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1.
Transcriptomics: A powerful tool to evaluate the behavior of foodborne pathogens in the food production chain.
Lamas, A, Regal, P, Vázquez, B, Miranda, JM, Franco, CM, Cepeda, A
Food research international (Ottawa, Ont.). 2019;:108543
Abstract
In recent years, the development of high-throughput transcriptomic tools such as RNA-seq and microarrays have revolutionized biological scientific research. Despite these techniques being widely used in biomedical research, their introduction into the field of food microbiology is still limited. However, transcriptomic research is of great importance to fully understand the resistance mechanisms and metabolic pathways involved in foodborne pathogen survival from farm to fork. Throughout this review, the main transcriptomic techniques available are described and discussed. Then, the main studies where transcriptomics were used to evaluate survival of foodborne pathogens in the different conditions of the food production chain are evaluated. Particularly, studies focused on biofilm formation, the food matrix and its environment, heat treatments, acid resistance, biocides, and food preservatives were specially reviewed. The data obtained from these studies are of great importance to develop new control strategies in any point of the food production chain.
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2.
Application of Computational Biology to Decode Brain Transcriptomes.
Li, J, Wang, GZ
Genomics, proteomics & bioinformatics. 2019;(4):367-380
Abstract
The rapid development of high-throughput sequencing technologies has generated massive valuable brain transcriptome atlases, providing great opportunities for systematically investigating gene expression characteristics across various brain regions throughout a series of developmental stages. Recent studies have revealed that the transcriptional architecture is the key to interpreting the molecular mechanisms of brain complexity. However, our knowledge of brain transcriptional characteristics remains very limited. With the immense efforts to generate high-quality brain transcriptome atlases, new computational approaches to analyze these high-dimensional multivariate data are greatly needed. In this review, we summarize some public resources for brain transcriptome atlases and discuss the general computational pipelines that are commonly used in this field, which would aid in making new discoveries in brain development and disorders.
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3.
MicroRNAs and response to therapy in leukemia.
Sharifi, H, Jafari Najaf Abadi, MH, Razi, E, Mousavi, N, Morovati, H, Sarvizadeh, M, Taghizadeh, M
Journal of cellular biochemistry. 2019;(9):14233-14246
Abstract
A variety of epigenetic factors involved in leukemia pathogenesis. Among various epigenetic factors, microRNAs (miRNAs) have emerged as important players, which affect a sequence of cellular and molecular signaling pathways. Leukemia is known as progressive cancer, which is related to many health problems in the world. It has been shown that the destruction of the blood-forming organs could lead to abnormal effects on the proliferation and development of leukocytes and their precursors. Despite many attempts for approved effective and powerful therapies for patients with leukemia, finding and developing new therapeutic approaches are required. One of the important aspects of leukemia therapy, identification of underlying cellular and molecular mechanisms involved in the pathogenesis of leukemia. Several miRNAs (ie, miR-103, miR-101, mit-7, let-7i, miR-424, miR-27a, and miR-29c) and play major roles in response to therapy in patients with leukemia. miRNAs exert their effects by targeting a variety of targets, which are associated with response to therapy in patients with leukemia. It seems that more understanding about the roles of miRNAs in response to therapy in patients with leukemia could contribute to better treatment of patients with leukemia. Here, for the first time, we summarized various miRNAs, which are involved in response to therapy in the treatment patients with leukemia.
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4.
Experimental design for single-cell RNA sequencing.
Baran-Gale, J, Chandra, T, Kirschner, K
Briefings in functional genomics. 2018;(4):233-239
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Abstract
Single-cell RNA sequencing (scRNA-seq) has opened new avenues for the characterization of heterogeneity in a large variety of cellular systems. As this is a relatively new technique, the field is fast evolving. Here, we discuss general considerations in experimental design and the two most popular approaches, plate-based Smart-Seq2 and microdroplet-based scRNA-seq at the example of 10x Chromium. We discuss advantages and disadvantages of both methods and point out major factors to consider in designing successful experiments.
