A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity.

Enhancers play a critical role in dynamically regulating spatial-temporal gene expression and establishing cell identity, underscoring the significance of designing them with specific properties for applications in biosynthetic engineering and gene therapy. Despite numerous high-throughput methods facilitating genome-wide enhancer identification, deciphering the sequence determinants of their activity remains challenging. Here, we present the DREAM (DNA cis-Regulatory Elements with controllable Activity design platforM) framework, a novel deep learning-based approach for synthetic enhancer design. Proficient in uncovering subtle and intricate patterns within extensive enhancer screening data, DREAM achieves cutting-edge sequence-based enhancer activity prediction and highlights critical sequence features implicating strong enhancer activity. Leveraging DREAM, we have engineered enhancers that surpass the potency of the strongest enhancer within the Drosophila genome by approximately 3.6-fold. Remarkably, these synthetic enhancers exhibited conserved functionality across species that have diverged more than billion years, indicating that DREAM was able to learn highly conserved enhancer regulatory grammar. Additionally, we designed silencers and cell line-specific enhancers using DREAM, demonstrating its versatility. Overall, our study not only introduces an interpretable approach for enhancer design but also lays out a general framework applicable to the design of other types of cis-regulatory elements.

Genome-wide association analysis identify candidate genes for feed efficiency and growth traits in Wenchang chickens.

BACKGROUND: Wenchang chickens are one of the most popular local chicken breeds in the Chinese chicken industry. However, the low feed efficiency is the main shortcoming of this breed. Therefore, there is a need to find a more precise breeding method to improve the feed efficiency of Wenchang chickens. In this study, we explored important candidate genes and variants for feed efficiency and growth traits through genome-wide association study (GWAS) analysis. RESULTS: Estimates of genomic heritability for growth and feed efficiency traits, including residual feed intake (RFI) of 0.05, average daily food intake (ADFI) of 0.21, average daily weight gain (ADG) of 0.24, body weight (BW) at 87, 95, 104, 113 days of age (BW87, BW95, BW104 and BW113) ranged from 0.30 to 0.44. Important candidate genes related to feed efficiency and growth traits were identified, such as PLCE1, LAP3, MED28, QDPR, LDB2 and SEL1L3 genes. CONCLUSION: The results identified important candidate genes for feed efficiency and growth traits in Wenchang chickens and provide a theoretical basis for the development of new molecular breeding technology.

Combined genome and transcriptome provides insight into the genetic evolution of an edible halophyte Suaeda salsa adaptation to high salinity.

Suaeda salsa L. is a typical halophyte with high value as a vegetable. Here, we report a 447.98 Mb, chromosomal-level genome of S. salsa, assembled into nine pseudomolecules (contig N50 = 1.36 Mb) and annotated with 27,927 annotated protein-coding genes. Most of the assembled S. salsa genome, 58.03%, consists of transposable elements. Some gene families including HKT1, NHX, SOS and CASP related to salt resistance were significantly amplified. We also observed expansion of genes encoding protein that bind the trace elements Zn, Fe, Cu and Mn, and genes related to flavonoid and α-linolenic acid metabolism. Many expanded genes were significantly up-regulated under salinity, which might have contributed to the acquisition of salt tolerance in S. salsa. Transcriptomic data showed that high salinity markedly up-regulated salt-resistance related genes, compared to low salinity. Abundant metabolic pathways of secondary metabolites including flavonoid, unsaturated fatty acids and selenocompound were enriched, which indicates that the species is a nutrient-rich vegetable. Particularly worth mentioning is that there was no significant difference in the numbers of cis-elements in the promoters of salt-related and randomly selected genes in S. salsa when compared with Arabidopsis thaliana, which may affirm that plant salt tolerance is a quantitative rather than a qualitative trait in terms of promoter evolution. Our findings provide deep insight into the adaptation of halophytes to salinity from a genetic evolution perspective.

Trajectory patterns and influencing factors of supportive care needs in stroke patients: A longitudinal study.

