CrossHub: a tool for multi-way analysis of The Cancer Genome Atlas (TCGA) in the context of gene expression regulation mechanisms.
Nucleic Acids Research 44(7):e62 (2016)
The contribution of different mechanisms to the regulation of gene expression varies for different tissues and tumors. Complementation of predicted mRNA-miRNA and gene-transcription factor (TF) relationships with the results of expression correlation analyses derived for specific tumor types out...
Identification, Expression Analysis, and Target Prediction of Flax Genotroph MicroRNAs Under Normal and Nutrient Stress Conditions.
Frontiers in Plant Science 7:399 (2016)
Cultivated flax (Linum usitatissimum L.) is an important plant valuable for industry. Some flax lines can undergo heritable phenotypic and genotypic changes (LIS-1 insertion being the most common) in response to nutrient stress and are called plastic lines. Offspring of plastic lines, which stab...
The Dysregulation of Polyamine Metabolism in Colorectal Cancer Is Associated with Overexpression of c-Myc and C/EBPβ rather than Enterotoxigenic Bacteroides fragilis Infection.
Oxidative Medicine & Cellular Longevity 2016:2353560 (2016)
Colorectal cancer is one of the most common cancers in the world. It is well known that the chronic inflammation can promote the progression of colorectal cancer (CRC). Recently, a number of studies revealed a potential association between colorectal inflammation, cancer progression, and infecti...
Microbial Community Structure of Activated Sludge in Treatment Plants with Different Wastewater Compositions.
Frontiers in Microbiology 7:90 (2016)
Activated sludge (AS) plays a crucial role in the treatment of domestic and industrial wastewater. AS is a biocenosis of microorganisms capable of degrading various pollutants, including organic compounds, toxicants, and xenobiotics. We performed 16S rRNA gene sequencing of AS and incoming sewag...
Basic mechanisms of longevity: A case study of Drosophila pro-longevity genes.
Ageing Research Reviews 24(Pt B):218 (2015)
Drosophila is one of the most convenient model organisms in the genetics of aging and longevity. Unlike the nematodes, which allow for the detection of new pro-aging genes by knockout and RNAi-mediated knock-down, Drosophila also provides an opportunity to find new pro-longevity genes by driver-...
Complete Genome Sequence of Bifidobacterium longum GT15: Identification and Characterization of Unique and Global Regulatory Genes.
Microbial Ecology 70(3):819 (2015)
In this study, we report the first completely annotated genome sequence of the Russia origin Bifidobacterium longum subsp. longum strain GT15. Comparative genomic analysis of this genome with other available completely annotated genome sequences of B. longum strains isolated from other countries...
Hot spots of DNA double-strand breaks and genomic contacts of human rDNA units are involved in epigenetic regulation.
Journal of Molecular Cell Biology 7(4):366 (2015)
DNA double-strand breaks (DSBs) are involved in many cellular mechanisms, including replication, transcription, and genome rearrangements. The recent observation that hot spots of DSBs in human chromosomes delimit DNA domains that possess coordinately expressed genes suggests a strong relationsh...
Excess fertilizer responsive miRNAs revealed in Linum usitatissimum L.
Biochimie 109:36 (2015)
Effective fertilizer application is necessary to increase crop yields and reduce risk of plant overdosing. It is known that expression level of microRNAs (miRNAs) alters in plants under different nutrient concentrations in soil. The aim of our study was to identify and characterize miRNAs with e...
Draft Genome Sequence of Rhodococcus ruber Strain P25, an Active Polychlorinated Biphenyl Degrader.
Genome Announcements 3(5) (2015)
We report the 5,728,255-bp draft genome sequence of Rhodococcus ruber P25, isolated from a soil polluted with halogenated aromatic compounds in the city of Perm, Russia. The strain degrades polychlorinated biphenyls and a broad range of aromatic compounds. It possesses genes that mediate the deg...
Tumor Suppressor Function of the SEMA3B Gene in Human Lung and Renal Cancers.
PLoS ONE 10(5):e0123369 (2015)
The SEMA3B gene is located in the 3p21.3 LUCA region, which is frequently affected in different types of cancer. The objective of our study was to expand our knowledge of the SEMA3B gene as a tumor suppressor and the mechanisms of its inactivation. In this study, several experimental approaches ...
Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis.
Disease Markers 2015:241301 (2015)
A significant need for reliable and accurate cancer diagnostics and prognosis compels the search for novel biomarkers that would be able to discriminate between indolent and aggressive tumors at the early stages of disease. The aim of this work was identification of potential diagnostic biomarke...
Retrotransposon-based molecular markers for analysis of genetic diversity within the Genus Linum.
BioMed Research International 2014:231589 (2014)
SSAP method was used to study the genetic diversity of 22 Linum species from sections Linum, Adenolinum, Dasylinum, Stellerolinum, and 46 flax cultivars. All the studied flax varieties were distinguished using SSAP for retrotransposons FL9 and FL11. Thus, the validity of SSAP method was demonstr...
Epigenetic alterations of chromosome 3 revealed by NotI-microarrays in clear cell renal cell carcinoma.
BioMed Research International 2014:735292 (2014)
This study aimed to clarify epigenetic and genetic alterations that occur during renal carcinogenesis. The original method includes chromosome 3 specific NotI-microarrays containing 180 NotI-clones associated with 188 genes for hybridization with 23 paired normal/tumor DNA samples of primary cle...
Complete Genome Sequence of Bifidobacterium longum GT15: Unique Genes for Russian Strains.
Genome Announcements 2(6) (2014)
In this study, we report the first completely annotated genome sequence of the Russian-origin Bifidobacterium longum subsp. longum strain GT15. We discovered 35 unique genes (UGs) which were detected from only the B. longum GT15 genome and were absent from other B. longum strain genomes (not of ...
Targeting VDAC-bound hexokinase II: a promising approach for concomitant anti-cancer therapy.
Expert Opinion on Therapeutic Targets 17(10):1221 (2013)
Enhancement of glucose metabolism and repression of oxidative phosphorylation followed by the Warburg effect is the common hallmark of cancer cells. Hexokinase II (HKII) plays a dual role - first, HKII up-regulation results in increased glycolysis rates. Second, association of VDAC and HKII cont...
Deregulation of glycolysis in cancer: glyceraldehyde-3-phosphate dehydrogenase as a therapeutic target.
Expert Opinion on Therapeutic Targets 17(6):681 (2013)
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a key glycolytic enzyme, but recent studies have shown its non-glycolytic role in cell death, survival mechanisms and diseases. Increase in glycolysis, in particular overexpression of GAPDH, has been considered an important feature of many type...
Novel tumor suppressor candidates on chromosome 3 revealed by NotI-microarrays in cervical cancer.
Epigenetics 8(4):409 (2013)
Genetic and epigenetic alterations in cervical carcinomas were investigated using NotI-microarrays containing 180 cloned sequences flanking all NotI-sites associated with genes on chromosome 3. In total, 48 paired normal/tumor DNA samples, specifically enriched in NotI-sites, were hybridized to ...
LRRC3B gene is frequently epigenetically inactivated in several epithelial malignancies and inhibits cell growth and replication.
Biochimie 94(5):1151 (2012)
Chromosome 3 specific NotI microarrays containing 180 NotI linking clones associated with 188 genes were hybridized to NotI representation probes prepared using matched tumor/normal samples from major epithelial cancers: breast (47 pairs), lung (40 pairs) cervical (43 pairs), kidney (34 pairs of...
Genetic and epigenetic analysis of non-small cell lung cancer with NotI-microarrays.
Epigenetics 7(5):502 (2012)
This study aimed to clarify genetic and epigenetic alterations that occur during lung carcinogenesis and to design perspective sets of newly identified biomarkers. The original method includes chromosome 3 specific NotI-microarrays containing 180 NotI clones associated with genes for hybridizati...
Differential expression of CHL1 gene during development of major human cancers.
PLoS ONE 6(3):e15612 (2011)
CHL1 gene (also known as CALL) on 3p26.3 encodes a one-pass trans-membrane cell adhesion molecule (CAM). Previously CAMs of this type, including L1, were shown to be involved in cancer growth and metastasis.
We used Clontech Cancer Profiling Arrays (19 different types of cancers, 395 samples) to...