RNxQuest: An Extension to the xQuest Pipeline Enabling Analysis of Protein–RNA Cross-Linking/Mass Spectrometry Data

Cross-linking and mass spectrometry (XL-MS) workflows are increasingly popular techniques for generating low-resolution structural information about interacting biomolecules. xQuest is an established software package for analysis of protein–protein XL-MS data, supporting stable isotope-labeled cross-linking reagents. Resultant paired peaks in mass spectra aid sensitivity and specificity of data analysis. The recently developed cross-linking of isotope-labeled RNA and mass spectrometry (CLIR-MS) approach extends the XL-MS concept to protein–RNA interactions, also employing isotope-labeled cross-link (XL) species to facilitate data analysis. Data from CLIR-MS experiments are broadly compatible with core xQuest functionality, but the required analysis approach for this novel data type presents several technical challenges not optimally served by the original xQuest package. Here we introduce RNxQuest, a Python package extension for xQuest, which automates the analysis approach required for CLIR-MS data, providing bespoke, state-of-the-art processing and visualization functionality for this novel data type. Using functions included with RNxQuest, we evaluate three false discovery rate control approaches for CLIR-MS data. We demonstrate the versatility of the RNxQuest-enabled data analysis pipeline by also reanalyzing published protein–RNA XL-MS data sets that lack isotope-labeled RNA. This study demonstrates that RNxQuest provides a sensitive and specific data analysis pipeline for detection of isotope-labeled XLs in protein–RNA XL-MS experiments

The pancreaticoduodenal arteries in human foetal development

Knowledge of the course of the pancreaticoduodenal arteries is of great importance in pancreatic surgery. Lack of care in the preparation of these vessels may lead to ischaemia or necrosis of the duodenum, the first loop of the jejunum, the head of the pancreas and even the liver, bile ducts and transverse colon. In such events, the surgeon would need to diagnose the course of the vessels and their anastomoses intraoperatively. Anatomical dissection in this special area diminishes the risk of early complications in the form of bleeding and late complications in the form of narrowing of the anastomoses, fistulas, necrosis and intestinal ileus after surgical resection or drainage. The aim of the present study was to determine the variability of the pancreaticoduodenal arteries in human foetuses. The material examined consisted of 60 human foetuses of both sexes (33 male, 27 female) from spontaneous abortion or stillbirth and ranging in age from the 16th to 38th week of prenatal life. White latex solution to of volume between 15 ml and 30 ml was injected into the thoracic aorta. The results of this were that a typical pancreatic supply from the coeliac trunk and superior mesenteric artery was observed in all cases. The coeliac trunk, splenic artery and gastroduodenal artery also appeared invariably. However, variability was observed in further generations of branches. The gastroduodenal artery with its branches, the anterior and posterior pancreaticoduodenal arteries, was constantly present. Irrespective of the sex of the foetus, in 10% of cases a large vessel was observed which ran horizontally on the anterior surface of the pancreas from head to tail and which originated in the anterior superior pancreaticoduodenal artery. We termed this vessel the "anterior pancreatic artery". In all cases there were anterior and posterior pancreaticoduodenal arcades, but in two cases (3.3%) a double anterior pancreaticoduodenal arcade was observed

Morphometry of the pancreas in human foetuses

With the use of conventional anatomical dissection, radiography, digital and statistical analysis, morphometry and skeletopy of the pancreas was carried out in 60 human foetuses of both sexes (28 female, 32 male) between the 17th and 40th week of intrauterine life. The material was fixed in a 10% formalin solution. The age of the foetuses was determined by crown-rump (CR) lenght measurement on the basis of the Iffy et al. tables. Photographic documentation was made and then digitally processed in the Computer Image Digital Analysis System. The following parameters were taken into account: the length and width of 3 parts of the pancreas, namely the head, corpus and tail. Additionally, radiograms were made to obtain a projection of the gland on the vertebral column. Development of the pancreas was correlated with the age of the foetuses calculated on the basis of crown-rump (CR) lenght measurements. The correlation coefficient with CR was 0.998 for the pancreas length, 0.709 for the width of the head, 0.703 for the width of the corpus and 0.712 for the width of tail. Gender dimorphism was not found (p > 0.05) with regard to the morphometry of the pancreas. In the material under examination the pancreas did not change its position in relation to the vertebral column. The head projected on the vertebral column in the range Th12–L2 (most frequently L1–L2), the corpus on Th12–L2 and the tail on Th11

Genetic Effect on Body Mass Index and Cardiovascular Disease Across Generations

BACKGROUND: Whether genetics contribute to the rising prevalence of obesity or its cardiovascular consequences in today\u27s obesogenic environment remains unclear. We sought to determine whether the effects of a higher aggregate genetic burden of obesity risk on body mass index (BMI) or cardiovascular disease (CVD) differed by birth year. METHODS: We split the FHS (Framingham Heart Study) into 4 equally sized birth cohorts (birth year before 1932, 1932 to 1946, 1947 to 1959, and after 1960). We modeled a genetic predisposition to obesity using an additive genetic risk score (GRS) of 941 BMI-associated variants and tested for GRS-birth year interaction on log-BMI (outcome) when participants were around 50 years old (N=7693). We repeated the analysis using a GRS of 109 BMI-associated variants that increased CVD risk factors (type 2 diabetes, blood pressure, total cholesterol, and high-density lipoprotein) in addition to BMI. We then evaluated whether the effects of the BMI GRSs on CVD risk differed by birth cohort when participants were around 60 years old (N=5493). RESULTS: Compared with participants born before 1932 (mean age, 50.8 yrs [2.4]), those born after 1960 (mean age, 43.3 years [4.5]) had higher BMI (median, 25.4 [23.3-28.0] kg/m CONCLUSIONS: The significant GRS-birth year interactions indicate that common genetic variants have larger effects on middle-age BMI and CVD risk in people born more recently. These findings suggest that the increasingly obesogenic environment may amplify the impact of genetics on the risk of obesity and possibly its cardiovascular consequences

