The dsRNA isolated from Escherichia coli infected with the MS2 bacteriophage induces the production of interferons.

Viral infections pose a significant threat to public health, and the production of interferons represents one of the most critical antiviral innate immune responses of the host. Consequently, the screening and identification of compounds or reagents that induce interferon production are of paramount importance. This study commenced with the cultivation of host bacterium 15,597, followed by the infection of Escherichia coli with the MS2 bacteriophage. Utilizing the J2 capture technique, a class of dsRNA mixtures (MS2+15,597) was isolated from the E. coli infected with the MS2 bacteriophage. Subsequent investigations were conducted on the immunostimulatory activity of the MS2+15,597 mixture. The results indicated that the dsRNA mixtures (MS2+15,597) extracted from E. coli infected with the MS2 bacteriophage possess the capability to activate innate immunity, thereby inducing the production of interferon-ß. These dsRNA mixtures can activate the RIG-I and TLR3 pattern recognition receptors, stimulating the expression of interferon stimulatory factors 3/7, which in turn triggers the NF-κB signaling pathway, culminating in the cellular production of interferon-ß to achieve antiviral effects. This study offers novel insights and strategies for the development of broad-spectrum antiviral drugs, potentially providing new modalities for future antiviral therapies.

Microbiomic signatures of anal fistula and putative sources of microbes.

Anal fistula is a common perianal disease that typically develops from an abscess caused by in-flammation in the area. It has long been believed that intestinal microbes play a significant role in its development, considering its close relation to the intestinal environment. This work attempts to identify the microbiomic signatures of anal fistula, and putative sources of microbes by analyzing microbiomes of 7 anal fistula-associated sites in 12 patients. This study found that microbes in anal fistulas may originate from the skin surface in addition to the intestinal tract. This finding was further validated by NMDS analysis, which also indicated that the microbial communities in the inner and outer openings of the fistula were more similar to their surrounding environments. Using MaAslin2, the characteristics of the microbiome were examined, demonstrating a higher similarity between the abundant bacteria in the anal fistula samples and those found on the skin surface. Moreover, pin-to-pair analysis conducted on all subjects consistently showed a higher abundance of skin-sourced bacteria in anal fistulas. This study identifies the microbiomic signatures of anal fistula, and provides novel insights into the origin of microorganisms in anal fistulas.

Genome-wide identification of GTE family proteins in sugarcane (Saccharum spontaneum) reveals that SsGTEL3a confers drought tolerance.

The bromodomain is a highly conserved protein domain that specifically binds to acetylated lysine residues in histones, thereby activating transcription of target genes. Although some progress in Global Transcription Factor Group E (GTE) has been achieved in numerous animals and a few plant species, no systematic analysis of GTE gene families has been reported yet in sugarcane. In our study, 37 GTE and GTE-Like (GTEL) genes were characterized in the Saccharum spontaneum. All SsGTE/SsGTEL members were heterogeneously located on all chromosomes of the sugarcane genome and divided into five groups. Transcriptome data showed that SsGTEL3a was expressed at significantly higher levels under drought stress in drought-resistant varieties than in drought-sensitive varieties. Moreover, the overexpression of SsGTEL3a significantly improved the drought tolerance in Arabidopsis through improving the scavenging ability of reactive oxygen species. Additionally, an interaction between ScFAR1 and SsGTEL3a was identified, with ScFAR1 showing a positive response to drought stress in bacterium. In summary, this systematic analysis of GTE gene family in sugarcane and functional research of SsGTEL3a broadened deeper insight into their evolutionary dynamics and functional properties and provided new candidate genes for drought-resistant molecular breeding of sugarcane.

Role of PDLIM1 in hepatic stellate cell activation and liver fibrosis progression.

