Changes In Nucleotide Sequence Research Articles

Investigation of resistance against to flumethrin using against Varroa destructor in Türkiye

The honeybee ectoparasite Varroa destructor is a major threat to apiculture when evaluating bee diseases and pests. While attempting to control this mite, beekeepers often depend on a small selection of authorized synthetic acaricides, such as flumethrin, which is widely used in Türkiye and globally. However, resistance to flumethrin develops due to incorrect and excessive use. In this study conducted at Ordu Beekeeping Research Institute, trial group were established including an untreated control group and group where flumethrin-based pesticides were applied. Dead varroas collected from pollen traps and live varroas collected from bees were obtained from these trial groups for molecular analysis as positive-negative controls. Varroa samples were collected from provinces representing different regions with intensive beekeeping activities such as Adana, Ankara, Bingöl, Muğla, Ordu, Şanlıurfa, Tekirdağ. Molecular methods were employed to investigate the resistance gene region for pyrethroids (specifically flumethrin) against V. destructor. In our study, individual DNA extractions were performed on dead parasites from colonies subjected to pyrethroid application (resistance negative control) and live parasites (resistance positive control). The DNA samples obtained were used in PCR reactions targeting the region encoding the 925th amino acid of the voltage-gated sodium channel (VGSC) gene, which is responsible for resistance formation. The DNA samples were subjected to gel electrophoresis to observe the amplification products of the expected target region. To examine the nucleotide sequence changes that encode leucine at the 925th amino acid, which is associated with resistance, DNA sequence analysis was applied to the amplification products. Out of 332 V. destructor parasites obtained from different provinces, 279 were analysed using molecular methods. It was observed that 31% of the samples showed sensitivity to flumethrin while 69% exhibited resistance to it. Among the resistant samples: 27% had homozygous isoleucine mutation; 28% had homozygous valine mutation; 2.8% had heterozygous isoleucine mutation; 8.5% had heterozygous valine mutation; and 2.8% had heterozygous methionine mutation, all of which were associated with flumethrin resistance. As a result, the rate of flumethrin resistance in parasites varied between 51% and 94% among different provinces.

Analysis of Mutations of the Maize Genes of Autonomous Embryo-, Endospermogenesis

The gynogenesis and parthenogenesis genes in Saratov maize lines was evaluated. In particular, the (Zm_Gex2, Zm_Gcs1, Zm_Pla1, Zm_CenH3, Zm_Dmp7) genes in haploid-inducing (ZMS-8, ZMSP) and (Zm_Chr106, Zm_Hdt104 and Zm_Fie1) genes in parthenogenetic (AT-1, AT-3, AT-4) and ordinary (KM, GPL-1) maize lines were sequenced. Using bioinformatic methods, gene sequences were compared in different maize lines and changes in nucleotide sequences were revealed. We suppose that it is possible to use Zm_Pla1, Zm_Gex2, and Zm_Fie1 genes for maize line genotyping.

A New Function of MbIAA19 Identified to Modulate Malus Plants Dwarfing Growth.

The primary determinants of apple (Malus) tree architecture include plant height and internode length, which are the significant criteria for evaluating apple dwarf rootstocks. Plant height and internode length are predominantly governed by phytohormones. In this study, we aimed to assess the mechanisms underlying dwarfism in a mutant of Malus baccata. M. baccata dwarf mutant (Dwf) was previously obtained through natural mutation. It has considerably reduced plant height and internode length. A comparative transcriptome analysis of wild-type (WT) and Dwf mutant was performed to identify and annotate the differentially expressed genes responsible for the Dwf phenotype using RNA-seq and GO and KEGG pathway enrichment analyses. Multiple DEGs involved in hormone signaling pathways, particularly auxin signaling pathways, were identified. Moreover, the levels of endogenous indole-3-acetic acid (IAA) were lower in Dwf mutant than in WT. The Aux/IAA transcription factor gene MbIAA19 was downregulated in Dwf mutant due to a single nucleotide sequence change in its promoter. Genetic transformation assay demonstrated strong association between MbIAA19 and the dwarf phenotype. RNAi-IAA19 lines clearly exhibited reduced plant height, internode length, and endogenous IAA levels. Our study revealed that MbIAA19 plays a role in the regulation of dwarfism and endogenous IAA levels in M. baccata.

