Integrated GWAS and transcriptome analysis reveals key genes associated with muscle fibre and fat traits in Gushi chicken.

1. In the following experiment meat quality traits of a Gushi-Anka F2 resource population were measured, and their heritability estimated. Intramuscular fat (IMF) had medium heritability (0.35) but leg muscle fibre density (LMD), leg muscle fibre diameter (LMF), breast muscle fibre density (BMD), fresh fat content (FFA), and absolute dry fat content (AFC) had low heritability (0-0.2). The IMF presented the most important genetic additive effect among the poultry meat quality-related traits studied.2. The phenotypic data of meat quality traits in the Gushi-Anka F2 resource population were combined with genotyping by sequencing (GBS) data to obtain genotype data. Six meat quality traits in 734 birds were analysed by GWAS. Based on these variants, 83 significant (-log10(p) > 4.42) single nucleotide polymorphisms and four quantitative trait loci (QTL) regions corresponding to 175 genes were identified. Further linkage disequilibrium (LD) analysis was conducted on chromosome 13 (Chr13) and chromosome 27 (Chr27) QTL regions.3. Based on the transcriptome data and GWAS results, 12 shared genes - ITGB3, DNAJC27, ETV4, C7orf50, FKBP1B, G3BP1, IGF2BP1, KCNH6, LOC416263, SCARA5, SMIM5 and TBL1XR1 were identified as candidate genes influencing muscle fibre and fat traits.

Genome-wide DNA methylation and transcriptome analyses reveal important epigenetic genes associated with valgus-varus deformity in broilers.

1. Valgus-varus deformity (VVD) is a common leg bone problem in broilers that causes serious economic losses to the breeding industry. The genetic aetiology of VVD is not clear, which restricts the genetic control of VVD.2. In this study, knee cartilage of 35-day-old VVD and normal broilers was sequenced by whole-genome bisulphite sequencing (WGBS). The unique whole-genome DNA methylation profile of VVD broilers was described, and the methylation data and transcription data were used for joint analysis.3. The mean methylation level of the VVD group was greater than that in the normal group. A total of 4315 differentially methylated regions (DMRs) were detected from methylation data, with the highest DMR density on chromosomes 25, 27, 31 and 33. DMRs were mainly located in introns, which accounted for more than 60%, followed by promoter and exon regions.4. A total of 2326 differentially methylated genes (DMGs) were identified from DMRs, including 1159 genes with upregulated DMRs, 936 genes with downregulated DMRs, and 231 genes with two types of DMRs.5. The ESPL1 gene may be an important epigenetic gene of VVD. The methylation of particular CpG17, CpG18 and CpG19 sites in the promoter region of the ESPL1 gene may hinder the binding of transcription factors and promoters and increase the expression of ESPL1.

Valgus-varus deformity induced abnormal tissue metabolism, inflammatory damage and apoptosis in broilers.

1. This study explored the tissue metabolic status and the relationship with inflammation in valgus-valgus deformity (VVD) broilers with increasing age.2. Tissue and blood from VVD and healthy broilers were collected at two, four and five weeks old. A fully automated biochemical analyser, real-time PCR, HE staining and enzyme-linked immunosorbent assay were used to detect tissue metabolic indexes, mRNA levels of inflammation and apoptosis cytokines in immune organs, histological changes and serum inflammation and immune-related protein contents in VVD broilers.3. The results showed that VVD increased the levels of total protein, albumin, alanine aminotransferase at five weeks of age, aspartate aminotransferase, urea and creatine kinase in blood at two weeks of age. It upregulated the gene expression of inflammatory factors IL-1ß, IL-6, IL-8, TNF-α, NF-κB and TGF-ß and apoptotic factors FAS, Bcl-2, caspase-3 and 9 in immune organs; increased levels of serum proteins TNF-α, IL-1ß and IL-6 and decreased levels of serum immunoglobulins IgY and CD3+.4. In addition, with increasing age, IL-10 gene expression gradually increased in the BF and decreased in the spleen.5. In conclusion, VVD broilers have disorders of liver and kidney metabolism, inflammation and apoptosis of immune organs and increased levels of serum inflammatory factor proteins.

[The value of nomogram for predicting microvascular invasion based on clinical and Gd-EOB-DTPA-enhanced magnetic resonance imaging features].

