scholarly journals Траектории кинков ДНК в последовательностях, содержащих кодирующие области генов

2017 ◽  
Vol 12 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Л.В. Якушевич ◽  
L.V. Yakushevich
Keyword(s):  
Gene Sequence ◽  
Initial Energy ◽  
Energy Profile ◽  
Coding Region ◽  
Quasi Particle ◽  
Coding Regions ◽  
Gene Coding ◽  
Initial Task ◽  
Convenient Approach ◽  
Open States

Coding regions (CDS) being an integral part of any gene sequence, play an important role in the process of transcription. One of the tasks associated with the CDS regions, consists in the modeling of the passage of transcription bubbles named also open states or DNA kinks through the coding regions. In this paper, we present a simple and convenient approach to the modeling of the passage. It includes the calculation of the energy profile of the sequence and reducing the initial task to the modeling of the movement of a quasi particle in the field with this energy profile. To illustrate the method, we present the results of the calculations of the trajectories of the DNA kinks moving in the sequence of gene coding interferon alpha 17 (IFNA17) that consists of the three regions: the coding region and the two regions with unknown functional properties. To analyze the kink dynamics, we apply approximation where the DNA parameters are being averaged separately over each of the three regions. In the absences of dissipation, the total kink energy is constant. At the same time the kink velocity is constant only inside each of the regions. In the presence of dissipation, the total kink energy decreases. It is shown that the greater the total initial energy of the kink, the faster the energy decrease. It is suggested that the proposed approach could be useful in finding the ways to govern the movement of transcription bubbles at the first stage of the process of transcription.

scholarly journals Analysis of the BRCA1 gene coding regions in patients with luminal B breast cancer

2020 ◽  
pp. 22-23
Author(s):  
А.М. Певзнер ◽  
М.К. Ибрагимова ◽  
М.М. Цыганов
Keyword(s):  
Breast Cancer ◽  
Tumor Tissue ◽  
Brca1 Gene ◽  
Germline Mutations ◽  
Coding Region ◽  
Luminal B ◽  
Coding Regions ◽  
Disease Prognosis ◽  
Gene Coding ◽  
Low Expression

Наши предыдущие исследования показали, что дефицит гена BRCA1, вызванный изменениями в опухоли, такими как низкая экспрессия, делеция, потеря гетерозиготности, может быть связан с эффективностью химиотерапии и прогнозом заболевания. Однако даже при отсутствии этих факторов эффективность терапии таксотером была переменной. Это может быть связано с наличием других соматических изменениий гена BRCA1 в опухолевой ткани, и их определение поможет определить индивидуальную стратегию лечения для каждого пациента с раком молочной железы. Здесь мы исследовали весь спектр герминальных и соматических мутаций кодирующей области генов BRCA1/2 в опухолевой ткани. В целом, наши результаты показывают, что имеет смысл принимать во внимание не только выявленные герминальные мутации, но и соматические изменения в генах BRCA1/2 при назначении терапии. Our previous studies have shown that BRCA1 gene deficiency caused by changes in the tumor such as low expression, deletion, loss of heterozygosity, etc., can be associated with the effectiveness of chemotherapy and the disease prognosis. However, even in the absence of these factors, the effectiveness of taxotere therapy was variable. This may be due to the availability of another BRCA1 gene somatic changes in the tumor tissue and their determination will help to define the personalize treatment strategy for each breast cancer patient. Here we investigated the entire spectrum germline and somatic mutation of coding region of the BRCA1/2 gene in tumor tissue. Overall, our results suggest that it makes sense to take into account not only identified germline mutations, but also somatic changes in the BRCA1/2 gene when appointment taxotere

scholarly journals A First-Stage Approximation to Identify New Imprinted Genes through Sequence Analysis of Its Coding Regions

2009 ◽  
Vol 2009 ◽  
pp. 1-7 ◽  
Author(s):  
Elias Daura-Oller ◽  
Maria Cabré ◽  
Miguel A. Montero ◽  
José L. Paternáin ◽  
Antoni Romeu
Keyword(s):  
Tandem Repeats ◽  
Cpg Islands ◽  
Imprinted Genes ◽  
Coding Region ◽  
Training Set ◽  
Principle Components Analysis ◽  
Coding Regions ◽  
Gene Coding ◽  
Components Analysis ◽  
Simple Repeats