Mitochondrial DNA Polymorphism in HV1 and HV2 Regions and 12S rDNA in Perimenopausal Hypertensive Women.

Estrogens enhance cellular mitochondrial activity. The diminution of female hormones during menopause may have an effect on the mitochondrial genome and the expression of mitochondrial proteins. Hence, oxidative stress and the pro-inflammatory state contribute to the formation of systemic illnesses including arterial hypertension (AH). This study aimed to determine the types and frequency of mutations in the mitochondrial DNA (mtDNA) nucleotide sequence in the hypervariable regions 1 and 2 (HV1 and HV2) and the 12S RNA coding sequence of the D-loop in postmenopausal women with hypertension. In our study, 100 women were investigated, 53 of whom were postmenopausal and 47 of whom were premenopausal (53.9 ± 3.7 years vs. 47.7 ± 4.2 years, respectively). Of those studied, 35 premenopausal and 40 postmenopausal women were diagnosed with AH. A medical checkup with 24 h monitoring of blood pressure (RR) and heart rate was undertaken (HR). The polymorphism of the D-loop and 12S rDNA region of mtDNA was examined. Changes in the nucleotide sequence of mtDNA were observed in 23% of the group of 100 women. The changes were identified in 91.3% of HV1 and HV2 regions, 60.9% of HV1 segments, 47.5% of HV2 regions, and 43.5% of 12S rDNA regions. The frequency of nucleotide sequence alterations in mtDNA was substantially higher in postmenopausal women (34%) than in premenopausal women (10.6%), p = 0.016. A higher frequency of changes in HV1 + HV2 sections in postmenopausal women (30.2%) compared to the premenopausal group (10.6%) was detected, p = 0.011. Only postmenopausal women were found to have modifications to the HV2 segment and the 12S rDNA region. After menopause, polymorphism in the mtDNA region was substantially more frequent in women with arterial hypertension than before menopause (p = 0.030; 37.5% vs. 11.5%). Comparable findings were observed in the HV2 and HV1 regions of the AH group (35% vs. 11.5%), p = 0.015, in the HV1 segment (25% vs. 11.5%), p = 0.529, and in the HV2 segment, 12S rDNA (25% vs. 0%). More than 80% of all changes in nucleotide sequence were homoplasmic. The mtDNA polymorphisms of the nucleotide sequence in the HV1 and HV2 regions, the HV2 region alone, and the 12S RNA coding sequence were associated with estrogen deficiency and a more severe course of arterial hypertension, accompanied by symptoms of adrenergic stimulation.

Type 1 Hemochromatosis: A Review of the History, Inheritance and Treatment of Iron Overload Disorder

Hereditary hemochromatosis (also known as type 1 hemochromatosis, iron overload disorder, or the Celtic Curse) is a genetic disorder characterized by an autosomal recessive inheritance pattern. This review project focused on gathering comprehensive data about the history, causes, inheritance, diagnosis, and treatment of iron overload disorder. Through such research, it was discovered that type 1 hemochromatosis may occur due to one of two nucleotide sequence changes (either the C282Y mutation or the H63D mutation) in the HFE gene, which codes for the construction of the homeostatic iron regulator protein and regulates production of the hormone hepcidin. As a result of these mutations, individuals affected by hemochromatosis have elevated iron levels and excess deposits of iron in tissues and organs. Such deposits may cause a variety of symptoms and complications, including fatigue, skin discoloration, heart failure, cirrhosis, liver cancer, and diabetes. Hemochromatosis is one of the most common genetic disorders in the world, affecting one in every three hundred individuals. The majority of hemochromatosis patients are of northern European descent. Currently, there is no cure for type 1 hemochromatosis; however, the primary treatment method for this disorder is phlebotomy. Due to the widespread prevalence of the disorder, researchers continue to explore experimental treatment methods, including gene therapy and iron chelation therapy.

