Алгоритмы обработки сигналов флуоресценции массового параллельного секвенирования нуклеиновых кислот

Определение нуклеотидной последовательности ДНК или РНК, содержащих от нескольких сотен до сотен миллионов звеньев мономеров позволяет получить подробную информацию о геноме человека, животных и растений. Расшифровывать структуру нуклеиновых кислот научились достаточно давно, однако первоначально методы расшифровки были низко производительными, неэффективными и дорогими. Методы расшифровки нуклеотидной последовательности нуклеиновых кислот принято называть методами секвенирования. Приборы, предназначенные для реализации методов секвенирования, называются секвенаторами. Секвенирование нового поколения, массовое параллельное секвенирование — это родственные термины, описывающие технологию высокопроизводительного секвенирования ДНК, при котором весь человеческий геном можно секвенировать в течение одного-двух дней. Предыдущая технология, используемая для расшифровки генома человека, потребовала более десяти лет, чтобы получить окончательные результаты. В Институте аналитического приборостроения РАН разрабатывается аппаратно-программный комплекс для расшифровки последовательности нуклеиновых кислот патогенных микроорганизмов методом массового параллельного секвенирования. Программное обеспечение, входящее в состав аппаратно-программного комплекса играет существенную роль в решении задач расшифровки генома. Цель статьи — показать необходимость создания алгоритмов программного обеспечения аппаратно-программного комплекса для обработки сигналов, получающихся в процессе генетического анализа при решении задач расшифровки генома, а также продемонстрировать возможности этих алгоритмов. В работе рассмотрены основные проблемы обработки сигналов и методы их решения. В их числе: автоматическая и полуавтоматическая фокусировка, коррекция изображения фона реакционной ячейки, обнаружение изображений кластеров, оценка координат их положений, создание шаблонов кластеров молекул нуклеиновых кислот на поверхности реакционной ячейки, коррекция влияния интенсивностей соседних оптических каналов и оценка достоверности результатов генетического анализа

Алгоритмы обработки сигналов флуоресценции массового параллельного секвенирования нуклеиновых кислот

Determination of the nucleotide sequence of DNA or RNA containing from several hundred to hundreds of millions of monomers units allows to obtain detailed information about the genome of humans, animals and plants. The deciphering of nucleic acids’ structure was learned quite a long time ago, but initially the decoding methods were low-performing, inefficient and expensive. Methods for decoding nucleotide nucleic acid sequences are usually called sequencing methods. Instruments designed to implement sequencing methods are called sequencers. Sequencing new generation (SNP), mass parallel sequencing are related terms that describe the technology of high-performance DNA sequencing in which the entire human genome can be sequenced within a day or two. The previous technology used to decipher the human genome required more than ten years to get final results. A hardware-software complex (HSC) is being developed to decipher the nucleic acid sequence (NA) of pathogenic microorganisms using the method of NGS in the Institute for Analytical Instrumentation of the Russian Academy of Sciences. The software included in the HSC plays an essential role in solving genome deciphering problems. The purpose of this article is to show the need to create algorithms for the software of the HSC for processing signals obtained in the process of genetic analysis when solving genome deciphering problems, and also to demonstrate the capabilities of these algorithms. The paper discusses the main problems of signal processing and methods for solving them, including: automatic and semi-automatic focusing, background correction, detection of cluster images, estimation of the coordinates of their positions, creation of templates of clusters of NA molecules on the surface of the reaction cell, correction of influence neighboring optical channels for intensities of signals and the assessment of the reliability of the results of genetic analysisОпределение нуклеотидной последовательности ДНК или РНК, содержащих от нескольких сотен до сотен миллионов звеньев мономеров позволяет получить подробную информацию о геноме человека, животных и растений. Расшифровывать структуру нуклеиновых кислот научились достаточно давно, однако первоначально методы расшифровки были низко производительными, неэффективными и дорогими. Методы расшифровки нуклеотидной последовательности нуклеиновых кислот принято называть методами секвенирования. Приборы, предназначенные для реализации методов секвенирования, называются секвенаторами. Секвенирование нового поколения, массовое параллельное секвенирование — это родственные термины, описывающие технологию высокопроизводительного секвенирования ДНК, при котором весь человеческий геном можно секвенировать в течение одного-двух дней. Предыдущая технология, используемая для расшифровки генома человека, потребовала более десяти лет, чтобы получить окончательные результаты. В Институте аналитического приборостроения РАН разрабатывается аппаратно-программный комплекс для расшифровки последовательности нуклеиновых кислот патогенных микроорганизмов методом массового параллельного секвенирования. Программное обеспечение, входящее в состав аппаратно-программного комплекса играет существенную роль в решении задач расшифровки генома. Цель статьи — показать необходимость создания алгоритмов программного обеспечения аппаратно-программного комплекса для обработки сигналов, получающихся в процессе генетического анализа при решении задач расшифровки генома, а также продемонстрировать возможности этих алгоритмов. В работе рассмотрены основные проблемы обработки сигналов и методы их решения. В их числе: автоматическая и полуавтоматическая фокусировка, коррекция изображения фона реакционной ячейки, обнаружение изображений кластеров, оценка координат их положений, создание шаблонов кластеров молекул нуклеиновых кислот на поверхности реакционной ячейки, коррекция влияния интенсивностей соседних оптических каналов и оценка достоверности результатов генетического анализа