Objective: To investigate the risk factors of microvascular invasion (MVI) in China liver cancer staging system stage Ⅰa (CNLC Ⅰa) hepatocellular carcinoma (HCC), and develop a nomogram for predicting MVI based on clinical and radiographic data. Methods: This retrospective study focused on CNLC Ⅰa HCC patients who underwent radical resection at the Cancer Hospital, Chinese Academy of Medical Sciences from January 2016 to December 2020. Patients' clinical characteristics and laboratory test results and pre-surgery gadolinium ethoxybenzyl diethylenetriamine pentaacetic acid (Gd-EOB-DTPA)-enhanced magnetic resonance imaging results were collected. The clinical and radiographic risk factors for MVI were identified by univariate and multivariate logistic regression analyses and used for the construction of the predictive nomogram. The nomogram model was then internally validated, and its performance was assessed. Results: A total of 104 patients were divided into the MVI-positive group (n=28) and the MVI-negative group (n=76). Multivariate logistic regression analysis at the P<0.1 level identified serum alpha-ferroprotein >7 ng/ml, total bilirubin >21 µmol/L, prothrombin time >12.5 s, non-smooth margin, and incomplete or absent capsule as risk factors of MVI, based on which a nomogram model was built. The model achieved an area under the curve (AUC) value of 0.867 (95% confidence interval, 0.791-0.944) in the internal validation. The sensitivity and specificity of the nomogram model were 0.786 and 0.829, respectively, with the prediction curve nearly overlapping the ideal curve. Based on the Hosmer-Lemeshow test, the predicted and real results were not significantly different (P=0.956). Conclusions: The probability of MVI of CNLC Ⅰa HCC can be objectively predicted by the monogram model that quantifies the clinical and radiographic risk factors. The model can also help clinicians select individualized surgical plans to improve the long-term prognosis of patients.

[Analysis of management efficacy in patients with heavy menstrual bleeding associated with antithrombotic therapy].

Objective: To evaluate different methods' efficacy of controlling acute bleeding and managing long-term menstruation in patients with heavy menstrual bleeding (HMB) associated with antithrombotic therapy. Methods: The clinical data of 22 cases with HMB associated with antithrombotic therapy admitted to Peking University People's Hospital from January 2010 to August 2022 were analyzed, aged 39 years old (26-46 years). Changes in menstrual volume, hemoglobin (Hb), and quality of life were collected after control of acute bleeding and long-term menstrual management. Menstrual volume was assessed by pictorial blood assessment chart (PBAC), and quality of life was assessed by menorrhagia multi-attribute scale (MMAS). Results: (1) Treatment of acute bleeding: of the 22 cases with HMB associated with antithrombotic therapy, 16 cases were treated in our hospital and 6 in other hospital for emergency bleeding; of the 16 cases treated in our hospital, 3 underwent emergency intrauterine Foley catheter balloon compression due to severe bleeding (Hb decreased by 20 to 40 g/L within 12 hours). Of the 22 cases with antithrombotic therapy-related HMB, 15 (including 2 cases with severe bleeding) underwent emergency aspiration or endometrial resection, and intraoperative placement of levonorgestrel-releasing intrauterine system (LNG-IUS) followed by a significant reduction in bleeding volume; 3 cases had controlled acute bleeding after rivaroxaban dose reduction and continued observation; 2 cases were given gonadotropin-releasing hormone agonists to control acute bleeding in other hospital, of which 1 case was temporarily treated with periodic blood transfusion, and the other one patient underwent total hysterectomy; and 2 cases had temporary amenorrhea with oral mifepristone after intrauterine balloon compression or oral norethindrone. (2) Long-term menstrual management: of the 22 cases with antithrombotic therapy-related HMB, 15 had LNG-IUS placement and 12 had LNG-IUS placement for 6 months, and menstrual volume was significantly reduced [PBAC scores were 365.0 (272.5-460.0) vs 25.0 (12.5-37.5), respectively; Z=4.593, P<0.001], Hb was significantly increased [91.5 g/L (71.8-108.2 g/L) vs 128.5 g/L (121.2-142.5 g/L); Z=4.695, P<0.001], and quality of life was significantly improved [MMAS scores were 415.0 (327.5-472.5) vs 580.0 (570.0-580.0), respectively; Z=-3.062, P=0.002] before placement compared with 6 months after placement. Three rivaroxaban dose reduction patients' PBAC scores decreased by 20 to 35 but remained >100, and perceived quality of life did not change significantly. Two cases with temporary amenorrhea treated with oral mifepristone felt significantly improved quality of life, and the MMAS scores increased by 220 and 180, respectively. Conclusion: Intrauterine Foley catheter balloon compression, aspiration or endometrial ablation could be used to control acute bleeding in patients with antithrombotic therapy-related HMB, and LNG-IUS for long-term management could reduce menstrual volume, increase hemoglobin, and improve the quality of life of patients.