Highly Sensitive Blocker Displacement Amplification for Detection of Low-Level JAK2V617F Variant.

Key criteria in the diagnostic workup and risk stratification for myeloproliferative neoplasms (MPN) include molecular testing for JAK2V617F and other mutant alleles. Multiple methods for quantitatively detecting nucleotide sequence changes exist, but the lower limit of detection can limit identification of the low-level allele fraction of a variant. We evaluated a recently developed blocker displacement amplification (BDA)-based quantitative PCR platform for detection and quantitation of JAK2V617F variant allele fraction (VAF). Clinical samples were tested using BDA, next-generation sequencing (NGS), and droplet digital PCR (ddPCR) in a head-to-head comparison of sensitivity and specificity in detecting the JAK2V617F variant. In total, 112 human genomic DNA specimens previously tested for JAK2V617F gene mutation status with NGS were analyzed, including 12 samples with low-level variants with VAF ≤2%, 6 samples with VAF >2%, and 94 samples with no variant previously identified by NGS. BDA and ddPCR results correlated well across a range of VAFs, with both methods identifying the JAK2V617F variant down to at least 0.05% VAF. NGS of routine sequencing depth was less sensitive, identifying JAK2V617F only at 0.6% VAF. BDA can provide a cost-effective alternative means to identify low-level variants using instrumentation commonly found in laboratories.

Identification and in silico analysis of noval alteration Arg420Gly in KIT proto oncogene among acute myeloid leukemia patients

A number of studies have reported frequent incidence of c-kit gene mutations in association with core binding factor acute myeloid leukemia (CBF-AML). These genetic changes have become important prognostic predictors in patients with abnormal karyotype. Aim of this study was the detection of nucleotide alterations in newly diagnosed acute myeloid leukemia patients for three exons of c-kit gene, including cytogenetically normal patients. Thirty-one de novo AML patients were screened for any possible variations in exon 8, 11 and 17 sequences of c-kit proto-oncogene leading to amino acid substitutions or frame shift. Sanger sequencing method was employed followed by sequence analysis. Mutation data was then correlated with clinical and hematological parameters of patients and prognostic significance of genetic changes was assessed as well. The computational tools were then used to further understand the extent of damage caused by these mutations to c-kit protein. Fifteen (48.4%) mutant patients were observed with single, double or multiple mutations in one, two or all three exons studied. The analysis revealed eight new alterations which were not reported previously. Significant variation among mutant and non-mutant group of patients was observed with respect to FAB subtypes (x2 = 12.524, p = 0.029), Spleen size (x2 = 4.288, p = 0.038) and Red blood cell count (x2 = 8.447, p = 0.007). The survival analysis indicates poor overall and event free survival outcomes in mutant individuals. Furthermore, the in silico analysis suggests that changes in nucleotide sequences can possibly damage the protein structure and effect it’s function. This study emphasizes the need to consider screening of c-kit gene alterations not only in CBF-AML but in cytogenetically normal AML patients as well. In current investigation the effect of mutation Arg420Gly on structure and function of c-kit protein was investigated, as this was the most observed substitution in present cohort. Various bioinformatics tools and techniques were employed, which determined that Arg420Gly is possibly non-pathogenic mutation.

