bluuebunny/crossref_metadata_2025 huggingface dataset:
Preventive effect of probiotics supplementation on occurrence of gestational diabetes mellitus: A systematic review and meta-analysis of randomized controlled trials
Authors: Pakmehr Azin , Ejtahed Hanieh-Sadat , Shirzad Nooshin , Hemmatabadi Mahboobeh , Farhat Sara , Larijani Bagher
Published: December 2022

Background

Gestational diabetes mellitus (GDM) is a health challenge during pregnancy and is associated with adverse effects. Dysbiosis of the gut microbiota may play a role in developing inflammation and insulin resistance observed in GDM. Probiotics are supposed to be influential in preventing GDM since they can alter the composition of microbiota in the intestine. Despite the existing studies on the therapeutic effects of probiotics in women with GDM, in this study we aim to systematically review and meta-analyze the results of randomized control trials (RCTs) on the beneficial effects of probiotics supplements on the prevention of GDM in healthy pregnant women.

Methods

Web of science, Scopus and PubMed databases were searched via a precise strategy to gather RCTs related to our study. Duplication removal, screening and data extraction were conducted by two researchers, independently. Quality assessment of eligible studies was conducted by Cochrane risk of bias tool. Meta-analysis was conducted using the random effects model due to substantial heterogeneity among studies.

Results

Ten articles met our eligibility criteria from our initial search of 451 articles. Two thousand nine hundred and twenty-one participants without previously diagnosed glucose disturbance were included in our analysis. Probiotics reduced GDM incidence by 33% (RR = 0.67, 95% CI: 0.47, 0.95), while greater effect was detected in trials using multiple-strains probiotics (RR = 0.65, 95% CI: 0.42, 0.99). We did not detect any significant benefits or harms related to probiotics supplements on secondary outcomes including GDM related infantile and maternal complications including preeclampsia, caesarian section, mothers' weight gain during pregnancy, prematurity, macrosomia, hypoglycemia, NICU admission, and birth weight.

Conclusion

Probiotics supplementation may reduce the incidence of GDM and help control glucose parameters in pregnant women. Further studies are warranted regarding the GDM-related maternal and infantile complications.

Systematic review registration

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022315550, identifier: CRD42022315550.
Analysis of the timing of endoscopic treatment for esophagogastric variceal bleeding in cirrhosis
Authors: Wu Kaini , Fu Yunfeng , Guo Zixiang , Zhou Xiaodong
Published: December 2022

Background

Existing guidelines recommend endoscopic treatment within 12 h or 12–24 h for patients with esophagogastric variceal bleeding (EGVB) in cirrhosis. In addition, research findings on the optimal time for endoscopy are inconsistent.

Aim

The aim of this study was to investigate the relationship between the timing of endoscopy and clinical outcomes in cirrhotic patients with EGVB and to analyze the risk factors for the composite outcomes after endoscopic treatment.

Methods

From January 2019 to June 2020, 456 patients with cirrhotic EGVB who underwent endoscopy were matched by a 1:1 propensity score. Finally, 266 patients were divided into two groups, including 133 patients within 12 h (urgent endoscopy group) of admission and after 12 h (non-urgent endoscopy group). Baseline data and clinical outcomes were compared. Logistic regression model analysis was used to determine risk factors for 30 days rebleeding and mortality.

Results

In 266 patients, the overall 30 days rebleeding rate and mortality were 10.9% (n = 29) and 3.4% (n = 9), respectively. Patients who underwent endoscopic treatment within 12 h had significantly higher 30 days rebleeding outcomes than those who underwent treatment beyond 12 h (15 vs. 6.8%, p = 0.003). However, 30 days mortality did not differ significantly between the two groups (3 vs. 3.8%, p = 0.736). Logistic regression analysis showed that age and shock on admission were independent risk factors for the composite outcome of 30 days rebleeding and mortality in patients with EGVB.

Conclusion

The 30 days rebleeding rate in patients with cirrhotic EGVB treated with urgent endoscopy was significantly higher than that in patients treated with non-urgent endoscopy, but there was no significant difference in 30 days mortality.
Bibliometric analysis and visualization of literature on assisted reproduction technology
Authors: Meng Fanchao , Deng Sheng , Wang Lu , Zhou Yumei , Zhao Mengjie , Li Haibin , Liu Dong , Gao Guojing , Liao Xiaoxing , Wang Jisheng
Published: December 2022

Introduction

Assisted reproductive technology (ART) is a method that uses various techniques to process sperm or ova. Assisted reproductive technology involves removing ova from a woman's ovaries, combining them with sperm in the laboratory, and returning them to the woman's body or donating them to another woman.

Methods

Based on the web of science core collection database, we firstly analyzed the quantity and quality of publications in the field of ART, secondly profiled the publishing groups in terms of country, institution, author's publication and cooperation network, and finally sorted out and summarized the hot topics of research.

Results

In total, 6,288 articles on ART were published between 2001 and 2022 in 1,013 journals. Most of these published articles represent the global research status, potential hotspots and future research directions. Publications and citations of research on assisted reproductive technology have steadily increased over the past few decades. Academic institutions in Europe and the United States have been leading in assisted reproductive technology research. The countries, institutions, journals, and authors with the most published articles were the United States (1864), Harvard Univ (108), Fertility and Sterility (819), and Stern, Judy E. (64). The most commonly used keywords are Assisted reproductive technology (3303) and in-vitro Fertilization (2139), Ivf (1140), Pregnancy (1140), Women (769), Intracytoplasmic Sperm injection (644), In Fertilization (632), Risk (545), and Outcome (423).