The role of interleukin-10 receptor alpha (IL10Rα) in Mycobacterium avium subsp. paratuberculosis infection of a mammary epithelial cell line

BackgroundJohne’s disease is a chronic wasting disease caused by the bacterium Mycobacterium avium subspecies paratuberculosis (MAP). Johne’s disease is highly contagious and MAP infection in dairy cattle can eventually lead to death. With no available treatment for Johne’s disease, genetic selection and improvements in management practices could help reduce its prevalence. In a previous study, the gene coding interleukin-10 receptor subunit alpha (IL10Rα) was associated with Johne’s disease in dairy cattle. Our objective was to determine how IL10Rα affects the pathogenesis of MAP by examining the effect of a live MAP challenge on a mammary epithelial cell line (MAC-T) that had IL10Rα knocked out using CRISPR/cas9. The wild type and the IL10Rα knockout MAC-T cell lines were exposed to live MAP bacteria for 72 h. Thereafter, mRNA was extracted from infected and uninfected cells. Differentially expressed genes were compared between the wild type and the IL10Rα knockout cell lines. Gene ontology was performed based on the differentially expressed genes to determine which biological pathways were involved.ResultsImmune system processes pathways were targeted to determine the effect of IL10Rα on the response to MAP infection. There was a difference in immune response between the wild type and IL10Rα knockout MAC-T cell lines, and less difference in immune response between infected and not infected IL10Rα knockout MAC-T cells, indicating IL10Rα plays an important role in the progression of MAP infection. Additionally, these comparisons allowed us to identify other genes involved in inflammation-mediated chemokine and cytokine signalling, interleukin signalling and toll-like receptor pathways.ConclusionsIdentifying differentially expressed genes in wild type and ILR10α knockout MAC-T cells infected with live MAP bacteria provided further evidence that IL10Rα contributes to mounting an immune response to MAP infection and allowed us to identify additional potential candidate genes involved in this process. We found there was a complex immune response during MAP infection that is controlled by many genes

An Examination of Bone Loss During Space Travel with Differential Gene Expression Analysis

Spaceflight poses many risks to human health due to the harsh conditions of microgravity, cosmic radiation, and confinement. One of the impacts that spaceflight entails is bone loss, which is a risk to astronauts as future space missions will require long travel durations. To elucidate the role of genetics in spaceflight bone loss, in this study differential gene expression analysis was performed using Nextflow-RCP, an adaptation of NASA Genelab’s RNA-Seq Consensus pipeline. The dataset for this project was GLDS-241, which contained samples from mice femoral skin. To gain a comprehensive understanding of the genes involved in bone loss, the results from the differential gene expression analysis were further analyzed using programs specifically for gene enrichment analysis. The findings demonstrated that there are many factors involved in bone loss under microgravity conditions. Altogether, the results from the gene enrichment analysis indicated a relationship between bone loss and glucose metabolism. However, additional studies on the mechanisms involved in bone loss are necessary to reduce bone loss in astronauts and assure their safe travel in space

The role of enrichment in decreasing diversity of mycobacteriophage genome databases