Natural genetic variation in the HAIRS ABSENT (H) gene increases type-VI glandular trichomes in both wild and domesticated tomatoes

Glandular trichomes produce and exude secondary metabolites, conferring insect resistance in many crop species. Whereas some of its wild relatives are insect-resistant, tomato (Solanum lycopersicum) is not. Identifying the genetic changes that altered trichome development and biochemistry during tomato domestication would contribute to breeding for insect resistance. A mutation in the HAIRS ABSENT (H) gene, which encodes a C2H2 zinc finger protein (ZFP8), leads to reduced trichome density. Several geographic accessions of S. pimpinellifolium, the wild ancestor of domesticated tomato, have glabrous organs that resemble the phenotype caused by h. Here, we investigated allelic diversity for H in tomato and S. pimpinellifolium accessions and their associated trichome phenotypes. We also evaluated how the developmental stage can affect trichome development in glabrous and non-glabrous plants. We found that glabrous accessions of S. pimpinellifolium have different ZFP8 nucleotide sequence changes, associated with altered trichome development and density. We also found that while the glabrous appearance of h mutants is caused by a lower density of long trichomes, the density of type-VI glandular trichomes is increased, particularly in the adult stages of plant development. These insights on the genetic control of trichome development may contribute to breeding for insect resistance in tomatoes and other crops.

CURRENT ISSUES OF VITAMIN D IN JUVENILE IDIOPATHIC ARTHRITIS

Background. Children with juvenile idiopathic arthritis (JIA) represent a special cohort of patients with chronic somatic pathology, characterized by severe damage to the musculoskeletal system and other vital organs and systems, which is associated with immune and metabolic changes in the body. Data regarding the provision of vitamin D (VD) in patients with JIA and the significance of its deficiency in the initiation, activation of the autoimmune process, the prognosis of the course of the disease, the risk of developing complications and the effectiveness of protocol therapy are contradictory. Objective. To investigate the body's supply of vitamin D in patients with juvenile idiopathic arthritis with the determination of the trigger factors of its deficiency, the assessment of the immune status and changes in the nucleotide sequence in the genes of innate immunity. Materials and methods. Research was conducted during 2016-2021 at the Institute in 119 patients with JIA aged 6 to 12 years. The concentration of 25OHD was determined in blood serum using commercial Vitamin D3 kits (Screeningkit, Switzerland). Immunological studies were performed by flow cytofluorimetry and enzyme immunoassay. For panel sequencing of 407 genes regulating immune functions, high-throughput panel exome sequencing was used on Illumina's HiSeq machine (made in the USA) at the Invitae laboratory (USA). The obtained digital data were processed by methods of statistical analysis using the Microsoft Excel computer package. Results. A high frequency of low supply of vitamin D in patients with JIA was revealed: vitamin D insufficiency was diagnosed in 96 (80.6 %), and its deficiency - in 38 (31.9 %) children. The lowest levels of 25ОНD concentration in blood serum (less than 15 ng/ml) are observed in patients with stage II–III disease activity, especially at the beginning of the pathological process. Vitamin D deficiency (DVD) was associated with the activity and severity of the clinical course, frequent exacerbation of the joint syndrome, the expressiveness of changes in the humoral and cellular immunity of patients. The main risk factors for reducing the body's supply of WD in patients with JIA have been determined, which must be taken into account during their observation and treatment. High activity of JIA in patients with VD deficiency in the body was associated with a significant increase in the number of CD3+ T-cells, CD3+CD4+ helper-inducer T-cells, activated HLA-DR+/CD3+ T-cells, ESR, C-reactive protein concentration (CRP), tumor necrosis factor (TNF), circulating immune complexes (CIC), immunoglobulins, which allows considering DWD as a likely predictor of severe and prognostically unfavorable course of rheumatic disease. Nucleotide sequence changes in the NOD2 gene were detected in 18.1 % of patients with JIA: c.2104C>T (p.Arg702Trp), c.3019dupC (p.Leu1007Profs*2). The of variable changes in patients with JIA is statistically significantly different from the population [VSh = 11.39; 95 % CI (2.39-54.22)]. DVD was detected in all children with mutations in the NOD2 gene – (17.2 ± 3.29) ng/ml, and in children without changes in the nucleotide sequence - in 23 (85.1 %) children [SS = 0.097; DI (0.03-0.31)], the concentration of VD is significantly higher - [(26.68 ± 2.34) ng/ml, p = 0.026]. Conclusions. The conducted studies confirm the presence of a decrease in the body's supply of vitamin D in patients with JIA, which is associated with a high activity of the pathological process and pronounced immunological changes in the body, which allows us to consider its deficiency as a likely predictor of a severe and prognostically unfavorable course of the disease. It has been proven that the concentration of vitamin D in JIA is higher in patients without changes in the nucleotide sequence in the NOD2 gene, which must be taken into account when predicting and evaluating the body's response to the treatment of juvenile arthritis. Key words: juvenile idiopathic arthritis, vitamin D, immunological status, genetic sequencing, children.

