Identifying canonical and replicable multi-scale intrinsic connectivity networks in 100k+ resting-state fMRI datasets.

Despite the known benefits of data-driven approaches, the lack of approaches for identifying functional neuroimaging patterns that capture both individual variations and inter-subject correspondence limits the clinical utility of rsfMRI and its application to single-subject analyses. Here, using rsfMRI data from over 100k individuals across private and public datasets, we identify replicable multi-spatial-scale canonical intrinsic connectivity network (ICN) templates via the use of multi-model-order independent component analysis (ICA). We also study the feasibility of estimating subject-specific ICNs via spatially constrained ICA. The results show that the subject-level ICN estimations vary as a function of the ICN itself, the data length, and the spatial resolution. In general, large-scale ICNs require less data to achieve specific levels of (within- and between-subject) spatial similarity with their templates. Importantly, increasing data length can reduce an ICN's subject-level specificity, suggesting longer scans may not always be desirable. We also find a positive linear relationship between data length and spatial smoothness (possibly due to averaging over intrinsic dynamics), suggesting studies examining optimized data length should consider spatial smoothness. Finally, consistency in spatial similarity between ICNs estimated using the full data and subsets across different data lengths suggests lower within-subject spatial similarity in shorter data is not wholly defined by lower reliability in ICN estimates, but may be an indication of meaningful brain dynamics which average out as data length increases.

A DNA methylation biomarker of alcohol consumption.

The lack of reliable measures of alcohol intake is a major obstacle to the diagnosis and treatment of alcohol-related diseases. Epigenetic modifications such as DNA methylation may provide novel biomarkers of alcohol use. To examine this possibility, we performed an epigenome-wide association study of methylation of cytosine-phosphate-guanine dinucleotide (CpG) sites in relation to alcohol intake in 13 population-based cohorts (ntotal=13 317; 54% women; mean age across cohorts 42-76 years) using whole blood (9643 European and 2423 African ancestries) or monocyte-derived DNA (588 European, 263 African and 400 Hispanic ancestry) samples. We performed meta-analysis and variable selection in whole-blood samples of people of European ancestry (n=6926) and identified 144 CpGs that provided substantial discrimination (area under the curve=0.90-0.99) for current heavy alcohol intake (⩾42 g per day in men and ⩾28 g per day in women) in four replication cohorts. The ancestry-stratified meta-analysis in whole blood identified 328 (9643 European ancestry samples) and 165 (2423 African ancestry samples) alcohol-related CpGs at Bonferroni-adjusted P<1 × 10-7. Analysis of the monocyte-derived DNA (n=1251) identified 62 alcohol-related CpGs at P<1 × 10-7. In whole-blood samples of people of European ancestry, we detected differential methylation in two neurotransmitter receptor genes, the γ-Aminobutyric acid-A receptor delta and γ-aminobutyric acid B receptor subunit 1; their differential methylation was associated with expression levels of a number of genes involved in immune function. In conclusion, we have identified a robust alcohol-related DNA methylation signature and shown the potential utility of DNA methylation as a clinically useful diagnostic test to detect current heavy alcohol consumption.

CPT1A methylation is associated with plasma adiponectin.

BACKGROUND AND AIMS: Adiponectin, an adipose-secreted protein that has been linked to insulin sensitivity, plasma lipids, and inflammatory patterns, is an established biomarker for metabolic health. Despite clinical relevance and high heritability, the determinants of plasma adiponectin levels remain poorly understood. METHODS AND RESULTS: We conducted the first epigenome-wide cross-sectional study of adiponectin levels using methylation data on 368,051 cytosine-phosphate-guanine (CpG) sites in CD4+ T-cells from the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN, n = 991). We fit linear mixed models, adjusting for age, sex, study site, T-cell purity, and family. We have identified a positive association (regression coefficient ± SE = 0.01 ± 0.001, P = 3.4 × 10-13) between plasma adiponectin levels and methylation of a CpG site in CPT1A, a key player in fatty acid metabolism. The association was replicated (n = 474, P = 0.0009) in whole blood samples from the Amish participants of the Heredity and Phenotype Intervention (HAPI) Heart Study as well as White (n = 592, P = 0.0005) but not Black (n = 243, P = 0.18) participants of the Bogalusa Heart Study (BHS). The association remained significant upon adjusting for BMI and smoking in GOLDN and HAPI but not BHS. We also identified associations between methylation loci in RNF145 and UFM1 and plasma adiponectin in GOLDN and White BHS participants, although the association was not robust to adjustment for BMI or smoking. CONCLUSION: We have identified and replicated associations between several biologically plausible loci and plasma adiponectin. These findings support the importance of epigenetic processes in metabolic traits, laying the groundwork for future translational applications.

