The Born in Guangzhou Cohort Study enables generational genetic discoveries.

Genomic research that targets large-scale, prospective birth cohorts constitutes an essential strategy for understanding the influence of genetics and environment on human health1. Nonetheless, such studies remain scarce, particularly in Asia. Here we present the phase I genome study of the Born in Guangzhou Cohort Study2 (BIGCS), which encompasses the sequencing and analysis of 4,053 Chinese individuals, primarily composed of trios or mother-infant duos residing in South China. Our analysis reveals novel genetic variants, a high-quality reference panel, and fine-scale local genetic structure within BIGCS. Notably, we identify previously unreported East Asian-specific genetic associations with maternal total bile acid, gestational weight gain and infant cord blood traits. Additionally, we observe prevalent age-specific genetic effects on lipid levels in mothers and infants. In an exploratory intergenerational Mendelian randomization analysis, we estimate the maternal putatively causal and fetal genetic effects of seven adult phenotypes on seven fetal growth-related measurements. These findings illuminate the genetic links between maternal and early-life traits in an East Asian population and lay the groundwork for future research into the intricate interplay of genetics, intrauterine exposures and early-life experiences in shaping long-term health.

Genome-wide association and Mendelian randomisation analysis among 30,699 Chinese pregnant women identifies novel genetic and molecular risk factors for gestational diabetes and glycaemic traits.

AIMS/HYPOTHESIS: Gestational diabetes mellitus (GDM) is the most common disorder in pregnancy; however, its underlying causes remain obscure. This study aimed to investigate the genetic and molecular risk factors contributing to GDM and glycaemic traits. METHODS: We collected non-invasive prenatal test (NIPT) sequencing data along with four glycaemic and 55 biochemical measurements from 30,699 pregnant women during a 2 year period at Shenzhen Baoan Women's and Children's Hospital in China. Genome-wide association studies (GWAS) were conducted between genotypes derived from NIPTs and GDM diagnosis, baseline glycaemic levels and glycaemic levels after glucose challenges. In total, 3317 women were diagnosed with GDM, while 19,565 served as control participants. The results were replicated using two independent cohorts. Additionally, we performed one-sample Mendelian randomisation to explore potential causal associations between the 55 biochemical measurements and risk of GDM and glycaemic levels. RESULTS: We identified four genetic loci significantly associated with GDM susceptibility. Among these, MTNR1B exhibited the highest significance (rs10830963-G, OR [95% CI] 1.57 [1.45, 1.70], p=4.42×10-29), although its effect on type 2 diabetes was modest. Furthermore, we found 31 genetic loci, including 14 novel loci, that were significantly associated with the four glycaemic traits. The replication rates of these associations with GDM, fasting plasma glucose levels and 0 h, 1 h and 2 h OGTT glucose levels were 4 out of 4, 6 out of 9, 10 out of 11, 5 out of 7 and 4 out of 4, respectively. Mendelian randomisation analysis suggested that a genetically regulated higher lymphocytes percentage and lower white blood cell count, neutrophil percentage and absolute neutrophil count were associated with elevated glucose levels and an increased risk of GDM. CONCLUSIONS/INTERPRETATION: Our findings provide new insights into the genetic basis of GDM and glycaemic traits during pregnancy in an East Asian population and highlight the potential role of inflammatory pathways in the aetiology of GDM and variations in glycaemic levels. DATA AVAILABILITY: Summary statistics for GDM; fasting plasma glucose; 0 h, 1 h and 2h OGTT; and the 55 biomarkers are available in the GWAS Atlas (study accession no.: GVP000001, https://ngdc.cncb.ac.cn/gwas/browse/GVP000001) .

Japanese medaka (Oryzias latipes) Nectin4 plays an important role against red spotted grouper nervous necrosis virus infection.