Deficiency in DDR1 Induces Pulmonary Hypertension and Impaired Alveolar Development.

Pulmonary hypertension (PH) is a multifaceted condition characterized by elevated pulmonary arterial pressure, which can result in right ventricular dysfunction and failure. Disorders of lung development can present with secondary PH, which is a leading cause of mortality in infants with bronchopulmonary dysplasia (BPD). DDR1 (discoidin domain receptor 1) is a collagen-binding receptor that regulates tissue fibrosis and inflammation and controls cellular growth and migration. However, the roles of DDR1 in lung development or the pathogenesis of PH are unknown. Studying mice with a DDR1 deletion (Ddr1-/-), we have noted 35% mortality between 1 and 4 months of age, and we demonstrate that DDR1 deficiency results in reduced right ventricular contractility and muscularization of distal pulmonary arteries, consistent with PH. Pathology analysis revealed enlarged alveolar spaces in Ddr1-/- mice by Postnatal Day 7, consistent with impaired alveolar development. Gene expression analysis showed that Ddr1-/- mice have reduced concentrations of alveologenesis factors and epithelial-to-mesenchymal transition markers. Mechanistic studies in vitro confirmed that DDR1 mediated epithelial-to-mesenchymal transition, migration, and growth of alveolar epithelial cells. Taken together, these data suggest that DDR1 plays important roles mediating alveolarization during lung development. Our studies also describe a new model of spontaneous PH and bronchopulmonary dysplasia in mice.

Multidonor analysis reveals structural elements, genetic determinants, and maturation pathway for HIV-1 neutralization by VRC01-class antibodies.

Antibodies of the VRC01 class neutralize HIV-1, arise in diverse HIV-1-infected donors, and are potential templates for an effective HIV-1 vaccine. However, the stochastic processes that generate repertoires in each individual of >10(12) antibodies make elicitation of specific antibodies uncertain. Here we determine the ontogeny of the VRC01 class by crystallography and next-generation sequencing. Despite antibody-sequence differences exceeding 50%, antibody-gp120 cocrystal structures reveal VRC01-class recognition to be remarkably similar. B cell transcripts indicate that VRC01-class antibodies require few specific genetic elements, suggesting that naive-B cells with VRC01-class features are generated regularly by recombination. Virtually all of these fail to mature, however, with only a few-likely one-ancestor B cell expanding to form a VRC01-class lineage in each donor. Developmental similarities in multiple donors thus reveal the generation of VRC01-class antibodies to be reproducible in principle, thereby providing a framework for attempts to elicit similar antibodies in the general population.

miR-181a-5p can inhibit the proliferation and promote the differentiation of chicken primary myoblasts.

1. Myoblast proliferation and differentiation is one of the most important biological processes in the development of skeletal muscle. MicroRNAs (miRNAs) play a crucial role in this process.2. In this study, the expression level of miR-181a-5p was detected, which found that miR-181a-5p was expressed differently in different tissues, different embryonic ages, and different differentiation stages of primary myoblasts in Gushi chickens.3. The effect of miR-181a-5p was further investigated on chicken primary myoblasts (CPMs). The results of cell counting kit-8 (CCK-8), 5-ethynyl-2'-deoxyuridine (EdU) and cell cycle showed that miR-181a-5p could inhibit the proliferation of CPM. The miR-181a-5p promoted the expression of MYOD, MYOG, and MYHC. MYHC protein immunofluorescence experiments showed that miR-181a-5p increased the area of myotubes.4. In total, 63 potential target genes of miR-181a-5p in mRNA transcriptome data analysis were identified. Functional enrichment analysis was performed on these target genes, and ASNS, SMYD1, and FOS were found to play regulatory roles in biological processes such as muscle development. It was speculated that miR-181a-5p played a role in myoblast development through these genes.5. In conclusion, miR-181a-5p can inhibit the proliferation of chicken myoblasts and promote the differentiation of chicken myoblasts. This study laid the foundation for further research on the regulatory mechanism of miR-181a-5p in the development of skeletal muscle and the formation of excellent meat quality traits in Gushi chicken.

