bluuebunny/crossref_metadata_2025 huggingface dataset:
Construction Immune Related Feed-Forward Loop Network Reveals Angiotensin II Receptor Blocker as Potential Neuroprotective Drug for Ischemic Stroke
Authors: Bo Chunrui , Cao Yuze , Li Shuang , Zhang Huixue , Lu Xiaoyu , Kong Xiaotong , Zhang Shuai , Gao Hongyu , Wang Jianjian , Wang Lihua
Published: March 2022

Ischemic stroke (IS) accounts for the leading cause of disability and mortality in China. Increasing researchers are studying the effects of neuroprotective agents on IS. However, the molecular mechanisms of feed-forward loops (FFLs) associated with neuroprotection in the pathogenesis of IS need to be further studied. A protein-protein interaction (PPI) network of IS immune genes was constructed to decipher the characters and excavate 3 hub genes (PI3K, IL6, and TNF) of immunity. Then, we identified two hub clusters of IS immune genes, and the cytokine-cytokine receptor interaction pathway was discovered on the pathway enrichment results of both clusters. Combined with GO enrichment analysis, the cytokines participate in the inflammatory response in the extracellular space of IS patients. Next, a transcription factor (TF)–miRNA–immune gene network (TMIGN) was established by extracting four regulatory pairs (TF–miRNA, TF–gene, miRNA–gene, and miRNA–TF). Then, we detected 3-node regulatory motif types in the TMIGN network. According to the criteria we set for defining 3-node motifs, the motif with the highest Z-score (3-node composite FFL) was picked as the statistically evident motif, which was merged to construct an immune-associated composite FFL motif-specific sub-network (IA-CFMSN), which contained 21 3-node FFLs composed of 13 miRNAs, 4 TFs, 9 immune genes, and 1 TF& immune gene, among which TP53 and VEGFA were prominent TF and immune gene, respectively. In addition, the immune genes in IA-CFMSN were used for identifying associated pathways and drugs to further clarify the immune regulation mechanism and neuroprotection after IS. As a result, 5 immune genes targeted by 20 drugs were identified and the Angiotensin II Receptor Blockers (ARBs) target AGTR1 was found to be a neuroprotective drug for IS. In the present study, the construction of IA-CFMSN provides IS immune-associated FFLs for further experimental studies, providing new prospects for the discovery of new biomarkers and potential drugs for IS.
Case Report: Exome and RNA Sequencing Identify a Novel de novo Missense Variant in HNRNPK in a Chinese Patient With Au-Kline Syndrome
Authors: Pan Xin , Liu Sihan , Liu Li , Zhang Xu , Yao Hong , Tan Bo
Published: March 2022

Au-Kline syndrome is a severe multisystemic syndrome characterized by several congenital defects, including intellectual disability. Loss-of-function and missense variants in the HNRNPK gene are associated with a range of dysmorphic features. This report describes an eleven-year-old Chinese boy with intellectual disability and developmental delays. Family-based whole-exome and Sanger sequencing identified a de novo missense variant in HNRNPK (NM_002140.3: c.143T > A, p. Leu48Val). In silico analysis predicted that this variant would be damaged in a highly conserved residue in the K homology 1 (KH1) domain. Bioinformatic analysis showed that the affinity change (ΔΔG) caused by this variant was -0.033 kcal/mol, indicating that it would have reduced affinity for RNA binding. Transcript analysis of the peripheral blood from this case found 42 aberrantly expressed and 86 aberrantly spliced genes (p-value <0.01). Functional enrichment analysis confirmed that the biological functions of these genes, including protein binding and transcriptional regulation, are associated with HNRNPK. In summary, this study identifies the first Chinese patient with a novel de novo heterozygous HNRNPK gene variant that contributes to Au-Kline syndrome and expands current knowledge of the clinical spectrum of HNRNPK variants.
Phospholipid Scramblases: Role in Cancer Progression and Anticancer Therapeutics
Authors: Behuria Himadri Gourav , Dash Sabyasachi , Sahu Santosh Kumar
Published: March 2022

Phospholipid scramblases (PLSCRs) that catalyze rapid mixing of plasma membrane lipids result in surface exposure of phosphatidyl serine (PS), a lipid normally residing to the inner plasma membrane leaflet. PS exposure provides a chemotactic eat-me signal for phagocytes resulting in non-inflammatory clearance of apoptotic cells by efferocytosis. However, metastatic tumor cells escape efferocytosis through alteration of tumor microenvironment and apoptotic signaling. Tumor cells exhibit altered membrane features, high constitutive PS exposure, low drug permeability and increased multidrug resistance through clonal evolution. PLSCRs are transcriptionally up-regulated in tumor cells leading to plasma membrane remodeling and aberrant PS exposure on cell surface. In addition, PLSCRs interact with multiple cellular components to modulate cancer progression and survival. While PLSCRs and PS exposed on tumor cells are novel drug targets, many exogenous molecules that catalyze lipid scrambling on tumor plasma membrane are potent anticancer therapeutic molecules. In this review, we provide a comprehensive analysis of scramblase mediated signaling events, membrane alteration specific to tumor development and possible therapeutic implications of scramblases and PS exposure.
Expression of a RhoA-Specific Guanine Nucleotide Exchange Factor, p190RhoGEF, in Mouse Macrophages Negatively Affects M1 Polarization and Inflammatory Responses
Authors: Choi So-Yeon , Ahn Yu Ri , Lee Eun-Bi , Yu Mi Jin , Lee Jong Ran
Published: March 2022