Nectins are adhesion molecules that play a crucial role in the organization of epithelial and endothelial junctions and function as receptors for the entry of herpes simplex virus. However, the role of Nectin4 remains poorly understood in fish. In this study, nectin4 gene was cloned from medaka (OlNectin4). OlNectin4 was located on chromosome 18 and contained 11 exons, with a total genome length of 25754 bp, coding sequences of 1689 bp, coding 562 amino acids and a molecular weight of 65.5 kDa. OlNectin4 contained four regions, including an Immunoglobulin region, an Immunoglobulin C-2 Type region, a Transmembrane region and a Coiled coil region. OlNectin4 shared 47.18 % and 25.00 % identity to Paralichthys olivaceus and Mus musculus, respectively. In adult medaka, the transcript of nectin4 was predominantly detected in gill. During red spotted grouper nervous necrosis virus (RGNNV) infection, overexpression of OlNectin4 in GE cells significantly increased viral gene transcriptions. Meanwhile, Two mutants named OlNectin4△4 (+4 bp) and OlNectin4△7 (-7 bp) medaka were established using CRISPR-Cas9 system. Nectin4-KO medaka had higher mortality than WT after infected with RGNNV. Moreover, the expression of RGNNV RNA2 gene in different tissues of the Nectin4-KO were higher than WT medaka after challenged with RGNNV. The brain and eye of Nectin4-KO medaka which RGNNV mainly enriched, exhibited significantly higher expression of interferon signaling genes than in WT. Taken together, the OlNectin4 plays a complex role against RGNNV infection by inducing interferon responses for viral clearance.

Large-scale inference of population structure in presence of missingness using PCA.

MOTIVATION: Principal component analysis (PCA) is a commonly used tool in genetics to capture and visualize population structure. Due to technological advances in sequencing, such as the widely used non-invasive prenatal test, massive datasets of ultra-low coverage sequencing are being generated. These datasets are characterized by having a large amount of missing genotype information. RESULTS: We present EMU, a method for inferring population structure in the presence of rampant non-random missingness. We show through simulations that several commonly used PCA methods cannot handle missing data arisen from various sources, which leads to biased results as individuals are projected into the PC space based on their amount of missingness. In terms of accuracy, EMU outperforms an existing method that also accommodates missingness while being competitively fast. We further tested EMU on around 100K individuals of the Phase 1 dataset of the Chinese Millionome Project, that were shallowly sequenced to around 0.08×. From this data we are able to capture the population structure of the Han Chinese and to reproduce previous analysis in a matter of CPU hours instead of CPU years. EMU's capability to accurately infer population structure in the presence of missingness will be of increasing importance with the rising number of large-scale genetic datasets. AVAILABILITY AND IMPLEMENTATION: EMU is written in Python and is freely available at https://github.com/rosemeis/emu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Lifestyle-based subtypes of childhood obesity and their association with cardiometabolic factors: A cluster analysis.

BACKGROUND: Lifestyle factors play an important role in the development and management of childhood obesity and its related cardiometabolic complications. OBJECTIVE/METHODS: We aimed to explore childhood obesity subtypes based on lifestyle factors and examine their association with cardiometabolic health. We included 1550 children with obesity from the National Health and Nutrition Examination Survey. Cluster analysis identified obesity subtypes based on four lifestyle factors (physical activity, diet quality, sedentary time and smoking). Multiple linear regression assessed their association with cardiometabolic factors. RESULTS: Five subtypes of childhood obesity were identified: unhealthy subtype (n = 571; 36.8%), physically active subtype (n = 185; 21.1%), healthy diet subtype (n = 404; 26.1%), smoking subtype (n = 125; 8.1%) and non-sedentary subtype (n = 265; 17.1%). Compared with the unhealthy subtype, the physically active subtype had lower insulin and HOMA-IR levels, and smoking subtype was associated with lower HDL levels. When compared with children with normal weight, all obesity subtypes had worse cardiometabolic profile, except the physically active subtype who had similar DBP, HbA1c and TC levels; smoking subtype who had similar TC levels; and healthy diet and non-sedentary subtypes who had similar DBP levels. CONCLUSION: Children of different lifestyle-based obesity subtypes might have different cardiometabolic risks. Our new classification system might help personalize assessment of childhood obesity.

Utilizing non-invasive prenatal test sequencing data for human genetic investigation.

Non-invasive prenatal testing (NIPT) employs ultra-low-pass sequencing of maternal plasma cell-free DNA to detect fetal trisomy. Its global adoption has established NIPT as a large human genetic resource for exploring genetic variations and their associations with phenotypes. Here, we present methods for analyzing large-scale, low-depth NIPT data, including customized algorithms and software for genetic variant detection, genotype imputation, family relatedness, population structure inference, and genome-wide association analysis of maternal genomes. Our results demonstrate accurate allele frequency estimation and high genotype imputation accuracy (R2>0.84) for NIPT sequencing depths from 0.1× to 0.3×. We also achieve effective classification of duplicates and first-degree relatives, along with robust principal-component analysis. Additionally, we obtain an R2>0.81 for estimating genetic effect sizes across genotyping and sequencing platforms with adequate sample sizes. These methods offer a robust theoretical and practical foundation for utilizing NIPT data in medical genetic research.

