seq of GBM cells and found that PTRF interacts with lncRNA NEAT1 and stabilizes its mRNA. PTRF also promoted the activity of NF-κB by suppressing UBXN1 expression via NEAT1 and enhanced the transcription of PD-L1 through NF-κB activation. Finally, PTRF promoted immune evasion in GBM cells by regulating PD-1 binding and PD-L1 mediated T cell cytotoxicity.

Conclusions

In summary, our study identified the PTRF-NEAT1-PD-L1 axis as a novel immune therapeutic target in GBM.
Distribution of Coomassie Blue Stainable Particles in the Pearl River Estuary, China, Insight Into the Nitrogen Cycling in Estuarine System
Authors: Sun Cui-Ci , Yue Wei-Zhong , Wang You-Shao , He Wei-Hong , Hong Yi-Guo , Sun Fu-Lin , Cheng Hao , Wu Mei-Lin , Jiang Zhao-Yu , Jiao Fei , Wang Yu-Tu
Published: January 2022

Distributions of Coomassie Blue stainable particles (CSP), the sources and transports, as well as their implications for nitrogen biogeochemical cycles in the Pearl River estuary (PRE) were investigated during two cruises in August 2016 and January 2017. CSPcolor concentrations (CSP concentration determined spectrophotometrically) were 73.7–685.3 μg BSA eq L–1 [μg Bovine serum albumin (BSA) equivalent liter–1] in August 2016 and 100.6–396.4 μg BSA eq L–1 in January 2017, respectively. CSP concentrations were high in low-salinity waters (<5), and declined from the river to the middle estuary by 80% in the wet season and 55.6% in the dry season, respectively, then increased again in the lower estuary due to high primary production. CSP concentrations were mainly associated with chlorophyll a (Chl a) concentration except for the turbid mixing zone, suggesting that autochthonous phytoplankton production served as the primary source of CSP in the PRE. The concentrations of nitrogen (N) as CSP in the PRE were comparable to the nitrogen content of particulate hydrolysable amino acids (PHAA). Pictures of CSP taken by microscopy and the correlation between composition of PHAA and the ratio of Chl a/CSPcolor showed that CSP were relatively degraded due to delivery of old terrestrial protein to river section and extensive microbial degradation during mixing at the upper and middle parts of the estuary, whereas CSP in lower estuary appeared to be more labile due to higher fresh algal production. The contribution of CSP nitrogen (CSP-N) to the particulate nitrogen (PN) pool was 34.98% in summer and 30.8% in winter. The conservative estimate of CSP-N input flux in the Pearl River Delta was about 6 × 106 mol N d–1. These results suggested that CSP was a significant pool of organic nitrogen in the PRE. The study of CSP composition in terms of nitrogen provides new insight into the roles of CSP on nitrogen biogeochemical processes in the turbid and productive estuarine system.
Spatial Distribution, Diversity, and Activity of Microbial Phototrophs in the Baltic Sea
Authors: Xu Peihang , Reeder Christian Furbo , Löscher Carolin Regina
Published: January 2022

Microbial plankton is essential for ocean biogeochemistry. As part of the prokaryotic phototrophic microbial community, both oxygenic phototrophs (OP) and anoxygenic phototrophs (AP) are widely distributed in the ocean and may play a significant role in carbon flow and oxygen production. However, comparative studies of microbial OP and AP have received very little attention, even though their different roles might be important in various marine environments, especially in oxygen minimum zones (OMZ). We explored the spatial distribution of the microbial community in the Baltic Sea, including an OMZ region, with a particular focus on the distribution and activity of OP and AP. We used 16S rRNA amplicon sequencing in combination with a qPCR-based quantification of photosynthesis marker genes. We found that specific bacterial groups dominated surface and intermediate depths, the OMZ, and deep waters, respectively. Salinity, temperature, oxygen, and depth were significant factors explaining the microbial community composition and distribution. A high diversity of OP and AP was observed, including OP-Chlorophyta, Diatoms, Cyanobacteria and Cryptomonads, and AP-Proteobacteria and Chloroflexota. OP were more abundant at most stations compared to AP. OP showed high photosynthetic activity and more photosynthesis activity in higher temperature and upper waters, while AP photosynthesis cannot be detected in most stations. Both, cyanobacterial and eukaryotic OP preferred to live in higher temperature and upper waters, but Cyanobacteria also preferred to live in oxic water while the whole OP community showed preference to live in higher salinity area. However, AP did not show any significant hydrochemical preference but prefer to live with OP community. The Baltic Sea is exposed to multiple climate change related stressors, such as warming, decreasing salinity, and deoxygenation. This study contributes to understanding and interpretation of how microbial community, especially phototrophic groups, might shift in their distribution and activity in a changing ocean like the Baltic Sea.
Coastal Erosion Vulnerability in Mainland China Based on Fuzzy Evaluation of Cloud Models
Authors: Cao Chao , Cai Feng , Qi Hongshuai , Liu Jianhui , Lei Gang , Zhu Kai , Mao Zijian
Published: January 2022