A RhoA-specific guanine nucleotide exchange factor, p190RhoGEF, was first cloned and identified in neuronal cells. In immune cells, we first reported the role of p190RhoGEF in B cells: expression of p190RhoGEF increased after CD40 stimulation and was required for CD40-mediated B cell activation and differentiation. We also showed that over-expression of p190RhoGEF negatively affected dendritic cell function in response to bacterial lipopolysaccharide (LPS). In this study, we examined the role of p190RhoGEF in macrophages using p190RhoGEF over-expressing transgenic (TG) mice. We found macrophages from TG mice to be more round than those from control mice, with enriched polymerized actin at the edge attached to the glass. TG macrophages also responded less to LPS: production of reactive oxygen species, phagocytosis, chemokine-dependent migration, and pro-inflammatory cytokine secretion were all reduced compared with the responses of macrophages from littermate (LTM) control mice. Furthermore, the classical M1 subset population was observed less in the peritoneal macrophages of TG mice than the LTM control mice during LPS-elicited peritoneal inflammation. When the activity of RhoA was inhibited in TG macrophages, their morphology and LPS responses became similar to those of the LTM macrophages. These results suggest that over-expression of p190RhoGEF in macrophages could reduce M1 polarization and inflammatory responses by regulating the actin cytoskeleton.
Bibliometric Analysis of Chimeric Antigen Receptor-Based Immunotherapy in Cancers From 2001 to 2021
Authors: Ou Zhanpeng , Qiu Ling , Rong Haixu , Li Bowen , Ren Siqi , Kuang Shijia , Lan Tianjun , Lin Hsinyu , Li Qunxing , Wu Fan , Cai Tingting , Yan Lingjian , Ye Yushan , Fan Song , Li Jinsong
Published: March 2022

Background

Chimeric antigen receptor (CAR)-based immunotherapy has shown great potential for the treatment of both hematopoietic malignancies and solid tumors. Nevertheless, multiple obstacles still block the development of CAR-based immunotherapy in the clinical setting. In this study, we aimed to summarize the research landscape and highlight the front lines and trends of this field.

Methods

Literature published from 2001 to 2021 was searched in the Web of Science Core Collection database. Full records and cited references of all the documents were extracted and screened. Bibliometric analysis and visualization were conducted using CiteSpace, Microsoft Excel 2019, VOSviewer and R software.

Results

A total of 5981 articles and reviews were included. The publication and citation results exhibited increasing trends in the last 20 years. Frontiers in Immunology and Blood were the most productive and most co-cited journals, respectively. The United States was the country with the most productive organizations and publications in the comprehensive worldwide cooperation network, followed by China and Germany. June, C.H. published the most papers with the most citations, while Maude, S.L. ranked first among the co-cited authors. The hotspots in CAR-based therapy research were multiple myeloma, safety and toxicity, solid tumors, CAR-engineered immune cells beyond T cells, and gene editing.

Conclusion

CAR-based immunotherapy is a promising treatment for cancer patients, and there is an emerging movement toward using advanced gene modification technologies to overcome therapeutic challenges, especially in solid tumors, and to generate safer and more effective universal CAR-engineered cell products.
Durable Expansion of TCR-δ Meta-Clonotypes After BCG Revaccination in Humans
Authors: James Charlotte A. , Yu Krystle K. Q. , Mayer-Blackwell Koshlan , Fiore-Gartland Andrew , Smith Malisa T. , Layton Erik D. , Johnson John L. , Hanekom Willem A. , Scriba Thomas J. , Seshadri Chetan
Published: March 2022

Mycobacterium bovis bacille Calmette-Guérin (BCG) has been used for 100 years and prevents disseminated tuberculosis and death in young children. However, it shows only partial efficacy against pulmonary tuberculosis (TB) in adults, so new vaccines are urgently needed. The protective efficacy of BCG depends on T cells, which are typically activated by pathogen-derived protein antigens that bind to highly polymorphic major histocompatibility complex (MHC) molecules. Some T cells recognize non-protein antigens via antigen presenting systems that are independent of genetic background, leading to their designation as donor-unrestricted T (DURT) cells. Whether live whole cell vaccines, like BCG, can induce durable expansions of DURT cells in humans is not known. We used combinatorial tetramer staining, multi-parameter flow cytometry, and immunosequencing to comprehensively characterize the effect of BCG on activation and expansion of DURT cell subsets. We examined peripheral blood mononuclear cells (PBMC) derived from a Phase I study of South African adults in which samples were archived at baseline, 3 weeks, and 52 weeks post-BCG revaccination. We did not observe a change in the frequency of total mucosal-associated invariant T (MAIT) cells, invariant natural killer T (iNKT) cells, germline encoded mycolyl-reactive (GEM) T cells, or γδ T cells at 52 weeks post-BCG. However, immunosequencing revealed a set of TCR-δ clonotypes that were expanded at 52 weeks post-BCG revaccination. These expanded clones expressed the Vδ2 gene segment and could be further defined on the basis of biochemical similarity into several ‘meta-clonotypes’ that likely recognize similar epitopes. Our data reveal that BCG vaccination leads to durable expansion of DURT cell clonotypes despite a limited effect on total circulating frequencies in the blood and have implications for defining the immunogenicity of candidate whole cell TB vaccines.
Computer-Based Immunoinformatic Analysis to Predict Candidate T-Cell Epitopes for SARS-CoV-2 Vaccine Design
Authors: Mei Xueyin , Gu Pan , Shen Chuanlai , Lin Xue , Li Jian
Published: March 2022