Breast Milk Constituents and the Development of Breast Milk Jaundice in Neonates: A Systematic Review.

Breast milk is tailored for optimal growth in all infants; however, in some infants, it is related to a unique phenomenon referred to as breast milk jaundice (BMJ). BMJ is a type of prolonged unconjugated hyperbilirubinemia that is often late onset in otherwise healthy-appearing newborns, and its occurrence might be related to breast milk itself. This review aims to systematically evaluate evidence regarding breast milk composition and the development of BMJ in healthy neonates. PubMed, Scopus and Embase were searched up to 13 February 2023 with key search terms, including neonates, hyperbilirubinemia, and breastfeeding. A total of 678 unique studies were identified and 12 were ultimately included in the systematic review with narrative synthesis. These included studies covered both nutritional compositions (e.g., fats and proteins) and bioactive factors (e.g., enzymes and growth factors) of breast milk and formally assessed the difference in the concentration (or presence) of various endogenous components of breast milk collected from mothers of BMJ infants and healthy infants. The results were inconsistent and inconclusive for most of the substances of interest, and there was only a single study available (e.g., total energy and mineral content, bile salts and cytokines); conflicting or even contradictory results arose when there were two or more studies on the subject matter (e.g., fats and free fatty acids contents and epidermal growth factor). The etiology of BMJ is likely multifactorial, and no single constituent of breast milk could explain all the BMJ cases observed. Further well-designed studies are warranted to investigate the complex interaction between maternal physiology, the breast milk system and infant physiology before this field could be progressed to uncover the etiology of BMJ.

Prevalence of High-Risk Human Papillomavirus by Subtypes Among Rural Women Aged 35-64 Years - Guangzhou City, Guangdong Province, China, 2019-2021.

What is already known about this topic?: Little is known about the infection pattern for high-risk human papillomavirus (hrHPV) subtypes in rural areas in southern China. What is added by this report?: The prevalence of HPV-16, 18, and the other 12 hrHPV subtypes were 0.71%, 0.34%, and 4.50%, respectively, among rural women in Guangzhou. The prevalence of HPV-16 and the other 12 hrHPV subtypes increased with age, but there was no evident age trend for HPV-18 prevalence. What are the implications for public health practice?: Epidemiological characteristics of hrHPV prevalence in rural Guangzhou should be considered to identify high-risk populations of hrHPV infection and determine follow-up strategies.

The Relationship between Bicultural Identity Integration, Self-Esteem, Academic Resilience, Interaction Anxiousness, and School Belonging among University Students with Vocational Qualifications.

Background: University students with a vocational pathway face greater cultural, psychological, cognitive, and behavioral challenges during the transition process than their counterparts with an academic route. Method: This study examined the predictive effect of bicultural identity integration, self-esteem, academic resilience, and interaction anxiousness on school belonging using a quantitative approach with 326 Chinese vocational pathway university student participants. Result: The participants had high levels of cultural adaptability, self-esteem, academic resilience, and school belonging, but they also displayed moderate interaction anxiousness. Bicultural identity integration (B = 0.24; p < 0.001), self-esteem (B = 0.35; p < 0.001), and academic resilience (B = 0.25; p < 0.001) significantly positively predicted school belonging, while interaction anxiousness (B = −0.17; p < 0.01) negatively predicted school belonging. Conclusions: Bicultural identity integration, self-esteem, academic resilience, and interaction anxiousness were crucial determinants of school belonging among Chinese university students with vocational qualifications. Effective measures should be initiated to boost their feelings of being recognized, respected, and connected to the university community.

Exploring the Associations between Perceived Organizational Support and Job Burnout among Chinese Academic Journal Editors: A Moderated Mediation Model.