In the present study, a positive training set of 30 known human imprinted gene coding regions are compared with a set of 72 randomly sampled human nonimprinted gene coding regions (negative training set) to identify genomic features common to human imprinted genes. The most important feature of the present work is its ability to use multivariate analysis to look at variation, at coding region DNA level, among imprinted and non-imprinted genes. There is a force affecting genomic parameters that appears through the use of the appropriate multivariate methods (principle components analysis (PCA) and quadratic discriminant analysis (QDA) to analyse quantitative genomic data. We show that variables, such as CG content, [bp]% CpG islands, [bp]% Large Tandem Repeats, and [bp]% Simple Repeats, are able to distinguish coding regions of human imprinted genes.

scholarly journals Identification of NURR1 (Exon 4) and FOXA1 (Exon 3) Haplotypes Associated with mRNA Expression Levels in Peripheral Blood Lymphocytes of Parkinson’s Patients in Small Indian Population

2017 ◽  
Vol 2017 ◽  
pp. 1-8 ◽  
Author(s):  
Jayakrishna Tippabathani ◽  
Jayshree Nellore ◽  
Vaishnavie Radhakrishnan ◽  
Somashree Banik ◽  
Sonia Kapoor
Keyword(s):  
Mrna Expression ◽  
Peripheral Blood ◽  
Peripheral Blood Lymphocytes ◽  
Coding Region ◽  
Male And Female ◽  
Blood Lymphocytes ◽  
Coding Regions ◽  
Significant Difference ◽  
Exon 4 ◽  
Foxa1 Expression

Here, we study the expression of NURR1 and FOXA1 mRNA in peripheral blood lymphocytes and its haplotypes in coding region in a small Chennai population of India. Thirty cases of Parkinson’s patients (PD) with anti-PD medications (20 males aged65.85±1.19and 10 females aged65.7±1.202) and 30 age matched healthy people (20 males aged68.45±1.282and 10 females aged65.8±1.133) were included. The expression of NURR1 and FOXA1 in PBL was detected by Q-PCR and haplotypes were identified by PCR-SSCP. In the 30 PD cases examined, NURR1 and FOXA1 expression was significantly reduced in both male and female PD patients. However, NURR1 (57.631% reduced in males; 28.93% in females) and FOXA1 (64.42% in males; 55.76% in females) mRNA expression did differ greatly between male and female PD patients. Polymorphisms were identified at exon 4 of the NURR1 and at exon 3 of the FOXA1, respectively, in both male and female patients. A near significant difference in SSCP patterns between genders of control and PD population was analyzed suggesting that further investigations of more patients, more molecular markers, and coding regions should be performed. Such studies could potentially reveal peripheral molecular marker of early PD and different significance to the respective genders.

Structure and expression of canary myc family genes

1991 ◽  
Vol 11 (3) ◽  
pp. 1770-1776
Author(s):  
R G Collum ◽  
D F Clayton ◽  
F W Alt
Keyword(s):  
Untranslated Region ◽  
Untranslated Regions ◽  
Coding Region ◽  
Protein Coding ◽  
Coding Regions ◽  
Neuronal Precursors ◽  
Myc Gene ◽  
Mature Neurons

We found that the canary N-myc gene is highly related to mammalian N-myc genes in both the protein-coding region and the long 3' untranslated region. Examined coding regions of the canary c-myc gene were also highly related to their mammalian counterparts, but in contrast to N-myc, the canary and mammalian c-myc genes were quite divergent in their 3' untranslated regions. We readily detected N-myc and c-myc expression in the adult canary brain and found N-myc expression both at sites of proliferating neuronal precursors and in mature neurons.

scholarly journals In silico analyses of CD14 molecule reveals significant evolutionary diversity potentially associated with speciation and variable immune response in mammals

2019 ◽  
Author(s):  
Olanrewaju B Morenikeji ◽  
Bolaji N Thomas
Keyword(s):  
Immune Response ◽  
Complex Disease ◽  
Mammalian Species ◽  
Coding Region ◽  
Protein Protein Interaction ◽  
Species Response ◽  
Gene Coding ◽  
Protein Interactome ◽  
Mutational Hotspots ◽  
Leucine Rich Repeats

