Exome sequencing and characterization of 49,960 individuals in the UK Biobank.

The UK Biobank is a prospective study of 502,543 individuals, combining extensive phenotypic and genotypic data with streamlined access for researchers around the world1. Here we describe the release of exome-sequence data for the first 49,960 study participants, revealing approximately 4 million coding variants (of which around 98.6% have a frequency of less than 1%). The data include 198,269 autosomal predicted loss-of-function (LOF) variants, a more than 14-fold increase compared to the imputed sequence. Nearly all genes (more than 97%) had at least one carrier with a LOF variant, and most genes (more than 69%) had at least ten carriers with a LOF variant. We illustrate the power of characterizing LOF variants in this population through association analyses across 1,730 phenotypes. In addition to replicating established associations, we found novel LOF variants with large effects on disease traits, including PIEZO1 on varicose veins, COL6A1 on corneal resistance, MEPE on bone density, and IQGAP2 and GMPR on blood cell traits. We further demonstrate the value of exome sequencing by surveying the prevalence of pathogenic variants of clinical importance, and show that 2% of this population has a medically actionable variant. Furthermore, we characterize the penetrance of cancer in carriers of pathogenic BRCA1 and BRCA2 variants. Exome sequences from the first 49,960 participants highlight the promise of genome sequencing in large population-based studies and are now accessible to the scientific community.

NAD+ supplementation prevents STING-induced senescence in CD8+ T cells by improving mitochondrial homeostasis.

Understanding the connection between senescence phenotypes and mitochondrial dysfunction is crucial in aging and premature aging diseases. Loss of mitochondrial function leads to a decline in T cell function, which plays a significant role in this process. However, more research is required to determine if improving mitochondrial homeostasis alleviates senescence phenotypes. Our research has shown an association between NAD+ and senescent T cells through the cGAS-STING pathway, which can lead to an inflammatory phenotype. Further research is needed to fully understand the role of NAD+ in T-cell aging and how it can be utilized to improve mitochondrial homeostasis and alleviate senescence phenotypes. We demonstrate here that mitochondrial dysfunction and cellular senescence with a senescence-associated secretory phenotype (SASP) occur in senescent T cells and tumor-bearing mice. Senescence is mediated by a stimulator of interferon genes (STING) and involves ectopic cytoplasmic DNA. We further show that boosting intracellular NAD+ levels with nicotinamide mononucleotide (NMN) prevents senescence and SASP by promoting mitophagy. NMN treatment also suppresses senescence and neuroinflammation and improves the survival cycle of mice. Encouraging mitophagy may be a useful strategy to prevent CD8+ T cells from senescence due to mitochondrial dysfunction. Additionally, supplementing with NMN to increase NAD+ levels could enhance survival rates in mice while also reducing senescence and inflammation, and enhancing mitophagy as a potential therapeutic intervention.

Effect of dietary koumine on the immune and antioxidant status of carp (Cyprinus carpio) after Aeromonas hydrophila infection.

Koumine (KM) has anxiolytic, anti-inflammatory and growth-promoting effects in pigs and sheep. Based on the growth-promoting and immunological effects of koumine, the present study was conducted on Cyprinus carpio (C. carpio) with four KM concentrations: 0 mg/kg, 0.2 mg/kg, 2 mg/kg, and 20 mg/kg for 10 weeks, followed by a 1-week Aeromonas hydrophila (A. hydrophila) infection experiment. The effect of KM on the immunity of A. hydrophila infected carp was analyzed by histopathology, biochemical assay, and qRT-PCR to assess the feasibility of KM in aquaculture. The results showed that the presence of KM alleviated pathogen damage to carp tissues. At 2 mg/kg and 20 mg/kg concentrations of KM successively and significantly elevated (p < 0.05) the SOD activities in the intestinal tract, hepatopancreas and kidney of carp. The expression levels of hepatopancreatic antioxidant genes Nrf2 and IGF-1 were significantly up-regulated in the same group (p < 0.05), while the expression levels of immune genes IL-8 and IL-10 were down-regulated. In summary, KM at concentrations of 2 mg/kg and 20 mg/kg could regulate the expression of antioxidant and immune genes in various tissues in an orderly and rapid manner, and significantly improve the antioxidant and immune abilities of carp, which is conducive to the improvement of the resilience of carp.