Conclusion

Frozen embryo transfer, intracytoplasmic sperm injection, and in vitro fertilization are the main research topics and hotspots in the field of assisted reproductive technology.
Case report: Acute oxalate nephropathy due to traditional medicinal herbs
Authors: Wang Lirui , Zhu Zhuxian , Li Jiangtao
Published: December 2022

Acute oxalate nephropathy (AON), defined as the association between acute kidney injury (AKI) and the deposition of oxalate crystals in the renal parenchyma, is a rare complication of hyperoxaluria. We report a rare case of AON in an adult due to medicinal herbs intake leading to crystal-induced AKI. We recommend that a thorough medication history including the use of medicinal herbs, should be obtained for all patients with a rapid loss of kidney function, especially in the absence of known risk factors for AKI. The use of medicinal herbs with unknown oxalate contents would increase the risk of AON and should be avoided.
Comparing the infection biology and gene expression differences of Plasmodiophora brassicae primary and secondary zoospores
Authors: Yang Hui , Sun Qianyu , Zhang Yihan , Zhang Yang , Zhao Yushan , Wang Xinyue , Chen Yanmei , Yuan Shu , Du Junbo , Wang Wenming
Published: December 2022

Plasmodiophora brassicae (Wor.) is an obligate plant pathogen affecting Brassicae worldwide. To date, there is very little information available on the biology and molecular basis of P. brassicae primary and secondary zoospore infections. To examine their roles, we used microscope to systematically investigate the infection differences of P. brassicae between samples inoculated separately with resting spores and secondary zoospores. The obvious development of P. brassicae asynchrony that is characterized by secondary plasmodium, resting sporangial plasmodium, and resting spores was observed at 12 days in Brassica rapa inoculated with resting spores but not when inoculated with secondary zoospores at the same time. Inoculation with resting spores resulted in much more development of zoosporangia clusters than inoculation with secondary zoospores in non-host Spinacia oleracea. The results indicated that primary zoospore infection played an important role in the subsequent development. To improve our understanding of the infection mechanisms, RNA-seq analysis was performed. Among 18 effectors identified in P. brassicae, 13 effectors were induced in B. rapa seedlings inoculated with resting spores, which suggested that the pathogen and host first contacted, and more effectors were needed. Corresponding to those in B. rapa, the expression levels of most genes involved in the calcium-mediated signaling pathway and PTI pathway were higher in plants inoculated with resting spores than in those inoculated with secondary zoospores. The ETI pathway was suppressed after inoculation with secondary zoospores. The genes induced after inoculation with resting spores were suppressed in B. rapa seedlings inoculated with secondary zoospores, which might be important to allow a fully compatible interaction and contribute to a susceptible reaction in the host at the subsequent infection stage. The primary zoospores undertook an more important interaction with plants.
Deletion of the primase-polymerases encoding gene, located in a mobile element in Thermus thermophilus HB27, leads to loss of function mutation of addAB genes
Authors: Verdú Carlos , Pérez-Arnaiz Patricia , Peropadre Ana , Berenguer José , Mencía Mario
Published: December 2022

DNA primase-polymerases (Ppol) have been shown to play active roles in DNA repair and damage tolerance, both in prokaryotes and eukaryotes. The ancestral thermophilic bacterium Thermus thermophilus strain HB27 encodes a Ppol protein among the genes present in mobile element ICETh2, absent in other T. thermophilus strains. Using different strategies we ablated the function of Ppol in HB27 cells, either by knocking out the gene through insertional mutagenesis, markerless deletion or through abolition of its catalytic activity. Whole genome sequencing of this diverse collection of Ppol mutants showed spontaneous loss of function mutation in the helicase-nuclease AddAB in every ppol mutant isolated. Given that AddAB is a major player in recombinational repair in many prokaryotes, with similar activity to the proteobacterial RecBCD complex, we have performed a detailed characterization of the ppol mutants in combination with addAB mutants. The results show that knockout addAB mutants are more sensitive to DNA damage agents than the wild type, and present a dramatic three orders of magnitude increase in natural transformation efficiencies with both plasmid and lineal DNA, whereas ppol mutants show defects in plasmid stability. Interestingly, DNA-integrity comet assays showed that the genome of all the ppol and/or addAB mutants was severely affected by widespread fragmentation, however, this did not translate in neat loss of viability of the strains. All these data support that Ppol appears to keep in balance the activity of AddAB as a part of the DNA housekeeping maintenance in T. thermophilus HB27, thus, playing a key role in its genome stability.
D1018 with higher stability and excellent lipopolysaccharide binding affinity has potent anti-bacterial and anti-inflammatory activity
Authors: Wu Runzhe , Dong Xunxi , Wang Qiang , Zhang Zirui , Wang Jianhua , Wang Xiao
Published: December 2022