Since the first outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019, its high infectivity led to its prevalence around the world in an exceptionally short time. Efforts have been made to control the ongoing outbreak, and among them, vaccine developments are going on high priority. New clinical trials add to growing evidence that vaccines from many countries were highly effective at preventing SARS-CoV-2 virus infection. One of them is B cell-based vaccines, which were common during a pandemic. However, neutralizing antibody therapy becomes less effective when viruses mutate. In order to tackle the problem, we focused on T-cell immune mechanism. In this study, the mutated strains of the virus were selected globally from India (B.1.617.1 and B.1.617.2), United Kingdom (B.1.1.7), South Africa (B.1.351), and Brazil (P.1), and the overlapping peptides were collected based on mutation sites of S-protein. After that, residue scanning was used to predict the affinity between overlapping peptide and HLA-A*11:01, the most frequent human leukocyte antigen (HLA) allele among the Chinese population. Then, the binding free energy was evaluated with molecular docking to further verify the affinity changes after the mutations happen in the virus genomes. The affinity test results of three epitopes on spike protein from experimental validation were consistent with our predicted results, thereby supporting the inclusion of the epitope 374FSTFKCYGL382 in future vaccine design and providing a useful reference route to improve vaccine development.
Autophagy May Allow a Cell to Forbear Pyroptosis When Confronted With Cytosol-Invasive Bacteria
Authors: Harvest Carissa K. , Miao Edward A.
Published: March 2022

Inflammatory caspases detect cytosol-invasive Gram-negative bacteria by monitoring for the presence of LPS in the cytosol. This should provide defense against the cytosol-invasive Burkholderia and Shigella species by lysing the infected cell via pyroptosis. However, recent evidence has shown caspase-11 and gasdermin D activation can result in two different outcomes: pyroptosis and autophagy. Burkholderia cepacia complex has the ability invade the cytosol but is unable to inhibit caspase-11 and gasdermin D. Yet instead of activating pyroptosis during infection with these bacteria, the autophagy pathway is stimulated through caspases and gasdermin D. In contrast, Burkholderia thailandensis can invade the cytosol where caspasae-11 and gasdermin D is activated but the result is pyroptosis of the infected cell. In this review we propose a hypothetical model to explain why autophagy would be the solution to kill one type of Burkholderia species, but another Burkholderia species is killed by pyroptosis. For pathogens with high virulence, pyroptosis is the only solution to kill bacteria. This explains why some pathogens, such as Shigella have evolved methods to inhibit caspase-11 and gasdermin D as well as autophagy. We also discuss similar regulatory steps that affect caspase-1 that may permit the cell to forbear undergoing pyroptosis after caspase-1 activates in response to bacteria with partially effective virulence factors.
Environmental Regulation of Photosynthetically Produced Dissolved Organic Carbon by Phytoplankton Along a Subtropical Estuarine Bay
Authors: Kang Jianhua , Luo Zhaohe , Mohamed Hala. F. , Lin Yili , Huang Shuhong , Wang Yu , Lan Wenlu
Published: March 2022

Photosynthetically produced dissolved organic carbon (PDOC) released by marine phytoplankton has an important significance on the marine carbon cycle and on the growth of heterotopic bacteria (HB). However, PDOC is often neglected in the estimation of global marine primary productivity and carbon sequestration capacity. This work studied the issue of PDOC and its environmental regulation mechanism through field investigation and lab experiments in an estuarine bay during southwest and northeast monsoon. We used the percentage of extracellular release (PER) as a key indicator to evaluate the contribution of PDOC to total primary productivity (TPP). We also compared PER among different seasons and sectors and then analyzed the inter-relationship between PDOC and bacterial carbon demand (BCD), size-fractionated phytoplankton, bacterial production (BP), and TPP. We finally discussed the impact factors of PDOC productivity. The results showed that the average contribution of PDOC to TPP in Qinzhou bay could reach 15% during two seasons, which satisfies about 25% of the carbon requirement by HB in the bay. Multiple factors contribute to the seasonal (SW monsoon 13% < NE monsoon 18%) and sectoral variation (outer bay 26% > middle bay 17% > inner bay 7%) in PER, the most significant of which are salinity and nitrogen to phosphorus ratios. PER is also related to phytoplankton community structure and nutrient limitation, the higher PER in the outer bay is attributed to the dual effect of picophytoplankton being the predominant species and a severe imbalance in the nitrogen to phosphorus ratio, both of which lead to increased phytoplankton PDOC release. On the other hand, the lower PER in the inner bay was mainly due to the dominance of microphytoplankton and nitrogen to phosphorus ratio which is close to the redfield ratio. There is still a non-uniform conclusion on the relationship between PER and TPP, suggesting that this relationship needs to be evaluated not only in a horizontal-independent way but also through seasonal and vertical dimensions. The non-linear relationship between PDOC and BCD found in this study potentially indicated weak coupling between phytoplankton exudation and bacterial metabolism. In addition to phytoplankton exudate, HB is still dependent on other sources of DOC to meet their carbon requirements.
Intrauterine Perfusion of Autologous Platelet-Rich Plasma Before Frozen-Thawed Embryo Transfer Improves the Clinical Pregnancy Rate of Women With Recurrent Implantation Failure
Authors: Xu Yangying , Hao Cuifang , Fang Jianye , Liu Xiaoqiang , Xue Pingping , Miao Ruichao
Published: March 2022

Objective

To evaluate whether the intrauterine perfusion of platelet-rich plasma (PRP) before frozen-thawed embryo transfer (FET) improves the pregnancy outcomes of patients with repeated implantation failure (RIF).