AIM: To investigate the trajectory patterns and influencing factors of supportive care needs in stroke patients. DESIGN: A longitudinal study. METHODS: In total, 207 stroke patients who received treatment at the Department of Neurology in a hospital in Xuzhou between July 2022 and July 2023 were recruited using convenience sampling. Questionnaires including supportive care needs, hospital anxiety and depression scale, and the Barthel index were investigated at baseline and at 1, 3, and 6 months. A latent class growth model was applied to identify the supportive care needs trajectories. Multiple logistic regression was used to determine the predictors for membership. This study adheres to STROBE reporting guidelines. RESULTS: Three patterns of supportive care needs trajectories were identified: A high needs slow decline group (20.8%), a medium needs stable group (56.5%) and a medium needs rapid decline group (22.7%). Based on further analysis, the findings indicated that age, education level, monthly income, comorbidity, activities of daily living, anxiety and depression were associated with the trajectory categories of supportive care needs with stroke patients. CONCLUSION: This study demonstrates heterogeneity in changes in supportive care needs among stroke patients. Healthcare providers need to consider these different categories of needs and develop individualized care measures based on the characteristics of different patients. IMPACT: Healthcare providers should be aware of the fluctuations in care needs of stroke patients at various stages. Additionally, the study aimed to identify patients' specific needs based on their circumstances, monitor the rehabilitation process and establish a more personalized and optimized care plan through multidisciplinary collaboration. The ultimate goal was to alleviate symptomatic distress and address the long-term care needs of patients. PATIENT OR PUBLIC CONTRIBUTION: No patient or public contribution.

Development of an automatic measurement system using atmospheric pressure photoionization ultrahigh-resolution mass spectrometry and application for on-line analysis of particulate matter.

On-line chemical characterization of atmospheric particulate matter (PM) with soft ionization technique and ultrahigh-resolution Mass Spectrometry (UHRMS) provides molecular information of organic constituents in real time. Here we describe the development and application of an automatic measurement system that incorporates PM2.5 sampling, thermal desorption, atmospheric pressure photoionization, and UHRMS analysis. Molecular formulas of detected organic compounds were deducted from the accurate (±10 ppm) molecular weights obtained at a mass resolution of 100,000, allowing the identification of small organic compounds in PM2.5. Detection efficiencies of 28 standard compounds were determined and we found a high sensitivity and selectivity towards organic amines with limits of detection below 10 pg. As a proof of principle, PM2.5 samples collected off-line in winter in the urban area of Beijing were analyzed using the Ionization Module and HRMS of the system. The automatic system was then applied to conduct on-line measurements during the summer time at a time resolution of 2 hr. The detected organic compounds comprised mainly CHON and CHN compounds below 350 m/z. Pronounced seasonal variations in elemental composition were observed with shorter carbon backbones and higher O/C ratios in summer than that in winter. This result is consistent with stronger photochemical reactions and thus a higher oxidation state of organics in summer. Diurnal variation in signal intensity of each formula provides crucial information to reveal its source and formation pathway. In summary, the automatic measurement system serves as an important tool for the on-line characterization and identification of organic species in PM2.5.

Impact of army morale on suicidal ideation: The mediating role of grit and the moderating role of social support in a Chinese Navy population.

This study constructed a moderated mediation model to examine whether increased army morale could reduce suicidal ideation. The mediating role of grit and the moderating role of social support were also examined. A total of 1029 male navy cadets in China were recruited to complete the survey. The measures used in the study included the Army Morale Scale, Grit Scale, Social Support Scale, and Self-rated Idea of Suicide Scale. The results indicated that: increased army morale could significantly reduce suicidal ideation; the impact of army morale on suicidal ideation could be partially mediated by grit; and social support moderated the impact of army morale on suicidal ideation. Specifically, relatively higher levels of social support could reduce suicidal ideation among individuals with lower levels of army morale, but the effect is not significant when the morale is at a high level. The study revealed that increased army morale could reduce suicidal ideation. Moreover, the mediating role of grit and the moderating role of social support were also revealed.