A novel 27-bp indel in the intron region of the YBX3 gene is associated with growth traits in chickens.

1. The DNA/RNA binding protein YBX3 is associated with gene transcription, DNA repair, and the progression of various diseases and is highly conserved from bacteria to humans.2. The following experiment found a 27-bp insertion/deletion polymorphism in the intron region of the YBX3 gene through resequencing. In cross-designed, F2 resource groups, the indel was significantly associated with broiler weight and body size at 0, 2, 4, 6, 8, 10 and 12 weeks of age and several other traits (semi evisceration weight (SEW), evisceration weight (EW), semi evisceration rate (SER), evisceration rate (ER), head weight (HW), claw weight (CLW), wing weight (DWW), gizzard weight (GW), pancreas weight (PW), chest muscle weight (CMW), leg weight (LW), leg muscle weight (LMW), shedding weight (SW), carcase weight (CW) and pectoral area (PA)) (P < 0.05).3. The insertion-insertion (II) genotype was significantly associated with the greatest growth traits and carcase traits, whereas the values associated with the insertion-deletion (ID) genotype were the lowest in the F2 reciprocal cross chickens.4. The mutation sites were genotyped in 3611 individuals from 13 different chicken breeds and cross-designed F2 resource groups. The II genotype is the most important in commercial broilers, and the I allele frequency observed in these breeds was relatively high. However, there is still considerable potential in breeding dual-purpose chickens and commercial laying hens.5. The mRNA expression of the YBX3 gene in tissues from different breeds and developmental stages demonstrated that the 27-bp indel may affect the entire development process of poultry by affecting muscle development. These findings are beneficial for elucidating the function of the YBX3 gene and facilitating enhanced production in the chicken industry.

miR-30a-3p can inhibit the proliferation and promote the differentiation of chicken primary myoblasts.

1. Chicken muscle is an important factor in meat quality and its development is controlled by a complex regulatory network.2. The following study examined the expression of miR-30a-3p in Gushi chicken breast muscle tissue and found that it was differentially expressed at different embryonic stages, reaching a peak in the 14-day-old embryo (E14).3. The effect of miR-30a-3p on chicken primary myoblasts (CPMs) was explored. Results from both cell counting kit-8 (CCK-8) and 5-ethynyl-2'-deoxyuridine (EdU) showed that this can inhibit the proliferation of myoblasts, and through cell cycle experiments, the inhibition of myoblast proliferation was found, which may be due to G0/G1 arrest in the cell cycle.4. The effect of miR-30a-3p on the differentiation of myoblasts was studied. The results showed that miR-30a-3p can promote the expression of MYOD, myogenin (MYOG), and myosin heavy chain (MYHC) genes to promote the differentiation of myoblasts. Through MYHC protein immunofluorescence experiments, it was found that miR-30a-3p can effectively increase the area of myotubes.5. Finally, mRNA transcriptome data was analysed, which showed that miR-30a-3p has 51 potential target genes. Among them, forkhead box O3 (FOXO3), ankyrin repeat domain 1 (ANKRD1), and insulin-induced 1 (INSIG1) genes were differentially expressed at different developmental stages and were enriched in Gene Ontology (GO) terms, such as cell differentiation and cellular developmental process. The data showed that tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein gamma (YWHAG), BUB1 mitotic checkpoint serine/threonine kinase (BUB1), and growth arrest and DNA damage-inducible 45 (GADD45) genes were enriched in the cell cycle pathway.6. It can be speculated that miR-30a-3p plays roles through these genes in myoblast development. This research provides information for further improving knowledge of the chicken muscle development regulation network.

Evaluation of colostrum bioactive protein transfer and blood metabolic traits in neonatal lambs in the first 24 hours of life.