Escherichia coli (E. coli) infection and LPS-induced inflammation are still of severe threat to human health. With the increasing problem of antibiotic resistance, there is a desperate need to develop new approaches to solve the problem. Antimicrobial peptide (AMP) IDR-1018 exhibited potential antimicrobial and immunoregulation activity. However, moderate antimicrobial efficiency and susceptibility to protease cleavage limited its therapeutic application. Therefore, the derived 1018M which has better activity against MRSA and whole sequence D-amino acids substitution peptides (D1018 and D1018M) were synthesized in this study. The resistance of D1018 and D1018M against tested proteases increased (2–4 times), particularly in D1018. The antibacterial activity of D1018 was the same as that of the parent peptide IDR-1018, but the antimicrobial activity of D1018M was slightly increased (2-fold). Though the hemolysis of IDR-1018 and D1018 was about 2%, at the concentration of 8×MIC, the cytotoxicity of IDR-1018, D1018, and 1018M was negligible. The peptides could interact with E. coli cell wall and cytoplasmic membrane, penetrate the membrane, cause leakage of contents, and disrupt genomic DNA. Among them, D1018 is the most prominent one. In addition, IDR-1018 and D1018 showed potent binding ability to LPS, thus leading to excellent inhibition capacity to LPS-induced proinflammation response. Taken together, these data demonstrate that D1018 is a promising peptide candidate for the treatment of E. coli infection.
Looking for the mechanism of arsenate respiration of Fusibacter sp. strain 3D3, independent of ArrAB
Authors: Acosta-Grinok Mauricio , Vázquez Susana , Guiliani Nicolás , Marín Sabrina , Demergasso Cecilia
Published: December 2022

The literature has reported the isolation of arsenate-dependent growing microorganisms which lack a canonical homolog for respiratory arsenate reductase, ArrAB. We recently isolated an arsenate-dependent growing bacterium from volcanic arsenic-bearing environments in Northern Chile, Fusibacter sp. strain 3D3 (Fas) and studied the arsenic metabolism in this Gram-positive isolate. Features of Fas deduced from genome analysis and comparative analysis with other arsenate-reducing microorganisms revealed the lack of ArrAB coding genes and the occurrence of two arsC genes encoding for putative cytoplasmic arsenate reductases named ArsC-1 and ArsC-2. Interestingly, ArsC-1 and ArsC-2 belong to the thioredoxin-coupled family (because of the redox-active disulfide protein used as reductant), but they conferred differential arsenate resistance to the E. coli WC3110 ΔarsC strain. PCR experiments confirmed the absence of arrAB genes and results obtained using uncouplers revealed that Fas growth is linked to the proton gradient. In addition, Fas harbors ferredoxin-NAD+ oxidoreductase (Rnf) and electron transfer flavoprotein (etf) coding genes. These are key molecular markers of a recently discovered flavin-based electron bifurcation mechanism involved in energy conservation, mainly in anaerobic metabolisms regulated by the cellular redox state and mostly associated with cytoplasmic enzyme complexes. At least three electron-bifurcating flavoenzyme complexes were evidenced in Fas, some of them shared in conserved genomic regions by other members of the Fusibacter genus. These physiological and genomic findings permit us to hypothesize the existence of an uncharacterized arsenate-dependent growth metabolism regulated by the cellular redox state in the Fusibacter genus.
Experimental inheritance of antibiotic acquired dysbiosis affects host phenotypes across generations
Authors: Kowallik Vienna , Das Ashutosh , Mikheyev Alexander S.
Published: December 2022

Microbiomes can enhance the health, fitness and even evolutionary potential of their hosts. Many organisms propagate favorable microbiomes fully or partially via vertical transmission. In the long term, such co-propagation can lead to the evolution of specialized microbiomes and functional interdependencies with the host. However, microbiomes are vulnerable to environmental stressors, particularly anthropogenic disturbance such as antibiotics, resulting in dysbiosis. In cases where microbiome transmission occurs, a disrupted microbiome may then become a contagious pathology causing harm to the host across generations. We tested this hypothesis using the specialized socially transmitted gut microbiome of honey bees as a model system. By experimentally passaging tetracycline-treated microbiomes across worker ‘generations’ we found that an environmentally acquired dysbiotic phenotype is heritable. As expected, the antibiotic treatment disrupted the microbiome, eliminating several common and functionally important taxa and strains. When transmitted, the dysbiotic microbiome harmed the host in subsequent generations. Particularly, naïve bees receiving antibiotic-altered microbiomes died at higher rates when challenged with further antibiotic stress. Bees with inherited dysbiotic microbiomes showed alterations in gene expression linked to metabolism and immunity, among other pathways, suggesting effects on host physiology. These results indicate that there is a possibility that sublethal exposure to chemical stressors, such as antibiotics, may cause long-lasting changes to functional host-microbiome relationships, possibly weakening the host’s progeny in the face of future ecological challenges. Future studies under natural conditions would be important to examine the extent to which negative microbiome-mediated phenotypes could indeed be heritable and what role this may play in the ongoing loss of biodiversity.
Gut microbiota in acute leukemia: Current evidence and future directions
Authors: Zhou Yao , Zhou Chendan , Zhang Aijun
Published: December 2022

Gut microbiota includes a large number of microorganisms inhabiting the human gastrointestinal tract, which show a wide range of physiological functions, including digestion, metabolism, immunity, neural development, etc., and are considered to play an increasingly important role in health and disease. A large number of studies have shown that gut microbiota are closely associated with the onset and development of several diseases. In particular, the interaction between gut microbiota and cancer has recently attracted scholars’ attention. Acute leukemia (AL) is a common hematologic malignancy, especially in children. Microbiota can affect hematopoietic function, and the effects of chemotherapy and immunotherapy on AL are noteworthy. The composition and diversity of gut microbiota are important factors that influence and predict the complications and prognosis of AL after chemotherapy or hematopoietic stem cell transplantation. Probiotics, prebiotics, fecal microbiota transplantation, and dietary regulation may reduce side effects of leukemia therapy, improve response to treatment, and improve prognosis. This review concentrated on the role of the gut microbiota in the onset and development of AL, the response and side effects of chemotherapy drugs, infection during treatment, and therapeutic efficacy. According to the characteristics of gut microbes, the applications and prospects of microbial preparations were discussed.
Cyclophilin A causes severe fever with thrombocytopenia syndrome virus-induced cytokine storm by regulating mitogen-activated protein kinase pathway
Authors: Huang Huaying , Jin Ke , Ouyang Ke , Jiang Zhengyi , Yang Zhan , Hu Nannan , Dai Yan , Zhang Yaqin , Zhang Qian , Han Ying , Zhao Jie , Lin Hong , Wang Chunhui , Wang Chunyan , Sun Xuewei , Lu Dafeng , Zhu Jin , Li Jun
Published: December 2022