Effect of Premedication With Pronase Before Upper Gastrointestinal Endoscopy: A Multicenter Prospective Randomized Controlled Study.

OBJECTIVES: This study aimed to confirm whether premedication with pronase before endoscopy improves mucosal visualization and increases precancerous lesion and cancer lesion detection rates. MATERIALS AND METHODS: From June 2018 to April 2019, out-patients scheduled for endoscopy from 13 hospitals were screened to be randomly allocated in a 2:1 ratio to premedication with pronase (group A) and water (group B). The primary endpoint was mucosal visibility scores, and the secondary endpoint was precancerous and cancer lesion detection rates. This trial was registered at Chinese Clinical Trial Registry, and the registration number was ChiCTR1800016853. RESULTS: Group A showed significantly lower mucosal visibility scores (better mucosal visibility) of esophagus, stomach, and duodenum than group B, with all P -values <0.001. The overall cancer detection rates between group A and group B were 0.83 and 1.08%, and overall detection rates of precancerous and cancer lesion were 4.4 and 4.9%, both without significant difference ( P =1.000 and 0.824). In addition, the flushing volume (milliliter) of group A (10.52±23.41) was less than group B (36.30±52.11) ( P <0.001), and the flushing frequency of group A (0.46±1.01) was fewer than group B (1.62±2.12) ( P <0.001). CONCLUSIONS: Premedication with pronase could achieve better mucosal visibility and decrease flushing frequency and volume, but may not increase lesion detection rates.

Gut microbiota and metabolic changes in children with idiopathic short stature.

BACKGROUND: Idiopathic short stature (ISS) is characterized by short stature with unknown causes. Recent studies showed different gut microbiota flora and reduced fecal short-chain fatty acids in ISS children. However, the roles of the microbiome and metabolites in the pathogenesis of ISS remains largely unknown. METHODS: We recruited 51 Chinese subjects, comprising 26 ISS children and 25 normal-height control individuals. Untargeted metabolomics was performed to explore the fecal metabolic profiles between groups. A shotgun metagenomic sequencing approach was used to investigate the microbiome at the strains level. Mediation analyses were done to reveal correlations between the height standard deviation (SD) value, the gut microbiome and metabolites. RESULTS: We detected marked differences in the composition of fecal metabolites in the ISS group, particularly a significant increase in erucic acid and a decrease in spermidine, adenosine and L-5-Hydroxytryptophan, when compared to those of controls. We further identified specific groups of bacterial strains to be associated with the different metabolic profile. Through mediation analysis, 50 linkages were established. KEGG pathway analysis of microbiota and metabolites indicated nutritional disturbances. 13 selected features were able to accurately distinguish the ISS children from the controls (AUC = 0.933 [95%CI, 79.9-100%]) by receiver operating characteristic (ROC) analysis. CONCLUSION: Our study suggests that the microbiome and the microbial-derived metabolites play certain roles in children's growth. These findings provide a new research direction for better understanding the mechanism(s) underlying ISS.

Chronic cauda equina syndrome decompression surgery recovery is very "bad"? Based on patient self-assessment.

BACKGROUND: Symptoms of cauda equina syndrome (CES) secondary to degenerative lumbar spine diseases are sometimes mild and tend to be ignored by patients, resulting in delayed treatment. In addition, the long-term efficacy of surgery is unclear. OBJECTIVE: To determine the predictive factors of CES and post-operative recovery in patients with symptoms lasting > 3 months. METHODS: From January 2011 to December 2020, data of 45 patients with CES secondary to lumbar disk herniation/lumbar spinal stenosis were collected from a single center. The patients had bladder, bowel or sexual dysfunction and decreased perineal sensation that lasted for > 3 months. A 2-year post-operative follow-up was conducted to evaluate recovery outcomes, which were measured by validated self-assessment questionnaires conducted by telephone and online. RESULTS: Overall, 45 CES patients (57.8% female; mean age, 56 years) were included. The duration of pre-operative CES symptoms was 79.6 weeks (range, 13-730 weeks). The incidence of saddle anesthesia before decompression was 71.1% (n = 32), bladder dysfunction 84.4% (n = 38), bowel dysfunction 62.2% (n = 28) and sexual dysfunction 64.4% (n = 29). The overall recovery rate of CES after a 2-year follow-up was 64.4%. The rates of the residual symptoms at the last follow-up were as follows: saddle anesthesia 22.2%, bladder dysfunction 33.3%, bowel dysfunction 24.4% and sexual dysfunction 48.9%. Pre-operative saddle anesthesia, overactive bladder and sexual dysfunction were risk factors for poor prognosis after decompression. CONCLUSION: CES patients with symptoms lasting > 3 months may recover after surgery. Sexual dysfunction has a high residual rate and should not be ignored during diagnosis and treatment.