While there is great genetic diversity among phages, a large proportion of mycobacteriopphages fall into only a few clusters. Does the observed distribution of members in clusters actually reflect what is present in nature or does the enrichment procedure cause a skew in diversity? We hypothesize that the enrichment procedure promotes the replication of phages belonging to only a few clusters, thus decreasing the diversity of phages identified from a sample. Using nanopore sequencing to conduct a metagenomics analysis of soil samples, a decrease in the number of clusters present in enriched samples, compared to unenriched samples, was observed. The data supports the hypothesis and demonstrates that enrichment promotes the growth of only a select few clusters and subclusters, making it more likely to isolate phages of these clusters and subclusters. With the growing potential and prevalence of phage applications, it is important to expand our knowledge on their diversity. Conducting studies on phage diversity not only leads to a larger array of phages to use for applications, but also gives us more information on how phages interact with their environment

Additional file 1 of Estimating Phred scores of Illumina base calls by logistic regression and sparse modeling

Supplementary information about the elastic net model. This file contains the following sections: S1 - Introduction to the elastic net model and its advantages. S2 - Results of the elastic net mode include training time, coefficients, consistency and empirical discrimination power. Table S1 - The coefficients of 74 predicted features of the elastic net model. Figure S1 - The consistency of the elastic net model with three different training sets. Figure S2 - The empirical discrimination power of the elastic net model with three different training sets. (PDF 164 kb

Characterising heterogeneity in the T-cell acute lymphoblastic leukaemia jurkat cell line in the context of the TAL1 locus

T-cell acute lymphoblastic leukaemia (T-ALL) is the hyperproliferative transformation of T-cell lymphoid progenitor cells within the blood and bone marrow and is extremely heterogeneous. T-ALL has been linked to the overexpression of transcription factors, such as TAL1, that is specific within the late-cortical subtype of T-ALL. This project has utilised clonal cell line populations for testing phenotypic intra-tumoural heterogeneity seen within cancer cell lines, such as the Jurkat cell line, to generate clonal populations relative to the parental cell line they are derived from at passages 1, 5 and 9 as a cost-effective model. We tested the phenotype of proliferation using a carboxyfluorescein succinimidyl ester (CFSE) assay which identified Jurkat clonal populations as highly proliferative and displayed lower expression of the TAL1 gene, relative to the parental cell line using real-time PCR analysis. We also identified four differentially bound putative regulatory element sites using bioinformatics analysis of publicly available data. This analysis displayed a Jurkat-specific predicted intragenic regulatory element and intergenic enhancer regions that map to the known upstream TAL1 Jurkat super-enhancer as stated by Mansour et al. (2014). DNA methylation is known to fine-tune intragenic and intergenic enhancer-mediated transcription. Thus, we used a methylation-sensitive restriction endonuclease (MSRE) assay that provided insight of dynamic and stable DNA methylation patterns at the intragenic and intergenic sites across the TAL1 locus between Jurkat clonal populations, respectively, at passages 1 and 9. Finally, using MinION nanopore sequencing, we identified single-nucleotide variants common between Jurkat clonal populations tested at passages 1 and 9, which map to regulatory elements, SNPs in linkage disequilibrium across the TAL1 locus and sites of predicted transcription factor binding, therefore suggesting regulatory functionality of these SNVs in the context of the TAL1-mediated T-ALL

Engineering a feedback-based synthetic gene circuit for targeted continuous evolution of a gene in E. coli

Directed evolution is an invaluable technique for engineering proteins to possess desired physical and chemical properties when very little structural and functional information is known. It is divided into two sequential steps: generating a library of protein variants using mutagenic techniques; and applying a screening or selection strategy to scan the library for variants displaying desired properties. Library generation is performed using either in vitro or in vivo techniques, while screening or selection typically occurs in a suitable host cell. Currently, in vitro methods like error-prone PCR are popular for library generation. However, these techniques can be labour intensive, prone to mutation biases, and generate limited library sizes for screening. In vivo mutagenic techniques overcome these limitations by enabling simultaneous library generation and selection within cells. By generating random mutations in the gene-of-interest within one cell cycle, each cell in a batch culture potentially represents a library variant. Such a continuous evolution system can run for weeks with minimal human intervention, greatly expanding the genetic search space for protein engineering. The challenge lies in developing a mutator system that specifically generates mutations in the target gene, while maintaining the cell’s genomic fidelity. With this goal in mind, a mutator system was engineered in E. coli that introduces targeted cytidine deamination damage and subsequently performs error-prone DNA repair by hijacking the base excision repair pathway. The targeted damage occurs via activation induced cytidine deaminase fused to T7 RNA polymerase, while the error-prone DNA repair is performed by a three-protein fusion comprising a 5’-3’-exonuclease, an AP-endonuclease and an error-prone DNA polymerase. The mutagenic characteristics of this system was tested by knocking out GFP expression and analysing the mutant library using next generation sequencing techniques. The system was also experimentally shown to generate functionally active mutations that reverted inactivated β-lactamase gene variants to confer ampicillin resistance.Open Acces