Interactions between maternal killer cell immunoglobulin receptor genes and foetal HLA ligand genes contribute to type 1 diabetes susceptibility in Han Chinese.

In this study, we aimed to test the hypothesis that KIR haplotypes (that interact with HLA class I molecules) are associated with susceptibility in patients with T1DM in utero through maternal-foetal interaction of KIR and their HLA class I ligands in Han Chinese population. We determined the KIR genes and KIR/ligand gene combination frequencies in 59 Han Chinese children with T1D and their mothers and compared it with 159 healthy control children and their mothers. The absence of KIR-2DS1 in the mother and the presence of HLA-C2 ligand in the child were negatively associated with type 1 diabetes in the child. Our results indicate that maternal KIR genes and their interaction with foetal HLA-C2 may contribute to the risk of type 1 diabetes among Han Chinese children.

High-density genotyping of immune loci in Kawasaki disease and IVIG treatment response in European-American case-parent trio study.

Kawasaki disease (KD) is a diffuse and acute small-vessel vasculitis observed in children, and has genetic and autoimmune components. We genotyped 112 case-parent trios of European decent (confirmed by ancestry informative markers) using the immunoChip array, and performed association analyses with susceptibility to KD and intravenous immunoglobulin (IVIG) non-response. KD susceptibility was assessed using the transmission disequilibrium test, whereas IVIG non-response was evaluated using multivariable logistic regression analysis. We replicated single-nucleotide polymorphisms (SNPs) in three gene regions (FCGR, CD40/CDH22 and HLA-DQB2/HLA-DOB) that have been previously associated with KD and provide support to other findings of several novel SNPs in genes with a potential pathway in KD pathogenesis. SNP rs838143 in the 3'-untranslated region of the FUT1 gene (2.7 × 10(-5)) and rs9847915 in the intergenic region of LOC730109 | BRD7P2 (6.81 × 10(-7)) were the top hits for KD susceptibility in additive and dominant models, respectively. The top hits for IVIG responsiveness were rs1200332 in the intergenic region of BAZ1A | C14orf19 (1.4 × 10(-4)) and rs4889606 in the intron of the STX1B gene (6.95 × 10(-5)) in additive and dominant models, respectively. Our study suggests that genes and biological pathways involved in autoimmune diseases have an important role in the pathogenesis of KD and IVIG response mechanism.

Genomic changes at the early stage of somatic hybridization.

A broad spectrum of genetic and epigenetic changes is induced by wide hybridization and subsequent polyploidization, but the timing of these events remains obscure because early hybrid cells are very difficult to harvest and analyze. Here, we used both cytological and genetic marker approaches to analyze the constitution of very young somatic hybrid cells between japonica rice (Oryza sativa L. subsp japonica) and indica rice (Oryza sativa L. subsp indica) and between japonica rice and bread wheat (Triticum aestivum L.). Chromatin elimination, simple sequence repeats, and retrotransposon profile deletions were already apparent within six days of the fusion event. The evidence we have presented suggests that genomic changes induced by genomic shock occur soon after the formation of hybrid cells.

Development and validation of a nomogram to predict postsurgical intra-abdominal infection in blunt abdominal trauma patients: A multicenter retrospective study.

BACKGROUND: Intra-abdominal infection is a common complication of blunt abdominal trauma. Early detection and intervention can reduce the incidence of intra-abdominal infection and improve patients' prognoses. This study aims to construct a clinical model predicting postsurgical intra-abdominal infection after blunt abdominal trauma. METHODS: This study is a retrospective analysis of 553 patients with blunt abdominal trauma from the Department of General Surgery of 7 medical centers (2011-2021). A 7:3 ratio was used to assign patients to the derivation and validation cohorts. Patients were divided into 2 groups based on whether intra-abdominal infection occurred after blunt abdominal trauma. Multivariate logistic regression and least absolute shrinkage and selection operator regression were used to select variables to establish a nomogram. The nomogram was evaluated, and the validity of the model was further evaluated by the validation cohort. RESULTS: A total of 113 were diagnosed with intra-abdominal infection (20.4%). Age, prehospital time, C-reactive protein, injury severity score, operation duration, intestinal injury, neutrophils, and antibiotic use were independent risk factors for intra-abdominal infection in blunt abdominal trauma patients (P < .05). The area under the receiver operating curve (area under the curve) of derivation cohort and validation cohort was 0.852 (95% confidence interval, 0.784-0.912) and 0.814 (95% confidence interval, 0.751-0.902). The P value for the Hosmer-Lemeshow test was .135 and .891 in the 2 cohorts. The calibration curve demonstrated that the nomogram had a high consistency between prediction and practical observation. The decision curve analysis also showed that the nomogram had a better potential for clinical application. To facilitate clinical application, we have developed an online at https://nomogramcgz.shinyapps.io/IAIrisk/. CONCLUSION: The nomogram is helpful in predicting the risk of postoperative intra-abdominal infection in patients with blunt abdominal trauma and provides guidance for clinical decision-making and treatment.