Introduction

Severe fever with thrombocytopenia syndrome (SFTS) has become a global threat to public health since its first report in China in 2009. However, the pathogenesis of SFTS virus (SFTSV) in humans remains unclear. Also, there are no effective therapeutics for SFTS. Cyclophilin A (CyPA) regulates protein folding and trafficking involved in various viral infectious diseases, but its role in SFTSV infection has not been elucidated.

Methods

We detected plasma CyPA levels in 29 healthy subjects and 30 SFTS patients by ELISA. In THP-1 cells and normal human peripheral blood mononuclear cells (PBMCs), SFTSV-induced extracellular CyPA (eCyPA) was also detected by ELISA. In THP-1, the effects of CyPA on Mitogen-activated protein kinase (MAPK) pathway and NF-κB were determined by Western blot. We validated the interaction between CypA and CD147 by human recombinant CyPA (hrCyPA) and the CD147 inhibitor. Effects of CyPA inhibitor Cyclosporine A (CsA) on cytokines and SFTSV replication in THP-1 cells was also detected. 8-week-old Interferon-α/β Receptor (IFNAR) knockout (IFNAR-/-) C57BL/6 mice were divided into mock group, 106TCID50 SFTSV (Untreated) group and 106TCID50 SFTSV+CsA (CsA-treated) group. The changes of body weight, animal behavior and survival time of each group were recorded. Blood samples were collected from tail vein regularly. After death, the liver, spleen, lung, kidney and brain were collected for pathological HE staining and SFTSV-NP immunohistochemical staining.

Results

Compared to healthy subjects and SFTS patients in the febrile phase of the disease, plasma CyPA levels in SFTS patients at the multi-organ dysfunction (MOD) phase showed significantly elevated (P < 0.01). Extracellular CyPA activates the MAPK pathway by binding to CD147 in THP-1 infected with SFTSV. CsA inhibits the pro-inflammatory and promoting replication effects of CyPA after SFTSV infection in vitro. In vivo, CsA can prolong the survival time and delay the weight loss of SFTSV mice. CsA reduces multi-organ dysfunction in IFNAR−/− mice infected with SFTSV.

Discussion

Our results indicate that CyPA is associated with SFTSV-induced cytokine storm, which can be a potential target for SFTS therapy.
Characterization and Identification of a novel chromosome-encoded metallo-β-lactamase WUS-1 in Myroides albus P34
Authors: Liu Shuang , Zhang Lei , Feng Chunlin , Zhu Jin , Li Anqi , Zhao Jingxuan , Zhang Yuan , Gao Mengdi , Shi Weina , Li Qiaoling , Zhang Xueya , Zhang Hailin , Xu Teng , Lu Junwan , Bao Qiyu
Published: December 2022

In this study, we identified and characterized a novel chromosomally-encoded class B metallo-β-lactamase (MBL) gene designated blaWUS-1 in a carbapenem-resistant isolate Myroides albus P34 isolated from sewage discharged from an animal farm. Comparative analysis of the deduced amino acid sequence revealed that WUS-1 shares the highest amino acid similarities with the function-characterized MBLs MUS-1 (AAN63647.1; 70.73%) and TUS-1 (AAN63648.1; 70.32%). The recombinant carrying blaWUS-1 exhibited increased MICs levels against a number of β-lactam antimicrobials such as carbenicillin, ampicillin and imipenem, and β-lactamase inhibitors (clavulanic acid and tazobactam). The metallo-β-lactamase WUS-1 could also hydrolyze these antimicrobials and the hydrolytic activities could be inhibited by EDTA. Genetic context analysis of blaWUS-1 revealed that no mobile genetic element was found in its surrounding region. The plasmid pMA84474 of Myroides albus P34 harbored 6 resistance genes (blaOXA-347, aadS, blaMYO-1, ereD, sul2 and ermF) within an approximately 17 kb multidrug resistance (MDR) region. These genes, however, were all related to mobile genetic elements.
Systematic analysis of Baobaoqu fermentation starter for Wuliangye Baijiu by the combination of metagenomics and metabolomics
Authors: Zhang Qingmei , Du Guocheng , Chen Jian , Li Jianghua , Qiao Zongwei , Zheng Jia , Zhao Dong , Zhao Xinrui
Published: December 2022

