Integrated study of copy number states and genotype calls using high-density SNP arrays

We propose a statistical framework, named genoCN, to simultaneously dissect copy number states and genotypes using high-density SNP (single nucleotide polymorphism) arrays. There are at least two types of genomic DNA copy number differences: copy number variations (CNVs) and copy number aberrations (CNAs). While CNVs are naturally occurring and inheritable, CNAs are acquired somatic alterations most often observed in tumor tissues only. CNVs tend to be short and more sparsely located in the genome compared with CNAs. GenoCN consists of two components, genoCNV and genoCNA, designed for CNV and CNA studies, respectively. In contrast to most existing methods, genoCN is more flexible in that the model parameters are estimated from the data instead of being decided a priori. GenoCNA also incorporates two important strategies for CNA studies. First, the effects of tissue contamination are explicitly modeled. Second, if SNP arrays are performed for both tumor and normal tissues of one individual, the genotype calls from normal tissue are used to study CNAs in tumor tissue. We evaluated genoCN by applications to 162 HapMap individuals and a brain tumor (glioblastoma) dataset and showed that our method can successfully identify both types of copy number differences and produce high-quality genotype calls.     

Highly B lymphocyte‐specific tamoxifen inducible transgene expression of CreERT2 by using the LC‐1 locus BAC vector

The generation of cell type specific inducible Cre transgenic mice is the most challenging and limiting part in the development of spatio‐temporally controlled knockout mouse models. Here we report the generation and characterization of a B lymphocyte‐specific tamoxifen‐inducible Cre transgenic mouse strain, LC‐1‐hCD19‐CreER^T2. We utilized the human CD19 promoter for expression of the tamoxifen‐inducible Cre recombinase (CreER^T2) gene, embedded in genomic sequences previously reported to give minimal position effects after transgenesis. Cre recombinase activity was evaluated by cross‐breeding the LC‐1‐hCD19‐CreER^T2 strain with a strain containing a floxed gene widely expressed in the hematopoietic system. Cre activity was only detected in the presence of tamoxifen and was restricted to B lymphocytes. The efficacy of recombination ranged from 27 to 61% in the hemizygous and homozygous mice, respectively. In conclusion, the LC‐1‐hCD19‐CreER^T2 strain is a powerful tool to study gene function specifically in B lymphocytes at any chosen time point in the lifecycle of the mouse. genesis 47:729–735, 2009. © 2009 Wiley‐Liss, Inc.     

Tinnitus Intensity Dependent Gamma Oscillations of the Contralateral Auditory Cortex

Background

Non-pulsatile tinnitus is considered a subjective auditory phantom phenomenon present in 10 to 15% of the population. Tinnitus as a phantom phenomenon is related to hyperactivity and reorganization of the auditory cortex. Magnetoencephalography studies demonstrate a correlation between gamma band activity in the contralateral auditory cortex and the presence of tinnitus. The present study aims to investigate the relation between objective gamma-band activity in the contralateral auditory cortex and subjective tinnitus loudness scores.

Methods and Findings

In unilateral tinnitus patients (N = 15; 10 right, 5 left) source analysis of resting state electroencephalographic gamma band oscillations shows a strong positive correlation with Visual Analogue Scale loudness scores in the contralateral auditory cortex (max r = 0.73, p<0.05).

Conclusion

Auditory phantom percepts thus show similar sound level dependent activation of the contralateral auditory cortex as observed in normal audition. In view of recent consciousness models and tinnitus network models these results suggest tinnitus loudness is coded by gamma band activity in the contralateral auditory cortex but might not, by itself, be responsible for tinnitus perception.     

Anthrax Lethal Toxin Induced Lysosomal Membrane Permeabilization and Cytosolic Cathepsin Release Is Nlrp1b/Nalp1b-Dependent

NOD-like receptors (NLRs) are a group of cytoplasmic molecules that recognize microbial invasion or ‘danger signals’. Activation of NLRs can induce rapid caspase-1 dependent cell death termed pyroptosis, or a caspase-1 independent cell death termed pyronecrosis. Bacillus anthracis lethal toxin (LT), is recognized by a subset of alleles of the NLR protein Nlrp1b, resulting in pyroptotic cell death of macrophages and dendritic cells. Here we show that LT induces lysosomal membrane permeabilization (LMP). The presentation of LMP requires expression of an LT-responsive allele of Nlrp1b, and is blocked by proteasome inhibitors and heat shock, both of which prevent LT-mediated pyroptosis. Further the lysosomal protease cathepsin B is released into the cell cytosol and cathepsin inhibitors block LT-mediated cell death. These data reveal a role for lysosomal membrane permeabilization in the cellular response to bacterial pathogens and demonstrate a shared requirement for cytosolic relocalization of cathepsins in pyroptosis and pyronecrosis.     

Extragonadal germ cell tumor presenting in a woman with systemic lupus erythematosus: a case report

Introduction

Esophageal intramural pseudodiverticulosis is a rare condition characterized by the dilatation of the submucosal glands.

Case presentation

We present a case of esophageal intramural pseudodiverticulosis in a 72-year-old Caucasian man who presented with dysphagia and with a background history of alcohol abuse. An upper gastrointestinal endoscopy of our patient showed an esophageal stricture with abnormal mucosal appearances, but no malignant cells were seen at biopsy. Appearances on a barium esophagram were pathognomonic for esophageal intramural pseudodiverticulosis.

Conclusion

We demonstrate the enduring usefulness of barium esophagography in the characterization of abnormal mucosal appearances at endoscopy.     

Production and characterization of the extracellular domain of recombinant human fibroblast growth factor receptor 4

Among the members of the fibroblast growth factor receptor family the FGFR4 has demonstrated strong dependence on heparin-like material for its activation by fibroblast growth factors. We have produced and characterized a recombinant human FGFR4 extracellular domain (FGFR4ed), in order to study its biochemical properties in isolated conditions. The FGFR4ed was expressed in an insect cell system and purified from the culture medium by Ni(2+)-affinity and gel filtration chromatography. Pure FGFR4ed was tested for FGF- and heparin-binding by covalent crosslinking experiments and by biosensor analysis. In solution, FGFR4ed formed complexes with acidic FGF (FGF-1) and basic FGF (FGF-2), both in the presence and absence of heparin. Immobilized FGFR4 also bound FGF-8 besides FGF-1 and FGF-2. Furthermore, heparin alone induced receptor oligomerization on the surface of the receptor coupled chip. Thus, the recombinant FGFR4ed revealed properties described for the cellular form of this receptor and can be used for interaction studies.     

Molecular docking analysis of SARS-CoV-2 linked RNA dependent RNA polymerase (RdRp) with compounds from Plectranthus amboinicus

It is of interest to document the moelcular docking analysis of SARS-CoV-2 linked RNA dependent RNA polymerase (RdRp) with compounds from Plectranthus amboinicus. Hence, we report the binding features of rutin, Luteolin, Salvianolic acid A, Rosmarinic acid and p-Coumaric acid with the target protein SARS-CoV-2 linked RNA dependent RNA polymerase (RdRp) for further consideration.