Assessment of ecological state for the north-eastern shelf of Sakhalin Island: hydrochemical analysis and bioassay

Results of ecological monitoring in the coastal waters at north-eastern Sakhalin are presented. Spatial patterns of water temperature, salinity, dissolved oxygen content, and concentrations of inorganic phosphate and silicon are described, geostrophic currents are calculated. Abnormalities of early embryogenesis are revealed for the sand dollar Scaphechinus mirabilis in the water sampled both at the coast and in the oil-producing areas but not in the areas distanced from the oil wells. Possible influence of natural environments and anthropogenic factors on marine biota in the area of monitoring is discussed: the abnormalities at the coast are possibly caused by low salinity, but those ones in the oil-producing areas have no any natural reasons, so far as salinity, temperature and nutrients concentration in these areas are the same as in the open-waters with normal results of the bioassay. Thus, anthropogenic impact on marine biota is detected for the areas of continued oil and gas production on the northeastern shelf of Sakhalin Island

Ecotoxicological assay of seawater quality on the western Kamchatka shelf

Ecotoxicological assay of seawater quality along the shelf of West Kamchatka, including the areas of oil and gas deposits, was conducted in the summer of 2014. Temperature and salinity conditions were usual for summer season, as well as the field of density currents. For introduction of modern and representative bioassay methods in practice of environmental monitoring in the regions of oil and gas production and transportation, embryogenesis of sand dollar Scaphechinus mirabilis was used for biotesting. The stations with high number of the embryos and larvae abnormalities had mosaic distribution - this effect may be connected with shipping of fishing and merchant vessels

Economic evaluation of biological resources and ecosystem services for the Okhotsk Sea

The total cost of commercial stocks of biological resources in the Okhotsk Sea is evaluated as US$23.5 · 109/year on the data on total allowable catch for the year 2014, taking into account the world prices for seafood. The potential cost of all known bioresources in the Sea, including pelagic and benthic fish and invertebrates (for a case of their total utilization), is determined as US$ 58.5 · 109/year. The total value of ecosystem services provided by the Okhotsk Sea is estimated as US$ 294.4 · 109/year, believing that their cost per unit area in the Okhotsk Sea is equal to mean value of ecosystem services per unit area in certain areas of the World Ocean with a known cost - this value for non-market ecosystem services exceeds the cost of traditionally used biological resources. Economic evaluation of ecosystem services presented in monetary units can be used as a tool to enhance conservation of natural complexes in the process of industrial projects implementation

Comparative study of the pharmacological effects of Venarus Plus, Venarus, and Detralex on L-NAME-induced endothelial dysfunction, venous tone and platelet aggregation

In the present study we compared the pharmacological activity of Venarus Plus, Venarus and Detralex 1000 mg on the reversion of endothelial dysfunction (ED), and on the effect on venous tone, vascular permeability, and platelet aggregation. We used 150 Wistar male rats, weighing 180-220 g, and 80 adult albino rabbits weighing 2800 - 3200 g. Endothelial dysfunction (ED) was induced with the non-selective inhibitor of NO synthase, N-nitro-L-arginine-methyl ether (L-NAME). Functional vascular tests and biochemical markers were used to determine the reversion of the functional disorders. The anti-inflammatory effects of the drugs was evaluated in rabbits using o-xylene. The venotonic effects of the compounds was carried out on an isolated segment of the rat portal vein with Ca2+ solutions at a concentration of 0.08-1.75 mM. Our results show that the maximum daily therapeutic dose of Venarus Plus, produces a significant decrease in the ED coefficient (СED), an increase in NO synthesis, and an extended ADP-induced platelet aggregation time. The studied drugs dose-dependently reduce vascular permeability disorders caused by the application of o-xylene, which was manifested in a profound decrease the size of spots and the extension of the time interval before their onset. To study the Ca2+-mediated smooth muscle response, showed that the maximum force of vein contraction occurs with a higher dosage of drugs in the presence of a lower concentration of Ca2+, the effects of the drugs are comparable