Global climate change-induced sea-level rise and storm wave intensification, along with the large population densities and high-intensity human development activities in coastal areas, have caused serious burden and damage to China’s coasts, led to the rapid growth of artificial shorelines development, and formed a “new Great Wall” of reinforced concrete against the laws of nature. After the last ice age, transgression formed the different features of China’s coast. Depending on the types of geological and landform features, coasts are divided into 36 evaluation units, and 10 indicators are selected from natural aspects (including tectonics, geomorphology, sediment, and storms) and aspects of social economy (population, GDP, Gross Domestic Product), and cloud model theory is used to build a coastal erosion vulnerability evaluation index system in China. The results show that high grade (V), high-middle grade (IV), middle grade (III), low-middle grade (II), and low grade (I) coastal erosion vulnerability degrees account for 5.56, 13.89, 41.67, 33.33, and 5.56% of the Chinese coastlines, respectively. The coastal erosion vulnerability of the subsidence zone is significantly higher than that of the uplift zone. Reverse cloud model and analytic hierarchy process calculation show that the main factors that control coastal erosion vulnerability since the transgression after the last ice age are geological structure, topography and lithological features, and in recent years, the decrease in sea sediment loads and increase in reclamation engineering. Mainland China must live with the basic situation of coastal erosion, and this study shows that the index system and method of cloud modeling are suitable for the evaluation of the coastal erosion vulnerability of the Chinese mainland. This study provides a scientific basis for the adaptive management of coastal erosion, coastal disaster assessment and the overall planning of land and sea.
Feasibility Study on Biomonitoring of Microplastics in Fish Gastrointestinal Tracts
Authors: De Witte Bavo , Catarino Ana I. , Vandecasteele Loes , Dekimpe Michael , Meyers Nelle , Deloof Daphné , Pint Steven , Hostens Kris , Everaert Gert , Torreele Els
Published: January 2022

Monitoring the occurrence and trends of microplastic contamination in the marine environment is key to establish microplastic (MP) data baselines, to work out policy mitigation measures, and to assess the effectiveness of waste regulations. To establish MP contamination baselines in the marine environment, marine biota species can be selected as monitoring matrices to track plastic pollution in the environment. The aim of this work was to evaluate the feasibility of biomonitoring MPs in fish gastrointestinal tract (GIT). A selection of suitable fish species was performed, based on species distribution, sampling effort, commercial value of species, sustainable development of fish populations, migration behaviour, and scientific evidence for occurrence of MPs in the fish GIT. Sampling and MP extraction protocols were developed and validated on fish GIT samples acquired in the Southern North Sea. The fish species selection protocol enabled the selection of ubiquitous distributed and non-endangered fish species relevant for MP monitoring in the North Sea. The fish GIT sampling protocol considered background contamination measures and sampling fillet as procedural blanks. Advantages and disadvantages of onboard dissection were discussed. The MPs extraction protocol was based on matrix digestion, density separation, and Nile red staining of particles followed by fluorescent microscopy observation. The confirmation of MPs identification and the analysis of the polymer composition was done using micro-Fourier transform infrared (μFTIR) spectroscopy. The MP analysis indicated a low number of MPs in the fish GIT. The mean number of particles per single fish GIT was 0.48 ± 0.81 (Nile red staining observations) to 0.26 ± 0.64 (corrected for background contamination). A power analysis (sampling effort) indicated that to detect significant differences, in a balanced-ANOVA type of analysis, between species and/or sampling areas, the sample size would require a minimum of 109 up to 370 individual fish. The feasibility of MP biomonitoring in fish GIT was assessed by a SWOT-analysis, which indicated that fish GIT is a suitable matrix for biomonitoring of MPs, but that the large number of samples needed to identify significant differences can be a major drawback. A potential implementation strategy for MP biomonitoring within Europe was suggested.
Inactivation Kinetics of Coxiella burnetii During High-Temperature Short-Time Pasteurization of Milk
Authors: Wittwer Marcel , Hammer Philipp , Runge Martin , Valentin-Weigand Peter , Neubauer Heinrich , Henning Klaus , Mertens-Scholz Katja
Published: January 2022

