Microbial communities such as those residing in the human gut are highly diverse and complex, and many with important implications for health and diseases. The effects and functions of these microbial communities are determined not only by their species compositions and diversities but also by the dynamic intra- and inter-cellular states at the transcriptional level. Powerful and scalable technologies capable of acquiring single-microbe-resolution RNA sequencing information in order to achieve a comprehensive understanding of complex microbial communities together with their hosts are therefore utterly needed. Here we report the development and utilization of a droplet-based smRNA-seq (single-microbe RNA sequencing) method capable of identifying large species varieties in human samples, which we name smRandom-seq2. Together with a triple-module computational pipeline designed for the bacteria and bacteriophage sequencing data by smRandom-seq2 in four human gut samples, we established a single-cell level bacterial transcriptional landscape of human gut microbiome, which included 29,742 single microbes and 329 unique species. Distinct adaptive response states among species in Prevotella and Roseburia genera and intrinsic adaptive strategy heterogeneity in Phascolarctobacterium succinatutens were uncovered. Additionally, we identified hundreds of novel host-phage transcriptional activity associations in the human gut microbiome. Our results indicated that smRandom-seq2 is a high-throughput and high-resolution smRNA-seq technique that is highly adaptable to complex microbial communities in real-world situations and promises new perspectives in the understanding of human microbiomes.
Humans ; Gastrointestinal Microbiome/genetics* ; Bacteriophages/physiology* ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, RNA/methods* ; Bacteria/virology*

Objective To explore the role and efficacy of VEGF and HGF gene adenovirus vector in promoting angiogenesis in ischemic tissue.Methods 84 Kunming mice were randomly divided into sham group,control group,VEGF group,HGF group and VEGF+HGF group,and the left lower limb ischemia model was established.The blood supply of ischemic tissue was observed by rheometer,and the expression levels of VEGF and HGF in each group were detected by Western Blot and ELISA.Immunohistochemical staining was used to detect angiogenesis(CD31,SMA)in ischemic tissues.Safety was assessed by side effects during treatment in mice.Results After the successful modeling,the blood flow velocity of the left lower limb in each group decreased significantly.On the 7th day after operation,the blood flow of the left lower limb in each group was significantly better than that on the 0th day after operation(P<0.05),and the blood flow of the left lower limb in Ad-VEGF-HGF group was significantly better than that in other groups(P<0.05).On the 28th day after operation,the blood flow of the left lower limb in Ad-VEGF-HGF group gradually stabilized,the blood flow in Ad-VEGF-HGF group was significantly better than that in other groups,and both VEGF group and HGF group were significantly better than the control group(P<0.05).On the 7th,14th,and 28th days following surgery,HGF and VEGF protein levels in the Ad-HGF,Ad-VEGF,and Ad-VEGF-HGF groups were substantially greater than those in the control group(P<0.05).The expression level in the Ad-VEGF-HGF group peaked on the 14th day(all P<0.001)and subsequently declined to preoperative levels on the 28th day after operation.Conclusion Ad-VEGF-HGF gene injection can effectively boost VEGF and HGF protein expression and rapidly reach the relative peak level,encour-aging angiogenesis after lower limb ischemia,increasing blood flow,and improving lower limb circulation.

BACKGROUND:Previous studies on cervical instability failed to explain the dynamic and static interaction relationship and pathological characteristics changes in the development of cervical lesions under the traditional imaging examination.In recent years,the emerging nuclear magnetic resonance imaging(MRI)radiomics can provide a new way for in-depth research on cervical instability. OBJECTIVE:To investigate the application value of MRI radiomics in the study of cervical instability. METHODS:Through recruitment advertisements and the Second Department of Spine of Wangjing Hospital,China Academy of Chinese Medical Sciences,young cervical vertebra unstable subjects and non-unstable subjects aged 18-45 years were included in the cervical vertebra nuclear magnetic image collection.Five specific regions of interest,including the intervertebral disc region,the facet region,the prevertebral muscle region,the deep region of the posterior cervical muscle group,and the superficial region of the posterior cervical muscle group,were manually segmented to extract and screen the image features.Finally,the cervical instability diagnosis classification model was constructed,and the effectiveness of the model was evaluated using the area under the curve. RESULTS AND CONCLUSION:(1)A total of 56 subjects with cervical instability and 55 subjects with non-instability were included,and 1 688 imaging features were extracted for each region of interest.After screening,300 sets of specific image feature combinations were obtained,with 60 sets of regions of interest for each group.(2)Five regions of interest diagnostic classification models for cervical instability were initially established.Among them,the support vector machine model for the articular process region and the support vector machine model for the deep cervical muscle group had certain accuracy for the classification of instability and non-instability,and the average area under the curve of ten-fold cross-validation was 0.719 7 and 0.703 3,respectively.(3)The Logistic model in the intervertebral disc region,the LightGBM model in the prevertebral muscle region,and the Logistic model in the superficial posterior cervical muscle region were generally accurate in the classification of instability and non-instability,and the average area under the curve of ten-fold cross-validation was 0.650 4,0.620 7,and 0.644 2,respectively.(4)This study proved the feasibility of MRI radiomics in the study of cervical instability,further deepened the understanding of the pathogenesis of cervical instability,and also provided an objective basis for the accurate diagnosis of cervical instability.