Liver fibrosis is caused by chronic hepatic injury and may lead to cirrhosis, and even hepatocellular carcinoma. When hepatic stellate cells (HSCs) are activated by liver injury, they transdifferentiate into myofibroblasts, which secrete extracellular matrix proteins that generate the fibrous scar. Therefore, it is extremely urgent to find safe and effective drugs for HSCs activation treatment to prevent liver against fibrosis. Here, we reported that PDZ and LIM domain protein 1 (PDLIM1), a highly conserved cytoskeleton organization regulator, was significantly up-regulated in fibrotic liver tissues and TGF-ß-treated HSC-T6 cells. Through transcriptome analysis, we found that knockdown of PDLIM1 resulted in a significant downregulation of genes related to inflammation and immune-related pathways in HSC-T6 cells. Moreover, PDLIM1 knockdown significantly inhibited the activation of HSC-T6 cells and the trans-differentiation of HSC-T6 cells into myofibroblasts. Mechanistically, PDLIM1 is involved in the regulation of TGF-ß-mediated signaling pathways in HSCs activation. Thus, targeting PDLIM1 may provide an alternative method to suppress HSCs activation during liver injury. CCCTC-binding factor (CTCF), a master regulator of genome architecture, is upregulated during HSCs activation. PDLIM1 knockdown also indirectly reduced CTCF protein expression, however, CTCF binding to chromatin was not significantly altered by CUT&Tag analysis. We speculate that CTCF may cooperate with PDLIM1 to activate HSCs in other ways. Our results suggest that PDLIM1 can accelerate the activation of HSCs and liver fibrosis progression and could be a potential biomarker for monitoring response to anti-fibrotic therapy.

Learning curve for flexible bronchoscope-guided orotracheal intubation for anesthesiology residents: A cumulative sum analysis.

BACKGROUND: Endotracheal intubation with a flexible bronchoscope is a well-recognized airway management technique that anesthesiologists must master. Skill acquisition and knowledge must reach an appropriate level before trainees perform independent practice on patients. There are a paucity of evidence-based outcome measures of trainee competence in performing flexible bronchoscopy. The objectives of this study were to 1) construct a learning curve for flexible bronchoscope-guided orotracheal intubation for anesthesiology residents using the CUSUM method and 2) determine the number of procedures required to achieve proficiency. METHODS: This study included 12 first-year anesthesiology residents with no previous experience with flexible bronchoscopic intubation. Trainees attended theoretical and simulation training and performed flexible bronchoscope-guided orotracheal intubation in adult patients with normal airways under general anesthesia. Number of intubation attempts, intubation success rate, time to intubation, and incidence of dental and mucosal injuries were recorded. The cumulative sum (CUSUM) method was used to evaluate the learning curve of flexible bronchoscope-guided orotracheal intubation. RESULTS: Trainees performed flexible bronchoscope-guided orotracheal intubation on 364 patients. First-attempt intubation success occurred in 317 (87.1%) patients. Second-attempt intubation success occurred in 23 (6.3%) patients. Overall, the flexible bronchoscope-guided orotracheal intubation success rate was 93.4% (range, 85.3% to 100%). The mean number of orotracheal intubation procedures per trainee was 31 ± 5 (range, 23 to 40). All trainees crossed the lower decision boundary (H0) after 15.1 ± 5.6 procedures (range, 8 to 25 procedures). There was a significant decrease in median intubation time [39s (IQR: 30, 50) vs. 76s (IQR: 54, 119)] (P < 0.001) after crossing the lower decision boundary (H0) compared to before. There were no dental, mucosa, arytenoid or vocal cord trauma events associated with intubation. CONCLUSIONS: Learning curves constructed with CUSUM analysis showed that all trainees (anesthesiologist residents) included in this study achieved competence (intubation success rates ≥ 80%) in flexible bronchoscope-guided orotracheal intubation. Trainees needed to perform 15 (range, 8 to 25) procedures to achieve proficiency. There was wide variability between trainees. TRIAL REGISTRATION: Trial registration: Chinese Clinical Trial Register, ChiCTR 2000032166.

Incidence of acute kidney injury after hematopoietic stem cell transplantation in children: a systematic review and meta-analysis.