Identification of Type 2 Diabetes Based on a Ten-Gene Biomarker Prediction Model Constructed Using a Support Vector Machine Algorithm.

Background: Type 2 diabetes is a major health concern worldwide. The present study is aimed at discovering effective biomarkers for an efficient diagnosis of type 2 diabetes. Methods: Differentially expressed genes (DEGs) between type 2 diabetes patients and normal controls were identified by analyses of integrated microarray data obtained from the Gene Expression Omnibus database using the Limma package. Functional analysis of genes was performed using the R software package clusterProfiler. Analyses of protein-protein interaction (PPI) performed using Cytoscape with the CytoHubba plugin were used to determine the most sensitive diagnostic gene biomarkers for type 2 diabetes in our study. The support vector machine (SVM) classification model was used to validate the gene biomarkers used for the diagnosis of type 2 diabetes. Results: GSE164416 dataset analysis revealed 499 genes that were differentially expressed between type 2 diabetes patients and normal controls, and these DEGs were found to be enriched in the regulation of the immune effector pathway, type 1 diabetes mellitus, and fatty acid degradation. PPI analysis data showed that five MCODE clusters could be considered as clinically significant modules and that 10 genes (IL1B, ITGB2, ITGAX, COL1A1, CSF1, CXCL12, SPP1, FN1, C3, and MMP2) were identified as "real" hub genes in the PPI network using algorithms such as Degree, MNC, and Closeness. The sensitivity and specificity of the SVM model for identifying patients with type 2 diabetes were 100%, with an area under the curve of 1 in the training as well as the validation dataset. Conclusion: Our results indicate that the SVM-based model developed by us can facilitate accurate diagnosis of type 2 diabetes.

The detection of SAS1B in serum provides clues for early diagnosis of thyroid cancer.

OBJECTIVE: The incidence of thyroid cancer is rising globally. Most patients progress slowly, but some patients develop lymph node and distant metastasis earlier, and their prognosis is poor. Therefore, early diagnosis and warning of malignancy are very meaningful for such patients. SAS1B gene is a newly discovered protein expressed on the surface of mature egg cells and has metalloendopeptidase activity. We aimed at exploring whether SAS1B is involved in the occurrence of thyroid cancer, and at providing evidence for early diagnosis and targeted therapy of thyroid cancer. PATIENTS AND METHODS: In this study, a rabbit anti-human SAS1B polyclonal antibody was prepared by gene recombination technology. The indirect ELISA method was used to detect the SAS1B protein expression in the serum of 69 patients with thyroid cancer and 55 normal controls, and the relevant pathological factors were analyzed. Immunohistochemistry and PCR technology were used to investigate the expression levels of SAS1B protein and mRNA in 30 thyroid cancer tissues and 23 control thyroid tissues. RESULTS: The titer of SAS1B recombinant antibody was 1:51200. The expression of SAS1B in the serum of patients with thyroid cancer was higher than that in the normal control group (p<0.01). The antibody had a good sensitivity in serum detection of cancer patients (p=0.008<0.01), the linear regression analysis result was that the expression of SAS1B gene was related to tumor envelope invasion and lymph node metastasis (p=0.003<0.01, p=0.003<0.01), and it was irrelevant to the patient's gender, age, tumor mass size, number of cancer foci, pathological stage, etc. (p>0.05). The results of immunohistochemistry showed that SAS1B protein was mainly located in the cytoplasm and membrane of thyroid cancer cells. The expression intensity in thyroid cancer tissues was higher than that in control tissues (p<0.05), but it was not expressed in normal thyroid tissues. Antibodies showed a good sensitivity that was used to detect thyroid cancer tissues (p=0.000<0.01). The results of ordinary PCR detection using thyroid cancer tissue and control thyroid tissue showed that the amplification products of the three domains (N-terminal, C-terminal and catalytic domain) of the SAS1B gene showed high expression in thyroid cancer tissue. q-PCR results showed that the expression of SAS1B gene in thyroid cancer and control thyroid tissue was higher than that in control group (p<0.05), and the genes of Aurora A and BARD1 related to centrosome replication and DNA replication forks protection during the proliferation were highly expressed in thyroid cancer tissue. The study results suggested that SAS1B was involved in the carcinogenesis of thyroid cancer. The Hum_mPLoc.2.0 software, PSORT Ⅱ software and UniProt software were used to predict that SAS1B protein had secretory protein properties. CONCLUSIONS: The above data indicate that the SAS1B gene is closely related to the process of thyroid cancer and can serve as a good tumor marker that can be used for early diagnosis and early warning of thyroid malignancy.