Methods

This retrospective study included 288 infertile women with RIF after undergoing in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) treatment from October 1, 2019, to January 1, 2021, at Qingdao Women and Children's Hospital. Patients were divided into two groups according to whether they received PRP intrauterine perfusion before embryo transfer in FET cycles. 138 women were in the PRP group, 150 women were in the control group. The primary outcome measure was live birth rates and the secondary outcome were clinical pregnancy, positive β hCG, miscarriage and implantation rates.

Results

No significant differences in baseline demographic and clinical characteristics were observed between the two groups. Overall, significantly more women in the PRP group than in the control group achieved a live birth rate (41 women; 29.71% vs. 27 women; 18%) and a clinical pregnancy (50 women; 36.23% vs. 37 women; 24.67%). The PRP group had a higher implantation rate and lower spontaneous miscarriage rate than the control group, but these differences were not statistically significant. No pregnancy outcome difference between two groups in PCOS patients with RIF.

Conclusion

Our results showed that intrauterine perfusion of PRP before embryo transfer in FET cycles can significantly increase the live birth and clinical pregnancy rates in patients with RIF.
Isoliquiritin Ameliorates Cisplatin-Induced Renal Proximal Tubular Cell Injury by Antagonizing Apoptosis, Oxidative Stress and Inflammation
Authors: Pei Zhiyin , Wu Meng , Yu Hanqing , Long Guangfeng , Gui Zhen , Li Xiaonan , Chen Hongbing , Jia Zhanjun , Xia Weiwei
Published: March 2022

Acute kidney injury (AKI) is a clinical syndrome characterized by morbidity, mortality, and cost. Cis-diamminedichloroplatinum (cisplatin) is a chemotherapeutic agent used to treat solid tumors and hematological malignancies, but its side effects, especially nephrotoxicity, limit its clinical application. Isoliquiritin (ISL), one of the major flavonoid glycoside compounds in licorice, has been reported to have anti-apoptotic, antioxidant, and anti-inflammatory activities. However, the effect and mechanism of ISL on cisplatin-induced renal proximal tubular cell injury remain unknown. In this study, mouse proximal tubular cells (mPTCs) and human proximal tubule epithelial cells (HK2) were administered increasing concentrations of ISL from 7.8125 to 250 μM. Moreover, mPTC and HK2 cells were pretreated with ISL for 6–8 h, followed by stimulation with cisplatin for 24 h. CCK-8 assay was performed to evaluate the cell viability. Apoptosis and reactive oxygen species (ROS) of cells were measured by using flow cytometer and western blotting. Our results showed that ISL had no obvious effect on cell viability. ISL decreased cisplatin-induced cell injury in a dose-dependent manner. ISL also protected against cisplatin-induced cell apoptosis. Meanwhile, the enhanced protein levels of Bax, cleaved caspase-3/caspase-3 ratio, levels of Pp-65/p-65, levels of IL-6, and the production of ROS induced by cisplatin were significantly attenuated by ISL treatment. Moreover, ISL markedly increased the protein levels of Bcl-2 and SOD2, which were reduced by cisplatin stimulation. These results showed that ISL ameliorated cisplatin-induced renal proximal tubular cell injury by antagonizing apoptosis, oxidative stress and inflammation.
Heterorhabditis and Photorhabdus Symbiosis: A Natural Mine of Bioactive Compounds
Authors: Parihar Ripu Daman , Dhiman Urvashi , Bhushan Anil , Gupta Prashant Kumar , Gupta Prasoon
Published: March 2022

Phylum Nematoda is of great economic importance. It has been a focused area for various research activities in distinct domains across the globe. Among nematodes, there is a group called entomopathogenic nematodes, which has two families that live in symbiotic association with bacteria of genusXenorhabdusandPhotorhabdus, respectively. With the passing years, researchers have isolated a wide array of bioactive compounds from these symbiotically associated nematodes. In this article, we are encapsulating bioactive compounds isolated from members of the family Heterorhabditidae inhabitingPhotorhabdusin its gut. Isolated bioactive compounds have shown a wide range of biological activity against deadly pathogens to both plants as well as animals. Some compounds exhibit lethal effects against fungi, bacteria, protozoan, insects, cancerous cell lines, neuroinflammation, etc., with great potency. The main aim of this article is to collect and analyze the importance of nematode and its associated bacteria, isolated secondary metabolites, and their biomedical potential, which can serve as potential leads for further drug discovery.
Screening of Potential Vibrio cholerae Bacteriophages for Cholera Therapy: A Comparative Genomic Approach
Authors: Barman Ranjan Kumar , Chakrabarti Alok Kumar , Dutta Shanta
Published: March 2022

Cholera continues to be a major burden for developing nations, especially where sanitation, quality of water supply, and hospitalization have remained an issue. Recently, growing antimicrobial-resistant strains of Vibrio cholerae underscores alternative therapeutic strategies for cholera. Bacteriophage therapy is considered one of the best alternatives for antibiotic treatment. For the identification of potential therapeutic phages for cholera, we have introduced a comprehensive comparative analysis of whole-genome sequences of 86 Vibrio cholerae phages. We have witnessed extensive variation in genome size (ranging from 33 to 148 kbp), GC (G + C) content (varies from 34.5 to 50.8%), and the number of proteins (ranging from 15 to 232). We have identified nine clusters and three singletons using BLASTn, confirmed by nucleotide dot plot and sequence identity. A high degree of sequence and functional similarities in both the genomic and proteomic levels have been observed within the clusters. Evolutionary analysis confirms that phages are conserved within the clusters but diverse between the clusters. For each therapeutic phage, the top 2 closest phages have been identified using a system biology approach and proposed as potential therapeutic phages for cholera. This method can be applied for the classification of the newly isolated Vibrio cholerae phage. Furthermore, this systematic approach might be useful as a model for screening potential therapeutic phages for other bacterial diseases.
Molecular Epidemiology and Colistin-Resistant Mechanism of mcr-Positive and mcr-Negative Escherichia coli Isolated From Animal in Sichuan Province, China
Authors: Li Fulei , Cheng Ping , Li Xiaoting , Liu Ruimeng , Liu Haibin , Zhang Xiuying
Published: March 2022