Colostrum is a unique resource that contributes to the passive transfer of immunity and plays a central role in the health status of neonatal ruminants. However, digestion and absorption of colostral proteins in the gut remain incompletely understood. Therefore, this study aimed to investigate the effect of bovine colostrum feeding on blood metabolic traits and to quantify colostral bioactive proteins in the gastrointestinal digesta and blood to evaluate intestinal transfer in neonatal lambs in the first 24 h of life. Fifty-four newborn lambs were used in this study, including 27 lambs fed pooled bovine colostrum and slaughtered at 6 (C6h), 12 (C12h), or 24 h (C24h) after birth; 18 lambs not fed any colostrum or milk and slaughtered at birth (N0h) or 24 h (N24h) after birth; and 9 milk-fed lambs slaughtered at 24 h (M24h) after birth. Lambs receiving colostrum or milk were bottle-fed within the first 2 h to obtain intakes of 8% of body weight at birth. Samples of blood and digesta from the abomasum, jejunum, and ileum were collected after slaughter. Serum concentrations of glucose, insulin, total protein, and aspartate aminotransferase were higher in colostrum-fed lambs than in N0h lambs. Serum concentrations of insulin, total protein, insulin-like growth factor 1, and γ-glutamyl transpeptidase were higher in C24h lambs than in N24h or M24h lambs. Apparent efficiencies of IgG absorption in C6h, C12h, and C24h lambs were 14.4, 26.8, and 17.2%, respectively, whereas apparent efficiencies of lactoferrin (LF), α-lactalbumin (α-LA), and ß-lactoglobulin (ß-LG) absorption were very low in colostrum-fed lambs, with mean values of 0.06, 0.002, and 0.003%, respectively. Concentrations of IgG, LF, α-LA, and ß-LG in the digesta of the abomasum, jejunum, and ileum rapidly decreased from C6h to C24h lambs, and the disappearance rates of IgG, LF, α-LA, and ß-LG were higher in lambs from C6h to C12h (62.1, 75.7, 91.3, and 95.0% for IgG, LF, α-LA, and ß-LG, respectively) than from C12h to C24h (34.6, 22.5, 7.5, and 2.2% for IgG, LF, α-LA, and ß-LG, respectively). These results indicated that bovine colostrum feeding improved the metabolic and immunological status of lambs, and that ingested colostral IgG was prone to intact uptake into the blood, whereas almost all ingested LF, α-LA, and ß-LG disappeared in the lumen of the gastrointestinal tract in a time-dependent manner. The findings provide novel information for exploring selective absorption of colostral compounds in the small intestine of lambs.

Changes in bacterial community and expression of genes involved in intestinal innate immunity in the jejunum of newborn lambs during the first 24 hours of life.

The newborn gut undergoes rapid colonization by commensal microorganisms and possible exposure to pathogens. The contribution of colostrum intake to host protection is well known; however, limited research exists on the intestinal innate immunity corresponding to colostrum intake during the passive immune transfer period in newborn ruminants. The aim of this study was to investigate the changes in bacterial community and expression of genes encoding toll-like receptors (TLR), mucins (MUC), antimicrobial peptides, and tight junctions in the jejunum of lambs that were fed colostrum during the first 24 h of life. Twenty-seven newborn lambs were used in this study, of which 18 lambs were bottle-fed pooled bovine colostrum within the first 2 h after birth to obtain an intake of approximately 8% of body weight. Lambs were slaughtered at 12 (n = 9) and 24 h (n = 9) after birth. The remaining 9 lambs without any feeding were slaughtered at 30 min after birth (0 h). Tissue and ligated segment samples from the jejunum were collected immediately after the lambs were slaughtered. The bacterial profile in the ligated jejunum segment was assessed using amplicon sequencing. The gene expression in the jejunum tissue was determined using quantitative real-time PCR. The relative abundances of Escherichia-Shigella, Lactobacillus, Lactococcus, and Streptococcus increased, whereas those of Sphingomonas, Phyllobacterium, Bradyrhizobium, and Rudaea decreased during the first 24 h of life. Expression of TLR2 and ß-defensin 109-like was upregulated at 12 h after birth, but a recovery was detected at 24 h; TLR3, TLR5, LYZ, MUC1, MUC13, MUC20, and CLDN7 showed a higher expression level in samples taken at 24 h than in those taken at 0 h. In addition, expression level of CLDN1, CLDN4, and the junctional adhesion molecule-1 tended to be higher at 24 h than at 0 h after birth. Correlation analysis indicated that TLR2 expression was negatively correlated with the relative abundance of Lactobacillus and Bradyrhizobium, whereas TLR5 expression was positively correlated with the relative abundance of Escherichia-Shigella and Pelagibacterium. These results suggest that TLR, MUC, antimicrobial peptides, and CLDN act together and play an important role in intestinal defense during the passive immune transfer period. They are potentially associated with microbial colonization. The findings from this study provide novel information to elucidate the role of colostrum components in regulating the development of the intestinal mucosal immune barrier in newborn lambs during the passive immune transfer period.