Anti-breast cancer activity of resveratrol encapsulated in liposomes.

Resveratrol (RES) is a naturally occurring and effective drug for tumor prevention and treatment. However, its low levels of aqueous solubility, stability, and poor bioavailability limit its application, especially when used as a free drug. In this study, RES was loaded into peptide and sucrose liposomes (PSL) to enhance the physico-chemical properties of RES and exploit RES delivery mediated by liposomes to effectively treat breast cancer. RES loaded PSL (the complex: PSL@RES) were stable, had a good RES encapsulation efficiency, and prolonged RES-release in vitro. PSL@RES was exceptionally efficient for inhibiting the growth of cancer cells, as the IC50 of PSL@RES in MCF-7 cells was found to be only 20.89 µmol L-1. The therapeutic efficacy of PSL@RES was evaluated in mice bearing breast cancer. The results showed that PSL@RES at a dosage of 5 mg kg-1 was more effective than 10 mg kg-1 free RES, and PSL@RES inhibited tumor growth completely at a dosage of 10 mg kg-1. PSL@RES induced apoptosis in breast tumor by upregulation of p53 expression. This then downregulated Bcl-2 and upregulated Bax, thereby inducing Caspase-3 activation. More importantly, encapsulation of RES within peptide liposomes greatly reduced the toxicity of free RES to mice. Overall, the simple formulation of liposomal nanocarriers of RES developed in this study produces satisfactory outcomes to encourage further applications of liposomal carriers for the treatment of breast cancer.

Prematurely condensed chromosome fragments in human lymphocytes induced by high doses of high-linear-energy-transfer irradiation.

This study provides a useful biodosimetry protocol for radiation accidents that involve high doses of heavy particle radiation. Human peripheral blood lymphocytes (PBLs) were irradiated in vitro with high doses (5-50 Gy) of charged heavy-ion particles (carbon ions, at an effective linear-energy-transfer (LET) of 34.6 keV/microm), and were then stimulated to obtain dividing cells. PBLs were treated with 100 nM calyculin A to force chromosomes to condense prematurely, and chromosome spreads were obtained and stained with Giemsa. The G2 prematurely condensed chromosome (G2-PCC) index and the number of G2-PCC including fragments (G2-PCC-Fs) per cell for each radiation dose point were scored. Dose-effect relationships were obtained by plotting the G2-PCC indices or G2-PCC-Fs numbers against radiation doses. The G2-PCC index was greater than 5% up to doses of 15 Gy; even after a 30 Gy radiation dose, the index was 1 to 2%. At doses higher than 30 Gy, however, the G2-PCC indices were close to zero. The number of G2-PCC-Fs increased steeply for radiation doses up to 30 Gy at a rate of 1.07 Gy(-1). At doses higher than 30 Gy, the numbers of G2-PCC-Fs could not be accurately indexed because of the limited numbers of cells for analysis. Therefore, the number of G2-PCC-Fs could be used to estimate radiation doses up to 30 Gy. In addition, a G2-PCC index close to zero could be used as an indicator for radiation doses greater than 40 Gy.

Population genetic data of 15 STR loci in Han population of Henan province (central China).