Abnormal TNS3 gene methylation in patients with congenital scoliosis

BackgroundCongenital scoliosis (CS) is a congenital deformity of the spine resulting from abnormal and asymmetrical development of vertebral bodies during pregnancy. However, the etiology and mechanism of CS remain unclear. Epigenetics is the study of heritable variations in gene expression outside of changes in nucleotide sequence. Among these, DNA methylation was described first and is the most characteristic and most stable epigenetic mechanism. Therefore, in this study, we aim to explore the association between genome methylation and CS which are not been studied before.MethodsTwo pairs of monozygotic twins were included, with each pair involving one individual with and one without CS. Agilent SureSelect XT Human Methyl-Sequencing was used for genome methylation sequencing. MethylTarget was used to detect methylation levels in target regions. Immunohistochemistry was performed to visualize expression of associated genes in candidate regions.ResultsA total of 75 differentially methylated regions were identified, including 24 with an increased methylation level and 51 with a decreased methylation level in the CS group. Nine of the differentially methylated regions were selected (TNS3, SEMAC3, GPR124, MEST, DLK1, SNTG1, PPIB, DEF8, and GRHL2). The results showed that the methylation level of the promoter region of TNS3 was 0.72 ± 0.08 in the CS group and 0.43 ± 0.06 in the control group (p = 0.00070 < 0.01). There was no significant difference in the degree of methylation of SEMAC3, GPR124, MEST, DLK1, SNTG1, PPIB, DEF8, or GRHL2 between the two groups. Immunohistochemistry showed significantly decreased TNS3 expression in the cartilage of the articular process in CS (CS: 0.011 ± 0.002; control: 0.018 ± 0.006, P = 0.003 < 0.01).ConclusionCompared with the control group, high-level methylation of the TNS3 promoter region and low TNS3 expression in the cartilage layer of the articular process characterize CS. Thus, DNA methylation and TNS3 may play important roles in the pathogenesis of CS.

Characterization of a Human Sapovirus Genotype GII.3 Strain Generated by a Reverse Genetics System: VP2 Is a Minor Structural Protein of the Virion.

We devised a reverse genetics system to generate an infectious human sapovirus (HuSaV) GII.3 virus. Capped/uncapped full-length RNAs derived from HuSaV GII.3 AK11 strain generated by in vitro transcription were used to transfect HuTu80 human duodenum carcinoma cells; infectious viruses were recovered from the capped RNA-transfected cells and passaged in the cells. Genome-wide analyses indicated no nucleotide sequence change in the virus genomes in the cell-culture supernatants recovered from the transfection or those from the subsequent infection. No virus growth was detected in the uncapped RNA-transfected cells, suggesting that the 5′-cap structure is essential for the virus’ generation and replication. Two types of virus particles were purified from the cell-culture supernatant. The complete particles were 39.2-nm-dia., at 1.350 g/cm3 density; the empty particles were 42.2-nm-dia. at 1.286 g/cm3. Two proteins (58-kDa p58 and 17-kDa p17) were detected from the purified particles; their molecular weight were similar to those of VP1 (~60-kDa) and VP2 (~16-kDa) of AK11 strain deduced from their amino acids (aa) sequences. Protein p58 interacted with HuSaV GII.3-VP1-specific antiserum, suggesting that p58 is HuSaV VP1. A total of 94 (57%) aa of p17 were identified by mass spectrometry; the sequences were identical to those of VP2, indicating that the p17 is the VP2 of AK11. Our new method produced infectious HuSaVs and demonstrated that VP2 is the minor protein of the virion, suggested to be involved in the HuSaV assembly.