Objective:To analyze the effects of SARS-CoV-2 infection and vaccination on virus mutation.Methods:The whole genome sequencing sequences of 2 659 local SARS-CoV-2 specimens from Jiangsu Province in 2023 were selected for analysis, and relevant information such as demographic and clinical characteristics were collected, and the effects of infection and vaccination on the genome-wide mutation rate and S gene′s selective pressure of the virus were analyzed by univariate and multivariate linear regression models.Results:The average age of these infected patients was 55.0 (31.0, 74.0) years, 1 150 cases (43.2%) in the age group of ≥60 years, 1 367 cases (51.4%) were males, 2 044 cases (76.9%) had a history of COVID-19 vaccination, and 1 629 cases (61.3%) had the first-time infection. The clinical symptoms of the infected patients were mainly mild, with a total of 2434 cases (91.5%), and 29 cases (1.1%) with severe symptoms or more. The average substitution rate of SARS-CoV-2 was 9.69 (9.38, 9.98)×10 -4 subs/site/year, and the dN/dS value of the S gene was 6.08 (5.56, 8.66), which was significantly greater than that of 1 ( P<0.001), indicating positive selection. The result of univariate and multivariate linear regression model analysis showed that the SARS-CoV-2 substitution rate was higher in those with vaccination history and reinfection, aged 20-30 years, ≥60 years, and the SARS-CoV-2 substitution rate was lower in males with moderate clinical symptoms and severe disease and above. Those with a history of vaccination and reinfection, aged 50-60 years old, ≥60 years old have smaller S gene dN/dS. Conclusions:Under the immune pressure exerted by vaccination and infection, the genome-wide mutation of SARS-COV-2 accelerated, but the non-synonymous mutation rate of the S gene decreased. The mechanism causing these phenomena needs further study.

Objective:To develop an integrated point-of-care testing (POCT) reagent for genotying respiratory syncytial virus (RSV) and evaluate its performance.Methods:Specific primers and probes were designed based on the conserved sequences of the genomes of RSV A and B as well as ON1 and BA9 genotypes. The PCR reaction system and conditions were optimized. The vitrification technology of reagents and multiplex detection platform were integrated to develop the RSV genotyping POCT reagent. The sensitivity, specificity, reproducibility, and clinical performance of the product were then evaluated.Results:The sensitivity of the developed integrated RSV genotyping POCT reagent reached 500 copies/ml. It exhibited good specificity with no cross-reaction with clinically similar pathogens. The coefficient of variation of Ct values for both inter-batch and intra-batch reproducibility was less than 5%, indicating good reproducibility. In testing 53 clinical samples, the detection results showed high consistency and concordance with the reference reagent, with a positive concordance rate of up to 98.11%.Conclusions:The developed integrated RSV genotyping POCT reagent incorporates nucleic acid extraction, purification, and detection into a single process, achieving a "sample in, result out" workflow. It is simple to operate and provides accurate, reliable, and stable detection results. This product can be used for the genotyping of RSV A and B in POCT, offering support for the prevention, control, and diagnosis of RSV.