Cluster differentiation gene (CD14) is a family of monocyte differentiating genes that works in conjunction with lipopolysaccharide binding protein (LBP), forming a complex with TLR4 or LY96 to mediate innate immune response to pathogens. In this paper, we used different computational methods to elucidate the evolution of CD14 gene coding region in 14 mammalian species. Our analyses identified leucine rich repeats (LRRs) as the only significant domain across the CD14 protein of the 14 species, presenting with frequencies ranging from 1-4. Importantly, we found signal peptides located at mutational hotspots demonstrating this gene is conserved across these species. Out of the 10 selected variants analyzed in this study, only 6 were predicted to possess significant deleterious effect. Our predicted protein interactome showed a significant varying protein-protein interaction with CD14 protein across the species. This may be important for drug target and therapeutic manipulation for the treatment of many diseases. We conclude that these results contribute to our understanding of the CD14 molecular evolution, which underlays varying species response to complex disease traits.

scholarly journals Identification of the Colletotrichum species associated with mango diseases and a universal LAMP detection method for C. gloeosporioides species complex

2021 ◽  
pp. 49-60
Author(s):  
Yukako Hattori ◽  
Chiharu Nakashima ◽  
Shunsuke Kitabata ◽  
Kosuke Naito ◽  
Ayaka Hieno ◽  
...  
Keyword(s):  
Species Complex ◽  
Plant Disease ◽  
Plant Pathogens ◽  
Colletotrichum Gloeosporioides ◽  
Detection Method ◽  
Coding Region ◽  
Gene Coding ◽  
Detectable Range ◽  
Amplification Assay ◽  
Colletotrichum Gloeosporioides Species Complex

Abstract: The Colletotrichum gloeosporioides species complex contains plant pathogens linked to Anthracnose diseases afflicting various crops. In this study, we designed a loop-mediated isothermal amplification assay (LAMP) primer set based on calmodulin gene coding region sequences from taxonomically authorized isolates of species from this complex to rapidly detect the presence of fungi associated with Anthracnose diseases. This test can be employed at any point between cultivation and sale. Moreover, we examined the specificity and detectable range of this primer set using isolates selected from species of the genus Colletotrichum. This test was able to specifically detect members of the C. gloeosporioides species complex, including C. gloeosporioides, C. aotearoa, C. fructicola, C. horii, C. kahawae, C. musae, C. siamense, C. theobromicola, and C. tropicale. Key Words: Anthracnose, diagnosis, phylogeny, plant disease

scholarly journals Genome-wide variations of SARS-CoV-2 infer evolution relationship and transmission route

2020 ◽  
Author(s):  
Lehai Zhang ◽  
Shifu Wang ◽  
Qian Ren ◽  
Junjie Yang ◽  
Yanqin Lu ◽  
...  
Keyword(s):  
Molecular Detection ◽  
Detection Efficiency ◽  
Evolutionary Relationship ◽  
Clinical Manifestations ◽  
Coding Region ◽  
Gene Coding ◽  
Genome Wide ◽  
Group A ◽  
Group B ◽  
Relationship Of

AbstractIn the epidemic evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the issues of mutation, origin, typing and the effect of mutation on molecular detection remain to be unrevealed. In order to identify the evolutionary relationship of SARS-CoV-2 and evaluate the detection efficiency of primers that are currently used in different countries, we retrieved genomic sequences of 373 SARS-CoV-2 strains from multiple databases and performed genome-wide variation analysis. According to the nucleotide C28144T variation, the SARS-CoV-2 can be divided into group A (117 strains) and group B (256 strains). The spike protein gene (S gene) coding region 1841 (total 23403) A1841G, formed a B1 subgroup (40 strains) in group B, of which 30 strains were from European and American countries in March (especially Washington, USA). These mutations are likely to be influenced by the environment or the immunization selection pressure of different populations. Although the mutation is not in the receptor binding region (RBD) and alkaline cleavage region, it may also affect the ability of transmission and pathogenicity; however, the significance is not yet clear. As the ratio of A / B strains in the epidemic months showed an increasing trend (0.35: 1 in January, 0.62: 1 in February and 0.76: 1 in March), it seems that the transmissibility of group A strains becomes stronger with time. Based on the variation of 11 nucleotide sites during the epidemic process, it is speculated that the Washington strain is more like an ancestor type, and the Wuhan strain is the offspring of the group A virus strain. By comparing the detection capabilities of primers in different countries, the SARS-CoV-2 nucleotide variation may only affect molecular detection of very few strains. The differences in the transmissibility, pathogenicity and clinical manifestations of different types of strains require further investigations.