Baobaoqu (BBQ) is a traditional fermenting power, which is widely applied in Nong-flavor Baijiu brewing. There are two different types of BBQ (premium BBQ and normal BBQ) used in industrial manufacture, but the reasons for the significant differences between two kinds of BBQ have not been clearly illuminated. In this study, the combination of metagenomics and metabolomics was performed to compare the differences in the composition of microbial communities and the components of flavors between premium BBQ and normal BBQ. The results showed that the glycosidase-producing microorganisms are the biomarkers of premium BBQ, contributing a better ability of carbon source utilization than normal BBQ. In addition, several important flavors (ethyl hexanoate, phenylethanol, ethyl acetate) were rich in normal BBQ, which have a significant positive correlation with the biomarkers (Lactobacillus and Pichia kudriavzevii) of normal BBQ. It suggests that the microbial community has an advantage in utilizing raw materials in premium BBQ, while the community was inclined to form flavors in normal BBQ. The differences between two types of BBQ at the microbial and flavor level have theoretical and practical guiding significance in the application of premium and normal BBQ and in the further improvements of taste and quality of Baijiu.
Individual and combined contamination of oxytetracycline and cadmium inhibited nitrification by inhibiting ammonia oxidizers
Authors: Cao Xiaoxu , Zhao Wei , Zhang He , Lin Jitong , Hu Jingying , Lou Yanhong , Wang Hui , Yang Quangang , Pan Hong , Zhuge Yuping
Published: December 2022

Introduction

The large-scale development of animal husbandry and industrialization lead to more and more serious co-contamination from heavy metals and antibiotics in soils. Ecotoxic effects of residues from antibiotics and heavy metals are of increasing concern.

Materials and Methods

In this study, oxytetracycline (OTC) and cadmium (Cd) were selected as target pollutants to evaluate the individual and combined effects on nitrification process using four different soil types sampled from North to South China through a 56-day incubation experiment.

Results and Discussion

The results demonstrated that the contaminations of OTC and Cd, especially combined pollution had significant inhibitory effects on net nitrification rates (NNRs) as well as on AOA and AOB abundance. The toxic effects of contaminants were greatly enhanced with increasing OTC concentration. AOB was more sensitive than AOA to exogenous contaminants. And the interaction effects of OTC and Cd on ammonia oxidizers were mainly antagonistic. Furthermore, Cd contaminant (with or without OTC) had indirect effects on nitrification activity via inhibiting mineral N and AOA/AOB, while OTC alone indirectly inhibited nitrification activity by inhibiting ammonia oxidizers. The results could provide theoretical foundation for exploring the eco-environmental risks of antibiotics and heavy metals, as well as their toxic effects on nitrification processes.
Biocontrol potential of Bacillus subtilis CTXW 7-6-2 against kiwifruit soft rot pathogens revealed by whole-genome sequencing and biochemical characterisation
Authors: Chen Tingting , Zhang Zhuzhu , Li Wenzhi , Chen Jia , Chen Xuetang , Wang Bince , Ma Jiling , Dai Yunyun , Ding Haixia , Wang Weizhen , Long Youhua
Published: December 2022

Soft rot causes significant economic losses in the kiwifruit industry. This study isolated strain CTXW 7-6-2 from healthy kiwifruit tissue; this was a gram-positive bacterium that produced the red pigment pulcherrimin. The phylogenetic tree based on 16S ribosomal RNA, gyrA, rpoB, and purH gene sequences identified CTXW 7-6-2 as a strain of Bacillus subtilis. CTXW 7-6-2 inhibited hyphal growth of pathogenic fungi that cause kiwifruit soft rot, namely, Botryosphaeria dothidea, Phomopsis sp., and Alternaria alternata, by 81.76, 69.80, and 32.03%, respectively. CTXW 7-6-2 caused the hyphal surface to become swollen and deformed. Volatile compounds (VOC) produced by the strain inhibited the growth of A. alternata and Phomopsis sp. by 65.74 and 54.78%, respectively. Whole-genome sequencing revealed that CTXW 7-6-2 possessed a single circular chromosome of 4,221,676 bp that contained 4,428 protein-coding genes, with a guanine and cytosine (GC) content of 43.41%. Gene functions were annotated using the National Center for Biotechnology Information (NCBI) non-redundant protein, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes, Clusters of Orthologous Groups of proteins, Gene Ontology, Pathogen–Host Interactions, Carbohydrate-Active enZYmes, and Rapid Annotations using Subsystem Technology databases, revealing non-ribosomal pathways associated with antifungal mechanisms, biofilm formation, chemotactic motility, VOC 3-hydroxy-2-butanone, cell wall-associated enzymes, and synthesis of various secondary metabolites. antiSMASH analysis predicted that CTXW 7-6-2 can produce the active substances bacillaene, bacillibactin, subtilosin A, bacilysin, and luminmide and has four gene clusters of unknown function. Quantitative real-time PCR (qRT-PCR) analysis verified that yvmC and cypX, key genes involved in the production of pulcherrimin, were highly expressed in CTXW 7-6-2. This study elucidates the mechanism by which B. subtilis strain CTXW 7-6-2 inhibits pathogenic fungi that cause kiwifruit soft rot, suggesting the benefit of further studying its antifungal active substances.
Nodule-associated diazotrophic community succession is driven by developmental phases combined with microhabitat of Sophora davidii
Authors: Ai Jiamin , Yu Tianfei , Liu Xiaodong , Jiang Yingying , Hao Ziwei , Zhao Xiaoyu , Wang Entao , Deng Zhenshan
Published: December 2022