Objective To investigate the expression and prognostic significance of serum protease C1 inhib-itor(SERPING1)and plasminogen activator inhibitor type 1(SERPINE1)in patients with sepsis.Methods A total of 132 patients with sepsis treated in the hospital from March 2018 to March 2020 were se-lected as the sepsis group.According to whether they died within 28 days of admission,they were divided into a death group(n=34)and a survival group(n=98).Enzyme linked immunosorbent assay was used to detect the expression of serum SERPING1 and SERPINE1.Multivariate Logistic regression model and receiver oper-ating characteristic curve were used to study the value of serum SERPING1 and serpine1 in evaluating the prognosis of patients'death.Results[Compared with the control group,serum SERPING1(331.12±51.80 ng/L vs.639.04±91.12 ng/L)was lower and serum serpine1(412.67±64.84 ng/L vs.42.33±10.32 ng/L)was higher in the sepsis group,and the differences were statistically significant(P＜0.05).[Compared to the survival group,the levels of serum SERPINE1,procalcitonin,C-reactive protein,Acute Physiology and Chronic Health Evaluation Ⅱ(APACHE Ⅱ)score and Sequential Organ Failure Assessment(SOFA)score in the death group were higher,while serum SERPING1 was lower,and the differences were statistically significant(all P＜0.05).Serum SERPING1 showed negative correlation with APACHE Ⅱ and SOFA scores(r=-0.779,-0.653,P＜0.05),while serum SERPINE1 showed positive correlation with APACHE Ⅱ and SO-FA scores(r=0.740,0.685,P＜0.05).APACHE Ⅱ score,SOFA score,and serum SERPINE1 were risk fac-tors affecting the prognosis of sepsis patients,while serum SERPING1 was a protective factor.The area under the curve of serum SERPING1 and SERPINE1 combined for the evaluation of the death in sepsis patients was 0.938(95％CI:0.893-0.968),which was significantly higher than 0.860(95％CI:0.812-0.899)and 0.838(95％CI:0.781-0.868)of the single detection,and the differences were statistically significant(Z=3.861,4.015,P＜0.001).Conclusion The elevated levels of serum SERPING1 and SERPINE1 in patients with sepsis are related to the severity of the patient's condition.The combination of the two has high prognos-tic value for sepsis patients.

Objective:To explore any effect of upper limb swing training guided by rhythmic auditory stimulation (RAS) on the walking ability of stroke survivors.Methods:Eighty stroke survivors were randomly divided into an observation group and a control group. Both groups received conventional rehabilitation treatment, including neuromuscular facilitation, muscle strength training, balance training and gait training, but the observation group was additionally provided with RAS-guided upper limb swing training for 20min once a day, 5d per week for 6 weeks. Before and after the intervention, balance and lower limb function were quantified in both groups using Holden′s walking function classification, the Fugl-Meyer lower extremity motor function scale (FMA-LE), the Berg Balance Scale (BBS) and the 10m walk test (10MWT). Limits of stability were also quantified.Results:After the treatment, the average Holden, FMA-LE and BBS scores, as well as the average 10MWT time were significantly better in the observation group than in the control group. The average stability limits and their maintenance were also superior.Conclusion:RAS-guided upper limb swing training can improve the gait, walking ability, walking stability, walking speed and balance of stroke survivors.

Objective:To document any effect of clinical rehabilitation pathway management on intubation time, dysfunction and medical expenditure associated with tracheotomy after a stroke.Methods:A total of 154 stroke survivors undergoing tracheotomy were randomly divided into an observation group and a control group, each of 77. Both groups were given routine rehabilitation, while the observation group was additionally provided with clinical rehabilitation pathway management during the rehabilitation intervention. Kaplan-Meier analysis was performed before the experiment and after 2, 4 and 6 weeks of treatment. Clinical pulmonary infection scores (CPISs), scores on the Chelsea Physical Function Assessment Scale (CPAx) and hospitalization cost were compared between the two groups.Results:The median extubation time of the observation group (2d) was significantly shorter than that of the control group (10d). After 2, 4 and 6 weeks of treatment, the average CPIS scores of the observation group were in each case significantly lower than those before treatment and the control group′s averages at the same time points, even though after 4 and 6 weeks of treatment the control group′s average CPIS scores had improved significantly. After 2, 4 and 6 weeks of treatment, the average CPAx scores of the observation group were significantly higher than those before treatment and better than the control group′s averages, even though the control group too had improved significantly compared with before the treatment. Hospitalization days, total hospitalization cost, antibiotic cost and laboratory examination cost of the observation group were, on average, significantly lower than those of the control group.Conclusion:Rehabilitation path management can shorten the period of intubation, prevent pulmonary infections, relieve dysfunction, and reduce medical expenses for stroke survivors after a tracheotomy. It is worthy of clinical promotion.