Nontarget Screening of Novel Urinary Biomarkers for Occupational Exposure to Toxic Chemicals from Coking Industry Using HPLC-QTOF-MS.

High-resolution mass spectrometry is an advanced technique for comprehensive screening of toxic chemicals. In this study, urine samples were collected from both an occupationally exposed population at a coking site and normal inhabitants to identify novel urinary biomarkers for occupational exposure to coking contaminants. A coking-site-appropriate analytical method was developed for unknown chemical screening. Through nontarget screening, 515 differential features were identified, and finally, 32 differential compounds were confirmed as candidates for the current study, including 13 polycyclic aromatic hydrocarbon (PAH) metabolites. Besides monohydroxy-PAHs (such as 1-&2-naphthol, 2-&9-hydroxyfluorene, 2-&4-phenanthrol, and 1-&2-hydroxypyrene), many other PAH metabolites including dihydroxy metabolites, PAH oxide, and sulfate conjugate were detected, suggesting that the quantification based solely on monohydroxy-PAHs significantly underestimated the human exposure to PAHs. Furthermore, several novel compounds were recognized that could be considered as biomarkers for the exposure to coking contaminants, including quinolin-2-ol (1.10 ± 0.44 ng/mL), naphthylmethanols (11.4 ± 5.47 ng/mL), N-hydroxy-1-aminonaphthalene (0.78 ± 0.43 ng/mL), hydroxydibenzofurans (17.4 ± 7.85 ng/mL), hydroxyanthraquinone (0.13 ± 0.053 ng/mL), and hydroxybiphenyl (2.70 ± 1.03 ng/mL). Despite their lower levels compared with hydroxy-PAHs (95.1 ± 30.8 ng/mL), their severe toxicities should not be overlooked. The study provides a nontarget screening approach to identify chemicals in human urine, which is crucial for accurately assessing the health risks of toxic chemicals in the coking industry.

Co-exposure health risk of benzo[a]pyrene with aromatic VOCs: Monoaromatic hydrocarbons inhibit the glucuronidation of benzo[a]pyrene.

Occupational workers and residents near petrochemical industry facilities are exposed to multiple contaminants on a daily basis. However, little is known about the co-exposure effects of different pollutants based on biotransformation. The study examined benzo[a]pyrene (BaP), a representative polycyclic aromatic hydrocarbon related to the petrochemical industry, to investigate changes in toxicity and co-exposure mechanism associated with different monoaromatic hydrocarbons (MAHs). A central composite design method was used to simulate site co-exposure scenarios to reveal biotransformation of BaP when co-exposed with benzene, toluene, chlorobenzene, or nitrobenzene in microsome systems. BaP metabolism depended on MAH concentration, and association of MAH with microsome concentration/incubation time. Particularly, MAH co-exposure negatively affected BaP glucuronidation, an important phase Ⅱ detoxification process. BaP metabolite intensities decreased to 43%-80% for OH-BaP-G, and 32%-71% for diOH-BaP-G in co-exposure system with MAHs, compared with control group. Furthermore, glucuronidation was affected by competitive and time-dependent inhibition. Co-exposure significantly decreased gene expression of UGT 1A10 and BCRP/ABCG2 in HepG2 cells, which are involved in BaP detoxification through metabolism and transmembrane transportation. Therefore, human co-exposure to multiple contaminants may deteriorate toxic effects of these chemicals by disturbing metabolic pathways. This study provides a reference for assessing toxic effects and co-exposure risks of pollutants.

Cxcl9l and Cxcr3.2 regulate recruitment of osteoclast progenitors to bone matrix in a medaka osteoporosis model.