Colistin is the last line of defense for the treatment of multidrug-resistant gram-negative bacterial infections. However, colistin resistance is gradually increasing worldwide, with resistance commonly regulated by two-component system and mcr gene. Thus, this study aimed to investigate molecular epidemiology and colistin-resistant mechanism of mcr-positive and mcr-negative Escherichia coli isolates from animal in Sichuan Province, China. In this study, a total of 101 colistin-resistant E. coli strains were isolated from 300 fecal samples in six farms in Sichuan Province. PCR was used to detect mcr gene (mcr-1 to mcr-9). The prevalence of mcr-1 in colistin-resistant E. coli was 53.47% (54/101), and the prevalence of mcr-3 in colistin-resistant E. coli was 10.89% (11/101). The colistin-resistant E. coli and mcr-1–positive E. coli showed extensive antimicrobial resistance profiles. For follow-up experiments, we used 30 mcr-negative and 30 mcr-1–positive colistin-resistant E. coli isolates and E. coli K-12 MG1655 model strain. Multi-locus sequence typing (MLST) of 30 strains carrying mcr-1 as detected by PCR identified revealed six strains (20%) of ST10 and three strains (10%) of each ST206, ST48, and ST155 and either two (for ST542 and 2539) or just one for all other types. The conjugation experiment and plasmid replicon type analysis suggest that mcr-1 was more likely to be horizontally transferred and primarily localized on IncX4-type and IncI2-type plasmid. The ST diversity of the mcr-1 indicated a scattered and non-clonal spreading in mcr-1–positive E. coli. Twenty-eight mcr-negative colistin-resistant E. coli isolates carried diverse amino acid alterations in PmrA, PmrB, PhoP, PhoQ, and MgrB, whereas no mutation was found in the remaining isolates. The finding showed the high prevalence of colistin resistance in livestock farm environments in Sichuan Province, China. Our study demonstrates that colistin resistance is related to chromosomal point mutations including the two-component systems PhoP/PhoQ, PmrA/PmrB, and their regulators MgrB. These point mutations may confer colistin resistance in mcr-negative E. coli. These findings help in gaining insight of chromosomal-encoded colistin resistance in E. coli.
Short-Term Grazing Exclusion Alters Soil Bacterial Co-occurrence Patterns Rather Than Community Diversity or Composition in Temperate Grasslands
Authors: Wang Fangfang , Li Zongming , Fu Bojie , Lü Yihe , Liu Guoping , Wang Dongbo , Wu Xing
Published: March 2022

Grazing exclusion is one of the most common practices for degraded grassland restoration worldwide. Soil microorganisms are critical components in soil and play important roles in maintaining grassland ecosystem functions. However, the changes of soil bacterial community characteristics during grazing exclusion for different types of grassland remain unclear. In this study, the soil bacterial community diversity and composition as well as the co-occurrence patterns were investigated and compared between grazing exclusion (4 years) and the paired adjacent grazing sites for three types of temperate grasslands (desert steppe, typical steppe, and meadow steppe) in the Hulunbuir grassland of Inner Mongolia. Our results showed that short-term grazing exclusion decreased the complexity and connectivity of bacterial co-occurrence patterns while increasing the network modules in three types of temperate grasslands. The effects of grazing exclusion on soil bacterial α-diversity and composition were not significant in typical steppe and meadow steppe. However, short-term grazing exclusion significantly altered the community composition in desert steppe, indicating that the soil bacteria communities in desert steppe could respond faster than those in other two types of steppes. In addition, the composition of bacterial community is predominantly affected by soil chemical properties, such as soil total carbon and pH, instead of spatial distance. These results indicated that short-term grazing exclusion altered the soil bacterial co-occurrence patterns rather than community diversity or composition in three types of temperate grasslands. Moreover, our study suggested that soil bacterial co-occurrence patterns were more sensitive to grazing exclusion, and the restoration of soil bacterial community might need a long term (>4 years) in our study area.
Singapore Grouper Iridovirus Induces Glucose Metabolism in Infected Cells by Activation of Mammalian Target of Rapamycin Signaling
Authors: Guo Xixi , Zheng Qi , Pan Zanbin , Huang Youhua , Huang Xiaohong , Qin Qiwei
Published: March 2022