The CIMP-high phenotype is associated with energy metabolism alterations in colon adenocarcinoma

Abstract Background CpG island methylator phenotype (CIMP) is found in 15–20% of malignant colorectal tumors and is characterized by strong CpG hypermethylation over the genome. The molecular mechanisms of this phenomenon are not still fully understood. The development of CIMP is followed by global gene expression alterations and metabolic changes. In particular, CIMP-low colon adenocarcinoma (COAD), predominantly corresponded to consensus molecular subtype 3 (CMS3, “Metabolic”) subgroup according to COAD molecular classification, is associated with elevated expression of genes participating in metabolic pathways. Methods We performed bioinformatics analysis of RNA-Seq data from The Cancer Genome Atlas (TCGA) project for CIMP-high and non-CIMP COAD samples with DESeq2, clusterProfiler, and topGO R packages. Obtained results were validated on a set of fourteen COAD samples with matched morphologically normal tissues using quantitative PCR (qPCR). Results Upregulation of multiple genes involved in glycolysis and related processes (ENO2, PFKP, HK3, PKM, ENO1, HK2, PGAM1, GAPDH, ALDOA, GPI, TPI1, and HK1) was revealed in CIMP-high tumors compared to non-CIMP ones. Most remarkably, the expression of the PKLR gene, encoding for pyruvate kinase participating in gluconeogenesis, was decreased approximately 20-fold. Up to 8-fold decrease in the expression of OGDHL gene involved in tricarboxylic acid (TCA) cycle was observed in CIMP-high tumors. Using qPCR, we confirmed the increase (4-fold) in the ENO2 expression and decrease (2-fold) in the OGDHL mRNA level on a set of COAD samples. Conclusions We demonstrated the association between CIMP-high status and the energy metabolism changes at the transcriptomic level in colorectal adenocarcinoma against the background of immune pathway activation. Differential methylation of at least nine CpG sites in OGDHL promoter region as well as decreased OGDHL mRNA level can potentially serve as an additional biomarker of the CIMP-high status in COAD

Immunohistochemistry and Mutation Analysis of SDHx Genes in Carotid Paragangliomas

Carotid paragangliomas (CPGLs) are rare neuroendocrine tumors often associated with mutations in SDHx genes. The immunohistochemistry of succinate dehydrogenase (SDH) subunits has been considered a useful instrument for the prediction of SDHx mutations in paragangliomas/pheochromocytomas. We compared the mutation status of SDHx genes with the immunohistochemical (IHC) staining of SDH subunits in CPGLs. To identify pathogenic/likely pathogenic variants in SDHx genes, exome sequencing data analysis among 42 CPGL patients was performed. IHC staining of SDH subunits was carried out for all CPGLs studied. We encountered SDHx variants in 38% (16/42) of the cases in SDHx genes. IHC showed negative (5/15) or weak diffuse (10/15) SDHB staining in most tumors with variants in any of SDHx (94%, 15/16). In SDHA-mutated CPGL, SDHA expression was completely absent and weak diffuse SDHB staining was detected. Positive immunoreactivity for all SDH subunits was found in one case with a variant in SDHD. Notably, CPGL samples without variants in SDHx also demonstrated negative (2/11) or weak diffuse (9/11) SDHB staining (42%, 11/26). Obtained results indicate that SDH immunohistochemistry does not fully reflect the presence of mutations in the genes; diagnostic effectiveness of this method was 71%. However, given the high sensitivity of SDHB immunohistochemistry, it could be used for initial identifications of patients potentially carrying SDHx mutations for recommendation of genetic testing