The Gram-negative, obligate intracellular bacterium Coxiella burnetii is the causative organism of the zoonosis Q fever and is known for its resistance toward various intra- and extracellular stressors. Infected ruminants such as cattle, sheep, and goats can shed the pathogen in their milk. Pasteurization of raw milk was introduced for the inactivation of C. burnetii and other milk-borne pathogens. Legal regulations for the pasteurization of milk are mostly based on recommendations of the Codex Alimentarius. As described there, C. burnetii is considered as the most heat-resistant non-spore-forming bacterial pathogen in milk and has to be reduced by at least 5 log10-steps during the pasteurization process. However, the corresponding inactivation data for C. burnetii originate from experiments performed more than 60 years ago. Recent scientific findings and the technological progress of modern pasteurization equipment indicate that C. burnetii is potentially more effectively inactivated during pasteurization than demanded in the Codex Alimentarius. In the present study, ultra-high heat-treated milk was inoculated with different C. burnetii field isolates and subsequently heat-treated in a pilot-plant pasteurizer. Kinetic inactivation data in terms of D- and z-values were determined and used for the calculation of heat-dependent log reduction. With regard to the mandatory 5 log10-step reduction of the pathogen, the efficacy of the established heat treatment regime was confirmed, and, in addition, a reduction of the pasteurization temperature seems feasible.
Eukaryotic Parasites Are Integral to a Productive Microbial Food Web in Oxygen-Depleted Waters
Authors: Suter Elizabeth A. , Pachiadaki Maria , Taylor Gordon T. , Edgcomb Virginia P.
Published: January 2022

Oxygen-depleted water columns (ODWCs) host a diverse community of eukaryotic protists that change dramatically in composition over the oxic-anoxic gradient. In the permanently anoxic Cariaco Basin, peaks in eukaryotic diversity occurred in layers where dark microbial activity (chemoautotrophy and heterotrophy) were highest, suggesting a link between prokaryotic activity and trophic associations with protists. Using 18S rRNA gene sequencing, parasites and especially the obligate parasitic clade, Syndiniales, appear to be particularly abundant, suggesting parasitism is an important, but overlooked interaction in ODWC food webs. Syndiniales were also associated with certain prokaryotic groups that are often found in ODWCs, including Marinimicrobia and Marine Group II archaea, evocative of feedbacks between parasitic infection events, release of organic matter, and prokaryotic assimilative activity. In a network analysis that included all three domains of life, bacterial and archaeal taxa were putative bottleneck and hub species, while a large proportion of edges were connected to eukaryotic nodes. Inclusion of parasites resulted in a more complex network with longer path lengths between members. Together, these results suggest that protists, and especially protistan parasites, play an important role in maintaining microbial food web complexity, particularly in ODWCs, where protist diversity and microbial productivity are high, but energy resources are limited relative to euphotic waters.
Temperature-Regulated IncX3 Plasmid Characteristics and the Role of Plasmid-Encoded H-NS in Thermoregulation
Authors: Baomo Liu , Lili Shui , Moran Robert A. , van Schaik Willem , Chao Zhuo
Published: January 2022