Nodule-associated nitrogen-fixing microorganisms (diazotrophs) residing in legume root nodules, and they have the potential to enhance legume survival. However, the succession characteristics and mechanisms of leguminous diazotrophic communities remain largely unexplored. We performed a high-throughput nifH amplicon sequencing with samples of root nodules and soil in the three developmental phases (young nodules, active nodules and senescent nodules) of the Sophora davidii (Franch.) Skeels root nodules, aiming to investigate the dynamics of nodule-endophytic diazotrophs during three developmental phases of root nodules. The results demonstrated the presence of diverse diazotrophic bacteria and successional community shifting dominated by Mesorhizobium and Bradyrhizobium inside the nodule according to the nodule development. The relative abundance decreased for Mesorhizobium, while decreased first and then increased for Bradyrhizobium in nodule development from young to active to senescent. Additionally, strains M. amorphae BT-30 and B. diazoefficiens B-26 were isolated and selected to test the interaction between them in co-cultured conditions. Under co-culture conditions: B. diazoefficiens B-26 significantly inhibited the growth of M. amorphae BT-30. Intriguingly, growth of B. diazoefficiens B-26 was significantly promoted by co’culture with M. amorphae BT-30 and could utilize some carbon and nitrogen sources that M. amorphae BT-30 could not. Additionally, the composition of microbial community varied in root nodules, in rhizosphere and in bulk soil. Collectively, our study highlights that developmental phases of nodules and the host microhabitat were the key driving factors for the succession of nodule-associated diazotrophic community.
Human liver tissue transcriptomics revealed immunometabolic disturbances and related biomarkers in hepatitis B virus-related acute-on-chronic liver failure
Authors: Yang Luo , Zhen Limin , Li Zhihui , Zhu Shu , Xu Wenxiong , Luo Qiumin , Peng Liang , Xie Chan
Published: December 2022

Acute-on-chronic liver failure (ACLF) is a major cause of liver-related death worldwide, but its key pathological features remain incompletely defined. This study aimed to reveal the molecular basis of hepatitis B virus-related ACLF (HBV-ACLF) by transcriptome sequencing of human liver tissue. A total of 18 human liver tissues from patients with different stages of HBV-related disease were collected for RNA sequencing, and liver tissues from patients and mouse models with ACLF were used for subsequent validation. Specifically, 6,853 differentially expressed genes (DEGs) and 5,038 differentially expressed transcripts were identified in patients with ACLF compared to patients with chronic hepatitis B (CHB) and normal controls (NCs). Investigation of functional by KEGG pathway enrichment analysis revealed prominent immune and metabolic dysregulation at the ACLF stage. We found that the key genes FGF19, ADCY8 and KRT17, which are related to immunometabolic disturbances, were significantly upregulated in the progression of ACLF. The three key genes were validated in human and mouse samples, indicating their prognostic and therapeutic potential in ACLF. In summary, our work reveals that immunometabolic disorder is involved in HBV-ACLF pathogenesis and indicates that FGF19, ADCY8 and KRT17 may be sensitive biomarkers for HBV-related ACLF.
Caspase-8 but not caspase-7 influences inflammasome activation to act in control of Brucella abortus infection
Authors: Santos Raiany A. , Cerqueira Daiane M. , Zamboni Dario S. , Oliveira Sergio C.
Published: December 2022

Programmed cell death (PCD) is an important mechanism of innate immunity against bacterial pathogens. The innate immune PCD pathway involves the molecules caspase-7 and caspase-8, among others. Brucella abortus is a gram-negative bacterium that causes a zoonotic disease termed brucellosis. The innate immune response against this pathogen involves activation of inflammasome components and induction of pyroptosis. However, no studies so far have revealed the role of caspase-7 or caspase-8 during this bacterial infection. Herein, we demonstrate that caspase-7 is dispensable for caspase-1 processing, IL-1β secretion and cell death in macrophages. Additionally, caspase-7 deficient animals control B. abortus infection as well as the wild type mice. Furthermore, we addressed the role of caspase-8 in inflammasome activation and pyroptosis during this bacterial infection. Macrophages deficient in caspase-8 secreted reduced amounts of IL-1β that parallels with diminished caspase-1 activity when compared to wild type cells. Additionally, caspase-8 KO macrophages showed reduced LDH release when compared to wild type, suggesting that caspase-8 may play an important role in pyroptosis in response to B. abortus. Finally, caspase-8 KO animals were more susceptible to Brucella infection when compared to wild type mice. Overall, this study contributes to a better understanding of the involvement of caspase-7 and caspase-8 in innate immunity against B. abortus infection.
Machine learning models for predicting one-year survival in patients with metastatic gastric cancer who experienced upfront radical gastrectomy
Authors: Zhang Cheng , Zhang Yi , Yang Ya-Hui , Xu Hui , Zhang Xiao-Peng , Wu Zhi-Jun , Xie Min-Min , Feng Ying , Feng Chong , Ma Tai
Published: December 2022