Polymorphisms, diet and nutrigenomics.

Every human being possesses an exclusive nutritional blueprint inside their genes. Bioactive food components and nutrients affect the expression of such genes. Nutrigenomics is the science that analyzes gene-nutrient interactions (nutrigenetics), which can lead to the development of personalized nutritional recommendations to maintain optimal health and prevent disease. Genomic diversity among various ethnic groups might affect nutrients bioavailability as well as their metabolism. Nutrigenomics combines different branches of science including nutrition, bioinformatics, genomics, molecular biology, molecular medicine, and epidemiology. Genes regulate intake and metabolism of different nutrients, while nutrients positively or negatively influence the expression of a number of genes; testing of specific genetic polymorphisms may therefore become a useful tool to manage weight loss and to fully understand gene-nutrient interactions. Indeed, several approaches are used to study gene-nutrient interactions: epigenetics, the study of genome modification not related to changes in nucleotide sequence; transcriptomics, the study of tissue-specific and time-specific RNA transcripts; proteomics, the study of proteins involved in biological processes; and metabolomics, the study of changes of primary and secondary metabolites in body fluids and tissues. Hence, the use of nutrigenomics to improve and optimize a healthy, balanced diet in clinical settings could be an effective approach for long-term lifestyle changes that might lead to consistent weight loss and improve quality of life.

Impact of anthocyanin on genetic stability in mammary adenocarcinoma-induced mice treated with methotrexate.

BackgroundGenetic instability leads to genome mutations, changes in nucleotide sequences, rearrangements, and gains or losses of part of the chromosomes. This instability can initiate and develop cancer. This study evaluated genomic stability in methotrexate and anthocyanin-treated mammary adenocarcinoma model. Seventy albino mice were divided into seven groups: negative control, anthocyanin, methotrexate, Ehrlich’s solid tumor; Ehrlich’s solid tumor and methotrexate; Ehrlich’s solid tumor and anthocyanin; and Ehrlich’s solid tumor, methotrexate, and anthocyanin groups.ResultsTumor weight and size were evaluated. Serum arylesterase activity was low in all the induced tumors and those treated with anthocyanin, methotrexate, or both. Poly[adenosine diphosphate (ADP)-ribose] polymerase activity was high, and glutathione S-transferase activity was low in the tumors treated with anthocyanin, methotrexate, or both, compared with that of the untreated tumor. There was an increase in DNA damage in the mice with solid tumors and those injected with methotrexate or methotrexate and anthocyanin, compared with that in the untreated mice.ConclusionsThere was a decrease in genetic instability and DNA damage in the tumor-bearing mice treated with anthocyanin, with a concomitant increase in nuclear poly[adenosine diphosphate (ADP)-ribose] polymerase activity, compared with those of the untreated group. Anthocyanin exerted positive effects in the treatment of mammary adenocarcinoma.

Conformation impact in the deformation of DNA TATA-box

The ability to undergo specific deformation in response to conformational changes of some sites of the macromolecule is the key element of DNA genetic activity regulation in biological cells. The deformation of the definite sequences in DNA chain provides an accurate reading of genetic information and the process of protein synthesis passing. The model based on the analysis of conformational changes of the TATA nucleotide sequence in DNA double helix is developed. In addition to elastic components (bending, twisting), the presented model includes the conformational rearrangements of the TATA-box. Obtained form, value, and energy of DNA cite deformation allow to offer the probable mechanism of recognition of key DNA sequences and makes it possible to explain the high accuracy of the processes of reproducing of genetic information in biological cells. The formulated physical mechanism of DNA deformation can be one of the main principles of genetic information realization.

Enhanced Production of a Thermostable Carbonic Anhydrase in Escherichia coli by Using a Modified NEXT Tag.