Carbapenem-resistant Enterobacteriaceae (CRE) are a critical public health problem worldwide. Globally, IncX3-type plasmids have emerged as the predominant vehicles carrying the metallo-β-lactamase gene blaNDM. Although blaNDM-bearing IncX3 plasmids have been found in various hosts from diverse environments, whether their transfer and persistence properties vary under different conditions and what factors influence any variation is unknown. By observing the effects of different temperatures on IncX3 plasmid conjugation rates, stability, and effects on host fitness in Escherichia coli, we demonstrate that temperature is an important determinant of plasmid phenotypes. The IncX3 plasmid pGZIncX3 transferred at highest frequencies, was most stable and imposed lower fitness costs at 37°C. Temperature-regulated variation in pGZIncX3 properties involved a thermoregulated plasmid-encoded H-NS-like protein, which was produced at higher levels at 30°C and 42°C and inhibited the expression of type IV secretion system genes involved in conjugation. These findings suggest that blaNDM-bearing IncX3 plasmids are adapted to carriage by enterobacteria that colonize mammalian hosts and could explain the rapid dissemination of these plasmids among human-associated species, particularly in hospital settings.
Analysis of Endophytic Bacterial Diversity From Different Dendrobium Stems and Discovery of an Endophyte Produced Dendrobine-Type Sesquiterpenoid Alkaloids
Authors: Wang Shan-Shan , Liu Jia-Meng , Sun Jing , Huang Ya-Tao , Jin Nuo , Li Min-Min , Liang Yan-Tian , Fan Bei , Wang Feng-Zhong
Published: January 2022

As the unique component of Dendrobium, dendrobine-type sesquiterpenoid alkaloids (DSAs) possess a variety of medicinal properties. It has been well documented that plant endophytes can in vitro synthesize secondary metabolites identical or similar to metabolites produced by their host plants. This study aimed to investigate the composition and distribution of endophytic bacteria of Dendrobium stems by Illumina MiSeq platform sequencing and cultivation-dependent methods and then to assess the potential for endophytic bacteria to produce DSAs. Results indicated that it was necessary to combine both cultivation-dependent and cultivation-independent methods to analyze the community structure of endophytic bacterial in plants comprehensively. The length of the Dendrobium stems influenced the endophytic bacterial community. The diversity and richness of endophytic bacteria in group J10_15cm of stems were the highest, which showed a significant difference from the other stem groups. However, there was no certain connection between the diversity and richness of endophytic bacteria and the content of dendrobine. It was most likely due to the influence of several specific endophytic bacteria genera, such as Sphingomonas and Rhodococcus. Athelia rolfsii, Myrothecium roridum, as pathogenic fungi, and Pectobacterium carotovorum subsp. actinidiae, as pathogenic bacteria of Dendrobium, were used to determine the antimicrobial activities. In these assays, six strains belonging to five genera showed antimicrobial activity against at least two phytopathogens. The strain BL-YJ10_15-29 (Paracoccus pueri THG-N2.35, 98.98%) showed the best antimicrobial activity against the three phytopathogens. In addition, 2 DSAs (6-hydroxydendrobine and nobilonine) were identified in the fermentation supernatant of the strain CM-YJ10_15-44 (Pseudomonas protegens CHA0, 99.24%), whereas the whole-genome analysis results further demonstrated that the precursors of the two DSAs [geranyl-PP and (E, E)-famesyl-PP] were synthesized mainly through the methyl-D-erythritol 4-phosphate pathway in this strain. This study provides new insight into the studies on the biosynthesis of DSAs and provides potential biocontrol bacteria.
The Depth-Depended Fungal Diversity and Non-depth-Depended Aroma Profiles of Pit Mud for Strong-Flavor Baijiu
Authors: Cai Wenchao , Xue Yu’ang , Tang Fengxian , Wang Yurong , Yang Shaoyong , Liu Wenhui , Hou Qiangchuan , Yang Xinquan , Guo Zhuang , Shan Chunhui
Published: January 2022

