[Idiopathic membranous nephropathy with focal segmental sclerosis].

Aim: To evaluate the clinical and pathological features and prognosis of idiopathic membranous nephropathy (IMN) with focal segmental sclerosis (FSGS) in a group of Russian patients.

Materials And Methods: 101 patients with morphologically verified IMN were enrolled in our single-center cohort retrospective study. The patients were divided into IMN group and IMN+FSGS group.

[Frailty and chronic kidney disease - the real problem of modern nephrology: A review].

The article deals with the syndrome of frailty or senile asthenia in patients with chronic kidney disease. The questions of prevalence, diagnosis, pathogenesis of this syndrome and its clinical consequences in chronic kidney disease are discussed.

[Clinical significance of the determination of antibodies to thrombospondin type 1 containing domain 7A (THSD7A) in membranous nephropathy].

Background: Membranous nephropathy (MN) is an immunocomplex glomerular disease, which is the most common cause of nephrotic syndrome in adults. Numerous studies have established that autoantibodies against the target podocyte autoantigens, including the thrombospondin type 1 domain containing 7A (THSD7A), play a leading role in the development of idiopathic MN.

Aim: To evaluate the prevalence of anti-THSD7A autoantibodies (anti-THSD7A AB) in a group of Russian patients with MN.

[Successful treatment of a rare variant of mesangioproliferative glomerulonephritis with IgM deposits with Cyclosporin A].

We present a case with a rare variant of glomerulonephritis, IgM nephropathy, which occurs mainly with nephrotic syndrome. The clinical features of this variant of kidney damage are characterized; the pathogenetic and the transformation of this form of nephritis into focal segmental glomerulosclerosis are discussed. The development of severe nephrotic syndrome at the beginning of the disease, the formation of secondary steroid resistance have confirmed this hypothesis and have justified the treatment with cyclosporin A aimed at the recovery of the function of the podocyte with remission of nephritis.

[Changes in metabolic parameters and glomerular filtration rate in patients with morbid obesity after bariatric surgery].

Aim: To study the effect of weight loss in the short term after bariatric surgery (BO) on metabolic parameters and glomerular filtration rate (GFR) in patients with morbid obesity.

Materials And Methods: We studied 40 adult (over 18 years) patients with morbid obesity who underwent bariatric surgery. Metabolic indices and calculated GFR according to the CKD-EPI formula in patients before and after bariatric surgery were compared.

Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer.

Current literature suggests that epigenetically regulated super-enhancers (SEs) are drivers of aberrant gene expression in cancers. Many tumor types are still missing chromatin data to define cancer-specific SEs and their role in carcinogenesis. In this work, we develop a simple pipeline, which can utilize chromatin data from etiologically similar tumors to discover tissue-specific SEs and their target genes using gene expression and DNA methylation data.

[Modern approaches to conservative therapy of polycystic kidney disease].

Polycystic kidney disease (PKD) is a genetically determined pathological process associated with the formation and growth of cysts originating from the epithelial cells of the tubules and/or collecting tubes. PBP is represented by two main types - autosomal dominant (ADPKD) and autosomal recessive PKD (ARPKD), which are different diseases. The main causes of ADPKD are mutations of the PKD1 and PKD2 genes, which encode the formation of polycystin-1 and polycystin-2 proteins.

Nephrological aspects of surgical weight correction in morbid obesity.

Obesity, including morbid obesity, is a growing worldwide problem. The adverse effect of obesity on the kidneys is associated with the development of comorbid conditions, such as insulin resistance (IR), metabolic syndrome (MS), diabetes mellitus (DM), arterial hypertension (AH), which are the recognized risk factors of chronic kidney disease (СKD). Obesity also causes direct kidney damage with the development of non-immune focal segmental glomerulosclerosis.

StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data.

Motivation: Genomics features with similar genome-wide distributions are generally hypothesized to be functionally related, for example, colocalization of histones and transcription start sites indicate chromatin regulation of transcription factor activity. Therefore, statistical algorithms to perform spatial, genome-wide correlation among genomic features are required.

Results: Here, we propose a method, StereoGene, that rapidly estimates genome-wide correlation among pairs of genomic features.

Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks.

Chromatin alterations mediate mutations and gene expression changes in cancer. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) has been utilized to study genome-wide chromatin structure in human cancer cell lines, yet numerous technical challenges limit comparable analyses in primary tumors. Here we have developed a new whole-genome analytic pipeline to optimize ChIP-Seq protocols on patient-derived xenografts from human papillomavirus-related (HPV) head and neck squamous cell carcinoma (HNSCC) samples.

[Chromatin and Polycomb: Biology and bioinformatics].

All cells of a multicellular eukaryotic organism carry almost the same genome, still they obviously demonstrate phenotypes of very divergent kinds. The most probable explanation of the divergence is that different groups of genes are expressed in cells of different types. Expression is regulated at all steps between DNA and a protein, but transcription regulation is the most common regulatory mechanism.

[Idiopathic membranous nephropathy: Evolution in understanding the problem].

The review highlights the evolution of ideas on the. mechanisms responsible for the 'development of membranous nephropathy(MN), glomerulopathy that is the most common cause of nephrotic syndrome in adults. Primary emphasis is placed on the primary form of MN.

Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus.

Background: Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in bacteria is one of the critical tasks of modern genomics. The Shewanella genus is comprised of metabolically versatile gamma-proteobacteria, whose lifestyles and natural environments are substantially different from Escherichia coli and other model bacterial species. The comparative genomics approaches and computational identification of regulatory sites are useful for the in silico reconstruction of transcriptional regulatory networks in bacteria.

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach.

RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept of a cluster of co-regulated orthologous operons allows the user to distribute the analysis of large regulons and to perform the comparative analysis of multiple clusters independently.

A basal promoter element recognized by free RNA polymerase sigma subunit determines promoter recognition by RNA polymerase holoenzyme.

During transcription initiation by bacterial RNA polymerase, the sigma subunit recognizes the -35 and -10 promoter elements; free sigma, however, does not bind DNA. We selected ssDNA aptamers that strongly and specifically bound free sigma(A) from Thermus aquaticus. A consensus sequence, GTA(C/T)AATGGGA, was required for aptamer binding to sigma(A), with the TA(C/T)AAT segment making interactions similar to those made by the -10 promoter element (consensus sequence TATAAT) in the context of RNA polymerase holoenzyme.

Two genetic algorithms for identification of regulatory signals.

There exist numerous algorithms for identification of regulatory signals in unaligned DNA fragments. Here we present two genetic algorithms for signal identification and describe their implementation and testing on simulated and real data. The first algorithm selects the start position of the signal in a given fragment.