Singapore grouper iridovirus (SGIV), a member of the Iridoviridae family, is an important marine cultured fish pathogen worldwide. Our previous studies have demonstrated that lipid metabolism was essential for SGIV entry and replication, but the roles of glucose metabolism during SGIV infection still remains largely unknown. In this study, we found that the transcription levels of key enzymes involved in glycolysis were regulated in varying degrees during SGIV infection based on the transcriptomic analysis. Quantitative PCR and western blot analysis also indicated that the expression of both glucose transporters (GLUT1 and GLUT2) and the enzymes of glucose metabolism (hexokinase 2, HK2 and pyruvate dehydrogenase complex, PDHX) were upregulated during SGIV infection in vivo or in vitro, suggesting that glycolysis might be involved in SGIV infection. Exogenous glucose supplementation promoted the expression of viral genes and infectious virion production, while glutamine had no effect on SGIV infection, indicating that glucose was required for SGIV replication. Consistently, pharmacological inhibition of glycolysis dramatically reduced the protein synthesis of SGIV major capsid protein (MCP) and infectious virion production, and promotion of glycolysis significantly increased SGIV infection. Furthermore, knockdown of HK2, PDHX, or GLUT1 by siRNA decreased the transcription and protein synthesis of SGIV MCP and suppressed viral replication, indicating that those enzymes exerted essential roles in SGIV replication. In addition, inhibition of mTOR activity in SGIV-infected cells effectively reduced the expression of glycolysis key enzymes, including HK2, PDHX, GLUT1, and GLUT2, and finally inhibited SGIV replication, suggesting that mTOR was involved in SGIV-induced glycolysis. Thus, our results not only provided new insights into the mechanism of how SGIV infection affects host cell glycolysis, but also contributed to further understanding of the iridovirus pathogenesis.
The CREB and AP-1–Dependent Cell Communication Network Factor 1 Regulates Porcine Epidemic Diarrhea Virus-Induced Cell Apoptosis Inhibiting Virus Replication Through the p53 Pathway
Authors: Zhou Hongchao , Zhang Yuting , Wang Jingjing , Yan Yuchao , Liu Yi , Shi Xiaojie , Zhang Qi , Xu Xingang
Published: March 2022

Porcine epidemic diarrhea virus (PEDV) infection causes severe diarrhea, dehydration, and high mortality in sick pigs, causing huge economic losses to the pig industry. However, the relationship between cell communication network factor 1 (CCN1) and PEDV infection has not been reported. In this study, we showed that the expression of CCN1 was enhanced by PEDV infection, and we observed that PEDV promotes the CREB and AP-1 activation to promote CCN1 expression. The PKA and p38 inhibitors significantly suppress CCN1 expression, indicating that PEDV-induced CCN1 expression may be through PKA and p38 pathway. Further tests confirmed that CREB and AP-1 are regulated by PKA and p38, respectively. Overexpression of CCN1 decreased the replication of PEDV, whereas knockdown of CCN1 increased the replication of PEDV. We proved that the overexpression of CCN1 increased the phosphorylation level of p53, promoted the expresion of Bax and the cleavage of caspase 9 and caspase 3, and inhibited the production of Bcl-2. CCN1 knockdown decreased the phosphorylation level of p53, inhibited the production of Bax and the cleavage of caspase 9 and caspase 3, and promoted the expression of Bcl-2. The treatment of PFT-α (p53 inhibitor) significantly suppressed the expression of cleaved caspase 9 and caspase 3, leading to the decrease of apoptosis. Together, these studies showed that PEDV promotes the activation of CREB and AP-1 to increase the expression of CCN1. Overexpression of CCN1 promotes apoptosis by elevating p53 protein phosphorylation and inhibits PEDV replication, and knockdown of CCN1 inhibits apoptosis by decreasing p53 protein phosphorylation and promotes PEDV replication. Our study could provide some reference for the molecular mechanisms of PEDV-induced CCN1 induction and supply a new therapeutic target for PEDV.
Short-Term Metformin Treatment Enriches Bacteroides dorei in an Obese Liver Steatosis Zucker Rat Model
Authors: Robeson Michael S. , Manna Kanishka , Randolph Christopher , Byrum Stephanie , Hakkak Reza
Published: March 2022

Obesity is the leading cause of health-related diseases in the United States and World. Previously, we reported that obesity can change gut microbiota using the Zucker rat model. Metformin is an oral anti-hyperglycemic agent approved by the FDA to treat type 2 diabetes (T2D) in adults and children older than 10 years of age. The correlation of short-term metformin treatment and specific alterations to the gut microbiota in obese models is less known. Short-term metformin has been shown to reduce liver steatosis. Here we investigate the effects of short-term metformin treatment on population of gut microbiota profile in an obese rat model. Five week old obese (n = 12) female Zucker rats after 1 week of acclimation, received AIN-93 G diet for 8 weeks and then rats were randomly assigned into two groups (6 rats/group): (1) obese without metformin (ObC), or (2) obese with metformin (ObMet). Metformin was mixed with AIN-93G diet at 1,000 mg/kg of diet. Rats were weighed twice per week. All rats were sacrificed at the end of metformin treatment at 10 weeks and fecal samples were collected and kept at −80°C. Total microbial DNA was collected directly from the fecal samples used for shotgun-metagenomics sequencing and subsequently analyzed using MetaPlAn and HUMAnN. After stringent data filtering and quality control we found significant differences (p = 0.0007) in beta diversity (Aitchison distances) between the ObC vs. ObMet groups. Supervised and unsupervised analysis of the log-ratios Bacteroides dorei and B. massiliensis vs. all other Bacteroides spp., revealed that B. dorei and B. massiliensis were enriched in the ObMet group, while the remaining Bacteroides spp. where enriched in the ObC group (p = 0.002). The contributional diversity of pathways is also significantly associated by treatment group (p = 0.008). In summary, in the obese Zucker rat model, short-term metformin treatment changes the gut microbiota profile, particularly altering the composition Bacteroides spp. between ObC and ObMet.
Association of Gut Microbiota With Metabolism in Rainbow Trout Under Acute Heat Stress
Authors: Zhou Changqing , Yang Shunwen , Ka Wei , Gao Pan , Li Yalan , Long Ruijun , Wang Jianlin
Published: March 2022