Microorganisms in pit mud are the essential factor determining the style of strong flavor Baijiu. The spatial distribution characteristics of fungal communities and aroma in the pit mud for strong flavor Baijiu from Xinjiang, China, were investigated using Illumina MiSeq high-throughput sequencing and electronic nose technology. A total of 138 fungal genera affiliated with 10 fungal phyla were identified from 27 pit mud samples; of these, Saccharomycopsis, Aspergillus, and Apiotrichum were the core fungal communities, and Aspergillus and Apiotrichum were the hubs that maintain the structural stability of fungal communities in pit mud. The fungal richness and diversity, as well as aroma of pit mud, showed no significant spatial heterogeneity, but divergences in pit mud at different depths were mainly in pH, total acid, and high abundance fungi. Moisture, NH4+, and lactate were the main physicochemical factors involved in the maintenance of fungal stability and quality in pit mud, whereas pH had only a weak effect on fungi in pit mud. In addition, the fungal communities of pit mud were not significantly associated with the aroma. The results of this study provide a foundation for exploring the functional microorganisms and dissecting the brewing mechanism of strong flavor Baijiu in Xinjiang, and also contributes to the improvement of pit mud quality by bioaugmentation and controlling environmental physicochemical factors.
Adaptation to Endoplasmic Reticulum Stress in Candida albicans Relies on the Activity of the Hog1 Mitogen-Activated Protein Kinase
Authors: Husain Farha , Pathak Prerna , Román Elvira , Pla Jesús , Panwar Sneh Lata
Published: January 2022

Adaptation to ER stress is linked to the pathogenicity of C. albicans. The fungus responds to ER stress primarily by activating the conserved Ire1-Hac1-dependent unfolded protein response (UPR) pathway. Subsequently, when ER homeostasis is re-established, the UPR is attenuated in a timely manner, a facet that is unexplored in C. albicans. Here, we show that C. albicans licenses the HOG (high-osmolarity glycerol) MAPK pathway for abating ER stress as evidenced by activation and translocation of Hog1 to the nucleus during tunicamycin-induced ER stress. We find that, once activated, Hog1 attenuates the activity of Ire1-dependent UPR, thus facilitating adaptation to ER stress. We use the previously established assay, where the disappearance of the UPR-induced spliced HAC1 mRNA correlates with the re-establishment of ER homeostasis, to investigate attenuation of the UPR in C. albicans. hog1Δ/Δ cells retain spliced HAC1 mRNA levels for longer duration reflecting the delay in attenuating Ire1-dependent UPR. Conversely, compromising the expression of Ire1 (ire1 DX mutant strain) results in diminished levels of phosphorylated Hog1, restating the cross-talk between Ire1 and HOG pathways. Phosphorylation signal to Hog1 MAP kinase is relayed through Ssk1 in response to ER stress as inactivation of Ssk1 abrogates Hog1 phosphorylation in C. albicans. Additionally, Hog1 depends on its cytosolic as well as nuclear activity for mediating ER stress-specific responses in the fungus. Our results show that HOG pathway serves as a point of cross-talk with the UPR pathway, thus extending the role of this signaling pathway in promoting adaptation to ER stress in C. albicans. Additionally, this study integrates this MAPK pathway into the little known frame of ER stress adaptation pathways in C. albicans.
Proteomics Analysis of Exosomes From Patients With Active Tuberculosis Reveals Infection Profiles and Potential Biomarkers
Authors: Zhang Min , Xie Yiping , Li Shasha , Ye Xiaojian , Jiang Yibiao , Tang Lijun , Wang Jianjun
Published: January 2022