While acute kidney injury (AKI) has been reported after hematopoietic stem cell transplantation (HCT) in children, the incidence of this condition in the pediatric population has not been fully addressed. To assess the incidence of pediatric AKI after HCT treatment,we conducted a systematic literature review. Databases PubMed, Embase, Cochrane Library, and WOS were searched as of June 2022 to identify studies on the incidence and the risk of death in AKI children undergoing HCT. Random effects and generic inverse variance methods were used, and effect estimates were subsequently derived from individual studies. Twelve cohort studies with 2 159 HCT cases were included in this analysis. The combined estimated incidence of AKI and severe AKI (stage AKI III) was 51% (95% confidence interval (CI) 39-64%) and 12% (95%CI 4-24%), respectively. The estimated incidence of AKI based on RIFLE (pRIFLE), AKIN, and KDIGO criteria was 61% (95%CI 40-82% score I 95.1%), 64% (95%CI 49-79% score I 90.4%), and 51% (95%CI 2-100% score 99.0%), respectively. However, we found no significant correlation between the years of publication of the included studies and the incidence of AKI.  Conclusions: AKI affects approximately half of the children after HCT. With the advancements in medical techniques, it is expected that AKI in this population will decrease gradually. What is Known: • Hematopoietic stem cell transplantation is recognized as a treatment for malignant and non-malignant diseases in children. • Hematopoietic stem cell transplantation causes acute kidney injury in children. What is New: • This metanalysis showed that the overall frequency of post-HCT AKI in children is 51%. • The frequency of severe AKI after HCT was found to be 12%.

Research on the Mechanism and Control Technology of Coal Wall Sloughing in the Ultra-Large Mining Height Working Face.

One of the primary factors affecting safe and effective mining in fully mechanized mining faces with large mining heights is coal wall sloughing. This paper establishes the mechanical model of the coal wall and uses the deflection theory for the mechanics of materials to find the maximum point of the deflection of the coal wall, which is the most easily deformed and damaged during the mining process, based on the mining production conditions of the 12-2up108 working face in the Jinjitan Coal Mine. In order to simulate the characteristics of the coal wall in the large mining height working face at various mining heights, the FLAC-3D numerical method was used. The stability of the mining area was assessed in conjunction with the multi-factor fuzzy comprehensive evaluation mathematical model, and the corresponding control of the coal wall was suggested. The study demonstrates that: (1) The working surface at Jinjitan Coal Mine 112-2up108 is a typical drum-out sloughing. The coal wall is most likely to sustain damage at the point where it contacts the roof when the frictional resistance between the coal seam and the roof and floor is less than the uniform load, and at 0.578 times the mining height when the frictional resistance between the coal seam and the roof and floor is greater than the uniform load. (2) In the working face with a large mining height, mining height of the coal wall is one of the significant influencing factors. With increasing mining height, the coal wall's height also rises nonlinearly, as does the depth of the coal wall in the working face with the large mining height. The growth is linear. The coal wall's maximum deflection value point moves up and the slab's height significantly increases when the mining height exceeds 7.5 m. (3) The Jinjitan Coal Mine should be supported by a pressurized and enhanced composite support bracket with a support force greater than 0.245 MPa and a support plate of 3500 mm because it belongs to a Class I stable coal wall, according to a thorough evaluation of a multi-factor fuzzy mathematical model. The working face's mining pressure is continuously and dynamically monitored, and the stress is released in a timely manner to prevent the occurrence of dynamic disasters.

FAIRE-MS reveals mitotic retention of transcriptional regulators on a proteome-wide scale.

Mitosis entails global and dramatic alterations, such as higher-order chromatin organization disruption, concomitant with global transcription downregulation. Cells reliably re-establishing gene expression patterns upon mitotic exit and maintaining cellular identities remain poorly understood. Previous studies indicated that certain transcription factors (TFs) remain associated with individual loci during mitosis and serve as mitotic bookmarkers. However, it is unclear which regulatory factors remain bound to the compacted mitotic chromosomes. We developed formaldehyde-assisted isolation of regulatory elements-coupled mass spectrometry (FAIRE-MS) that combines FAIRE-based open chromatin-associated protein pull-down and mass spectrometry (MS) to quantify the open chromatin-associated proteome during the interphase and mitosis. We identified 189 interphase and mitosis maintained (IM) regulatory factors using FAIRE-MS and found intrinsically disordered proteins and regions (IDP(R)s) are highly enriched, which plays a crucial role in liquid-liquid phase separation (LLPS) and chromatin organization during the cell cycle. Notably, in these IDP(R)s, we identified mitotic bookmarkers, such as CEBPB, HMGB1, and TFAP2A, and several factors, including MAX, HMGB3, hnRNP A2/B1, FUS, hnRNP D, and TIAL1, which are at least partially bound to the mitotic chromosome. Furthermore, it will be essential to study whether these IDP(R)s through LLPS helps cells transit from mitosis to the G1 phase during the cell cycle.

