Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations

We conducted a joint (pooled) analysis of three genome-wide association studies (GWAS) 1-3 of esophageal squamous cell carcinoma (ESCC) in ethnic Chinese (5,337 ESCC cases and 5,787 controls) with 9,654 ESCC cases and 10,058 controls for follow-up. In a logistic regression model adjusted for age, sex, study, and two eigenvectors, two new loci achieved genome-wide significance, marked by rs7447927 at 5q31.2 (per-allele odds ratio (OR) = 0.85, 95% CI 0.82-0.88; P=7.72x10−20) and rs1642764 at 17p13.1 (per-allele OR= 0.88, 95% CI 0.85-0.91; P=3.10x10−13). rs7447927 is a synonymous single nucleotide polymorphism (SNP) in TMEM173 and rs1642764 is an intronic SNP in ATP1B2, near TP53. Furthermore, a locus in the HLA class II region at 6p21.32 (rs35597309) achieved genome-wide significance in the two populations at highest risk for ESSC (OR=1.33, 95% CI 1.22-1.46; P=1.99x10−10). Our joint analysis identified new ESCC susceptibility loci overall as well as a new locus unique to the ESCC high risk Taihang Mountain region

Parental Factors Associated With Internet Gaming Disorder Among First-Year High School Students: Longitudinal Study

BackgroundParents play central roles in adolescents’ socialization, behavioral development, and health, including the development of internet gaming disorder (IGD). However, longitudinal research on the parental predictors of adolescent IGD is limited. ObjectiveThis study aimed to investigate the reciprocal associations between various parental factors and adolescent IGD using 2-wave cross-lagged models. MethodsA sample of 1200 year-one high school students in central China completed a baseline assessment in 2018 (mean age 15.6 years; 633/1200, 52.8% male) and a follow-up survey in 2019. IGD was measured using the 9-item DSM-5 IGD Symptoms checklist. Perceptions related to parental variables, including psychological control, parental abuse, parental support, and the parent-child relationship, were also collected from the adolescents. ResultsOf all the participants, 12.4% (148/1200) and 11.7% (140/1200) were classified as having IGD at baseline (T1) and follow-up (T2), respectively. All 4 cross-lagged models fit the data well (range for the comparative fit index .91-.95; range for the standardized root mean square residual .05-.06). Parental support (β=–.06, P=.02) and parental abuse (β=.08, P=.002) at T1 predicted IGD symptoms at T2, while parental psychological control (β=.03, P=.25) and a positive relationship with parents (β=–.05, P=.07) at T1 had nonsignificant effects on IGD symptoms at T2, when controlling for background variables. In addition, IGD symptoms at T1 did not predict parental factors at T2. ConclusionsThe findings suggest that parental factors may be significant predictors of adolescent IGD. Health interventions should consider involving parents to increase the effectiveness of treatment to prevent and reduce adolescent IGD

The complete chloroplast genome sequence of Mentha canadensis (Labiatae), a traditional Chinese herbal medicine

Mentha canadensis is a well-known resource of traditional Chinese herbal medicine, belonging to the Mentha of the Labiatae family. In this study, the whole chloroplast genome of the M. canadensis chloroplast genome was sequenced, assembled and annotated, which contains 134 unique genes, including 89 protein-coding genes, 37 tRNA genes and 8 rRNA genes. A maximum likelihood phylogenetic tree based on 11 complete chloroplast genomes revealed that M. canadensis is closely related to M. longifolia and M. spicata. The chloroplast genome could be used for variety identification, genetic engineering and effective protection of germplasm resources

The complete chloroplast genome of Gentiana apiata (Gentianaceae), an endemic species to Qinba Mountain in China

Gentiana apiata N. E. Br., is a perennial medicinal plant in the family Gentianaceae, which is recorded as near-threatened (NT) species in the Red List and endemic species only distributed in Qinba Mountain, China. The complete chloroplast genome sequence of G. apiata was sequenced using the Illumina Hiseq 4000 platform. The size of the G. apiata chloroplast genome is 151,069 bp, with an average GC content of 37.6%. This circular molecule has a typical quadripartite structure containing a large single-copy (LSC) region of 83,023 bp, a small single-copy (SSC) region of 17,256 bp, and two inverted (IRs) repeat regions of 25,395 bp. A total of 134 genes were successfully annotated containing 86 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 3 pseudogenes (rps19, ycf1, infA). A maximum likelihood (ML) phylogenetic tree supported the fact that the chloroplast genome of G. apiata is closely related to that of Gentiana hexaphylla

Relationship Between Illness Representations and Symptoms of Internet Gaming Disorder Among Young People: Cross-Lagged Model

BackgroundThe common-sense model of illness suggests that mental representations of health threats may affect one’s behavioral reactions to them and health status. Internet gaming disorder is a newly defined mental disorder. Illness representations of internet gaming disorder may affect one’s risk of internet gaming disorder. In turn, symptoms of internet gaming disorder may affect one’s perceptions of the disorder. ObjectiveThis study aimed to investigate the relationships between illness representations and symptoms of internet gaming disorder in college students. MethodsA 1-year longitudinal study was conducted with a convenience sample of Chinese college students (n=591; 342/591, 57.9% female). ResultsOf the participants, 10.1% (60/591) and 9.1% (54/591) were classified as having probable internet gaming disorder at baseline (T1) and follow-up (T2), respectively. The correlations between some dimensions of illness representations regarding internet gaming disorder (ie, consequence, timeline, personal control, treatment control, and concern) at T1 and symptoms of internet gaming disorder at T2 and between symptoms of internet gaming disorder at T1 and the dimensions of illness representations at T2 (ie, consequence, timeline, personal control, and emotional response) were statistically significant. The cross-lagged model fit the data well ((χ2/df=2.28, comparative fit index=.95, root mean square error of approximation=.06) and showed that internet gaming disorder at T1 was positively associated with unfavorable illness representations at T2. ConclusionsIndividuals with more severe symptoms of internet gaming disorder had more pessimistic perceptions about the disorder. Such cognitive perceptions may affect one’s emotional and behavioral reactions towards the disorder (eg, greater levels of depression and low self-control intention) and should be modified by educational programs and psychological interventions

Selection of Reference Genes in Transcription Analysis of Gene Expression of the Mandarin Fish, Siniperca chuasti

At present，transcription analysis of gene expression commonly uses housekeeping genes as control for normalization．In this study, the expression levels of three housekeeping genes including GAPDH, β-actin, and 18S rRNA in six tissues and five developmental stages of the Mandarin fish Siniperca chuasti were assayed with quantitative real-time PCR (qPCR)．Differences in expression levels were analyzed using geNorm program. The results demonstrate that β-actin is the most stable gene at developmental stages and GAPDH is the most stable in different tissues. While 18S rRNA expression during development is differentially regulated, which indicates it is suitable as an internal control for gene expression normalization at the developmental level. Overall, the data suggest that the two most stable housekeeping genes are enough to accurately calibrate gene expression in S. chuatsi. The significance of this study provided convincing references and methodology for housekeeping gene selection and normalization in gene expression analysis with regular PCR or qPCR