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Current Issues in Molecular Biology

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https://www.readbyqxmd.com/read/29648541/horizontal-gene-transfers-in-mycoplasmas-mollicutes
#1
C Citti, E Dordet-Frisoni, L X Nouvel, C H Kuo, E Baranowski
The class Mollicutes (trivial name "mycoplasma") is composed of wall-less bacteria with reduced genomes whose evolution was long thought to be only driven by gene losses. Recent evidences of massive horizontal gene transfer (HGT) within and across species provided a new frame to understand the successful adaptation of these minimal bacteria to a broad range of hosts. Mobile genetic elements are being identified in a growing number of mycoplasma species, but integrative and conjugative elements (ICEs) are emerging as pivotal in HGT...
April 12, 2018: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/29648540/editorial-ice-and-small
#2
Adam P Roberts
Bacterial genomes vary considerably in terms of size and gene content. The proportion of a genome composed of horizontally acquired DNA or mobile genetic elements also varies, but follows an ecological pattern with more mobile genetic element genes being found in facultative intracellular bacteria than those considered extracellular and both containing more than obligately intracellular bacteria.
April 12, 2018: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/29648539/horizontal-gene-transfer-in-thermus-spp
#3
Alba Blesa, Beate Averhoff, José Berenguer
The small amount of genetic content in thermophiles generally limits their adaptability to environmental changes. In Thermus spp., very active horizontal gene transfer (HGT) mechanisms allow the rapid spread of strain-specific adaptive gene modules among the entire population. Constitutive expression of a rather particular and highly efficient DNA transport apparatus (DTA) is at the center of this HGT-mediated enhanced adaptability. The function of the DTA is dependent on the integrity and longevity of the extracellular DNA (eDNA) being transformed, which can be improved by the production of extracellular vesicles (EV) through lysis of a fraction of the population...
April 12, 2018: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/29428910/a-review-of-crispr-based-genome-editing-survival-evolution-and-challenges
#4
Hafiz Ishfaq Ahmad, Muhammad Jamil Ahmad, Akhtar Rasool Asif, Muhammad Adnan, Muhammad Kashif Iqbal, Khalid Mehmood, Sayyed Aun Muhammad, Ali Akbar Bhuiyan, Abdelmotaleb Elokil, Xiaoyong Du, Changzhi Zhao, Xiangdong Liu, Shengsong Xie
Precise nucleic acid editing technologies have facilitated the research of cellular function and the development of novel therapeutics, especially the current programmable nucleases-based editing tools, such as the prokaryotic clustered regularly interspaced short palindromic repeats (CRISPR)-associated nucleases (Cas). As CRISPR-based therapies are advancing toward human clinical trials, it is important to understand how natural genetic variation in the human population may affect the results of these trials and even patient safety...
February 11, 2018: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/29388553/snapshots-endoplasmic-reticulum-stress-in-lipid-metabolism-and-cardiovascular-disease
#5
Tian Li, Shuai Jiang, Chenxi Lu, Wei Hu, Ting Ji, Mengzhen Han, Yang Yang, Zhenxiao Jin
The endoplasmic reticulum (ER) is an organelle present in most eukaryotic cells and plays a pivotal role in lipid metabolism. ER dysfunction, specifically ER stress (ERS), is a pathophysiological response involved in lipid metabolism and cardiovascular lesions. Therefore, suppression of ERS may improve lipid metabolic disorders and reduce cardiovascular risk. Herein, we focus on novel breakthroughs regarding the roles of ERS in lipid metabolism and cardiovascular disease (CVD), as well as the internal mechanisms of ERS and its status as a potential therapeutic target...