Bone homeostasis requires continuous remodeling of bone matrix to maintain structural integrity. This involves extensive communication between bone-forming osteoblasts and bone-resorbing osteoclasts to orchestrate balanced progenitor cell recruitment and activation. Only a few mediators controlling progenitor activation are known to date and have been targeted for intervention of bone disorders such as osteoporosis. To identify druggable pathways, we generated a medaka (Oryzias latipes) osteoporosis model, where inducible expression of receptor-activator of nuclear factor kappa-Β ligand (Rankl) leads to ectopic formation of osteoclasts and excessive bone resorption, which can be assessed by live imaging. Here we show that upon Rankl induction, osteoblast progenitors up-regulate expression of the chemokine ligand Cxcl9l. Ectopic expression of Cxcl9l recruits mpeg1-positive macrophages to bone matrix and triggers their differentiation into osteoclasts. We also demonstrate that the chemokine receptor Cxcr3.2 is expressed in a distinct subset of macrophages in the aorta-gonad-mesonephros (AGM). Live imaging revealed that upon Rankl induction, Cxcr3.2-positive macrophages get activated, migrate to bone matrix, and differentiate into osteoclasts. Importantly, mutations in cxcr3.2 prevent macrophage recruitment and osteoclast differentiation. Furthermore, Cxcr3.2 inhibition by the chemical antagonists AMG487 and NBI-74330 also reduced osteoclast recruitment and protected bone integrity against osteoporotic insult. Our data identify a mechanism for progenitor recruitment to bone resorption sites and Cxcl9l and Cxcr3.2 as potential druggable regulators of bone homeostasis and osteoporosis.

COVID-19 and risk spillovers of China's major financial markets: Evidence from time-varying variance decomposition and wavelet coherence analysis.

COVID-19 has influenced financial markets drastically; however, this influence has received little attention, particularly in China. This study investigates risk spillovers across China's financial and shipping markets through dynamic spillover measures based on time-varying parameter vector autoregression and generalized forecast error variance decompositions. Stock, fund, and futures markets are identified as major risk senders, whereas other markets are identified as major risk receivers. Surprisingly, bonds, gold, and shipping are safe havens that facilitate portfolio optimization. Furthermore, using wavelet coherence analysis, we find that the coherence between dynamic total spillover and COVID-19 varies across time and frequency domains.

Integrative analysis of transcriptomics and metabolomics to reveal the melanogenesis pathway of muscle and related meat characters in Wuliangshan black-boned chickens.

BACKGROUND: Melanin is an important antioxidant in food and has been used in medicine and cosmetology. Chicken meat with high melanin content from black-boned chickens have been considered a high nutritious food with potential medicinal properties. The molecular mechanism of melanogenesis of skeletal muscle in black-boned chickens remain poorly understood. This study investigated the biological gene-metabolite associations regulating the muscle melanogenesis pathways in Wuliangshan black-boned chickens with two normal boned chicken breeds as control. RESULTS: We identified 25 differentially expressed genes and 11 transcription factors in the melanogenesis pathways. High levels of the meat flavor compounds inosine monophosphate, hypoxanthine, lysophospholipid, hydroxyoctadecadienoic acid, and nicotinamide mononucleotide were found in Wuliangshan black-boned chickens. CONCLUSION: Integrative analysis of transcriptomics and metabolomics revealed the dual physiological functions of the PDZK1 gene, involved in pigmentation and/or melanogenesis and regulating the phospholipid signaling processes in muscle of black boned chickens.

A Novel Strategy Based on Permanent Protein Modifications Induced by Formaldehyde for Food Safety Analysis.

The illegal additions of chemicals in food products are serious incidents threatening current public safety. To date, ideal methods to determine permanent traces of prohibited chemicals in foods are still lacking. For example, formaldehyde (FA) can be added illegally as a food preservative. However, most current methods that are dependent on the direct detection of FA are not able to determine if FA has ever been added once food products are rinsed completely. Herein, we present a novel approach relying upon protein modifications induced by FA (PMIF) to examine FA in foods. We reveal the entire catalog of PMIFs in food products by combining mass spectrometry analysis with unrestrictive identification of protein modifications. Consequently, four obvious PMIFs were identified and confirmed as markers to discriminate the addition of FA in foods. Our study demonstrates that the approach based on PMIFs enables detecting the imprinted trace of FA even if the food products have been washed thoroughly. Our work presents a novel strategy for analysis of chemical additives, offering broad potential applications in protein analysis and food safety.