Tumor metastasis is a common event in patients with gastric cancer (GC) who previously underwent curative gastrectomy. It is meaningful to employ high-volume clinical data for predicting the survival of metastatic GC patients. We aim to establish an improved machine learning (ML) classifier for predicting if a patient with metastatic GC would die within 12 months. Eligible patients were enrolled from a Chinese GC cohort, and the complete detailed information from medical records was extracted to generate a high-dimensional dataset. Appropriate feature engineering and feature filter were conducted before modeling with eight algorithms. A 10-fold cross validation (CV) nested in a holdout CV (8:2) was employed for hyperparameter tuning and model evaluation. Model selection was based on the area under the receiver operating characteristic (AUROC) curve, recall, and precision. The selected model was globally explained using interpretable surrogate models. Of the total 399 cases (median survival of 8.2 months), 242 patients survived less than 12 months. The linear discriminant analysis (LDA), support vector machine (SVM), and random forest (RF) model had the highest AUROC (0.78 ± 0.021), recall (0.93 ± 0.031), and precision (0.80 ± 0.026), respectively. The LDA model created a new function that generally separated the two classes. The predicted probability of the SVM model was interpreted using a linear regression model visualized by a nomogram. The predicted class of the RF model was explained using a decision tree model. In summary, analyzing high-volume medical data by ML is helpful to produce an improved model for predicting the survival in patients with metastatic GC. The algorithm should be carefully selected in different practical scenarios.
A primary rodent triculture model to investigate the role of glia-neuron crosstalk in regulation of neuronal activity
Authors: Phadke Leela , Lau Dawn H. W. , Aghaizu Nozie D. , Ibarra Shania , Navarron Carmen M. , Granat Lucy , Magno Lorenza , Whiting Paul , Jolly Sarah
Published: December 2022

Neuroinflammation and hyperexcitability have been implicated in the pathogenesis of neurodegenerative disease, and new models are required to investigate the cellular crosstalk involved in these processes. We developed an approach to generate a quantitative and reproducible triculture system that is suitable for pharmacological studies. While primary rat cells were previously grown in a coculture medium formulated to support only neurons and astrocytes, we now optimised a protocol to generate tricultures containing neurons, astrocytes and microglia by culturing in a medium designed to support all three cell types and adding exogenous microglia to cocultures. Immunocytochemistry was used to confirm the intended cell types were present. The percentage of ramified microglia in the tricultures decreases as the number of microglia present increases. Multi-electrode array recordings indicate that microglia in the triculture model suppress neuronal activity in a dose-dependent manner. Neurons in both cocultures and tricultures are responsive to the potassium channel blocker 4-aminopyridine, suggesting that neurons remained viable and functional in the triculture model. Furthermore, suppressed neuronal activity in tricultures correlates with decreased densities of dendritic spines and of the postsynaptic protein Homer1 along dendrites, indicative of a direct or indirect effect of microglia on synapse function. We thus present a functional triculture model, which, due to its more complete cellular composition, is a more relevant model than standard cocultures. The model can be used to probe glia-neuron interactions and subsequently aid the development of assays for drug discovery, using neuronal excitability as a functional endpoint.
Alpha retinal ganglion cells in pigmented mice retina: number and distribution
Authors: Gallego-Ortega Alejandro , Norte-Muñoz María , Di Pierdomenico Johnny , Avilés-Trigueros Marcelino , de la Villa Pedro , Valiente-Soriano Francisco Javier , Vidal-Sanz Manuel
Published: December 2022

Purpose: To identify and characterize numerically and topographically the population of alpha retinal ganglion cells (αRGCs) and their subtypes, the sustained-response ON-center αRGCs (ONs-αRGCs), which correspond to the type 4 intrinsically photosensitive RGCs (M4-ipRGCs), the transient-response ON-center αRGCs (ONt-αRGCs), the sustained-response OFF-center αRGCs (OFFs-αRGCs), and the transient-response OFF-center αRGCs (OFFt-αRGCs) in the adult pigmented mouse retina.

Methods: The αRGC population and its subtypes were studied in flat-mounted retinas and radial sections immunodetected against non-phosphorylated high molecular weight neurofilament subunit (SMI-32) or osteopontin (OPN), two αRGCs pan-markers; Calbindin, expressed in ONs-αRGCs, and amacrines; T-box transcription factor T-brain 2 (Tbr2), a key transcriptional regulator for ipRGC development and maintenance, expressed in ipRGCs and GABA-displaced amacrine cells; OPN4, an anti-melanopsin antibody; or Brn3a and Brn3c, markers of RGCs. The total population of RGCs was counted automatically and αRGCs and its subtypes were counted manually, and color-coded neighborhood maps were used for their topographical representation.

Results: The total mean number of αRGCs per retina is 2,252 ± 306 SMI32+αRGCs and 2,315 ± 175 OPN+αRGCs (n = 10), representing 5.08% and 5.22% of the total number of RGCs traced from the optic nerve, respectively. αRGCs are distributed throughout the retina, showing a higher density in the temporal hemiretina. ONs-αRGCs represent ≈36% [841 ± 110 cells (n = 10)] of all αRGCs and are located throughout the retina, with the highest density in the temporal region. ONt-αRGCs represent ≈34% [797 ± 146 cells (n = 10)] of all αRGCs and are mainly located in the central retinal region. OFF-αRGCs represent the remaining 32% of total αRGCs and are divided equally between OFFs-αRGCs and OFFt-αRGCs [363 ± 50 cells (n = 10) and 376 ± 36 cells (n = 10), respectively]. OFFs-αRGCs are mainly located in the supero-temporal peripheral region of the retina and OFFt-αRGCs in the mid-peripheral region of the retina, especially in the infero-temporal region.