Clinical outcomes of radiofrequency ablation using a radiofrequency needle device for varicose ulcer: A non-randomized controlled prospective study.

OBJECTIVE: To evaluate the short-term clinical outcomes of radiofrequency ablation (RFA) using a radiofrequency (RF) needle device for varicose ulcers. METHODS: From September 2020 to September 2021, a total of 80 patients with varicose ulcers were included in this study. Based on the different surgical methods, the patients were divided into RF group and control groups, with 40 cases in each group. In the RF group, RFA was performed using an RF needle device and foam sclerotherapy was used for superficial veins. The control group was treated with conventional high-ligation stripping. The surgical data, hospitalization data, clinical efficacy, and postoperative complications of two groups were compared. Meanwhile, the correlation between RBC, HB, HCT, and ulcer healing time was analyzed. RESULTS: Compared to the control group, RF group had shorter surgery time, duration in the hospital, and less intraoperative bleeding (p < .05). The VCSS and CIVIQ scores in RF group were significantly higher than that in control group (p < .05). The healing time of ulcers was shorter in the RF group (x2 = 19.766, p = .000). The RF group had fewer postoperative complications. There was a positive correlation between RBC, HB, and HCT, and ulcer healing time (p < .05). CONCLUSION: The use of the RF needle device for RFA to treat patients with varicose ulcers showed acceptable short-term clinical outcomes with less incidence of trauma, faster recovery, and fewer complications.

The effectiveness of problem-based learning and case-based learning teaching methods in clinical practical teaching in TACE treatment for hepatocellular carcinoma in China: a bayesian network meta-analysis.

PURPOSE: To investigate the effectiveness of problem-based learning (PBL) and case-based learning (CBL) teaching methods in clinical practical teaching in transarterial chemoembolization (TACE) treatment in China. MATERIALS AND METHODS: A comprehensive search of PubMed, the Chinese National Knowledge Infrastructure (CNKI) database, the Weipu database and the Wanfang database up to June 2023 was performed to collect studies that evaluate the effectiveness of problem-based learning and case-based learning teaching methods in clinical practical teaching in TACE treatment in China. Statistical analysis was performed by R software (4.2.1) calling JAGS software (4.3.1) in a Bayesian framework using the Markov chain-Monte Carlo method for direct and indirect comparisons. The R packages "gemtc", "rjags", "openxlsx", and "ggplot2" were used for statistical analysis and data output. RESULTS: Finally, 7 studies (five RCTs and two observational studies) were included in the meta-analysis. The combination of PBL and CBL showed more effectiveness in clinical thinking capacity, clinical practice capacity, knowledge understanding degree, literature reading ability, method satisfaction degree, learning efficiency, learning interest, practical skills examination scores and theoretical knowledge examination scores. CONCLUSIONS: Network meta-analysis revealed that the application of PBL combined with the CBL teaching mode in the teaching of liver cancer intervention therapy significantly improves the teaching effect and significantly improves the theoretical and surgical operations, meeting the requirements of clinical education.

Evaluation of Different Fixation Methods Combinations After L-Shaped Osteotomy Reduction Malarplasty: An In Vitro Biomechanical Study.