Global warming is one of the most common environmental challenges faced by cold-water fish farming. Heat stress seriously affects the feeding, growth, immunity, and disease resistance of fish. These changes are closely related to the destruction of intestinal barrier function, the change of intestinal microbiota, and metabolic dysfunction. However, the causal relationship between the phenotypic effects of heat stress as well as intestinal and metabolic functions of fish is unknown. In the current study, the optimal growth temperature (16°C) of rainbow trout was used as the control group, while the fish treated at 22.5°C, 23.5°C, and 24.5°C for 24 h, respectively, were the treatment groups. The 16S rRNA gene sequencing analysis showed that with the increase in temperature, the relative abundance and diversity of intestinal microbiota decreased significantly, while the number of Mycoplasma, Firmicutes, and Tenericutes increased significantly. Non-targeted metabolomics analysis by liquid chromatography-mass spectrometry analysis and correlation analysis showed that the changes of metabolites related to amino acids, vitamins, and short-chain fatty acids in serum of rainbow trout under acute heat stress were strongly correlated with the decrease of relative abundance of various intestinal microbiota, especially Morganella, Enterobacter, Lactobacillus, Lawsonia, and Cloacibacterium. In addition, we also found that acute heat stress seriously affected the intestinal structure and barrier function, and also caused the pathological damage of epithelial cells. These results indicate that the gut microbiome of acute heat-stressed rainbow trout could mediate metabolite transfer through the gut barrier by affecting its integrity. Significant changes in gut morphology, permeability, antioxidant capacity, and pro-inflammatory cytokine levels were observed. Therefore, it is necessary to explore the changes of intestinal microbiota under heat stress to help understand the regulatory mechanism of heat stress and protect the intestinal health of rainbow trout from the negative effects of rising water temperature.
Effects of Three Pesticides on the Earthworm Lumbricus terrestris Gut Microbiota
Authors: Astaykina Angelika , Streletskii Rostislav , Maslov Mikhail , Krasnov George , Gorbatov Victor
Published: March 2022

Earthworms play a vital role in the terrestrial ecosystem functioning and maintenance of soil fertility. However, many pesticides, for example, imidacloprid, benomyl, and metribuzin that are world-widely used in agriculture, may be potentially dangerous to earthworms. At the same time, standard tests for pesticides acute and chronic toxicity do not reflect all aspects of their negative impact and might not be enough sensitive for effective assessment. In this paper, we studied the effects of non-lethal concentrations of imidacloprid, benomyl, and metribuzin on the gut bacterial community of Lumbricus terrestris using high-throughput sequencing approach. We found that pesticides reduced the total bacterial diversity in the earthworm’s gut even at the recommended application rate. Under the applied pesticides, the structure of the gut prokaryotic community underwent changes in the relative abundance of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Planctomyces, Verrucomicrobia, and Cyanobacteria, as well as the genera Haliangium, Gaiella, Paenisporosarcina, Oryzihumus, Candidatus Udaeobacter, and Aquisphaera. Moreover, the pesticides affected the abundance of Verminephrobacter—the earthworms’ nephridia specific symbionts. In general, the negative impact of pesticides on bacterial biodiversity was significant even under pesticides content, which was much lower than their acute and chronic toxicity values for the earthworms. These results highlighted the fact that the earthworm’s gut microbial community is highly sensitive to soil contamination with pesticides. Therefore, such examination should be considered in the pesticide risk assessment protocols.
Different Drugs, Same End: Ultrastructural Hallmarks of Autophagy in Pathogenic Protozoa
Authors: Pedra-Rezende Yasmin , Macedo Isabela S. , Midlej Victor , Mariante Rafael M. , Menna-Barreto Rubem F. S.
Published: March 2022

Protozoan parasites interact with a wide variety of organisms ranging from bacteria to humans, representing one of the most common causes of parasitic diseases and an important public health problem affecting hundreds of millions of people worldwide. The current treatment for these parasitic diseases remains unsatisfactory and, in some cases, very limited. Treatment limitations together with the increased resistance of the pathogens represent a challenge for the improvement of the patient’s quality of life. The continuous search for alternative preclinical drugs is mandatory, but the mechanisms of action of several of these compounds have not been described. Electron microscopy is a powerful tool for the identification of drug targets in almost all cellular models. Interestingly, ultrastructural analysis showed that several classes of antiparasitic compounds induced similar autophagic phenotypes in trypanosomatids, trichomonadids, and apicomplexan parasites as well as in Giardia intestinalis and Entamoeba spp. with the presence of an increased number of autophagosomes as well as remarkable endoplasmic reticulum profiles surrounding different organelles. Autophagy is a physiological process of eukaryotes that maintains homeostasis by the self-digestion of nonfunctional organelles and/or macromolecules, limiting redundant and damaged cellular components. Here, we focus on protozoan autophagy to subvert drug effects, discussing its importance for successful chemotherapy.
Two (p)ppGpp Synthetase Genes, relA and spoT, Are Involved in Regulating Cell Motility, Exopolysaccharides Production, and Biofilm Formation of Vibrio alginolyticus
Authors: Yin Wen-Liang , Xie Zhen-Yu , Zeng Yan-Hua , Zhang Ju , Long Hao , Ren Wei , Zhang Xiang , Cai Xiao-Ni , Huang Ai-You
Published: March 2022