Novel potential causative genes in carotid paragangliomas

Abstract Background Carotid paragangliomas (CPGLs) are rare neuroendocrine tumors that arise from the paraganglion at the bifurcation of the carotid artery and are responsible for approximately 65% of all head and neck paragangliomas. CPGLs can occur sporadically or along with different hereditary tumor syndromes. Approximately 30 genes are known to be associated with CPGLs. However, the genetic basis behind the development of these tumors is not fully elucidated, and the molecular mechanisms underlying CPGL pathogenesis remain unclear. Methods Whole exome and transcriptome high-throughput sequencing of CPGLs was performed on an Illumina platform. Exome libraries were prepared using a Nextera Rapid Capture Exome Kit (Illumina) and were sequenced under 75 bp paired-end model. For cDNA library preparation, a TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) was used; transcriptome sequencing was carried out with 100 bp paired-end read length. Obtained data were analyzed using xseq which estimates the influence of mutations on gene expression profiles allowing to identify potential causative genes. Results We identified a total of 16 candidate genes (MYH15, CSP1, MYH3, PTGES3L, CSGALNACT2, NMD3, IFI44, GMCL1, LSP1, PPFIBP2, RBL2, MAGED1, CNIH3, STRA6, SLC6A13, and ATM) whose variants potentially influence their expression (cis-effect). The strongest cis-effect of loss-of-function variants was found in MYH15, CSP1, and MYH3, and several likely pathogenic variants in these genes associated with CPGLs were predicted. Conclusions Using the xseq probabilistic model, three novel potential causative genes, namely MYH15, CSP1, and MYH3, were identified in carotid paragangliomas

Mutational load in carotid body tumor

Abstract Background Carotid body tumor (CBT) is a rare neoplasm arising from paraganglion located near the bifurcation of the carotid artery. There is great intra-tumor heterogeneity, and CBT development could be associated with both germline and somatic allelic variants. Studies on the molecular genetics of CBT are limited, and the molecular mechanisms of its pathogenesis are not fully understood. This work is focused on the estimation of mutational load (ML) in CBT. Methods Using the NextSeq 500 platform, we performed exome sequencing of tumors with matched lymph node tissues and peripheral blood obtained from six patients with CBT. To obtain reliable results in tumors with low ML, we developed and successfully applied a complex approach for the analysis of sequencing data. ML was evaluated as the number of somatic variants per megabase (Mb) of the target regions covered by the Illumina TruSeq Exome Library Prep Kit. Results The ML in CBT varied in the range of 0.09–0.28/Mb. Additionally, we identified several pathogenic/likely pathogenic somatic and germline allelic variants across six patients studied (including TP53 variants). Conclusions Using the developed approach, we estimated the ML in CBT, which is much lower than in common malignant tumors. Identified variants in known paraganglioma/pheochromocytoma-causative genes and novel genes could be associated with the pathogenesis of CBT. The obtained results expand our knowledge of the mutation process in CBT as well as the biology of tumor development

HK3 overexpression associated with epithelial-mesenchymal transition in colorectal cancer

Abstract Background Colorectal cancer (CRC) is a common cancer worldwide. The main cause of death in CRC includes tumor progression and metastasis. At molecular level, these processes may be triggered by epithelial-mesenchymal transition (EMT) and necessitates specific alterations in cell metabolism. Although several EMT-related metabolic changes have been described in CRC, the mechanism is still poorly understood. Results Using CrossHub software, we analyzed RNA-Seq expression profile data of CRC derived from The Cancer Genome Atlas (TCGA) project. Correlation analysis between the change in the expression of genes involved in glycolysis and EMT was performed. We obtained the set of genes with significant correlation coefficients, which included 21 EMT-related genes and a single glycolytic gene, HK3. The mRNA level of these genes was measured in 78 paired colorectal cancer samples by quantitative polymerase chain reaction (qPCR). Upregulation of HK3 and deregulation of 11 genes (COL1A1, TWIST1, NFATC1, GLIPR2, SFPR1, FLNA, GREM1, SFRP2, ZEB2, SPP1, and RARRES1) involved in EMT were found. The results of correlation study showed that the expression of HK3 demonstrated a strong correlation with 7 of the 21 examined genes (ZEB2, GREM1, TGFB3, TGFB1, SNAI2, TWIST1, and COL1A1) in CRC. Conclusions Upregulation of HK3 is associated with EMT in CRC and may be a crucial metabolic adaptation for rapid proliferation, survival, and metastases of CRC cells