BACKGROUND: This in vitro study compared the stability of different fixation method combinations for the zygomatic complex after simulated L-shaped osteotomy reduction malarplasty, a common facial contouring surgery in East Asia with high postoperative complications due to poor fixation methods. MATERIALS AND METHODS: The study used 108 zygoma replicas with various fixation methods combinations in the zygomatic body (L-shaped plate with short wing on zygoma and on the maxilla, two bicortical screws, one bicortical screw with L-shaped plate, square plate, and rectangular plate) and zygomatic arch (Mortise-Tenon structure, 3-hole plate, and Mortise-Tenon structure plus short screw). The failure force under incremental load was applied through the Instron tensile machine to a well-stabilized model using a rubber band simulating the masseter muscle and recorded the increasing force digitally. ANOVA test was used for comparison between recorded values (P < 0.05). RESULTS: The results showed that the most stable combination was a six-hole rectangular plate and a Mortise-Tenon structure plus one short screw (358.55 ± 51.64 N/mm2). The results also indicated that the placement vector of the fixation methods around the L-shaped osteotomy and the use of the two-bridge fixation method were important factors in enhancing the stability of the zygomatic complex. CONCLUSION: The study suggested that surgeons should choose appropriate fixation methods based on these factors to reduce postoperative complications and improve surgical outcomes. NO LEVEL ASSIGNED: This journal requires that authors assign a level of evidence to each submission to which Evidence-Based Medicine rankings are applicable. This excludes Review Articles, Book Reviews, and manuscripts that concern Basic Science, Animal Studies, Cadaver Studies, and Experimental Studies. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

Dietary kelp meal improves serum antioxidants, intestinal immunity, and lipid metabolism in hybrid snakehead (Channa maculata ♀ × Channa argus ♂).

BACKGROUND: Dietary kelp possesses a variety of useful biological qualities but does not have a toxic effect on the host. In this study, we examine how kelp dietary supplementation enhances the serum biochemistry, intestinal immunity, and metabolism of hybrid snakehead. A total of 810 juvenile hybrid snakeheads (Channa maculata ♀ × Channa argus ♂), with an initial average weight of 11.4 ± 0.15 g, were allocated randomly to three treatment groups (three replicates per group). The fish were fed for 60 days with isonitrogenous and isolipidic diets. The groups were the control group (C) (20% high-gluten flour), the medium replacement group (MR) (10% high-gluten flour and 10% kelp meal), and the full replacement group (FR) (0% high-gluten flour and 15% kelp meal). RESULTS: The results showed that dietary kelp increased the activity of serum antioxidant enzymes significantly and decreased the content of serum malondialdehyde (MDA) in hybrid snakeheads, with significant changes in the FR group (P < 0.05). The intestinal morphology results showed that dietary kelp helped to increase the specific surface area of intestinal villi, which was beneficial for intestinal digestion and absorption. According to transcriptome and quantitative real-time polymerase chain reaction (qRT-PCR) analysis, dietary kelp can improve the expression of intestinal immunity and metabolism-related pathways. Among them, immune-related genes MHC1 and HSPA1 were significantly up-regulated, and IGH, MHC2, and IL-8 were significantly down-regulated (P < 0.05). Lipid metabolism-related genes DGAT2, FABP2, RXRα, and PLPP1 were all significantly up-regulated (P < 0.05). CONCLUSION: Dietary kelp can effectively improve the antioxidant function of hybrid snakeheads, improve intestinal morphology, reduce intestinal inflammation, and promote intestinal lipid synthesis and transportation, thereby improving intestinal immunity and metabolic functions. © 2024 Society of Chemical Industry.

The effect of fine particulate matter (PM2.5) pollution on health inequality: an intergenerational perspective.

Air pollution poses a serious challenge to public health and simultaneously exacerbating regional & intergenerational health inequality. This research introduces PM2.5 pollution into the intergenerational health transmission model, and estimates its impact on health inequality in China using Ordered Logit Regression (OLR) and Multi-scale Geographically Weighted Regression (MGWR) model. The results indicate that PM2.5 pollution exacerbate the intergenerational health inequality, and its impacts show inconsistency across family income levels, parental health insurance status, and area of residence. Specifically, it is more difficult for offspring in low-income families to escape from the influence of unhealthy family to become upwardly mobile. Additionally, this health inequality is more significant in households in which at least one parent does not have health insurance. Moreover, the intergenerational solidification caused by PM2.5 pollution is higher in the east and lower in the west. Both the PM2.5 level and solidification effect are high in Beijing-Tianjin-Hebei region, Yangtze River Delta region and central areas of China, which is the focus of air pollution management. These findings suggest that more emphasis should be placed on family-based health promotion. In areas with high PM2.5 pollution levels, resources, subsidies and air pollution protection should be provided for less healthy families with lower incomes and no health insurance.