Although mycobacterial proteins in exosomes from peripheral serum of patients with tuberculosis (TB) have been identified, other exact compositions of exosomes remain unknown. In the present study, a comprehensive proteomics analysis of serum exosomes derived from patients with active TB (ATB) was performed. Exosomes from patients with ATB were characterized using nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), and western blotting analysis. Then identified protein components were quantified by label-free proteomics and were determined via bioinformatics analysis. A total of 123 differential proteins were identified in ATB serum exosomes and analyzed with Gene Ontology (GO) analysis. Among these proteins heat shock protein70 (HSP70), CD81, major histocompatibility complex-I (MHC-I ) and tumor susceptibility gene101 (TSG101) were present in exosomes of ATB and normal individuals confirmed via western blotting. In addition, among identified exosomal proteins lipopolysaccharide binding protein (LBP) increased significantly, but CD36 and MHC-I decreased significantly in ATB exosomes. Meanwhile, MHC-I was down-expressed in serum and peripheral blood mononuclear cells (PBMCs) of ATB, but interestingly CD36 was down-regulated in serum and up-expressed in PBMCs of ATB patients validated with ELISA and flow cytometry. CD36 was up-regulated by M. tuberculosis H37Ra infection in macrophages and suppressed in exosomes from H37Ra infected macrophages detected by western blotting. This study provided a comprehensive description of the exosome proteome in the serum of patients with ATB and revealed certain potential biomarkers associated with TB infection.
Establishment and Evaluation of a Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Pseudomonas fluorescens in Raw Milk
Authors: Bu Yushan , Qiao Wenjun , Zhai Zhengyuan , Liu Tongjie , Gong Pimin , Zhang Lanwei , Hao Yanling , Yi Huaxi
Published: January 2022

Raw milk is susceptible to microbial contamination during transportation and storage. Pseudomonas fluorescens producing heat-resistant enzymes have become the most common and harmful psychrophilic microorganisms in the cold chain logistics of raw milk. To rapidly detect P. fluorescens in raw milk, the protease gene aprX was selected as a detection target to construct a set of primers with strong specificity, and a loop-mediated isothermal amplification (LAMP) assay was established. The detection thresholds of the LAMP assay for pure cultured P. fluorescens and pasteurized milk were 2.57 × 102 and 3 × 102 CFU/mL, respectively. It had the advantages over conventional method of low detection threshold, strong specificity, rapid detection, and simple operation. This LAMP assay can be used for online monitoring and on-site detection of P. fluorescens in raw milk to guarantee the quality and safety of dairy products.
Surveillance, Epidemiology and Impact of EV-A71 Vaccination on Hand, Foot, and Mouth Disease in Nanchang, China, 2010–2019
Authors: He Fenglan , Rui Jia , Deng Zhiqiang , Zhang Yanxia , Qian Ke , Zhu Chunhui , Yu Shanshan , Tu Junling , Xia Wen , Zhu Qingxiong , Chen Shengen , Chen Tianmu , Zhou Xianfeng
Published: January 2022

After the first national-scale outbreak of Hand, foot, and mouth disease (HFMD) in China, a national surveillance network was established. Here we described the epidemiology and pathogenic profile of HFMD and the impact of EV-A71 vaccination on pathogen spectrum of enteroviruses in the southeastern Chinese city of Nanchang during 2010–2019. A total of 7,951 HFMD cases from sentinel hospitals were included, of which 4,800 EV-positive cases (60.4%) were identified by real-time RT-PCR. During 2010–2012, enterovirus 71 (EV-A71) was the main causative agent of HFMD, causing 63.1% of cases, followed by 19.3% cases associated with coxsackievirus A16 (CV-A16). Since 2013, the proportion of other enteroviruses has increased dramatically, with the sub genotype D3 strain of Coxsackievirus A6 (CV-A6) replacing the dominance of EV-A71. These genetically diverse native strains of CV-A6 have co-transmitted and co-evolved in Nanchang. Unlike EV-A71 and CV-A16, most CV-A6 infections were concentrated in autumn and winter. The incidence of EV-A71 infection negatively correlated with EV-A71 vaccination (r = −0.990, p = 0.01). And severe cases sharply declined as the promotion of EV-A71 vaccines. After 2-year implementation of EV-A71 vaccination, EV-A71 is no longer detected from the reported HFMD cases in Nanchang. In conclusion, EV-A71 vaccination changed the pattern of HFMD epidemic, and CV-A6 replaced the dominance of EV-A71 over time.
Critical Role of Astrocytic Polyamine and GABA Metabolism in Epileptogenesis
Authors: Kovács Zsolt , Skatchkov Serguei N. , Veh Rüdiger W. , Szabó Zsolt , Németh Krisztina , Szabó Pál T. , Kardos Julianna , Héja László
Published: January 2022

