scholarly journals Identification of mRNA degradome variation dependent on divergent muscle mass in different pig breeds

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Katarzyna L. Piórkowska ◽  
Tomasz Szmatoła ◽  
Klaudia Pawlina-Tyszko ◽  
Artur Gurgul ◽  
Grzegorz Żak ◽  
...  

AbstractThe search for the molecular processes associated with the development and metabolism of skeletal muscles is still actual. Selection conducted in farm animals is focused on high muscle mass because it delivers higher economic profit. The present study aimed to shed light on mRNA degradome signals that could be characteristic for molecular processes associated with an abundance of muscle mass and to identify miRNA regulatory networks controlling these processes in pigs applying next-generation-sequencing (NGS). In the study, over 10,000 degraded transcripts were identified per sample, with the highest abundance for genes encoding mitochondrial proteins (COXs, NDs, CYTB, ATP6 and ATP8). Moreover, only 26% of the miRNA targets were found whithin this degraded transcript pool, which suggested for miRNAs other molecular mechanism at different level of gene expression than mRNA degradation.On the other hand, a small share of the identified degraded transcripts associated with miRNA regulation suggests a different mechanism of mRNA degradation for identified degraded transcropts. Subsequently, most of the miRNA gene degraded targets, such as ENO3, CKM, CRYAB and ADAM19 encode proteins involved in the mascle mass control. The present study showed an interesting dependence between miRNAs and their targets. Nevertheless, the complete view of the miRNA regulatory network could be a subject of further advanced research, which would employ a miRNA transfection procedure in skeletal muscle cell cultures.

Author(s):  
Н.Н. Чакова ◽  
С.С. Ниязова ◽  
С.М. Комиссарова ◽  
Л.И. Плащинская ◽  
А.А. Савченко ◽  
...  

Методом высокопроизводительного секвенирования у пациентов с синдромом Бругада проведен поиск мутаций в генах, ассоциированных с наследственными аритмиями. Половина нуклеотидных замен локализована в генах, кодирующих белки натриевых и калиевых ионных каналов (SCN5A, KCNJ2, KCNJ8, HCN4, KCNQ1). Выявлены мутации в генах, ассоциированных преимущественно с другими каналопатиями и аритмогенными кардиомиопатиями. Mutation detection in the coding sequences of genes associated with inherited arrhythmias was performed by next generation sequencing (NGS) in patients with Brugada syndrome. Half of the mutations are located in the genes encoding the sodium and potassium ion channel proteins (SCN5A, KCNJ2, KCNJ8, HCN4, KCNQ1). In the genes associated predominantly with other canalopathies and arrhythmogenic cardiomyopathies the mutations were found.


Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 750
Author(s):  
Jutta Kasurinen ◽  
Cindy M. Spruit ◽  
Anu Wicklund ◽  
Maria I. Pajunen ◽  
Mikael Skurnik

Bacteriophage vB_EcoM_fHy-Eco03 (fHy-Eco03 for short) was isolated from a sewage sample based on its ability to infect an Escherichia coli clinical blood culture isolate. Altogether, 32 genes encoding hypothetical proteins of unknown function (HPUFs) were identified from the genomic sequence of fHy-Eco03. The HPUFs were screened for toxic properties (toxHPUFs) with a novel, Next Generation Sequencing (NGS)-based approach. This approach identifies toxHPUF-encoding genes through comparison of gene-specific read coverages in DNA from pooled ligation mixtures before electroporation and pooled transformants after electroporation. The performance and reliability of the NGS screening assay was compared with a plating efficiency-based method, and both methods identified the fHy-Eco03 gene g05 product as toxic. While the outcomes of the two screenings were highly similar, the NGS screening assay outperformed the plating efficiency assay in both reliability and efficiency. The NGS screening assay can be used as a high throughput method in the search for new phage-inspired antimicrobial molecules.


Author(s):  
Н.Н. Чакова ◽  
С.М. Комиссарова ◽  
С.С. Ниязова ◽  
Т.В. Долматович ◽  
Е.С. Ребеко