Robust, Ultrafast and Reversible Photoswitching in Bulk Polymers Enabled by Octupolar Molecule Design.

Improving the photoswitching rate and robustness of photochromic molecules in bulk solids is paramount for practical applications but remains an on-going challenge. Here, we introduce an octupolar design paradigm to develop a new family of visible light organic photoswitches, namely multi-branched octupolar Stenhouse Adducts (MOPSAs) featuring a C3-symmetrical A3-(D-core) architecture with a dipolar donor-acceptor (D-A) photochrome in each branch. Our design couples multi-dimensional geometric and electronic effects of MOPSAs to enable robust ultrafast reversible photoswitching in bulk polymers. Specifically, the optimal MOPSA (4 wt %) in commercial polyurethane films accomplishes nearly 100 % discoloration in 6 s under visible light with ∼ 100 % thermal-recovery in 17.4 s at 60 °C, while the acquired kinetics constants are 3∼7 times that of dipolar DASA counterpart and 1∼2 orders of magnitude higher than those of reported DASAs in polymers. Importantly, the MOPSA-doped polymer films sustain 500 discoloration/recovery cycles with slow degradation, superior to the existing DASAs in polymers (≤30 cycles). We discover that multi-dipolar coupling in MOPSA enables enhanced polarization and electron delocalization, promoting the rate-determining thermal cyclization, while the branched and non-planar geometry of MOPSA induces large free volume to facilitate the isomerization. This design can be extended to develop spiropyran or azobenzene-based ultrafast photochromic films. The superior photoswitching performance of MOPSAs together with their high-yield and scalable synthesis and facile film processing inspires us to explore their versatile uses as smart inks or labels for time-temperature indicators, optical logic encryption and multi-levelled data encryption.

Characterization of Exome Variants and Their Metabolic Impact in 6,716 American Indians from the Southwest US.

Applying exome sequencing to populations with unique genetic architecture has the potential to reveal novel genes and variants associated with traits and diseases. We sequenced and analyzed the exomes of 6,716 individuals from a Southwestern American Indian (SWAI) population with well-characterized metabolic traits. We found that the SWAI population has distinct allelic architecture compared to populations of European and East Asian ancestry, and there were many predicted loss-of-function (pLOF) and nonsynonymous variants that were highly enriched or private in the SWAI population. We used pLOF and nonsynonymous variants in the SWAI population to evaluate gene-burden associations of candidate genes from European genome-wide association studies (GWASs) for type 2 diabetes, body mass index, and four major plasma lipids. We found 19 significant gene-burden associations for 11 genes, providing additional evidence for prioritizing candidate effector genes of GWAS signals. Interestingly, these associations were mainly driven by pLOF and nonsynonymous variants that are unique or highly enriched in the SWAI population. Particularly, we found four pLOF or nonsynonymous variants in APOB, APOE, PCSK9, and TM6SF2 that are private or enriched in the SWAI population and associated with low-density lipoprotein (LDL) cholesterol levels. Their large estimated effects on LDL cholesterol levels suggest strong impacts on protein function and potential clinical implications of these variants in cardiovascular health. In summary, our study illustrates the utility and potential of exome sequencing in genetically unique populations, such as the SWAI population, to prioritize candidate effector genes within GWAS loci and to find additional variants in known disease genes with potential clinical impact.

Microenvironment Modulation of Metal-Organic Frameworks (MOFs) for Coordination Olefin Oligomerization and (co)Polymerization.