[Analysis of risk factors and construction of predictive nomogram for early recurrence after radiofrequency ablation of hepatocellular carcinoma].

Objective: To assess the optimal cut-off value between early recurrence and late recurrence of patients with hepatocellular carcinoma (HCC) after radiofrequency ablation (RFA), and to construct a nomogram to predict early recurrence. Methods: A total of 119 patients with HCC who recurred after RFA in Cancer Hospital, Chinese Academy of Medical Sciences from January 2012 to December 2017 were identified. The optimal cut-off value to distinguish early and late recurrence was determined based on differences in post recurrence survival (PRS) by minimum P-value approach. The clinical and radiographic risk factors for early recurrence were identified by univariate and multivariate Logistic regression analysis. The predictive nomogram was constructed by these factors and internally validated. Results: The optimal cut-off value to distinguish early recurrence and late recurrence was 12 months after RFA (P=0.005). The patients were divided into early recurrence group (47 cases) and late recurrence group (72 cases). The lower quartile PRS (Q1-PRS) and lower quartile overall survival (Q1-OS) were 11.1 and 19.1 months in the early recurrence group, which were shorter than 31.6 and 81.0 months in the late recurrence group (P=0.005 and P<0.001, respectively). The independent risk factors of early recurrence were alpha fetoprotein (AFP) (OR=8.459, 95%CI: 2.231-32.073), albumin(ALB) (OR=0.251, 95%CI: 0.047-1.339), number of lesions (OR=3.842, 95%CI: 1.424-10.365) and peritumoral enhancement (OR=8.05, 95%CI: 1.23-52.80), which were further incorporated into constructing the predictive nomogram of early recurrence of HCC after RFA. Internal validation results showed the area under the curve, sensitivity, specificity of the receiver operating characteristic (ROC) curve were 0.839, 68.1% and 93.1%, respectively. The calibration curve showed the predicted curve of nomogram was close to the ideal curve. Hosmer-Lemeshow test showed there was no significant difference between the predicted results of nomogram and the actual results (P=0.424). Conclusions: An interval of 12 months after RFA is the optimal cut-off value for defining early recurrence and late recurrence. The nomogram is integrated by clinical and radiographic features, which can potentially predict early recurrence of HCC after RFA and may offer useful guidance for individual treatment or follow up.

[Prevalence and influencing factors of deciduous dental caries among preschool children in Qingdao city in 2019].

In 2019, the rate of primary tooth caries rate among 1 598 preschool children in Shinan District and Shibei District of Qingdao was 59.4%. The multivariate logistic regression model showed that compared with children ≤ 2 years old with history of iron deficiency anemia (IDA), suffering IDA, breastfeeding to 2 years old and no tooth melanin, children ≤ 2 years old without history of IDA, not suffering IDA, breastfeeding to less than 2 years old and heavy tooth melanin had a lower risk of primary tooth caries, with OR (95%CI) values about 0.328 (0.197-0.549), 0.354 (0.208-0.603), 0.636 (0.437-0.926) and 0.301 (0.143-0.635), respectively.

Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies.

Antibodies capable of neutralizing HIV-1 often target variable regions 1 and 2 (V1V2) of the HIV-1 envelope, but the mechanism of their elicitation has been unclear. Here we define the developmental pathway by which such antibodies are generated and acquire the requisite molecular characteristics for neutralization. Twelve somatically related neutralizing antibodies (CAP256-VRC26.01-12) were isolated from donor CAP256 (from the Centre for the AIDS Programme of Research in South Africa (CAPRISA)); each antibody contained the protruding tyrosine-sulphated, anionic antigen-binding loop (complementarity-determining region (CDR) H3) characteristic of this category of antibodies. Their unmutated ancestor emerged between weeks 30-38 post-infection with a 35-residue CDR H3, and neutralized the virus that superinfected this individual 15 weeks after initial infection. Improved neutralization breadth and potency occurred by week 59 with modest affinity maturation, and was preceded by extensive diversification of the virus population. HIV-1 V1V2-directed neutralizing antibodies can thus develop relatively rapidly through initial selection of B cells with a long CDR H3, and limited subsequent somatic hypermutation. These data provide important insights relevant to HIV-1 vaccine development.

Label-free quantitative proteomics analysis reveals the fate of colostrum proteins in the intestine of neonatal calves.