Objective:To identify the differentially expressed long-chain non-coding RNA(lncRNA) and mRNA using ribonucleic acid sequencing(RNA-seq), and construct a competing endogenous RNA(ceRNA) regulatory network in mice with sepsis-associated encephalopathy.Methods:Ten clean-grade healthy male C57BL/6 mice, aged 6-8 weeks, weighing 20-25 g, were divided into 2 groups( n=5 each) using a random number table method: sham operation group(group Sham) and sepsis group(group Sepsis). Sepsis was induced by cecal ligation and puncture(CLP) in group Sepsis, while group Sham only underwent laparotomy without CLP. Morris water maze test and contextual fear conditioning test were performed to detect the cognitive function on 1 day before CLP and 3 days after CLP. Three mice were randomly sacrificed in group Sham, and 3 mice with the worst results in the cognitive function test were sacrificed in group Sepsis. The hippocampal tissues were obtained for RNA-seq via the BGISEQ-500 platform, and the differentially expressed mRNA and lncRNA were identified. The differentially expressed mRNAs and lncRNAs were visualized and analyzed by Dr. Tom platform provided by Shenzhen BGI Technology Service Co., Ltd., and the ceRNA regulatory network was constructed using the online visualization tool Cytoscape software. Results:Compared with group Sham, the escape latency was significantly prolonged, and the percentage of time of staying at the target quadrants and percentage of time spent freezing were decreased in group Sepsis( P<0.05). A total of 62 differentially expressed lncRNAs were obtained from RNA-seq, of which the expression of 45 lncRNAs was up-regulated and the expression of 17 lncRNAs was down-regulated.There were 282 differentially expressed mRNAs identified from RNA-seq, of which the expression of 173 mRNAs was up-regulated, and the expression of 109 mRNAs was down-regulated.Gene Ontology enrichment analysis revealed that the differentially expressed mRNAs were involved in biological processes such as memory, learning or memory, inflammatory responses, regulation of aging-related behavioral decline, and regulation of synaptic plasticity. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that differentially expressed mRNAs were enriched in IL-17 signaling pathway, TNF signaling pathway, NF-κB signaling pathway and etc. KDA analysis was performed on the differentially expressed mRNAs to identify the key driver genes, and the results showed that Ch25h, Il6ra, Lcn2, Sgk1, Nr4a3, Osm, Saa3, Ccl7, Sqle, Dhcr24 were the key SAE genes.A competing endogenous RNA regulatory network was successfully constructed based on 9 lncRNAs, 28 mRNAs and 134 miRNAs in the hippocampus of mice with SAE. Conclusions:The results of RNA-seq find that 10 mRNAs including Ch25h, Il6ra, Lcn2, Sgk1, Nr4a3, Osm, Saa3, Ccl7, Sqle, Dhcr24 and lncRNAs such as Rian, Gm35874 and Gm34347 are key genes regulating SAE in mice. Meanwhile, a ceRNA regulatory network based on lncRNA-miRNA-mRNA is successfully constructed in the hippocampus of mice with SAE.

The cell cycle is a complex process that involves DNA replication, protein expression, and cell division. Dysregulation of the cell cycle is associated with various diseases. Cyclin-dependent kinases (CDKs) and their corresponding cyclins are major proteins that regulate the cell cycle. In contrast to inhibition, a new approach called proteolysis-targeting chimeras (PROTACs) and molecular glues can eliminate both enzymatic and scaffold functions of CDKs and cyclins, achieving targeted degradation. The field of PROTACs and molecular glues has developed rapidly in recent years. In this article, we aim to summarize the latest developments of CDKs and cyclin protein degraders. The selectivity, application, validation and the current state of each CDK degrader will be overviewed. Additionally, possible methods are discussed for the development of degraders for CDK members that still lack them. Overall, this article provides a comprehensive summary of the latest advancements in CDK and cyclin protein degraders, which will be helpful for researchers working on this topic.
Humans ; Cell Cycle/physiology* ; Cell Division ; Cyclin-Dependent Kinases/metabolism* ; Cyclins/metabolism*