scholarly journals Distinct expression of select and transcriptome-wide isolated 3’UTRs suggests critical roles in development and transition states

2020 ◽  
Author(s):  
Shaoyi Ji ◽  
Ze Yang ◽  
Leonardi Gozali ◽  
Thomas Kenney ◽  
Arif Kocabas ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Gene Regulation ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Specific Gene ◽  
Coding Region ◽  
Proliferating Cells ◽  
Coding Regions ◽  
Micro Rnas

AbstractMature mRNA molecules are typically considered to be comprised of a 5’UTR, a 3’UTR and a coding region (CDS), all attached until degradation. Unexpectedly, however, there have been multiple recent reports of widespread differential expression of mRNA 3’UTRs and their cognate coding regions, resulting in the expression of isolated 3’UTRs (i3’UTRs); these i3’UTRs can be highly expressed, often in reciprocal patterns to their cognate CDS. Similar to the role of other lncRNAs, isolated 3’UTRs are likely to play an important role in gene regulation but little is known about the contexts in which they are deployed. To begin to parse the functions of i3’UTRs, here we carry out in vitro, in vivo and in silico analyses of differential 3’UTR/CDS mRNA ratio usage across tissues, development and cell state changes both for a select list of developmentally important genes as well as through unbiased transcriptome-wide analyses. Across two developmental paradigms we find a distinct switch from high i3’UTR expression of stem cell related genes in proliferating cells compared to newly differentiated cells. Our unbiased transcriptome analysis across multiple gene sets shows that regardless of tissue, genes with high 3’UTR to CDS ratios belong predominantly to gene ontology categories related to cell-type specific functions while in contrast, the gene ontology categories of genes with low 3’UTR to CDS ratios are similar and relate to common cellular functions. In addition to these specific findings our data provide critical information from which detailed hypotheses for individual i3’UTRs can be tested-with a common theme that i3’UTRs appear poised to regulate cell-specific gene expression and state.Significance StatementThe widespread existence and expression of mRNA 3’ untranslated sequences in the absence of their cognate coding regions (called isolated 3’UTRs or i3’UTRs) opens up considerable avenues for gene regulation not previously envisioned. Each isolated 3’UTR may still bind and interact with micro RNAs, RNA binding proteins as well as other nucleic acid sequences, all in the absence or low levels of cognate protein production. Here we document the expression, localization and regulation of i3’UTRs both within particular biological systems as well as across the transcriptome. As this is an entirely new area of experimental investigation these early studies are seminal to this burgeoning field.

scholarly journals Rapid and efficient generation of PCR-derived riboprobe templates for in situ hybridization histochemistry.

1993 ◽  
Vol 41 (5) ◽  
pp. 773-776 ◽  
Author(s):  
J H Sitzmann ◽  
P K LeMotte
Keyword(s):  
In Situ Hybridization ◽  
Coding Region ◽  
Biopsy Material ◽  
Hybridization Histochemistry ◽  
In Situ Hybridization Histochemistry ◽  
Gene Coding ◽  
Suprabasal Cell ◽  
Cell Layers ◽  
Negative Controls

In situ hybridization histochemistry (ISH) using cRNA probes (riboprobes) has become a powerful technique for the examination of gene expression in tissue sections. The construction of plasmid templates for the synthesis of riboprobes with phage RNA polymerases is often a difficult and time-consuming step. We have therefore developed a rapid, efficient, and flexible method to generate totally artificial riboprobe templates by the polymerase chain reaction (PCR). We have made riboprobe templates using self-priming oligonucleotide primers spanning 146 BP of the 3' end of the human cytokeratin 1 (K1) gene coding region flanked by T7 and T3 promoters. These PCR-derived riboprobe templates were used to synthesize 35S-labeled anti-sense riboprobes as well as sense riboprobes as negative controls. The riboprobes were then applied in ISH to human skin sections made from routinely fixed and paraffin-embedded clinical biopsy material. Consistent with published results, we observed strong expression of K1 mRNA in the suprabasal cell layers of the epidermis but only weak to undetectable signals in the basal and cornified cell layers and in the dermis. With this experimental procedure we see no decrease in probe efficiency or quality compared to conventional methods. The use of PCR-derived riboprobe templates for ISH makes it possible to detect expression of any desired gene of known sequence rapidly and efficiently.

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