Allele frequencies of the 15 STR loci were determined in 208 unrelated individuals from Han population living in Henan, China (central China). All loci except D5S818 were found no deviation from Hardy-Weinberg equilibrium. The combined power of discrimination (PD) and the combined chance of exclusion (CE) for the 15 studied loci were >0.9999999 and 0.999996119, respectively. Our data were statistically compared with the previously reported data from other Chinese population groups, and significant difference was found between central Han Chinese (n=208) and eastern Chinese (n=100) at vWA, or between central Han Chinese (n=208) and southeast Chinese (n=122) at D13S317.

Replacement of quaternary ammonium headgroups by tri-ornithine in cationic lipids for the improvement of gene delivery in vitro and in vivo.

Headgroups in cationic lipids play very important roles in determining transfection efficiency and toxicity in gene delivery. To better understand the influence of headgroups on gene delivery, a tri-peptide-based lipid was synthesized, wherein the usual quaternary ammonium was replaced by a tri-peptide. Though both the tri-peptide-based lipid (DAO3) and the quaternary ammonium-based lipid (DDCTMA) successfully mediated gene transfection, DAO3 was superior to DDCTMA in both in vitro and in vivo studies. Following their preparation into liposomes, the particle size, zeta potential, and DNA-binding capacity of the liposomes and lipoplexes were characterized to evaluate the efficiency of DAO3 compared to DDCTMA with regard to gene interactions. The expression of luciferase from pDNA mediated by DAO3 was 2-fold greater than than that with DDCTMA in Hep-2 cells, and DAO3/siRNA lipoplexes could silence about 60% luciferase in A549 cancer cells expressing firefly luciferase. DAO3/Luc-siRNA treatment exhibited 3-fold the efficiency of DDCTMA/Luc-siRNA in terms of in vivo luciferase RNAi with the bare density ratio of 0.54 at 48 h. Furthermore, DAO3 could mediate IGF-1R siRNA to inhibit tumor growth through silencing the expression of the IGF-1R protein, whereas DDCTMA showed nearly no effects. Most importantly, DAO3 had no obvious toxicity in vitro and in vivo, due to the biocompatibility of the peptide headgroups. In conclusion, these results demonstrated that the replacement of the quaternary ammonium headgroup by tri-ornithine may increase transfection efficiency and decrease toxicity.

Helicobacter pylori infection is associated with an altered gastric microbiota in children.

The intestinal microbiome in early life influences development of the mucosal immune system and predisposition to certain diseases. Because less is known about the microbiome in the stomach and its relationship to disease, we characterized the microbiota in the stomachs of 86 children and adults and the impact of Helicobacter pylori infection on the bacterial communities. The overall composition of the gastric microbiota in children and adults without H. pylori infection was similar, with minor differences in only low abundance taxa. However, the gastric microbiota in H. pylori-infected children, but not infected adults, differed significantly in the proportions of multiple high abundance taxa compared with their non-infected peers. The stomachs of H. pylori-infected children also harbored more diverse microbiota, smaller abundance of Firmicutes, and larger abundance of non-Helicobacter Proteobacteria and several lower taxonomic groups than stomachs of H. pylori-infected adults. Children with restructured gastric microbiota had higher levels of FOXP3, IL10, and TGFß expression, consistent with increased T-regulatory cell responses, compared with non-infected children and H. pylori-infected adults. The gastric commensal bacteria in children are altered during H. pylori infection in parallel with more tolerogenic gastric mucosae, potentially contributing to the reduced gastric disease characteristic of H. pylori-infected children.

Continuous monitoring of brain tissue oxygen pressure in patients with severe head injury during moderate hypothermia.

BACKGROUND: We studied the change of brain tissue oxygen pressure (PbrO2) value within 24 hours after trauma and during moderate hypothermia in patients with severe head injury. The PbrO2 value was used to differentiate patients at risk of brain ischemia and to predict outcome. METHODS: A flexible microcatheter to be used for continuous monitoring of brain tissue oxygen was inserted into the normal frontal white matter, along with a thermocouple, in 14 patients with severe head injury within 1.5-12 hours (mean 6.1 +/- 5.2 hours) after trauma. Moderate hypothermia was also used within 24 hours in these patients. RESULTS: (1) No complications related to the microcatheter were seen. (2) Low initial PbrO2 values (mean values <10 mmHg) were noted after severe head injury. (3) The occurrence of low initial PbrO2 values (< or = 5 mmHg) was significantly correlated with a poor outcome. (4) Moderate hypothermia can increase PbrO2, but hyperventilation reduced PbrO2. (5) The difference between RT and BT increased during moderate hypothermia. CONCLUSIONS: The PbrO2 values were low in severe head injury, but hypothermia may improve these values. The technique of continuously monitoring brain tissue oxygen pressure may give better insight into cerebral oxygenation and warn of impending ischemia of brain tissue, especially in patients treated with hyperventilation. It will help to improve the management and final outcome of patients with severe head injuries.