The contribution of intestinally absorbed colostral immunoglobulins to the transmission of passive immunity is widely reported in neonatal calves. However, changes in the colostral proteome in the gastrointestinal digesta remain unclear. Therefore, this study aimed to investigate changes in colostral proteome affected by gastrointestinal proteases in neonatal calves. Twenty-one neonatal Holstein calves were used in this study, including 18 colostrum-fed calves slaughtered at 8 (CI, n = 6), 24 (CII, n = 6), and 36 h (CIII, n = 6) postpartum and 3 milk-fed calves slaughtered 24 h postpartum (MI, n = 3). The ingested colostrum and milk samples were collected from the mid-jejunum segment, following the sacrifice. The undigested colostrum or milk along with their ingested colostrum or milk samples were investigated using a label-free proteomics approach. Hierarchical clustering and principal component analysis of the quantified proteins revealed that the ingested colostrum from the CII and CIII groups and the ingested mature milk from the MI group appeared to share similar patterns. Analysis of the intestinal digesta revealed a time-dependent decrease in caseins, lactoferrin, and osteopontin protein levels, and an increase in cationic trypsin, chymotrypsin, and carboxypeptidase. Several protease inhibitors, such as α-1-antiproteinase, α-2-antiplasmin, and early lactation protein, were identified in the colostrum and intestinal digesta. In addition, we detected identical levels in the intestinal digesta and colostrum for albumin, α-1-acid glycoprotein, and plasminogen. Pathway analysis indicated that proteins increased in the intestinal digesta belonged to the following categories: biosynthesis of antibiotics, carbon metabolism, and biosynthesis of amino acids. These results indicated that selected colostral proteins were digested by gastrointestinal proteases, contributing to their intestinal absorption in calves. These findings provide new insights into the fate of the colostral proteome in the gastrointestinal tract and may aid in the identification of factors contributing to health management in neonatal calves.

Association of growth traits with a structural variation downstream of the KCNJ11 gene: a large population-based study in chickens.

1. The potassium voltage-gated channel subfamily J member 11 gene (KCNJ11) is involved in the insulin secretion pathway. Studies have shown that mutation in this gene is associated with muscle weakness. The objective of the present study was to establish the association between KCNJ11 gene polymorphism and chicken growth performance and to analyse its expression pattern. 2. A novel 163-bp insertion/deletion (indel) polymorphism was identified in the region downstream of the KCNJ11 gene in 2330 individuals from ten populations by polymerase chain reaction (PCR). An F2 resource population was used to investigate the genetic effects of the chicken KCNJ11 gene. Association analysis showed that the indel was significantly associated with chicken growth traits and that the phenotypic value of the ins-ins (II) genotype is higher than that of the ins-del (ID) and del-del (DD) genotypes. 3. Gene expression for different genotypes showed that birds carrying the II allele had a higher expression level than the DD genotypes. Analysis of tissue and spatiotemporal expression patterns indicated that the KCNJ11 gene was highly expressed in muscle tissues, with the highest levels in muscle tissue at one week of age, and that a 10% crude protein diet reduced the expression of this gene, average daily gain and muscle fibre diameter. 4. The results suggested that this novel 163-bp indel has the potential to become a new target for marker-assisted selection.

[Characteristic and clinical significance of microRNA expression between 144 Uygur and Han women with endometrial carcinoma].

OBJECTIVE: To compare the expression patterns of microRNA (miRNA) between 144 Uygur and Han women with endometrial carcinoma and to investigate their clinical significance. METHODS: Taqman miRNA low-density array was used to compare miRNA profiles between Uygur and Han women with non-endometrioid endometrial carcinoma (NEEC). Five miRNAs were further analyzed in the 144 endometrial cancers including 62 Uygur and 82 Han samples via real-time PCR to determine their expression patterns. RESULTS: MiRNA expression profiles revealed that many miRNAs overexpressed or downregula-ted in one ethnic group, but did not express or changed slightly in the other ethnic group. Further detection in the 144 endometrial cancers showed that miR-141, miR-200a, and miR-205 overexpressed in both ethnic groups. In Uygur endometrioid endometrial carcinoma (EEC), tumors with miR-141/200a overexpression tended to be more aggressive in behavior, whereas in the Han group, EEC with miR-200a overexpression was relative mild. However, the NEEC with miR-200a overexpression also had aggressive clinicopathologic features in the Han women. MiR-145 and miR-143 expressed differentially between Uygur and Han groups, they overexpressed in the former and decreased in the latter (P<0.05). In the Uygur women miR-145/143 increased significantly in NEEC and there was a trend that NEEC exhibiting favorable clinicopathologic factors had higher miR-145 expression, and was statistically significant in tumors with myometrial invasion less than 1/2 thickness (P=0.042). By contrary, miR-145/143 decreased in Han group and EEC with worse clinicopathologic variables had lower expression although without statistical significance. NEEC in Han group had no such tendency. CONCLUSION: Uygur and Han women might have different miRNA expression profiles. MiR-141/200a/205 overexpressed in endometrial carcinomas and miR-141/200a might behave differently between these two ethnic groups as well as in EEC and in NEEC. Although miR-145/143 showed inverse expression patterns between Uygur and Han women with endometrial cancer, they all exerted tumor suppression effect on endometrial cancer.