The majority of commercial polyolefins are produced by coordination polymerization using early or late transition metal catalysts. Molecular catalysts containing these transition metals (Ti, Zr, Cr, Ni, and Fe, etc.) are loaded on supports for controlled polymerization behavior and polymer morphology in slurry or gas phase processes. Within the last few years, metal-organic frameworks (MOFs), a class of unique porous crystalline materials constructed from metal ions/clusters and organic ligands, have been designed and utilized as excellent supports for heterogeneous polymerization catalysis whose high density and uniform distribution of active sites would benefit the modulations of molecular weight distributions of high-performance olefin oligomers and (co)polymers. Impressive efforts have been made to modulate the microenvironment surrounding the active centers at the atomic level for improved activities of MOFs-based catalysts and controlled selectivity of olefin insertion. This review aims to draw a comprehensive picture of MOFs for coordination olefin oligomerization and (co)polymerization in the past decades with respect to different transition metal active centers, various incorporation sites, and finally microenvironment modulation. In consideration of more efforts are needed to overcome challenges for further industrial and commercial application, a brief outlook is provided.

MST4 as a novel therapeutic target for autophagy and radiosensitivity in gastric cancer.

BACKGROUND: Mammalian ste20-like kinase 4 (MST4) and autophagy have been implicated in ailments such as inflammatory and cancers. METHODS: In this study, the expression of MST4 data was extracted from TCGA, GTEx, and GEPIA. The infiltration of immune cells and methylation level of MST4 in tumor and normal tissues were extracted from GEPIA 2021, TISIDB, UALCAN, EWAS, MethSurv, and MEXPRESS database. We also predict the efficacy of outcome prediction with receiver operating characteristic curve (ROC). All proteins expressions of MST4, P62, and LC3 were detected by immunohistochemistry (IHC) in paired Gastric cancer (GC) and para-cancerous normal tissue samples. We verify the effects of MST4 on irradiation-induced gastric death, and also investigate effects of MST4 activating autophagy in GC cell lines with various in vitro assays using western blotting. RESULTS: We have confirmed the high transcription level of MST4 from TCGA, USLCAN, HPA, and other portals, but a rapid decrease in protein level. More, MST4 can be considered as an independent prognostic molecule, which has significant prognostic significance in tumor grade, anti-tumor treatment, histological type, and time-dependent ROC curve. The methylation degree of MST4 promoter region in tumor is much lower than that in normal tissue, which may be the main reason for the remarkably high transcription level of MST4. In addition, MST4 transcription level was significantly inversely proportional to the infiltration level of most immune cells. The MST4 up-regulation and the positive association of MST4 with autophagy expression were cross-validated in open-access datasets. CONCLUSIONS: MST4, as an autophagy-associated protein, plays a potential role in inducing cell death by increasing protein content in radiotherapy.

Phylogenomic analyses reveal incongruences between divergence times and fossil records of freshwater snails in East Asia.

Fossils provide important insight into our understanding of phylogenetic history by serving as calibration points for divergence time estimation. However, uncertainties in the fossil record due to parallel evolution and convergent evolution can critically affect estimates of node ages. Here, we compare and contrast estimates of phylogenetic divergence with geologic and fossil history for two freshwater snail genera of the family Viviparidae in East Asia (Cipangopaludina and Margarya). Cipangopaludina species are commonly widely distributed species in East Asia, but extant Margarya species are endemic to the ancient lakes in Yunnan, China. According to some previous studies, parallel evolution or convergent evolution of shell morphology has occurred in the family several times which may affect divergence time estimation using fossil records. In this study, we used SNP data derived from ddRAD-seq loci to investigate population demographic history of both genera. Our results show a common pattern of lake endemic lineages diversifying from widely distributed lineages in the Miocene, and multiple colonization to a single ancient lake occurred in the Pleistocene. Our results indicate substantial incongruence among estimated phylogenomic divergence times, some fossil records, and formation ages of ancient lakes. These findings suggest some fossil records may be misidentified in these groups and highlight the need to carefully evaluate geological evidence and fossil records when using these for divergence time estimation.

Taxonomic insights and evolutionary history in East Asian terrestrial slugs of the genus Meghimatium.