Carbonic anhydrase (CA) is an ultrafast enzyme that catalyzes the reversible conversion of carbon dioxide (CO2) to bicarbonate. CA is considered to be a green catalyst for enzyme-based CO2 capture and utilization. In particular, the CA of Thermovibrio ammonificans (taCA) has attracted increasing attention as a highly stable enzyme. However, the poor solubility and the low expression level in Escherichia coli have hampered further utilization of taCA. In a recent study, these limitations were partly resolved by using a small solubility-enhancing fusion tag named NEXT, which originates from the N-terminal extension of Hydrogenovibrio marinus CA. In this study, the NEXT tag was engineered by adding small peptides to the N terminus to further increase the production yield of NEXT-tagged taCA. The addition of ng3 peptide (His-Gly-Asn) originating from the N-terminal sequence of Neisseria gonorrhoeae CA improved the expression of NEXT-taCA, while the previously developed translation-enhancing element (TEE) and Ser-Lys-Ile-Lys (SKIK) tag were not effective. The expression test with all 16 codon combinations for the ng3 sequence revealed that the change in translation initiation rate brought about by the change in nucleotide sequence was not the primary determinant for the change in expression level. The modified ng3-NEXT tag may be applied to increase the production yields of various recombinant proteins.

Spectrum and frequency of connexin 26 & connexin 30 gene mutations in patients with congenital hearing loss from Ladakh India

BackgroundCongenital hearing loss refers to prenatal hearing impairment, which is the commonly shared problem among sensory disorders that ranges from slight to profound. In this study, we screened the involvement of connexin 26 & connexin 30 gene in congenital hearing loss patients from the Kargil district of Ladakh, India by target gene sequencing. Materials and methodsThe peripheral blood sample of the patients was collected followed by DNA extraction and PCR of the target gene of interest. The amplified target gene was then sequenced and analysed for any changes in nucleotide sequence. ResultsIn this study, the connexin 26 & connexin 30 are the target gene that are associated with hearing loss and in this study, we found mutations in the connexin 26 gene and none of the mutations were found in the connexin 30 gene. The mutations found in the connexin 26 gene are “NM_004004:c.71G>A, “NM_004004:c.223C>T, “NM_004004:c230G>A, “NM_004004:c.380G>A, and “NM_004004:c.439G>A which change the amino acids to W24X, R75W, W77X, R127H, and E147K respectively and the frequency of the connexin 26 mutations in patients was 23% and the overall mutations in the cohort were 14.5%. This study found that “NM_004004:c.71G>A (W24X) nucleotide variant as common mutation. Both homozygous as well as heterozygous variants were found. R127H was the only mutation observed in control samples. A significant association was seen between connexin 26 gene mutations and familial history of congenital hearing loss and consanguinity with the p-value P<0.001. Conclusion and significanceAlthough the etiology has been found to be multifactorial. However, the role of any nucleotide variant in the gene of interest needs to be thoroughly investigated to study the genetic etiology of the anomalies. The results of this study showed a positive association between congenital hearing loss and the connexin 26 gene. However, we did not find any role of the connexin 30 gene in congenital hearing loss.

Adaptive evolution at mRNA editing sites in soft-bodied cephalopods.