Methodological approaches in the investigation of sex & gender in cardiovascular disease

Background: Differences exist in the presentation, pathophysiology, management, and outcomes of cardiovascular conditions in men and women. These differences may arise from sex-dependent factors such as chromosomal complement, regulation of sex hormones, and sex-specific factors like pregnancy. Beyond sex, gender, a multifaceted psychosocial concept, also has an impact on cardiovascular health and disease. Transgender individuals experience incongruence between the sex they were assigned at birth and their gender identity. These individuals may engage with gender-affirming hormone therapy (GAHT), such as oestrogen or testosterone, and the effects of such treatments upon cardiovascular health have yet to be determined, and may provide insight into cardiovascular pathophysiology. Aims: This thesis aims to enhance our understanding of the role of sex and gender in cardiovascular disease, including transgender cardiovascular health, through a range of methodological approaches. Methods: Chapter 3) A systematic review assessing the influence of GAHT upon the blood pressure of transgender individuals is undertaken; Chapter 4) The Gender and Sex Determinants of Cardiovascular Disease: From Bench to BeyondPremature Acute Coronary Syndrome (GENESIS-PRAXY) gender stratification questionnaire is adapted and applied to a UK sample of cisgender individuals (n=446) to construct a gender score via principal component analysis (PCA); Chapter 5) A bioinformatic analysis of sex and gender stratified differentially expressed microRNA (miRNAs) in human plasma of individuals (n=36), derived from the original GENESIS-PRAXY study, who have experienced acute coronary syndrome (ACS) is undertaken; Chapter 6) A descriptive analysis of the Vascular Effects of Sex Steroids in Transgender Adults (VESSEL) study, which utilises a range of vascular phenotyping procedures (e.g. flow-mediated dilatation, peripheral artery tonometry, and pulse wave analysis (PWA) and velocity (PWV)) in transgender individuals using long-term GAHT compared to cisgender individuals is presented. Results: Chapter 3) The systematic review identified 14 studies including 1,309 transgender individuals, which demonstrated broadly no change in blood pressure in transmasculine individuals using testosterone. Both increases and decreases were observed within the transfeminine population using oestrogen therapy. These studies were of limited quality due to their uncontrolled pre-post design, lack of intervention and blood pressure measurement standardisation, inadequate follow up and small sample sizes; Chapter 4) The gender stratification analysis demonstrated a continuum of gender scores in this population derived from five gender-related questionnaire instruments. Gender score distributions were distinct from the GENESIS-PRAXY analysis, highlighting that gender and its related factors are dynamic and context dependent; Chapter 5) miR-664a-5p, miR-36135p, miR-382-5p, miR-134-5p, miR-10b-5p, miR-885-5p, miR-206, and miR-32-5p were found to be differentially expressed in females versus males in ACS. Many of these miRNA and associated gene networks demonstrate a number of roles important to ACS pathophysiology including the regulation of vascular smooth muscle cell proliferation, endothelial injury and inflammation, atherosclerosis progression. miR-3605-5p and miR-4467 were differentially expressed in males with feminine versus masculine gender characteristics; Chapter 6) Due to the impact of coronavirus disease 2019 (COVID-19), the VESSEL study was discontinued prematurely, however, the feasibility of local recruitment of transgender participants is demonstrated. Discussion: This thesis expands our appreciation of the means by which gender can be measured and its potential influence, in addition to sex, upon epigenomic regulation in cardiovascular disease. Moreover, it improves our understanding of limitations and barriers in conducting research in transgender populations. Overall, this thesis provides valuable insight into the methodological approaches used the investigation of sex and gender in cardiovascular disease, which can be applied in future cardiovascular research in cisgender and transgender populations