Mapping Polyclonal HIV-1 Antibody Responses via Next-Generation Neutralization Fingerprinting.

Computational neutralization fingerprinting, NFP, is an efficient and accurate method for predicting the epitope specificities of polyclonal antibody responses to HIV-1 infection. Here, we present next-generation NFP algorithms that substantially improve prediction accuracy for individual donors and enable serologic analysis for entire cohorts. Specifically, we developed algorithms for: (a) selection of optimized virus neutralization panels for NFP analysis, (b) estimation of NFP prediction confidence for each serum sample, and (c) identification of sera with potentially novel epitope specificities. At the individual donor level, the next-generation NFP algorithms particularly improved the ability to detect multiple epitope specificities in a sample, as confirmed both for computationally simulated polyclonal sera and for samples from HIV-infected donors. Specifically, the next-generation NFP algorithms detected multiple specificities in twice as many samples of simulated sera. Further, unlike the first-generation NFP, the new algorithms were able to detect both of the previously confirmed antibody specificities, VRC01-like and PG9-like, in donor CHAVI 0219. At the cohort level, analysis of ~150 broadly neutralizing HIV-infected donor samples suggested a potential connection between clade of infection and types of elicited epitope specificities. Most notably, while 10E8-like antibodies were observed in infections from different clades, an enrichment of such antibodies was predicted for clade B samples. Ultimately, such large-scale analyses of antibody responses to HIV-1 infection can help guide the design of epitope-specific vaccines that are tailored to take into account the prevalence of infecting clades within a specific geographic region. Overall, the next-generation NFP technology will be an important tool for the analysis of broadly neutralizing polyclonal antibody responses against HIV-1.

Antimicrobial resistance and virulence genes of Streptococcus isolated from dairy cows with mastitis in China.

Streptococcus is a major mastitis-causing pathogen in dairy cows. To investigate the prevalence, antimicrobial resistance and virulence gene of Streptococcus in mastitic milk, a total of 735 mastitic raw milk samples from dairy cows in 11 provinces of China were collected and tested. Antimicrobial resistance of Streptococcus isolates was determined by disc diffusion against 8 classes 29 antimicrobial agents, and Streptococcus resistant genes and virulence genes were determined by PCR and agarose gel electrophoresis. A total of 64 (8.71%) isolates of Streptococcus were isolated and identified using biochemical profiling, including 22 isolates of Streptococcus agalactiae, 13 isolates of Streptococcus dysgalactiae, and 29 isolates of Streptococcus uberis. Out of 64 resistant Streptococcus isolates, all isolates (100%) were resistant to 3 or more antimicrobials. The most frequency (n = 18, 28.12%) of the isolates were multi-resistant to 5-7 antimicrobials and the highest multi-resistant number was 29 (n = 1, 1.56%). Streptococcus isolates had the highest resistance rate to tetracycline (98.44%) and oxacillin (98.44%), followed by penicillin G (96.88%) and doxycycline (96.88%), and the lowest resistance was observed with respect to ciprofloxacin (1.56%). A total of 16 antimicrobials resistance genes with 25 combination patterns were detected in the isolates. The gene combination of Sul1/Sul2/Sul3 + gyrA/parC + cat1/cat2 was the most common pattern (12.5%). The correlation between resistant phenotypes and resistance genes in Streptococcs was 35.87%. A total of 7 virulence genes were detected and 59 (92.19%) isolates harbored at least one gene. Twenty-four classes of gene patterns were found in the isolates and the patterns of bca (9.38%) and cfb (9.38%) were the most prevalent form. In conclusion, the issue of drug resistance of Streptococcus is still a great concern in cattle health in China.