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5.
Comparative Genomics and Transcriptome Profiling in Primary Aldosteronism.
Aristizabal Prada, ET, Castellano, I, Sušnik, E, Yang, Y, Meyer, LS, Tetti, M, Beuschlein, F, Reincke, M, Williams, TA
International journal of molecular sciences. 2018;(4)
Abstract
Primary aldosteronism is the most common form of endocrine hypertension with a prevalence of 6% in the general population with hypertension. The genetic basis of the four familial forms of primary aldosteronism (familial hyperaldosteronism FH types I-IV) and the majority of sporadic unilateral aldosterone-producing adenomas has now been resolved. Familial forms of hyperaldosteronism are, however, rare. The sporadic forms of the disease prevail and these are usually caused by either a unilateral aldosterone-producing adenoma or bilateral adrenal hyperplasia. Aldosterone-producing adenomas frequently carry a causative somatic mutation in either of a number of genes with the KCNJ5 gene, encoding an inwardly rectifying potassium channel, a recurrent target harboring mutations at a prevalence of more than 40% worldwide. Other than genetic variations, gene expression profiling of aldosterone-producing adenomas has shed light on the genes and intracellular signalling pathways that may play a role in the pathogenesis and pathophysiology of these tumors.
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6.
Renaissance in phytomedicines: promising implications of NGS technologies.
Sharma, S, Shrivastava, N
Planta. 2016;(1):19-38
Abstract
Medicinal plant research is growing significantly in faith to discover new and more biologically compatible phytomedicines. Deposition of huge genome/trancriptome sequence data assisted by NGS technologies has revealed the new possibilities for producing upgraded bioactive molecules in medicinal plants. Growing interest of investors and consumers in the herbal drugs raises the need for extensive research to open the facts and details of every inch of life canvas of medicinal plants to produce improved quality of phytomedicines. As in agriculture crops, knowledge emergence from medicinal plant's genome/transcriptome, can be used to assure their amended quality and these improved varieties are then transported to the fields for cultivation. Genome studies generate huge sequence data which can be exploited further for obtaining information regarding genes/gene clusters involved in biosynthesis as well as regulation. This can be achieved rapidly at a very large scale with NGS platforms. Identification of new RNA molecules has become possible, which can lead to the discovery of novel compounds. Sequence information can be combined with advanced phytochemical and bioinformatics tools to discover functional herbal drugs. Qualitative and quantitative analysis of small RNA species put a light on the regulatory aspect of biosynthetic pathways for phytomedicines. Inter or intra genomic as well as transcriptomic interactive processes for biosynthetic pathways can be elucidated in depth. Quality management of herbal material will also become rapid and high throughput. Enrichment of sequence information will be used to engineer the plants to get more efficient phytopharmaceuticals. The present review comprises of role of NGS technologies to boost genomic studies of pharmaceutically important plants and further, applications of sequence information aiming to produce enriched phytomedicines. Emerging knowledge from the medicinal plants genome/transcriptome can give birth to deep understanding of the processes responsible for biosynthesis of medicinally important compounds.
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7.
Microarray: gateway to unravel the mystery of abiotic stresses in plants.
Gul, A, Ahad, A, Akhtar, S, Ahmad, Z, Rashid, B, Husnain, T
Biotechnology letters. 2016;(4):527-43
Abstract
Environmental factors, such as drought, salinity, extreme temperature, ozone poisoning, metal toxicity etc., significantly affect crops. To study these factors and to design a possible remedy, biological experimental data concerning these crops requires the quantification of gene expression and comparative analyses at high throughput level. Development of microarrays is the platform to study the differential expression profiling of the targeted genes. This technology can be applied to gene expression studies, ranging from individual genes to whole genome level. It is now possible to perform the quantification of the differential expression of genes on a glass slide in a single experiment. This review documents recently published reports on the use of microarrays for the identification of genes in different plant species playing their role in different cellular networks under abiotic stresses. The regulation pattern of differentially-expressed genes, individually or in group form, may help us to study different pathways and functions at the cellular and molecular level. These studies can provide us with a lot of useful information to unravel the mystery of abiotic stresses in important crop plants.