Inhibiting effect of moderate hypothermia on cell apoptosis after diffuse brain injury in rats.

OBJECTIVE: To explore the variant processes of cell apoptosis and the inhibiting effect of moderate hypothermia on cell apoptosis after diffuse brain injury. METHODS: Models of diffuse brain injury were induced by the trauma device reported by Marmarou. A total of 128 Wistar rats were divided into 4 groups: the uninjured group (Group A, n=8), the severely injured group (Group B, n=60), the mildly injured group (Group C, n=30) and the mild hypothermia group (Group D, n=30). In Group D, the severely injured rats were treated with moderate hypothermia to keep the rectal temperature at 32 degrees C (standard deviation for 0.1 degree C) for 6 hours. Then the morphology, the characteristics and the quantity of apoptotic cells in the cerebral cortex and in the hippocampus regions after different severities of craniocerebral injuries were observed and compared under an electronic microscope, with terminal deoxynucleotidyl nick end labeling (TUNEL) in DNA fragmentation and with agarose gel electrophoresis. RESULTS: TUNEL showed apoptotic cells increased according to the injury severity, and they peaked at 48 hours after injury and then declined. In Group C, apoptosis was located in the CA(2) and CA(3) areas of the hippocampus. And in Group B, apoptosis increased evidently, and located in the whole hippocampus and in the frontal and parietal cortex regions. The hypothermia-treated rats had some apoptotic cells, too. However, even at 24, 48 and 72 hours after injury there were significantly fewer apoptotic cells in the cortex and in the hippocampus in Group D than that in the non-treated groups. Electron microscopy showed that the apoptotic cells were round and shrunken in morphology and the nuclei were round and condensed at 24 and 48 hours after injury. And the apoptosis at 48 hours was more severe than that at 24 hours. The hypothermia-treated rats had no apoptotic cells. Gel electrophoresis showed that characteristic DNA "ladders" were observed in the cortex and in the hippocampus at 48 hours after severe injury. But there was no DNA "ladder" at other time points in the severely injured group, in the mildly injured group and in the hypothermia-treated group. CONCLUSIONS: It suggests that apoptosis occurs after diffuse brain injury and apoptotic cells increase with the injury severity. Moderate hypothermia has a specific inhibiting effect on cell apoptosis after diffuse brain injury in rats.

Screening genes crucial for pediatric pilocytic astrocytoma using weighted gene coexpression network analysis combined with methylation data analysis.

To identify novel genes associated with pediatric pilocytic astrocytoma (PA) for better understanding the molecular mechanism underlying the pediatric PA pathogenesis. Gene expression profile data of GSE50161 and GSE44971 and the methylation data of GSE44684 were downloaded from Gene Expression Omnibus. The differentially expressed genes (DEGs) between PA and normal control samples were screened using the limma package in R, and then used to construct weighted gene coexpression network (WGCN) using the WGCN analysis (WGCNA) package in R. Significant modules of DEGs were selected using the clustering analysis. Function enrichment analysis of the DEGs in significant modules were performed using the WGCNA package and clusterprofiler package in R. Correlation between methylation sites of DEGs and PA was analyzed using the CpGassoc package in R. Totally, 3479 DEGs were screened in PA samples. Thereinto, 3424 DEGs were used to construct the WGCN. Several significant modules of DEGs were selected based on the WGCN, in which the turquoise module was positively related to PA, whereas blue module was negatively related to PA. DEGs (for example, DOCK2 (dedicator of cytokinesis 2), DOCK8 and FCGR2A (Fc fragment of IgG, low affinity IIa)) in blue module were mainly involved in Fc gamma R-mediated phagocytosis pathway and natural killer cell-mediated cytotoxicity pathway. Methylations of 14 DEGs among the top 30 genes in blue module were related to PA. Our data suggest that DOCK2, DOCK8 and FCGR2A may represent potential therapeutic targets in PA that merits further investigation.

Whole-exome sequencing and an iPSC-derived cardiomyocyte model provides a powerful platform for gene discovery in left ventricular hypertrophy.