Deubiquitinating enzyme Josephin-2 stabilizes PHGDH to promote a cancer stem cell phenotype in hepatocellular carcinoma.

BACKGROUND: Deubiquitinating enzymes (DUBs) have been shown to be possible targets for hepatocellular carcinoma (HCC) treatment. OBJECTIVE: This study was designed to reveal the effect and underlying mechanism of Josephin-2, a relatively newly defined DUB, in HCC progression. METHODS: SNU-387 and PLC/PRF/5 cells were used for in vitro functional assays. The levels of Josephin-2 and phosphoglycerate dehydrogenase (PHGDH) were determined using RT-qPCR and western blotting. Cell proliferation, migration and invasion were assessed by CCK-8, colony formation and Transwell. Spheroid-forming assay was performed to assess the cancer stem cell (CSC)-phenotype of HCC cells. A xenograft mice model was applied to verify the effect of Josephin-2 on HCC cell growth in vivo. RESULTS: Herein, we showed that Josephin-2 expression was negatively correlated with HCC patient survival in data from the online database. Cell experiments indicated that knockdown of Josephin-2 attenuated HCC cell malignant biological behaviors. Besides, Josephin-2 silencing also decreased the spheroid-formation while inhibited the expression of CSC biomarkers (CD133, OCT4, SOX2 and EpCAM) in HCC cells. Mechanistically, Josephin-2 had a deubiquitinating activity towards the regulation of PHGDH protein, the rate-limiting enzyme in the first step of serine biosynthesis pathway. Depletion of Josephin-2 enhanced the ubiquitination degradation of PHGDH and ultimately inhibited the proliferation and CSC-phenotype of HCC in vitro and in vivo. CONCLUSION: Our work uncovered the regulatory effects of Josephin-2 on PHGDH protein stability and profiled its contribution in HCC malignant progression, which might provide a potential therapeutic target for HCC.

Targeted screening of genetic associations with COVID-19 susceptibility and severity.

The COVID-19 pandemic has resulted in great morbidity and mortality worldwide and human genetic factors have been implicated in the susceptibility and severity of COVID-19. However, few replicate researches have been performed, and studies on associated genes mainly focused on genic regions while regulatory regions were a lack of in-depth dissection. Here, based on previously reported associated variants and genes, we designed a capture panel covering 1,238 candidate variants and 25 regulatory regions of 19 candidate genes and targeted-sequenced 96 mild and 145 severe COVID-19 patients. Genetic association analysis was conducted between mild and severe COVID-19 patients, between all COVID-19 patients and general population, or between severe COVID-19 patients and general population. A total of 49 variants were confirmed to be associated with susceptibility or severity of COVID-19 (p < 0.05), corresponding to 18 independent loci. Specifically, rs1799964 in the promoter of inflammation-related gene TNF, rs9975538 in the intron of interferon receptor gene IFNAR2, rs429358 in the exon of APOE, rs1886814 in the intron of FOXP4-AS1 and a list of variants in the widely reported 3p21.31 and ABO gene were confirmed. It is worth noting that, for the confirmed variants, the phenotypes of the cases and controls were highly consistent between our study and previous reports, and the confirmed variants identified between mild and severe patients were quite different from those identified between patients and general population, suggesting the genetic basis of susceptibility and severity of SARS-CoV-2 infection might be quite different. Moreover, we newly identified 67 significant associated variants in the 12 regulatory regions of 11 candidate genes (p < 0.05). Further annotation by RegulomeDB database and GTEx eQTL data filtered out two variants (rs11246060 and rs28655829) in the enhancer of broad-spectrum antiviral gene IFITM3 that might affect disease severity by regulating the gene expression. Collectively, we confirmed a list of previously reported variants and identified novel regulatory variants associated with susceptibility and severity of COVID-19, which might provide biological and clinical insights into COVID-19 pathogenesis and treatment.

Pilot genome-wide association study of antibody response to inactivated SARS-CoV-2 vaccines.