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8.
[Functional annotation of rice WRKY transcription factors based on their transcriptional features].
Li, LY, Shi, JN, Yang, S, Sun, CQ, Liu, GZ
Yi chuan = Hereditas. 2016;(2):126-36
Abstract
Transcription factors regulate alteration of transcription levels. Recently, huge amount of transcriptomic data are accumulated via the application of high throughput sequencing technology, and it is reasonable to postulate that in-depth analysis of transcription data could be used to enhance gene annotation. In this study, we chose the gene family of rice WRKY transcription factors. Based on literature search, the transcriptional data under different biological processes, including biotic and abiotic stress, development, and nutrient absorption and hormone treatments were analyzed systematically. To the end, we summarize the list of differentially expressed WRKY genes. We also expect that such information will enrich their functional annotation and also provide direct clues for subsequent functional studies.
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Molecular ecological tools to decipher the role of our microbial mass in obesity.
Hermes, GD, Zoetendal, EG, Smidt, H
Beneficial microbes. 2015;(1):61-81
Abstract
After birth, our gastrointestinal (GI) tract is colonised by a highly complex assemblage of microbes, collectively termed the GI microbiota, that develops intimate interactions with our body. Recent evidence indicates that the GI microbiota and its products may contribute to the development of obesity and related diseases. This, coupled with the current worldwide epidemic of obesity, has moved microbiome research into the spotlight of attention. Although the main cause of obesity and its associated metabolic complications is excess caloric intake compared with expenditure, differences in GI tract microbial ecology between individuals might be an important biomarker, mediator or new therapeutic target. This can be investigated using a diverse set of complementary so called -omics technologies, such as 16S ribosomal RNA gene-targeted composition profiling, metabolomics, metagenomics, metatranscriptomics and metaproteomics. This review aims to describe the different molecular approaches and their contributions to our understanding of the role of the GI microbiota in host energy homeostasis. Correspondingly, we highlight their respective strengths, but also try to create awareness for their specific limitations. However, it is currently still unclear which bacterial groups play a role in the development of obesity in humans. This might partly be explained by the heterogeneity in genotype, lifestyle, diet and the complex ethology of obesity and its associated metabolic disorders (OAMD). Nevertheless, recent research on this matter has shown a conceptual shift by focusing on more homogenous subpopulations, through the use of both anthropometric (weight, total body fat) as well as biochemical variables (insulin resistance, hyperlipidaemia) to define categories. Combined with technological advances, recent data suggests that an OAMD associated microbiota can be characterised by a potential pro-inflammatory composition, with less potential for the production of short chain fatty acids and butyrate in particular.
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10.
[Gene expression analyses and their possible clinical benefit in head and neck cancer].
Dietz, A, Loeffler, M, Rosolowski, M, Kreuz, M, Lordick, F, Knödler, M, Mozet, C, Wichmann, G
HNO. 2015;(11):773-85
Abstract
Systems biology approaches for mutational (exome analysis and targeted sequencing) and gene expression analysis (transcriptome-wide gene expression profiling) represent a new and growing scientific field in head and neck oncology. In addition to medical biological expertise, bioinformatic assistance is increasingly required. For squamous cell head and neck cancer (HNSCC), the recent molecular genetic single-gene and signal pathway observations represent basic research. Important aspects of this have now been significantly enhanced by systems biology approaches, which have grown into relevant areas of translational clinical research. It is now known that HPV16 is associated with genetic alterations at various locations, but also that it functionally affects genes not altered in their base sequence at the level of methylation. In transcriptome analyses, various consortia found matching clusters of gene expression and HPV16 association with the spectrum of somatic mutations. The differential methylation of gene promoters discovered in HPV16-driven HNSCC proved predictive for survival—even in HNSCC patients without HPV detection. The authors present an overview of some translationally relevant findings and venture an outlook on possible future clinical developments.