SPOP promotes ubiquitination and degradation of MyD88 to suppress the innate immune response.

As a canonical adaptor for the Toll-like receptor (TLR) family, myeloid differentiation primary response protein 88 (MyD88) has crucial roles in host defense against infection by microbial pathogens, and its dysregulation might induce autoimmune diseases. Here, we demonstrate that the chicken Cullin 3-based ubiquitin ligase adaptor Speckle-type BTB-POZ protein (chSPOP) recognizes the intermediate domain of chicken MyD88 (chMyD88) and degrades it through the proteasome pathway. Knockdown or genetic ablation of chSPOP leads to aberrant elevation of chMyD88 protein. Through this interaction, chSPOP negatively regulates NF-κB pathway activity and thus the production of IL-1ß upon LPS challenge in chicken macrophages. Furthermore, Spop-deficient mice are more susceptible to infection with Salmonella typhimurium. Collectively, these findings demonstrate MyD88 as a bona fide substrate of SPOP and uncover a mechanism by which SPOP regulates MyD88 abundance and disease susceptibility.

New Insights into Human Biotransformation of BDE-209: Unique Occurrence of Metabolites of Ortho-Substituted Hydroxylated Higher Brominated Diphenyl Ethers in the Serum of e-Waste Dismantlers.

Extremely high levels of decabromodiphenyl ether (BDE-209) are frequently found in the serum of occupationally exposed groups, such as e-waste dismantlers and firefighters. However, the metabolism of BDE-209 in the human body is not adequately studied. In this study, 24 serum samples were collected from workers at a typical e-waste recycling workshop in Taizhou, Eastern China, and the occurrence and fate of these higher brominated diphenyl ethers (PBDEs) were investigated. The median concentration of the total PBDEs in the serum was 199 ng/g lipid weight (lw), ranging from 125 to 622 ng/g lw. Higher brominated octa- to deca-BDEs accounted for more than 80% of the total PBDEs. Three ortho-hydroxylated metabolites of PBDEs─6-OH-BDE196, 6-OH-BDE199, and 6'-OH-BDE206─were widely detected with a total concentration (median) of 92.7 ng/g lw. The concentrations of the three OH-PBDEs were significantly higher than their octa- and nona-PBDE homologues, even exceeding those of the total PBDEs in several samples, indicating that the formation of OH-PBDEs was a major metabolic pathway of the higher brominated PBDEs in occupationally exposed workers. An almost linear correlation between 6-OH-BDE196 and 6-OH-BDE199 (R = 0.971, P < 0.001) indicates that they might undergo a similar biotransformation pathway in the human body or may be derived from the same precursor. In addition, the occurrence of a series of penta- to hepta- ortho-substituted OH-PBDEs was preliminarily identified according to their unique "predioxin" mass spectral profiles by GC-ECNI-MS. Taken together, the tentative metabolic pathway for BDE-209 in e-waste dismantlers was proposed. The oxidative metabolism of BDE-209 was mainly observed at the ortho positions to form 6'-OH-BDE-206, which later underwent a consecutive loss of bromine atoms at the meta or para positions to generate other ortho-OH-PBDEs. Further studies are urgently needed to identify the chemical structures of these ortho-OH-PBDE metabolites, and perhaps more importantly to clarify the potentially toxic effects, along with their underlying molecular mechanisms.

Comparison of genomic prediction methods for residual feed intake in broilers.