Conclusions: The combination of specific antibodies is a useful tool to identify and study αRGCs and their subtypes. αRGCs are distributed throughout the retina presenting higher density in the temporal area. The sustained ON and OFF response subtypes are mainly located in the periphery while the transient ON and OFF response subtypes are found in the central regions of the retina.
Label-free designed nanomaterials enrichment and separation techniques for phosphoproteomics based on mass spectrometry
Authors: Rejeeth Chandrababu , Sharma Alok
Published: December 2022

The surface chemical characteristics of nanomaterials have a substantial impact on the affinity probe used to enrich proteins and peptides for MALDI-MS analysis of a real human sample. Detecting phosphoproteins involved in signalling is always difficult, even with recent developments in mass spectrometry, because protein phosphorylation is often temporary from complicated mixtures. This review summarizes current research on the successful enrichment of various intriguing glycoproteins and glycol peptides using surface affinity materials with distinctive qualities such as low cost, excellent structural stability, diversity, and multifunction. As a consequence, this review will provide a quick overview of the scholars from various backgrounds who are working in this intriguing interdisciplinary field. Label-free cancer biomarkers and other diseases will benefit from future challenges.
Prognostic value of susceptibility-weighted imaging of prominent veins in acute ischemic stroke: A systematic review and meta-analysis
Authors: Xiang Wei , Liang Zhigang , Zhang Manman , Wei Hongchun , Sun Zhongwen , Lv Yaodong , Meng Yuedan , Li Wei , Zheng Huaguang , Zhang Hongxia
Published: December 2022

Background

The prominent veins sign (PVS) on susceptibility-weighted imaging (SWI) has been suggested to be related to the prognosis of patients with acute ischemic stroke (AIS). This meta-analysis aims to clarify the association between PVS and the prognosis of patients with AIS.

Methods

This meta-analysis was registered in PROSPERO (no. CRD42022343795). We performed systematic research in PubMed, Web of Science, EMBASE, and Cochrane Library databases for studies investigating the prognostic value of PVS. Based on the enrolled studies, patients were divided into two groups as follows: those with PVS cohort and those without PVS cohort. Outcomes were unfavorable functional outcome, early neurological deterioration (END), and hemorrhagic transformation (HT). The random-effects models were used for the meta-analytical pooled. Heterogeneity was estimated using Cochran's Q-test and I2 value. Subgroup and sensitivity analyses were also performed to explore the potential sources of heterogeneity. Publication bias was assessed with funnel plots and using Begger's and Egger's tests.

Results

A total of 19 studies with 1,867 patients were included. PVS was correlated with an unfavorable functional outcome in patients with AIS (risk ratio [RR] 1.61, 95% CI 1.28–2.02), especially in those receiving recanalization therapy (RR 2.00, 95% CI 1.52–2.63), but not in those treated conservatively (RR 1.33, 95% CI 0.87–2.04). Moreover, PVS was related to END (RR 2.77, 95% CI 2.21–3.46), while without an increased risk of HT (RR 0.97, 95% CI 0.64–1.47).

Conclusion

PVS was associated with an unfavorable prognosis of patients with AIS and increased the risk of END, while not correlated with an increased risk of HT. PVS might be useful for predicting functional outcomes of patients with AIS as a novel imaging maker.

Systematic review registration

https://www.crd.york.ac.uk/PROSPERO/, identifier: CRD42022343795.
Neurodevelopmental outcomes and volumetric analysis of brain in preterm infants with isolated cerebellar hemorrhage
Authors: Kim Seh Hyun , Shin Seung Han , Yang Hyo Ju , Park Seul Gi , Lim Soo Yeon , Choi Young Hun , Kim Ee-Kyung , Kim Han-Suk
Published: December 2022

Background

Cerebellar hemorrhage (CBH) is a major form of cerebellar injury in preterm infants. We aimed to investigate the risk factors and neurodevelopmental outcomes of isolated CBH and performed volumetric analysis at term-equivalent age.

Methods

This single-centered nested case-control study included 26 preterm infants with isolated CBH and 52 infants without isolated CBH and any significant supratentorial injury.

Results

Isolated CBH was associated with PCO2 fluctuation within 72 h after birth (adjusted odds ratio 1.007, 95% confidence interval 1.000–1.014). The composite score in the motor domain of the Bayley Scales of Infant and Toddler Development at 24 month of corrected age was lower in the punctate isolated CBH group than that in the control group (85.3 vs. 94.5, P = 0.023). Preterm infants with isolated CBH had smaller cerebellum and pons at term-equivalent age compared to the control group. Isolated CBH with adverse neurodevelopment had a smaller ventral diencephalon and midbrain compared to isolated CBH without adverse neurodevelopmental outcomes.

Conclusions

In preterm infants, isolated CBH with punctate lesions were associated with abnormal motor development at 24 months of corrected age. Isolated CBH accompanied by a smaller ventral diencephalon and midbrain at term equivalent had adverse neurodevelopmental outcomes.
Optogenetics: Emerging strategies for neuropathic pain treatment
Authors: Li Siyu , Feng Xiaoli , Bian Hui
Published: December 2022

Neuropathic pain (NP) is a chronic health condition that presents a significant burden on patients, society, and even healthcare systems. However, in recent years, an emerging field in the treatment of neuropathic pain – optogenetic technology has dawned, heralding a new era in the field of medicine, and which has brought with it unlimited possibilities for studying the mechanism of NP and the treatment of research. Optogenetics is a new and growing field that uses the combination of light and molecular genetics for the first time ever. This rare combination is used to control the activity of living cells by expressing photosensitive proteins to visualize signaling events and manipulate cell activity. The treatments for NP are limited and have hardly achieved the desirable efficacy. NP differs from other types of pain, such as nociceptive pain, in that the treatments for NP are far more complex and highly challenging for clinical practice. This review presents the background of optogenetics, current applications in various fields, and the findings of optogenetics in NP. It also elaborates on the basic concepts of neuropathy, therapeutic applications, and the potential of optogenetics from the bench to the bedside in the near future.