East Asia, specifically the Japanese Archipelago, is a biodiversity hotspot of both vertebrates and invertebrates. Mollusks represent a burst of species diversity in this region due to the effects of biotic and abiotic factors on their morphological traits, such as shell shape and size. However, the evolutionary history of terrestrial slugs in East Asia remains unknown. In the present study, we investigated the molecular phylogeny of terrestrial slugs of the genus Meghimatium. This genus includes three described and eight undescribed species, and our study used all except for two. Based on phylogeny and the species delimitation tests, the genus Meghimatium was split into many putative species, suggesting higher species diversity than previously thought based on morphological and anatomical studies and that almost undescribed species may be inappropriate. Therefore, morphological traits, such as body size and colour, conventionally considered for classification may easily vary or be similar across geographic region. Moreover, the divergence time of this genus is almost concordant with the geographical time scale of the formation of the Japanese mainland. Our findings suggest that molecular phylogenetics helps classify Japanese Meghimatium slugs, but comprehensive taxonomic revisions using multi-locus analyses are needed.

AP2/ERF Transcription Factors Integrate Age and Wound Signals for Root Regeneration.

Age and wounding are two major determinants for regeneration. In plants, the root regeneration is triggered by wound-induced auxin biosynthesis. As plants age, the root regenerative capacity gradually decreases. How wounding leads to the auxin burst and how age and wound signals collaboratively regulate root regenerative capacity are poorly understood. Here, we show that the increased levels of three closely-related miR156-targeted Arabidopsis (Arabidopsis thaliana) SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors, SPL2, SPL10, and SPL11, suppress root regeneration with age by inhibiting wound-induced auxin biosynthesis. Mechanistically, we find that a subset of APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) transcription factors including ABSCISIC ACID REPRESSOR1 and ERF109 is rapidly induced by wounding and serves as a proxy for wound signal to induce auxin biosynthesis. In older plants, SPL2/10/11 directly bind to the promoters of AP2/ERFs and attenuates their induction, thereby dampening auxin accumulation at the wound. Our results thus identify AP2/ERFs as a hub for integration of age and wound signal for root regeneration.

Enhancing prognostic accuracy in head and neck squamous cell carcinoma chemotherapy via a lipid metabolism-related clustered polygenic model.

OBJECTIVE: Systemic chemotherapy is the first-line therapeutic option for head and neck squamous cell carcinoma (HNSCC), but it often fails. This study aimed to develop an effective prognostic model for evaluating the therapeutic effects of systemic chemotherapy. METHODS: This study utilized CRISPR/cas9 whole gene loss-of-function library screening and data from The Cancer Genome Atlas (TCGA) HNSCC patients who have undergone systemic therapy to examine differentially expressed genes (DEGs). A lipid metabolism-related clustered polygenic model called the lipid metabolism related score (LMRS) model was established based on the identified functionally enriched DEGs. The prediction efficiency of the model for survival outcome, chemotherapy, and immunotherapy response was evaluated using HNSCC datasets, the GEO database and clinical samples. RESULTS: Screening results from the study demonstrated that genes those were differentially expressed were highly associated with lipid metabolism-related pathways, and patients receiving systemic therapy had significantly different prognoses based on lipid metabolism gene characteristics. The LMRS model, consisting of eight lipid metabolism-related genes, outperformed each lipid metabolism gene-based model in predicting outcome and drug response. Further validation of the LMRS model in HNSCCs confirmed its prognostic value. CONCLUSION: In conclusion, the LMRS polygenic prognostic model is helpful to assess outcome and drug response for HNSCCs and could assist in the timely selection of the appropriate treatment for HNSCC patients. This study provides important insights for improving systemic chemotherapy and enhancing patient outcomes.

Genomic and biological characteristics of a novel lytic phage, vB_MscM-PMS3, infecting the opportunistic zoonotic pathogen Mammaliicoccus sciuri.

Mammaliicoccus sciuri is an opportunistic zoonotic pathogen in humans and animals. We isolated the Mammaliicoccus phage vB_MscM-PMS3, which was also able to infect and lyse M. sciuri and M. lentus. The phage genome is a linear dsDNA that is 147,811 bp in length and contains 206 ORFs and three tRNA genes. It showed low genome coverage (< 17%) and sequence identity (< 91.3%) to other phage genomes. Phylogenetic analysis based on the whole genome and major capsid protein revealed that this phage clustered with members of the subfamily Twortvirinae of the family Herelleviridae, but it was distinctly separated from the other members, indicating its uniqueness.