February 1, 2018: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/29388552/pgc-1-the-energetic-regulator-in-cardiac-metabolism
#6
Wencheng Di, Jianjun Lv, Shuai Jiang, Chenxi Lu, Zhi Yang, Zhiqiang Ma, Wei Hu, Yang Yang, Biao Xu
The peroxisome proliferator-activated receptor γ (PPARγ) coactivator-1s (PGC-1s) can induce the expression of several downstream genes that play pivotal roles in the regulation of mitochondrial biogenesis and metabolism in the heart. Moreover, PGC-1 signaling pathways have also been reported to play a critical role in cardioprotection. Given the significance of PGC-1 coactivators, we summarize the current literature on the molecular mechanisms and roles of PGC-1s in cardiac metabolism. Thus, in this review, we first introduce the basic knowledge regarding PGC-1 signaling pathways...
February 1, 2018: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28894039/translational-approaches-in-cardiovascular-diseases-by-omics
#7
Vahideh Rabani, Siamak Davani
Cardiovascular diseases are among the leading causes of morbidity and mortality. Despite scientific and technical progress in risk prediction, diagnostics, prognostication and therapy of cardiovascular pathologies, new biomarkers and therapeutic targets remain the subject of intense research to reduce the burden of these diseases. High throughput analyses, termed "omics", are a promising avenue of research. These recently developed technical fields have revolutionized biological and medical research in a very short time...
September 12, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28885183/from-microscopy-to-genomic-approach-in-soil-biodiversity-assessment
#8
Lucia Popescu, Zhi-Ping Cao
Soil biota represents a major component of the earth's biodiversity and for over 200 years, the microscopy approach was the only way to explore it. In the last decade, the DNA-based technique has been adopted in soil ecology. Due to the rapid development of cutting-edge technology, the field is transitioning from barcoding individuals to metabarcoding communities. With the advent of next-generation sequencing and a rapid decline in sequencing cost, it has become feasible to assess soil biodiversity at species level...
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28885182/cataloging-plant-genome-structural-variations
#9
Xingtan Zhang, Xuequn Chen, Pingping Liang, Haibao Tang
Structural variation (SV) is a type of genetic variation identified through the comparison of genome structures which often have direct and significant associations with phenotypic variations. Building on the next generation sequencing (NGS) technologies, research on plant structural variations are gaining momentum and have revolutionized our view on the functional impact of the 'hidden' diversity that were largely understudied before. Herein, we first describe the current state of plant genomic SV research based on NGS and in particular focus on the biological insights gained from the large-scale identification of various types of plant SVs...
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28885181/chip-seq-a-powerful-tool-for-studying-protein-dna-interactions-in-plants
#10
Xifeng Chen, Vijai Bhadauria, Bojun Ma
DNA-binding proteins, including transcription factors, epigenetic and chromatin modifiers, control gene expressions in plants. To pinpoint the binding sits of DNA-binding proteins in genome is crucial for decoding gene regulatory networks. Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-Seq) is a widely used approach to identify the DNA regions bound by a specific protein in vivo. The information generated from ChIP-Seq has tremendously advanced our understanding on the mechanism of transcription factors, cofactors and histone modifications in regulating gene expression...
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28885180/next-generation-sequencing-sheds-new-light-on-small-rnas-in-plant-reproductive-development
#11
Xiaobai Li
Reproductive development is a key step of the plant life cycles and indicates the start of a new life cycle. The reproductive organs including flower, fruit and seed, have diverse and complex structures, which is a syndrome in the evolution of angiosperms. The development of plant reproductive organs depends on the correct spatial and temporal expression of numerous genes acting in concert to form regulatory networks. Small non-coding RNAs (sRNAs) play a key role in the reproductive development through different modes of sequence-specific interaction with their targets...
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28885179/dual-rna-sequencing-to-elucidate-the-plant-pathogen-duel
#12
Sanushka Naidoo, Erik Andrei Visser, Lizahn Zwart, Yves du Toit, Vijai Bhadauria, Louise Simone Shuey
RNA-sequencing technology has been widely adopted to investigate host responses during infection with pathogens. Dual RNA-sequencing (RNA-seq) allows the simultaneous capture of pathogen specific transcripts during infection, providing a more complete view of the interaction. In this review, we focus on the design of dual RNA-seq experiments and the application of downstream data analysis to gain biological insight into both sides of the interaction. Recent literature in this area demonstrates the power of the dual RNA-seq approach and shows that it is not limited to model systems where genomic resources are available...