Residual feed intake (RFI) is a measure of the feed efficiency of animals. Previous studies have identified SNPs associated with RFI. The objective of this study was to compare the GBLUP model with the GA-BLUP model including previously identified associated SNPs. The nine associated SNPs were obtained from the genome-wide association study on a discovery population as preselection information. These models were analysed using ASREML software using a 5-fold cross-validation method on a validation population. With the genetic architecture (GA) matrix used, which was conducted with the nine RFI-associated SNPs, the prediction accuracy of RFI was improved compared with the original GBLUP model. The calculated optimal ω was 0.981 for RFI, which is in line with the optimal range from 0.9 to 1.0 in the gradient test. The prediction accuracy increased by 2% in the GA-BLUP model with ω being 0.981 compared with the GBLUP model. In conclusion, the GA-BLUP with the nine RFI-associated SNPs and an optimal ω can improve the prediction accuracy for a specific trait compared with GBLUP.

A life cycle assessment of an enterprise's low-carbon emissions model: The Xinjiang Shihezi pig farm faecal treatment biogas project as a case study.

The requirement of carbon emission reduction promotes the continuous implementation and development of low carbon emission mode in typical high-carbon industry aquaculture, especially in the resourceful treatment of terminal waste. However, the previous studies usually focus on a single process or chain, the difference between the long-chain (LC) and automated integration (AI) in the overall environmental impact needs to be quantified and standardised. This paper intends to make a comparative study on two waste treatment biogas projects of aquaculture, a typical industry with high resource consumption and pollution emission in industry and agriculture, and a typical production mode case of aquaculture. The life cycle assessment method is adopted to analyse the environmental impact intensity, identify key link materials, and put forward targeted improvement and optimization schemes. The study found the LC system's comprehensive environmental impact (CEI) is smaller, which is 59.73% less than the AI system. Biogas slurry returning to the field can effectively avoid inorganic fertilizer input. The pretreatment and storage of feces are the key stages. The key substances are NH3 and nitrogen oxides. Suggestions were put forward to optimize the manure management process. In practical pig farms, the process of dry-cleaning manure pre-treatment, automatic fermentation gas production and final biogas slurry filtration drip irrigation should be promoted.

Integrated analysis of the methylome and transcriptome of chickens with fatty liver hemorrhagic syndrome.

BACKGROUND: DNA methylation, a biochemical modification of cytosine, has an important role in lipid metabolism. Fatty liver hemorrhagic syndrome (FLHS) is a serious disease and is tightly linked to lipid homeostasis. Herein, we compared the methylome and transcriptome of chickens with and without FLHS. RESULTS: We found genome-wide dysregulated DNA methylation pattern in which regions up- and down-stream of gene body were hypo-methylated in chickens with FLHS. A total of 4155 differentially methylated genes and 1389 differentially expressed genes were identified. Genes were focused when a negative relationship between mRNA expression and DNA methylation in promoter and gene body were detected. Based on pathway enrichment analysis, we found expression of genes related to lipogenesis and oxygenolysis (e.g., PPAR signaling pathway, fatty acid biosynthesis, and fatty acid elongation) to be up-regulated with associated down-regulated DNA methylation. In contrast, genes related to cellular junction and communication pathways (e.g., vascular smooth muscle contraction, phosphatidylinositol signaling system, and gap junction) were inhibited and with associated up-regulation of DNA methylation. CONCLUSIONS: In the current study, we provide a genome-wide scale landscape of DNA methylation and gene expression. The hepatic hypo-methylation feature has been identified with FLHS chickens. By integrated analysis, the results strongly suggest that increased lipid accumulation and hepatocyte rupture are central pathways that are regulated by DNA methylation in chickens with FLHS.

Identification of QTL regions and candidate genes for growth and feed efficiency in broilers.