Синдром удлиненного интервала QT (LQTS) представляет собой генетически детерминированное заболевание, характеризующееся удлинением интервала QT на электрокардиограмме, высоким риском жизнеугрожающих аритмий и внезапной сердечной смерти. Причиной данного синдрома являются мутации в генах, кодирующих белки ионных каналов, а также протеины, опосредованно связанные с ионными каналами. От 4,5 до 8% пациентов с LQTS имеют более одной мутации в генах, связанных с развитием каналопатий. Цель работы: описание двух клинических случаев пациентов с жизнеугрожающими аритмиями, у которых выявлено сочетание редких мутантных аллелей в генах, ассоциированных с LQTS. Клиническое обследование включало ЭКГ в 12 отведениях, ЭхоКГ, МРТ сердца с отсроченным контрастированием и суточное мониторирование ЭКГ (СМ ЭКГ). Генетическое тестирование выполнено методом высокопроизводительного секвенирования (NGS) с использованием набора реагентов «TruSight™ Cardio Sequencing Panel» (Illumina). Оба пациента без отягощенного семейного анамнеза имели злокачественные желудочковые тахиаритмии, которые потребовали имплантации кардиовертера-дефибриллятора. В результате проведенного генотипирования методом NGS у пациента с идиопатической желудочковой тахикардией выявлено сочетание замен в генах ANK2 (c.9161C>G, p.Ala3054Gly, rs139007578) и KCNE1 (c.253G>A, p.Asp85Asn, rs1805128). У пациента с идиопатической фибрилляцией желудочков обнаружен аллельный вариант также в гене ANK2 (c.1397C>T, p.Thr466Met, rs786205722) и дополнительная замена в гене SNTA1 (c.787G>T, (p.Ala263Ser), rs150576530). При наличии у пациентов нескольких генетических дефектов может наблюдаться «кумулятивный эффект» мутаций, фенотипически проявляющийся тяжелым течением заболевания с неблагоприятными исходами. Показано, что при генотипировании пациентов с идиопатическими жизнеугрожающими тахиаритмиями использование панелей с большим количеством генов, ассоциированных с сердечно-сосудистой патологией, является вполне оправданным. Комплексное исследование генов позволяет увеличить диагностическую и прогностическую ценность генетического скрининга. Long QT syndrome (LQTS) is the genetically determined disease characterized by the QT interval elongation at the electrocardiogram, a high risk of life-threatening arrhythmias and sudden cardiac death. This syndrome is determined by mutations in genes encoding ion channel proteins, as well as proteins indirectly associated with ion channels. 4.5-8% of patients with LQTS have more than one mutation in the genes associated with the development of channelopathies. Purpose of work: description of two clinical cases of patients with life-threatening arrhythmia in which a combination of rare mutant alleles in the genes associated with LQTS was detected. The clinical examination included 12-lead ECG, echocardiography, cardiac MRI with delayed contrast, and 24-hour ECG monitoring (SM ECG). Genetic testing was performed by next generation sequencing (NGS) using the TruSight ™ Cardio Sequencing Panel reagent kit (Illumina). Both patients with no burdened family history had malignant ventricular tachyarrhythmias, which required the implantation of a cardioverter defibrillator. The NGS method allowed to detect a combination of substitutions in the genes ANK2 (c.9161C>G, p.Ala3054Gly, rs139007578) and KCNE1 (c.253G>A, p.Asp85Asn, rs1805128) in a patient with idiopathic ventricular tachycardia. In the patient with idiopathic ventricular fibrillation, the allelic variant was also found in the gene ANK2 (c.1397C>T, p.Thr466Met, rs786205722) and an additional substitution in the gene SNTA1 (c.1877>T, (p.Ala263Ser), rs150576530). If patients have several genetic defects, a “cumulative effect” of mutations can be observed, phenotypically manifested by a severe course of the disease with unfavorable outcomes. It has been shown that when genotyping patients with idiopathic life-threatening tachyarrhythmias, the use of panels with a large number of genes associated with cardiovascular pathology is quite justified. A comprehensive study of genes can increase the diagnostic and prognostic value of genetic screening.


Author(s):  
Altuğ Koç ◽  
Elçin Bora ◽  
Tayfun Cinleti ◽  
Gizem Yıldız ◽  
Meral Torun Bayram ◽  
...  

2020 ◽  
Vol 16 ◽  
Author(s):  
Pelin Telkoparan-Akillilar ◽  
Dilek Cevik

Background: Numerous sequencing techniques have been progressed since the 1960s with the rapid development of molecular biology studies focusing on DNA and RNA. Methods: a great number of articles, book chapters, websites are reviewed, and the studies covering NGS history, technology and applications to cancer therapy are included in the present article. Results: High throughput next-generation sequencing (NGS) technologies offer many advantages over classical Sanger sequencing with decreasing cost per base and increasing sequencing efficiency. NGS technologies are combined with bioinformatics software to sequence genomes to be used in diagnostics, transcriptomics, epidemiologic and clinical trials in biomedical sciences. The NGS technology has also been successfully used in drug discovery for the treatment of different cancer types. Conclusion: This review focuses on current and potential applications of NGS in various stages of drug discovery process, from target identification through to personalized medicine.


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