Vaccines are a key weapon against the COVID-19 pandemic caused by SARS-CoV-2. However, there are inter-individual differences in immune response to SARS-CoV-2 vaccines and genetic contributions to these differences have barely been investigated. Here, we performed genome-wide association study (GWAS) of antibody levels in 168 inactivated SARS-CoV-2 vaccine recipients. A total of 177 SNPs, corresponding to 41 independent loci, were identified to be associated with IgG, total antibodies or neutral antibodies. Specifically, the rs4543780, the intronic variant of FAM89A gene, was associated with total antibodies level and was annotated as a potential regulatory variant affecting gene expression of FAM89A, a biomarker differentiating bacterial from viral infections in febrile children. These findings might advance our knowledge of the molecular mechanisms driving immunity to SARS-CoV-2 vaccine.

Profiling and characterization of constitutive chromatin-enriched RNAs.

RNA species act as architectural scaffolds for nuclear structures including chromatin in eukaryotic cells. However, the composition and dynamics of tightly bound chromatin-associated RNAs during mitosis remains elusive. Here we report the identification of chromatin-enriched RNA (cheRNAs) by biochemical nuclear fractionation coupled with RNA sequencing in both interphase and mitotic phase of A549 and HeLa-S3 cell lines. We show that highly abundant cheRNAs, mostly small noncoding RNAs, are largely maintained in mitotic chromatin, and constitute a substantial part of chromatin RNA throughout cell cycle. We also show that the mitotic retained cheRNAs tend to be cell type nonspecific and might be involved in chromatin accessibility and epigenetic memory of gene expression control. Therefore, we reveal an unexpected set of cell type-nonspecific mitotic retained chromatin-enriched RNAs. We anticipate that the landscape of RNA composition of chromatin both in interphase and mitotic phase would help understanding structure and function of chromatin.

The role of ZNF143 overexpression in rat liver cell proliferation.

BACKGROUND: Zinc finger protein 143(ZNF143), a member of the Krüppel C2H2-type zinc finger protein family, is strongly associated with cell cycle regulation and cancer development. A recent study suggested that ZNF143 plays as a transcriptional activator that promotes hepatocellular cancer (HCC) cell proliferation and cell cycle transition. However, the exact biological role of ZNF143 in liver regeneration and normal liver cell proliferation has not yet been investigated. METHODS: In our study, we constructed a stable rat liver cell line (BRL-3A) overexpressing ZNF143 and then integrated RNA-seq and Cleavage Under Targets and Tagmentation (CUT&Tag) data to identify the mechanism underlying differential gene expression. RESULTS: Our results show that ZNF143 expression is upregulated during the proliferation phase of liver regeneration after 2/3 partial hepatectomy (PH). The cell counting kit-8 (CCK-8) assay, EdU staining and RNA-seq data analyses revealed that ZNF143 overexpression (OE) significantly inhibited BRL-3A cell proliferation and cell cycle progression. We then performed CUT&Tag assays and found that approximately 10% of ZNF143-binding sites (BSs) were significantly changed genome-wide by ZNF143 OE. However, CCCTC-binding factor (CTCF) binding to chromatin was not affected. Interestingly, the integration analysis of RNA-seq and CUT&Tag data showed that some of genes affected by ZNF143 differential BSs are in the center of each gene regulation module. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that these genes are critical in the maintenance of cell identity. CONCLUSION: These results indicated that the expression level of ZNF143 in the liver is important for the maintenance of cell identity. ZNF143 plays different roles in HCC and normal liver cells and may be considered as a potential therapeutic target in liver disease.

Flexible Bronchoscope versus Video Laryngoscope for Orotracheal Intubation During Upper Gastrointestinal Endoscopic Surgery in Left Lateral Position: A Randomized Controlled Trial.

Purpose: Endoscopic submucosal dissection (ESD) has become the primary treatment for early upper gastrointestinal tract lesions. During endoscopic surgery, endotracheal intubation is generally performed in the patients' supine position, and patients are shifted to the left lateral position for endoscopic surgery. This study compared the efficacy of flexible bronchoscope-guided intubation with that of video laryngoscope-guided intubation in the left lateral position. Patients and Methods: Forty-eight patients receiving ESD were randomly divided into the flexible bronchoscope group (group F) or the video laryngoscope group (group V). Tracheal intubation was performed by a trained anesthetist with a flexible bronchoscope (group F) or unchanneled video laryngoscope (group V) in the left lateral position. Primary outcomes included the intubation duration and success rate. Secondary outcomes included the ease of intubation technique and the occurrence of complications. Results: Twenty-four (100%) patients in group F and twenty-three (95.8%) in group V were successfully intubated (P = 1.000). The median intubation time in group F was 37s (interquartile range, 33.0, 44.5), which was significantly shorter compared to group V (53s [45.5, 66.5]; P < 0.001). The flexible bronchoscope was significantly easier to manage than the video laryngoscope, as reflected by the users scoring system (9 [9, 10] vs 8 [7, 8]; P < 0.001). The presence of perioperative adverse events and complications were comparable between the two groups. Conclusion: Both flexible bronchoscope- and video laryngoscope-guided intubation in patients' left lateral position achieved high success rates and comparable complication rates. However, intubation with the flexible bronchoscope was completed more quickly.

