CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse

Diversified histone modifications (HMs) are essential epigenetic features. They play important roles in fundamental biological processes including transcription, DNA repair and DNA replication. Chromatin regulators (CRs), which are indispensable in epigenetics, can mediate HMs to adjust chromatin structures and functions. With the development of ChIP-Seq technology, there is an opportunity to study CR and HM profiles at the whole-genome scale. However, no specific resource for the integration of CR ChIP-Seq data or CR-HM ChIP-Seq linkage pairs is currently available. Therefore, we constructed the CR Cistrome database, available online at http://compbio.tongji.edu.cn/cr and http://cistrome.org/cr/, to further elucidate CR functions and CR-HM linkages. Within this database, we collected all publicly available ChIP-Seq data on CRs in human and mouse and categorized the data into four cohorts: the reader, writer, eraser and remodeler cohorts, together with curated introductions and ChIP-Seq data analysis results. For the HM readers, writers and erasers, we provided further ChIP-Seq analysis data for the targeted HMs and schematized the relationships between them. We believe CR Cistrome is a valuable resource for the epigenetics community

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

BACKGROUND: RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells. The increase in use of RNA-seq technology has led to the continuous development of new tools for every step of analysis from alignment to downstream pathway analysis. However, effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts. RESULTS: Using the workflow management system Snakemake we have developed a user friendly, fast, efficient, and comprehensive pipeline for RNA-seq analysis. VIPER (Visualization Pipeline for RNA-seq analysis) is an analysis workflow that combines some of the most popular tools to take RNA-seq analysis from raw sequencing data, through alignment and quality control, into downstream differential expression and pathway analysis. VIPER has been created in a modular fashion to allow for the rapid incorporation of new tools to expand the capabilities. This capacity has already been exploited to include very recently developed tools that explore immune infiltrate and T-cell CDR (Complementarity-Determining Regions) reconstruction abilities. The pipeline has been conveniently packaged such that minimal computational skills are required to download and install the dozens of software packages that VIPER uses. CONCLUSIONS: VIPER is a comprehensive solution that performs most standard RNA-seq analyses quickly and effectively with a built-in capacity for customization and expansion

Complete Strain Mapping of Nanosheets of Tantalum Disulfide

Quasi-two-dimensional (quasi-2D) materials hold promise for future electronics because of their unique band structures that result in electronic and mechanical properties sensitive to crystal strains in all three dimensions. Quantifying crystal strain is a prerequisite to correlating it with the performance of the device, and calls for high resolution but spatially resolved rapid characterization methods. Here we show that using fly-scan nano X-ray diffraction we can accomplish a tensile strain sensitivity below 0.001% with a spatial resolution of better than 80 nm over a spatial extent of 100 $\mu$m on quasi 2D flakes of 1T-TaS2. Coherent diffraction patterns were collected from a $\sim$ 100 nm thick sheet of 1T-TaS2 by scanning 12keV focused X-ray beam across and rotating the sample. We demonstrate that the strain distribution around micron and sub-micron sized 'bubbles' that are present in the sample may be reconstructed from these images. The experiments use state of the art synchrotron instrumentation, and will allow rapid and non-intrusive strain mapping of thin film samples and electronic devices based on quasi 2D materials

Treatment of complex limb fractures with 3D printing technology combined with personalized plates: a retrospective study of case series and literature review

BackgroundIn recent years, 3D printing technology has made significant strides in the medical field. With the advancement of orthopedics, there is an increasing pursuit of high surgical quality and optimal functional recovery. 3D printing enables the creation of precise physical models of fractures, and customized personalized steel plates can better realign and more comprehensively and securely fix fractures. These technologies improve preoperative diagnosis, simulation, and planning for complex limb fractures, providing patients with better treatment options.Patients and methodsFive typical cases were selected from a pool of numerous patients treated with 3D printing technology combined with personalized custom steel plates at our hospital. These cases were chosen to demonstrate the entire process of printing 3D models and customizing individualized steel plates, including details of the patients' surgeries and treatment procedures. Literature reviews were conducted, with a focus on highlighting the application of 3D printing technology combined with personalized custom steel plates in the treatment of complex limb fractures.Results3D printing technology can produce accurate physical models of fractures, and personalized custom plates can achieve better fracture realignment and more comprehensive and robust fixation. These technologies provide patients with better treatment options.ConclusionThe use of 3D printing models and personalized custom steel plates can improve preoperative diagnosis, simulation, and planning for complex limb fractures, realizing personalized medicine. This approach helps reduce surgical time, minimize trauma, enhance treatment outcomes, and improve patient functional recovery

Omega-3 fatty acids and genome-wide interaction analyses reveal DPP10-pulmonary function association