BACKGROUND: Feed accounts for about 70% of the total cost of poultry meat production. Residual feed intake (RFI) has become the preferred measure of feed efficiency because it is phenotypically independent of growth rate and body weight. In this study, our aim was to estimate genetic parameters and identify quantitative trait loci (QTL) for feed efficiency in 3314 purebred broilers using a genome-wide association study. Broilers were genotyped using a custom 55 K single nucleotide polymorphism (SNP) array. RESULTS: Estimates of genomic heritability for seven growth and feed efficiency traits, including body weight at 28 days of age (BW28), BW42, average daily feed intake (ADFI), RFI, and RFI adjusted for weight of abdominal fat (RFIa), ranged from 0.12 to 0.26. Eleven genome-wide significant SNPs and 15 suggestively significant SNPs were detected, of which 19 clustered around two genomic regions. A region on chromosome 16 (2.34-2.66 Mb) was associated with both BW28 and BW42, and the most significant SNP in this region, AX_101003762, accounted for 7.6% of the genetic variance of BW28. The other region, on chromosome 1 (91.27-92.43 Mb) was associated with RFI and ADFI, and contains the NSUN3 and EPHA6 as candidate genes. The most significant SNP in this region, AX_172588157, accounted for 4.4% of the genetic variance of RFI. In addition, a genomic region containing the gene AGK on chromosome 1 was found to be associated with RFIa. The NSUN3 and AGK genes were found to be differentially expressed in breast muscle, thigh muscle, and abdominal fat between male broilers with high and low RFI. CONCLUSIONS: We identified QTL regions for BW28 and BW42 (spanning 0.32 Mb) and RFI (spanning 1.16 Mb). The NSUN3, EPHA6, and AGK were identified as the most likely candidate genes for these QTL. These genes are involved in mitochondrial function and behavioral regulation. These results contribute to the identification of candidate genes and variants for growth and feed efficiency in poultry.

Template-based modeling and ab-initio docking using CoDock in CAPRI.

Integration of template-based modeling, global sampling and precise scoring is crucial for the development of molecular docking programs with improved accuracy. We combined template-based modeling and ab-initio docking protocol as hybrid docking strategy called CoDock for the docking and scoring experiments of the seventh CAPRI edition. For CAPRI rounds 38-45, we obtained acceptable or better models in the top 10 submissions for eight out of the 16 evaluated targets as predictors, nine out of the 16 targets as scorers. Especially, we submitted acceptable models for all of the evaluated protein-oligosaccharide targets. For the CASP13-CAPRI experiment (round 46), we obtained acceptable or better models in the top 5 submissions for 10 out of the 20 evaluated targets as predictors, 11 out of the 20 targets as scorers. The failed cases for our group were mainly the difficult targets and the protein-peptide systems in CAPRI and CASP13-CAPRI experiments. In summary, this CAPRI edition showed that our hybrid docking strategy can be efficiently adapted to the increasing variety of challenges in the field of molecular interactions.

Identification of diverse cell populations in skeletal muscles and biomarkers for intramuscular fat of chicken by single-cell RNA sequencing.

BACKGROUND: The development of skeletal muscle is closely related to the efficiency of meat production and meat quality. Chicken skeletal muscle development depends on myogenesis and adipogenesis and occurs in two phases-hyperplasia and hypertrophy. However, cell profiles corresponding to the two-phase muscle development have yet to be determined. Single-cell RNA-sequencing (scRNA-seq) can elucidate the cell subpopulations in tissue and capture the gene expression of individual cells, which can provide new insights into the myogenesis and intramuscular adipogenesis. RESULTS: Ten cell clusters at the post-hatching developmental stage at Day 5 and seven cell clusters at the late developmental stage at Day 100 were identified in chicken breast muscles by scRNA-seq. Five myocyte-related clusters and two adipocyte clusters were identified at Day 5, and one myocyte cluster and one adipocyte cluster were identified at Day 100. The pattern of cell clustering varied between the two stages. The cell clusters showed clear boundaries at the terminal differentiation stage at Day 100; by contrast, cell differentiation was not complete at Day 5. APOA1 and COL1A1 were selected from up-regulated genes in the adipocyte cluster and found to be co-expressed with the ADIPOQ adipocyte marker gene in breast muscles by RNA in situ hybridization. CONCLUSIONS: This study is the first to describe the heterogeneity of chicken skeletal muscle at two developmental stages. The genes APOA1 and COL1A1 were identified as biomarkers for chicken intramuscular fat cells.