Changes in Higher-Order Chromosomal Structure of Klebsiella pneumoniae Under Simulated Microgravity.

Our previous work have shown that certain subpopulations of Klebsiella pneumoniae exhibit significant phenotypic changes under simulated microgravity (SMG), including enhanced biofilm formation and cellulose synthesis, which may be evoked by changes in gene expression patterns. It is well known that prokaryotic cells genomic DNA can be hierarchically organized into different higher-order three-dimensional structures, which can highly influence gene expression. It is remain elusive whether phenotypic changes induced by SMG in the subpopulations of K. pneumoniae are driven by genome higher-order structural changes. Here, we investigated the above-mentioned issue using the wild-type (WT) K. pneumoniae (WT was used as a control strain and continuously cultivated for 2 weeks under standard culture conditions of normal gravity) and two previous identified subpopulations (M1 and M2) obtained after 2 weeks of continuous incubation in a SMG device. By the combination of genome-wide chromosome conformation capture (Hi-C), RNA-seq and whole-genome methylation (WGS) analyses, we found that the along with the global chromosome interactions change, the compacting extent of M1, M2 subpopulations were much looser under SMG and even with an increase in active, open chromosome regions. In addition, transcriptome data showed that most differentially expressed genes (DEGs) were upregulated, whereas a few DEGs were downregulated in M1 and M2. The functions of both types DEGs were mainly associated with membrane fractions. Additionally, WGS analysis revealed that methylation levels were lower in M1 and M2. Using combined analysis of multi-omics data, we discovered that most upregulated DEGs were significantly enriched in the boundary regions of the variable chromosomal interaction domains (CIDs), in which genes regulating biofilm formation were mainly located. These results suggest that K. pneumoniae may regulate gene expression patterns through DNA methylation and changes in genome structure, thus resulting in new phenotypes in response to altered gravity.

dbGSRV: A manually curated database of genetic susceptibility to respiratory virus.

Human genetics has been proposed to play an essential role in inter-individual differences in respiratory virus infection occurrence and outcomes. To systematically understand human genetic contributions to respiratory virus infection, we developed the database dbGSRV, a manually curated database that integrated the host genetic susceptibility and severity studies of respiratory viruses scattered over literatures in PubMed. At present, dbGSRV contains 1932 records of genetic association studies relating 1010 unique variants and seven respiratory viruses, manually curated from 168 published articles. Users can access the records by quick searching, batch searching, advanced searching and browsing. Reference information, infection status, population information, mutation information and disease relationship are provided for each record, as well as hyperlinks to public databases in convenient of users accessing more information. In addition, a visual overview of the topological network relationship between respiratory viruses and associated genes is provided. Therefore, dbGSRV offers a convenient resource for researchers to browse and retrieve genetic associations with respiratory viruses, which may inspire future studies and provide new insights in our understanding and treatment of respiratory virus infection. Database URL: http://www.ehbio.com/dbGSRV/front/.

Abutment Pressure Distribution Law and Support Analysis of Super Large Mining Height Face.

Under the condition of the shallow coal seam, the laws of roof activity after large mining height longwall face mining and prevention measures for large-area roof weighting are problems that need to be solved urgently. In the background of the super large mining height working face in the upper 108 working face of Jinjitan Coal Mine 12-2, the spatial distribution characteristics of the development and change of the mining-induced abutment pressure and the related support design in the 8.2 m super large mining height and fully mechanized mining face were conducted. It reveals the distribution characteristics of the dynamic stress field and internal and external stress fields. The influence range of the abutment pressure of the super high mining height working face was measured on site. The numerical simulation is carried out, the roadway support structure is analyzed, and the improvement measures are proposed. The research results demonstrate that: The influence range of abutment pressure is 234 m, the obvious influence range of the leading pressure is 47-60 m, and the peak position of the influence of the leading pressure is 15-20 m. The 5 m range is the lateral inward stress field of the coal pillar, the 10-15 m range is the outward stress field of the coal pillar, and the 20 m range is the original rock stress field of the coal pillar. Therefore, it is proposed that the reasonable size of the coal pillar for roadway protection is 20-22 m. Adjusting the distance between screw steel and FRP bolts from 1000 mm to 1200 mm, the length of the roof prestressed anchor cable should be appropriately reduced to 5.5-6 m according to the lithology of the roof.