Rationale: Omega-3 polyunsaturated fatty acids (n-3 PUFAs) have anti-inflammatory properties that could benefit adults with comprised pulmonary health. Objective: To investigate n-3 PUFA associations with spirometric measures of pulmonary function tests (PFTs) and determine underlying genetic susceptibility. Methods: Associations of n-3 PUFA biomarkers (a-linolenic acid, eicosapentaenoic acid, docosapentaenoic acid [DPA], and docosahexaenoic acid [DHA]) were evaluated with PFTs (FEV1, FVC, and FEV1/FVC) in meta-analyses across seven cohorts from the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium (N=16,134 of European or African ancestry). PFT-associated n-3 PUFAs were carried forward to genome-wide interaction analyses in the four largest cohorts (N=11,962) and replicated in one cohort (N=1,687). Cohort-specific results were combined using joint 2 degree-of-freedom (2df) meta-analyses of SNPassociations and their interactions with n-3PUFAs. Results: DPA and DHA were positively associated with FEV1 and FVC (P < 0.025), with evidence for effect modification by smoking and by sex. Genome-wide analyses identified a novel association of rs11693320-an intronic DPP10 SNP-with FVC when incorporating an interaction with DHA, and the finding was replicated (P-2df = 9.4 x 10(-9) across discovery and replication cohorts). The rs11693320-A allele (frequency, similar to 80%) was associated with lower FVC (P-SNP = 2.1 x 10(-9); beta(SNP) = 2161.0 ml), and the association was attenuated by higher DHA levels (P-SNPxDHA interaction = 2.1x10(-7); beta(SNPxDHA interaction) = 36.2 ml). Conclusions: We corroborated beneficial effects of n-3 PUFAs on pulmonary function. By modeling genome-wide n-3 PUFA interactions, we identified a novel DPP10 SNP association with FVC that was not detectable in much larger studies ignoring this interaction

Genome wide association study of apparent treatment resistant hypertension in the CHARGE consortium: the CHARGE pharmacogenetics working group

Background: Only a handful of genetic discovery efforts in apparent treatment-resistant hypertension (aTRH) have been described. Methods: We conducted a case–control genome-wide association study of aTRH among persons treated for hypertension, using data from 10 cohorts of European ancestry (EA) and 5 cohorts of African ancestry (AA). Cases were treated with 3 different antihypertensive medication classes and had blood pressure (BP) above goal (systolic BP ≥ 140 mm Hg and/or diastolic BP ≥ 90 mm Hg) or 4 or more medication classes regardless of BP control (nEA = 931, nAA = 228). Both a normotensive control group and a treatment-responsive control group were considered in separate analyses. Normotensive controls were untreated (nEA = 14,210, nAA = 2,480) and had systolic BP/diastolic BP &lt; 140/90 mm Hg. Treatment-responsive controls (nEA = 5,266, nAA = 1,817) had BP at goal (&lt;140/90 mm Hg), while treated with one antihypertensive medication class. Individual cohorts used logistic regression with adjustment for age, sex, study site, and principal components for ancestry to examine the association of single-nucleotide polymorphisms with case–control status. Inverse variance-weighted fixed-effects meta-analyses were carried out using METAL. Results: The known hypertension locus, CASZ1, was a top finding among EAs (P = 1.1 × 10−8) and in the race-combined analysis (P = 1.5 × 10−9) using the normotensive control group (rs12046278, odds ratio = 0.71 (95% confidence interval: 0.6–0.8)). Single-nucleotide polymorphisms in this locus were robustly replicated in the Million Veterans Program (MVP) study in consideration of a treatment-responsive control group. There were no statistically significant findings for the discovery analyses including treatment-responsive controls. Conclusion: This genomic discovery effort for aTRH identified CASZ1 as an aTRH risk locus

Facies variations in the pyroclastic density currents (PDCs) produced by the Millennium Eruption of the Changbaishan Tianchi volcano, NE China

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Gα12 and Gα13: Versatility in Physiology and Pathology.

G protein-coupled receptors (GPCRs), as the largest family of receptors in the human body, are involved in the pathological mechanisms of many diseases. Heterotrimeric G proteins represent the main molecular switch and receive cell surface signals from activated GPCRs. Growing evidence suggests that Gα12 subfamily (Gα12/13)-mediated signaling plays a crucial role in cellular function and various pathological processes. The current research on the physiological and pathological function of Gα12/13 is constantly expanding, Changes in the expression levels of Gα12/13 have been found in a wide range of human diseases. However, the mechanistic research on Gα12/13 is scattered. This review briefly describes the structural sequences of the Gα12/13 isoforms and introduces the coupling of GPCRs and non-GPCRs to Gα12/13. The effects of Gα12/13 on RhoA and other signaling pathways and their roles in cell proliferation, migration, and immune cell function, are discussed. Finally, we focus on the pathological impacts of Gα12/13 in cancer, inflammation, metabolic diseases, fibrotic diseases, and circulatory disorders are brought to focus