BACKGROUND: Job burnout (JB) has become a prevalent emotional and psychological syndrome across diverse contexts, especially in the face of the COVID-19 pandemic. This study aimed to examine the relationship between perceived organizational support (POS), job satisfaction (JS), self-efficacy (SE), and JB, alongside their mechanism of interplay. METHODS: We took 210 Chinese academic journal editors as the research participants and designed a moderated mediation model to examine the posited construct. All the data were gathered online and analyzed with the statistical software SPSS and SmartPLS. RESULTS: The participants comprised 117 women (55.71%) and 93 men (44.29%). There were significant differences among observed variables in age, experience, and title. POS had a significant negative predictive effect on JB (95% CI = -0.43; -0.06). JS mediated the relationship between POS and JB (95% CI = -0.48; -0.11). SE moderated the association between JS and JB (95% CI = 0.04; 0.75) but did not function as a moderator in the relationship between POS and JS (95% CI = -0.01; 0.24). CONCLUSIONS: POS, JS, and SE were crucial determinants of JB among Chinese academic journal editors. Targeted interventions should be initiated to diminish editors' feelings of being unappreciated, inefficient, dissatisfied, and unaccomplished at work.

The trans-omics landscape of COVID-19.

The outbreak of coronavirus disease 2019 (COVID-19) is a global health emergency. Various omics results have been reported for COVID-19, but the molecular hallmarks of COVID-19, especially in those patients without comorbidities, have not been fully investigated. Here we collect blood samples from 231 COVID-19 patients, prefiltered to exclude those with selected comorbidities, yet with symptoms ranging from asymptomatic to critically ill. Using integrative analysis of genomic, transcriptomic, proteomic, metabolomic and lipidomic profiles, we report a trans-omics landscape for COVID-19. Our analyses find neutrophils heterogeneity between asymptomatic and critically ill patients. Meanwhile, neutrophils over-activation, arginine depletion and tryptophan metabolites accumulation correlate with T cell dysfunction in critical patients. Our multi-omics data and characterization of peripheral blood from COVID-19 patients may thus help provide clues regarding pathophysiology of and potential therapeutic strategies for COVID-19.

Association Between Social Support and Job Satisfaction Among Mainland Chinese Ethnic Minority Kindergarten Teachers: The Mediation of Self-Efficacy and Work Engagement.

Grounded on the social exchange theory (SET), social cognitive theory (SCT), and self-determination theory (SDT), this study aims to explore the mediating role of self-efficacy (SE) and work engagement (WE) on the effect of social support (SS) on job satisfaction (JS) among Chinese ethnic minority kindergarten teachers (KTs). The results show that: (1) SS has a directly significant effect on JS; (2) WE mediates the relationship between SS and JS; and (3) SE mediates the relationship between SS and WE. Although the mediation of SE on the relationship between SS and JS is not found, the posited multiple mediations of SE and WE on the relationship between SS and JS are totally accepted. The results reveal that SS mainland Chinese ethnic minority KTs received can not only have a direct effect on JS but also have an indirect impact through the one-path mediating role of WE and the chain mediating role of SE and WE. The results suggest that governments, supervisors, and sponsors should work together to provide ethnic minority KTs with more prioritized SS from both cultural psychology and financial material and opportunities for facilitating professional knowledge and skills in order to enhance their SE, inspire their WE, and eventually accumulate their JS.

[Sensitivity of Oncomelania snail to niclosamide in China].

OBJECTIVE: To understand the variation in response of Oncomelania hupensis to niclosamide. METHODS: Snails were collected from 37 sampling areas distributed in 10 provinces (municipalities) using random environmental sampling methods in accordance with the different types and categories of snail habitats. In laboratory the snails were immersed in solutions of niclosamide for 24 and 48 hours at 25 degrees C. RESULTS: 1.0 mg/L niclosamide showed 100% killing effect on snails in 24 hours. The LC50 concentrations for snails immersed for 24 hours ranged from 0.0320 to 0.1689 mg/L with a mean value of 0.0920 mg/L. 0.5 mg/L niclosamide showed 100% killing effect on snails in 48 hours. The LC50 values for snails immersed for 48 hours ranged between 0.0299 and 0.1114 mg/L with a mean of 0.0627 mg/L. There is a significant difference in snail sensitivity to niclosamide between sampling areas. CONCLUSION: The sensitivity to niclosamide varied in snails from different sampling fields, but the chemical in a concentration of 1.0 mg/L showed 100% effect of killing snails, which is consistent to the manual of schistosomiasis control.