In vivo structure and dynamics of the SARS-CoV-2 RNA genome.

The dynamics of SARS-CoV-2 RNA structure and their functional relevance are largely unknown. Here we develop a simplified SPLASH assay and comprehensively map the in vivo RNA-RNA interactome of SARS-CoV-2 genome across viral life cycle. We report canonical and alternative structures including 5'-UTR and 3'-UTR, frameshifting element (FSE) pseudoknot and genome cyclization in both cells and virions. We provide direct evidence of interactions between Transcription Regulating Sequences, which facilitate discontinuous transcription. In addition, we reveal alternative short and long distance arches around FSE. More importantly, we find that within virions, while SARS-CoV-2 genome RNA undergoes intensive compaction, genome domains remain stable but with strengthened demarcation of local domains and weakened global cyclization. Taken together, our analysis reveals the structural basis for the regulation of replication, discontinuous transcription and translational frameshifting, the alternative conformations and the maintenance of global genome organization during the whole life cycle of SARS-CoV-2, which we anticipate will help develop better antiviral strategies.

Changes in Vibrio natriegens Growth Under Simulated Microgravity.

The growth rate of bacteria increases under simulated microgravity (SMG) with low-shear force. The next-generation microbial chassis Vibrio natriegens (V. natriegens) is a fast-growing Gram-negative, non-pathogenic bacterium with a generation time of less than 10 min. Screening of a V. natriegens strain with faster growth rate was attempted by 2-week continuous long-term culturing under SMG. However, the rapid growth rate of this strain made it difficult to obtain the desired mutant strain with even more rapid growth. Thus, a mutant with slower growth rate emerged. Multi-omics integration analysis was conducted to explore why this mutant grew more slowly, which might inform us about the molecular mechanisms of rapid growth of V. natriegens instead. The transcriptome data revealed that whereas genes related to mechanical signal transduction and flagellin biogenesis were up-regulated, those involved in adaptive responses, anaerobic and nitrogen metabolism, chromosome segregation and cell vitality were down-regulated. Moreover, genome-wide chromosome conformation capture (Hi-C) results of the slower growth mutant and wide type indicated that SMG-induced great changes of genome 3D organization were highly correlated with differentially expressed genes (DEGs). Meanwhile, whole genome re-sequencing found a significant number of structure variations (SVs) were enriched in regions with lower interaction frequency and down-regulated genes in the slower growth mutant compared with wild type (WT), which might represent a prophage region. Additionally, there was also a decreased interaction frequency in regions associated with well-orchestrated chromosomes replication. These results suggested that SMG might regulate local gene expression by sensing stress changes through conformation changes in the genome region of genes involved in flagellin, adaptability and chromosome segregation, thus followed by alteration of some physiological characteristics and affecting the growth rate and metabolic capacity.

miR-25-3p inhibition impairs tumorigenesis and invasion in gastric cancer cells in vitro and in vivo.

Deregulated expression of microRNAs (miRNAs) plays a role in the pathogenesis and progression of gastric cancer (GC). Among upregulated miRNAs, miR-25-3p has oncogenic potential and therefore represents an attractive target for the treatment of GC. Here, we investigated the role of miR-25-3p on GC cells in vitro and in vivo. We found that miR-25-3p overexpression significantly promoted growth and invasion of gastric cancer cells in vitro. Conversely, targeting miR-25-3p triggered significant inhibition of growth, invasion and migration in GC cells in vitro. In vivo delivery of miR-25-3p inhibitors induced significant anti-tumor activity in SCID mice bearing human GC xenografts. Our findings showed the evidence that in vivo antagonism of miR-25-3p impaired tumorigenesis, providing the rationale for clinical development of miR-25-3p inhibitors in GC.