The stringent response mediated by the signal molecule (p)ppGpp is involved in response to multiple environmental stresses and control of various physiological processes. Studies have revealed that (p)ppGpp strongly affects the formation and maintenance of several bacterial biofilms. However, the specific regulatory roles of (p)ppGpp in biofilms, especially in the expression of genes related to cell motility and exopolysaccharides (EPSs) production, remain poorly understood. We recently reported two (p)ppGpp synthetase genes relA and spoT from the epizootic pathogen Vibrio alginolyticus. Herein, we found that the (p)ppGpp synthetase genes of V. alginolyticus contributed to biofilm formation at low cell density and biofilm detachment at high cell density, respectively, in polystyrene microtiter plates. Quantitative reverse transcription PCR (qRT-PCR) analysis revealed that the expression levels of both EPSs and motility associated genes were consistent with the development of biofilms. Besides, the (p)ppGpp synthetase gene spoT was found to be closely involved in the regulation of flagellum, smooth/translucent colony morphology and spotty pellicle at the air-liquid interface. Interestingly, pleiotropic phenotypes of ΔrelAΔspoT were similar to that of the rpoN (σ54) deletion mutant. Meanwhile, the absence of (p)ppGpp synthetase genes significantly reduced the expression levels of rpoN at low cell density, suggesting that (p)ppGpp may mediate the formation via positively affecting the alternative sigma factor RpoN. These findings allow us to propose (p)ppGpp as a crucial regulator for biofilm development in V. alginolyticus, in view of the regulatory roles of relA and spoT in cell motility and EPSs production.
Prognostic Implications and Immune Infiltration Characteristics of Chromosomal Instability-Related Dysregulated CeRNA in Lung Adenocarcinoma
Authors: Guo Shengnan , Li Tianhao , Xu Dahua , Xu Jiankai , Wang Hong , Li Jian , Bi Xiaoman , Cao Meng , Xu Zhizhou , Xia Qianfeng , Cui Ying , Li Kongning
Published: March 2022

An accumulating body of research indicates that long-noncoding RNAs (lncRNAs) regulate the target genes and act as competitive endogenous RNAs (ceRNAs) playing an indispensable role in lung adenocarcinoma (LUAD). LUAD is frequently accompanied by the feature of chromosomal instability (CIN); however, CIN-related ceRNAs have not been investigated yet. We systematically analyzed and integrated CIN-related dysregulated ceRNAs characteristics in LUAD samples for the first time. In TCGA LUAD cohort, CIN in tumor samples was significantly higher than that in those of adjacent, and patients with high CIN risk tended to have worse clinical outcomes. We constructed a double-weighted CIN-related dysregulated ceRNA network, in which edge weight and node weight represented the disorder extent of ceRNA and the correlation of RNA expression level and prognosis, respectively. After module mining and analysis, a potential prognostic biomarker composed of 12 RNAs (8 mRNAs and 4 lncRNAs) named CIN-related dysregulated ceRNAs (CRDC) was obtained. The CRDC risk score had a positive relation with clinical stage and CIN, and patients with high CRDC risk scores exhibited poor prognosis. Moreover, CRDC tended to be an independent risk factor with high robustness to overcome the effect of multicollinearity among other explanatory variables for disease-specific survival (DSS) in TCGA and two GEO cohorts. The result of functional analysis indicated that CRDC was involved in multiple cancer progresses, especially immune-related pathways. The patients with lower CRDC risk had higher B cell, T cell CD4+, T cell CD8+, neutrophil, macrophage, and myeloid dendritic cell infiltration than the patients with higher CRDC risk. Meanwhile, patients with lower CRDC risk could get more benefits from immunological therapy. The results suggested that the CRDC could be a potential prognostic biomarker and an immunotherapy predictor for lung adenocarcinoma.
The Legacy of the TTASAAN Report—Premature Conclusions and Forgotten Promises: A Review of Policy and Practice Part I
Authors: Pavel Dan G. , Henderson Theodore A. , DeBruin Simon
Published: March 2022

Brain perfusion single photon emission computed tomography (SPECT) scans were initially developed in 1970's. A key radiopharmaceutical, hexamethylpropyleneamine oxime (HMPAO), was originally approved in 1988, but was unstable. As a result, the quality of SPECT images varied greatly based on technique until 1993, when a method of stabilizing HMPAO was developed. In addition, most SPECT perfusion studies pre-1996 were performed on single-head gamma cameras. In 1996, the Therapeutics and Technology Assessment Subcommittee of the American Academy of Neurology (TTASAAN) issued a report regarding the use of SPECT in the evaluation of neurological disorders. Although the TTASAAN report was published in January 1996, it was approved for publication in October 1994. Consequently, the reported brain SPECT studies relied upon to derive the conclusions of the TTASAAN report largely pre-date the introduction of stabilized HMPAO. While only 12% of the studies on traumatic brain injury (TBI) in the TTASAAN report utilized stable tracers and multi-head cameras, 69 subsequent studies with more than 23,000 subjects describe the utility of perfusion SPECT scans in the evaluation of TBI. Similarly, dementia SPECT imaging has improved. Modern SPECT utilizing multi-headed gamma cameras and quantitative analysis has a sensitivity of 86% and a specificity of 89% for the diagnosis of mild to moderate Alzheimer's disease—comparable to fluorodeoxyglucose positron emission tomography. Advances also have occurred in seizure neuroimaging. Lastly, developments in SPECT imaging of neurotoxicity and neuropsychiatric disorders have been striking. At the 25-year anniversary of the publication of the TTASAAN report, it is time to re-examine the utility of perfusion SPECT brain imaging. Herein, we review studies cited by the TTASAAN report vs. current brain SPECT imaging research literature for the major indications addressed in the report, as well as for emerging indications. In Part II, we elaborate technical aspects of SPECT neuroimaging and discuss scan interpretation for the clinician.