Accumulating evidence indicate that astrocytes are essential players of the excitatory and inhibitory signaling during normal and epileptiform activity via uptake and release of gliotransmitters, ions, and other substances. Polyamines can be regarded as gliotransmitters since they are almost exclusively stored in astrocytes and can be released by various mechanisms. The polyamine putrescine (PUT) is utilized to synthesize GABA, which can also be released from astrocytes and provide tonic inhibition on neurons. The polyamine spermine (SPM), synthesized form PUT through spermidine (SPD), is known to unblock astrocytic Cx43 gap junction channels and therefore facilitate astrocytic synchronization. In addition, SPM released from astrocytes may also modulate neuronal NMDA, AMPA, and kainate receptors. As a consequence, astrocytic polyamines possess the capability to significantly modulate epileptiform activity. In this study, we investigated different steps in polyamine metabolism and coupled GABA release to assess their potential to control seizure generation and maintenance in two different epilepsy models: the low-[Mg2+] model of temporal lobe epilepsy in vitro and in the WAG/Rij rat model of absence epilepsy in vivo. We show that SPM is a gliotransmitter that is released from astrocytes and significantly contributes to network excitation. Importantly, we found that inhibition of SPD synthesis completely prevented seizure generation in WAG/Rij rats. We hypothesize that this antiepileptic effect is attributed to the subsequent enhancement of PUT to GABA conversion in astrocytes, leading to GABA release through GAT-2/3 transporters. This interpretation is supported by the observation that antiepileptic potential of the Food and Drug Administration (FDA)-approved drug levetiracetam can be diminished by specifically blocking astrocytic GAT-2/3 with SNAP-5114, suggesting that levetiracetam exerts its effect by increasing surface expression of GAT-2/3. Our findings conclusively suggest that the major pathway through which astrocytic polyamines contribute to epileptiform activity is the production of GABA. Modulation of astrocytic polyamine levels, therefore, may serve for a more effective antiepileptic drug development in the future.
Admission Lower Serum Phosphate Ion Levels Predict Acute Hydrocephalus of Aneurysmal Subarachnoid Hemorrhage
Authors: Zhang Yibin , Zheng Shufa , Wang Haojie , Chen Guogong , Li Chunwang , Lin Yuanxiang , Yao Peisen , Kang Dezhi
Published: January 2022

Introduction: The relationship between serum phosphate ion (sPi) and the occurrence of acute hydrocephalus (aHCP) in aneurysmal subarachnoid hemorrhage (aSAH) remains largely unknown and controversial. The primary aim of this study was to investigate the association between sPi on admission and aHCP following aSAH.

Methods: The study included 635 patients over the age of 19 years diagnosed with aSAH in our institution from September 2012 to June 2018. Data on clinical characteristics, laboratory parameters, treatments, and outcomes were collected and analyzed. The association between lower sPi levels and aHCP was assessed in univariate and multivariate analyses. Propensity-score matching (PSM) analysis was performed to reduce significant differences in baseline characteristics between the aHCP group and non-HCP group.

Results: The overall incidence of aHCP following aSAH was 19.37% (123/512). Lower sPi levels were detected in patients with aHCP compared with those without [0.86 (0.67–1.06) vs. 1.04 (0.84–1.21) mmol/L] in the univariate analysis. In the multivariate analysis, lower sPi level, high modified Fisher (mFisher) grade, and high Hunt-Hess grade were associated with aHCP [odds ratios (OR) 1.729, 95% confidence interval (CI) 1.139–2.623, p = 0.01; mFisher OR 0.097,95% CI 0.055–0.172, p < 0.001; Hunt-Hess, OR 0.555, 95% CI 0.320–0.961, P = 0.036]. After PSM, the matched aHCP group had a significantly lower sPi level than the matched non-aHCP group [0.86 (0.67–1.06) vs. 0.94 (0.76–1.12) mmol/L, p = 0.044]. The area under the curve (AUC) of the sPi level and the logistic regression model based on these predictors (sPi, Hunt-Hess grade, and mFisher grade) was 0.667 and 0.840 (sensitivity of 88.6% and specificity of 68.4%) for predicting aHCP, respectively.

Conclusions: Lower sPi levels predict the occurrence of aHCP, and the model constructed by sPi levels, Hunt-Hess grade, and mFisher grade markedly enhances the prediction of aHCP after aSAH.