BackgroundThe bulk of variability in mRNA sequence arises due to mutation—change in DNA sequence which is heritable if it occurs in the germline. However, variation in mRNA can also be achieved by post-transcriptional modification including mRNA editing, changes in mRNA nucleotide sequence that mimic the effect of mutations. Such modifications are not inherited directly; however, as the processes affecting them are encoded in the genome, they have a heritable component, and therefore can be shaped by selection. In soft-bodied cephalopods, adenine-to-inosine RNA editing is very frequent, and much of it occurs at nonsynonymous sites, affecting the sequence of the encoded protein.MethodsWe study selection regimes at coleoid A-to-I editing sites, estimate the prevalence of positive selection, and analyze interdependencies between the editing level and contextual characteristics of editing site.ResultsHere, we show that mRNA editing of individual nonsynonymous sites in cephalopods originates in evolution through substitutions at regions adjacent to these sites. As such substitutions mimic the effect of the substitution at the edited site itself, we hypothesize that they are favored by selection if the inosine is selectively advantageous to adenine at the edited position. Consistent with this hypothesis, we show that edited adenines are more frequently substituted with guanine, an informational analog of inosine, in the course of evolution than their unedited counterparts, and for heavily edited adenines, these transitions are favored by positive selection. Our study shows that coleoid editing sites may enhance adaptation, which, together with recent observations on Drosophila and human editing sites, points at a general role of RNA editing in the molecular evolution of metazoans.

Combined Influences of Genetic Factors and Attention Deficit Hyperactivity Disorder on the Development of Dependence on Synthetic Cannabinoids

Objectives. To create a complex model of the individual risk of developing dependence on synthetic cannabinoids taking account of the combined influences of genetic predisposition and attention deficit hypera-ctivity disorder (ADHD). Materials and methods. A total of 146 male adolescents consuming synthetic cannabinoids and 136 healthy subjects (controls) were observed. Genetic studies assessed cases with the combination of these dependencies with ADHD. DNA was collected and six polymorphic loci of genes of the dopaminergic and serotoninergic systems were determined; results were analyzed using a series of special statistical methods. Results and conclusions. These data demonstrate the important role of the dopaminergic and serotoninergic systems in the pathogenesis of dependence on psychoactive substances and the significance of changes in the nucleotide sequences of the DRD2, SLC6A3, and HTR2A genes in the development of dependence on synthetic cannabinoids in males with ADHD.

Enrichment in conservative amino acid changes among fixed and standing missense variations in slowly evolving proteins.

The process of molecular evolution has many elements that are not yet fully understood. Evolutionary rates are known to vary among protein coding and noncoding DNAs, and most of the observed changes in amino acid or nucleotide sequences are assumed to be non-adaptive by the neutral theory of molecular evolution. However, it remains unclear whether fixed and standing missense changes in slowly evolving proteins are more or less neutral compared to those in fast evolving genes. Here, based on the evolutionary rates as inferred from identity scores between orthologs in human and Rhesus Macaques (Macaca mulatta), we found that the fraction of conservative substitutions between species was significantly higher in their slowly evolving proteins. Similar results were obtained by using four different methods of scoring conservative substitutions, including three that remove the impact of substitution probability, where conservative changes require fewer mutations. We also examined the single nucleotide polymorphisms (SNPs) by using the 1000 Genomes Project data and found that missense SNPs in slowly evolving proteins also had a higher fraction of conservative changes, especially for common SNPs, consistent with more non-conservative substitutions and hence stronger natural selection for SNPs, particularly rare ones, in fast evolving proteins. These results suggest that fixed and standing missense variants in slowly evolving proteins are more likely to be neutral.

New Aspects of the Epigenetics of Pancreatic Carcinogenesis.

Pancreatic cancer remains among the deadliest forms of cancer with a 5 year survival rate less than 10%. With increasing numbers being observed, there is an urgent need to elucidate the pathogenesis of pancreatic cancer. While both contribute to disease progression, neither genetic nor environmental factors completely explain susceptibility or pathogenesis. Defining the links between genetic and environmental events represents an opportunity to understand the pathogenesis of pancreatic cancer. Epigenetics, the study of mitotically heritable changes in genome function without a change in nucleotide sequence, is an emerging field of research in pancreatic cancer. The main epigenetic mechanisms include DNA methylation, histone modifications and RNA interference, all of which are altered by changes to the environment. Epigenetic mechanisms are being investigated to clarify the underlying pathogenesis of pancreatic cancer including an increasing number of studies examining the role as possible diagnostic and prognostic biomarkers. These mechanisms also provide targets for promising new therapeutic approaches for this devastating malignancy.