The SWI/SNF ATP-Dependent Chromatin Remodeling Complex in Arabidopsis Responds to Environmental Changes in Temperature-Dependent Manner

SWI/SNF ATP-dependent chromatin remodeling complexes (CRCs) play important roles in the regulation of transcription, cell cycle, DNA replication, repair, and hormone signaling in eukaryotes. The core of SWI/SNF CRCs composed of a SWI2/SNF2 type ATPase, a SNF5 and two of SWI3 subunits is sufficient for execution of nucleosome remodeling in vitro. The Arabidopsis genome encodes four SWI2/SNF2 ATPases, four SWI3, a single SNF5 and two SWP73 subunits. Genes of the core SWI/SNF components have critical but not fully overlapping roles during plant growth, embryogenesis, and sporophyte development. Here we show that the Arabidopsis swi3c mutant exhibits a phenotypic reversion when grown at lower temperature resulting in partial restoration of its embryo, root development and fertility defects. Our data indicates that the swi3c mutation alters the expression of several genes engaged in low temperature responses. The location of SWI3C-containing SWI/SNF CRCs on the ICE1, MYB15 and CBF1 target genes depends on the temperature conditions, and the swi3c mutation thus also influences the transcription of several cold-responsive (COR) genes. These findings, together with genetic analysis of swi3c/ice1 double mutant and enhanced freezing tolerance of swi3c plants illustrate that SWI/SNF CRCs contribute to fine-tuning of plant growth responses to different temperature regimes

Genome-wide interaction study of early-life smoking exposure on time-to-asthma onset in childhood

BACKGROUND: Asthma, a heterogeneous disease with variable age of onset, results from the interplay between genetic and environmental factors. Early-life tobacco smoke (ELTS) exposure is a major asthma risk factor. Only a few genetic loci have been reported to interact with ELTS exposure in asthma. OBJECTIVE: Our aim was to identify new loci interacting with ELTS exposure on time-to-asthma onset (TAO) in childhood. METHODS: We conducted genome-wide interaction analyses of ELTS exposure on time-to-asthma onset in childhood in five European-ancestry studies (totaling 8,273 subjects) using Cox proportional-hazard model. The results of all five genome-wide analyses were meta-analyzed. RESULTS: The 13q21 locus showed genome-wide significant interaction with ELTS exposure (P=4.3x10-8 for rs7334050 within KLHL1 with consistent results across the five studies). Suggestive interactions (P<5x10-6 ) were found at three other loci: 20p12 (rs13037508 within MACROD2; P=4.9x10-7 ), 14q22 (rs7493885 near NIN; P=2.9x10-6 ) and 2p22 (rs232542 near CYP1B1; P=4.1x10-6 ). Functional annotations and the literature showed that the lead SNPs at these four loci influence DNA methylation in the blood and are located nearby CpG sites reported to be associated with exposure to tobacco smoke components, which strongly support our findings. CONCLUSION AND CLINICAL RELEVANCE: We identified novel candidate genes interacting with ELTS exposure on time-to-asthma onset in childhood. These genes have plausible biological relevance related to tobacco smoke exposure. Further epigenetic and functional studies are needed to confirm these findings and to shed light on the underlying mechanisms. This article is protected by copyright. All rights reserved

Evaluation of the role of downregulation of SNF5/INI1 core subunit of SWI/SNF complex in clear cell renal cell carcinoma development

Clear cell renal cell carcinoma (ccRCC) is characterized by stabilization of hypoxia-inducible factor (HIF1), and mutations in von Hippel-Lindau (VHL) gene. Additionally, in about 40% of ccRCC cases the mutation in PBRM1 (POLYBROMO1) gene coding for a non-core subunit of SWI/SNF chromatin remodeling complex was found suggesting potential impairment of this complex function in ccRCC. In this study we assessed the extent to which the core SWI/SNF complex subunit - INI1 (hSNF5/SMARCB1) is affected in ccRCC and whether it has any consequences on the development of this type of cancer. The evaluation of INI1 protein level in samples from 50 patients with diagnosed ccRCC, including three displaying rhabdoid features, showed the INI1 positive staining in rhabdoid cells while the conventional ccRCC cells exhibited reduced INI1 level. This indicated the rhabdoid component of ccRCC as distinct from other known rhabdoid tumors. The reduced INI1 protein level observed in all conventional ccRCC cases used in this study correlated with decreased SMARCB1 gene expression at the transcript level. Consistently, the overexpression of INI1 protein in A498 ccRCC cell line resulted in the elevation of endogenous SMARCB1 transcript level indicating that the INI1-dependent regulatory feedback loop controlling expression of this gene is affected in ccRCC Moreover, the set of INI1 target genes including i.e. CXCL12/CXCR7/CXCR4 chemokine axis was identified to be affected in ccRCC. In summary, we demonstrated that the inactivation of INI1 may be of high importance for ccRCC development and aggressiveness