RATIONALE: Left ventricular hypertrophy (LVH) is a heritable predictor of cardiovascular disease, particularly in blacks. OBJECTIVE: Determine the feasibility of combining evidence from two distinct but complementary experimental approaches to identify novel genetic predictors of increased LV mass. METHODS: Whole-exome sequencing (WES) was conducted in seven African-American sibling trios ascertained on high average familial LV mass indexed to height (LVMHT) using Illumina HiSeq technology. Identified missense or nonsense (MS/NS) mutations were examined for association with LVMHT using linear mixed models adjusted for age, sex, body weight, and familial relationship. To functionally assess WES findings, human induced pluripotent stem cell-derived cardiomyocytes (induced pluripotent stem cell-CM) were stimulated to induce hypertrophy; mRNA sequencing (RNA-seq) was used to determine gene expression differences associated with hypertrophy onset. Statistically significant findings under both experimental approaches identified LVH candidate genes. Candidate genes were further prioritized by seven supportive criteria that included additional association tests (two criteria), regional linkage evidence in the larger HyperGEN cohort (one criterion), and publically available gene and variant based annotations (four criteria). RESULTS: WES reads covered 91% of the target capture region (of size 37.2 MB) with an average coverage of 65×. WES identified 31,426 MS/NS mutations among the 21 individuals. A total of 295 MS/NS variants in 265 genes were associated with LVMHT with q-value <0.25. Of the 265 WES genes, 44 were differentially expressed (P < 0.05) in hypertrophied cells. Among the 44 candidate genes identified, 5, including HLA-B, HTT, MTSS1, SLC5A12, and THBS1, met 3 of 7 supporting criteria. THBS1 encodes an adhesive glycoprotein that promotes matrix preservation in pressure-overload LVH. THBS1 gene expression was 34% higher in hypertrophied cells (P = 0.0003) and a predicted conserved and damaging NS variant in exon 13 (A2099G) was significantly associated with LVHMT (P = 4 × 10(-6)). CONCLUSION: Combining evidence from cutting-edge genetic and cellular experiments can enable identification of novel LVH risk loci.

Boty-like retrotransposons in the filamentous fungus Botrytis cinerea contain the additional antisense gene brtn.

Long-terminal repeat (LTR) retrotransposons typically contain gag, pol, or gag-pol, and in some case env genes. In this work, we used data mining of the Botrytis cinerea genomic sequence and a molecular approach to identify Boty-like LTR retrotransposons in B. cinerea containing an antisense gene (brtn) between pol and the 3'-LTR. Reverse transcriptase PCR (RT-PCR) revealed that some brtn-like genes could be expressed, at least in B. cinerea T4. We conducted BLAST comparisons and conserved-domain analysis, but the function of putative BRTN is presently unknown. Boty-like LTR retrotransposons in Sclerotinia sclerotiorum, called ScscLRET and containing brtn homologs at positions similar to brtn, were detected by homology searches and data mining of the S. sclerotiorum 1980 genomic sequence. Thus, this study demonstrated that some fungal LTR retrotransposons contain additional antisense genes.

Biodosimetry estimate for high-LET irradiation.

The purpose of this paper is to prepare for an easy and reliable biodosimeter protocol for radiation accidents involving high-linear energy transfer (LET) exposure. Human peripheral blood lymphocytes were irradiated using carbon ions (LET: 34.6 keV microm(-1)), and the chromosome aberrations induced were analyzed using both a conventional colcemid block method and a calyculin A induced premature chromosome condensation (PCC) method. At a lower dose range (0-4 Gy), the measured dicentric (dics) and centric ring chromosomes (cRings) provided reasonable dose information. At higher doses (8 Gy), however, the frequency of dics and cRings was not suitable for dose estimation. Instead, we found that the number of Giemsa-stained drug-induced G2 prematurely condensed chromosomes (G2-PCC) can be used for dose estimation, since the total chromosome number (including fragments) was linearly correlated with radiation dose (r = 0.99). The ratio of the longest and the shortest chromosome length of the drug-induced G2-PCCs increased with radiation dose in a linear-quadratic manner (r = 0.96), which indicates that this ratio can also be used to estimate radiation doses. Obviously, it is easier to establish the dose response curve using the PCC technique than using the conventional metaphase chromosome method. It is assumed that combining the ratio of the longest and the shortest chromosome length with analysis of the total chromosome number might be a valuable tool for rapid and precise dose estimation for victims of radiation accidents.