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28885178/a-rice-genetic-improvement-boom-by-next-generation-sequencing
#13
Xiangchun Zhou, Xufeng Bai, Yongzhong Xing
Rice (Oryza sativa L.) is a staple food crop for people worldwide, and a key goal has been to increase its grain yield. An increasing population that relies on a decreasing level of farmland has rendered the traditional method for the isolation and use of genetic loci in rice breeding unsatisfactory. Recently, the rapid development in next generation sequencing (NGS) has boosted the number of genome sequences for hundreds to thousands of rice varieties. A MutMap strategy and bulk segregation analysis (BSA) has been developed to directly identify candidate genes based on NGS...
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28885177/quantitative-genetics-of-disease-resistance-in-wheat
#14
Vijai Bhadauria, Lucia Popescu
Wheat (Triticum aestivum L.) is one of the top three global food security crops. Fusarium head blight is one of the major constraints in sustainable wheat production and resistance to the disease is polygenic. This review provides an overview of recent efforts in mapping these genes/loci with the objective to aid marker-assisted selection breeding.
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28885176/applications-of-bioinformatics-to-plant-biotechnology
#15
Diego F Gomez-Casati, María V Busi, Julieta Barchiesi, Diego A Peralta, Nicolás Hedin, Vijai Bhadauria
Bioinformatics encompasses many tools and techniques that today are essential for all areas of research in the biological sciences. New databases with a wealth of information about genomes, proteins, metabolites, and metabolic pathways appear almost daily. Particularly, for scientists who carry out research in plant biology, the amount of information has multiplied exponentially due to the large number of databases available for many individual plant species. In this sense, bioinformatics together with next generation sequencing and 'omics' approaches, can provide tools for plant breeding and the genetic engineering of plants...
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28885175/bioinformatics-resources-for-plant-genomics-opportunities-and-bottlenecks-in-the-omics-era
#16
Luca Ambrosino, Chiara Colantuono, Francesco Monticolo, Maria Luisa Chiusano
The sudden exponential increase of biological data concerning genome structure and functionalities, also fostered by the advent of Next Generation Sequencing (NGS) technologies, while expanding the opportunity to highlight still uncovered molecular aspects, challenges bioinformatics in several repects. Data management, processing, updating, dissemination and integration are the major areas of concern. The rapid increase in various omics technologies causes two major issues, which may even appear contrasting: the dissemination of poorly curated datasets, still in the form of raw collections or preliminary draft results, and the fast updating of information that, as a consequence, affects the establishment of stable reliable resources...
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28885174/advanced-applications-of-next-generation-sequencing-technologies-to-orchid-biology
#17
Chuan-Ming Yeh, Zhong-Jian Liu, Wen-Chieh Tsai
Next-generation sequencing technologies are revolutionizing biology by permitting, transcriptome sequencing, whole-genome sequencing and resequencing, and genome-wide single nucleotide polymorphism profiling. Orchid research has benefited from this breakthrough, and a few orchid genomes are now available; new biological questions can be approached and new breeding strategies can be designed. The first part of this review describes the unique features of orchid biology. The second part provides an overview of the current next-generation sequencing platforms, many of which are already used in plant laboratories...
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28885173/next-generation-sequencing-promoted-the-release-of-reference%C3%A2-genomes-and-discovered%C3%A2-genome-evolution-in-cereal-crops
#18
Yong Huang, Haiyang Liu, Yongzhong Xing
In recent decades, next-generation sequencing (NGS) was developed and brought biology into a new era. Rice, maize, wheat, sorghum and barley are the most important cereal crops and feed most of the world's population. Great progress in the study of cereal genomes has been made with the help of NGS. Reference genome sequence assembly and re-sequencing have grown exponentially. Thus, evolution and comparative genomics are renewed, including origin verification, evolution tracking and so on. In this review, we briefly record the development of sequencing technology, the comparison of next-generation sequencing methods and platforms and summarize the bioinformatics tools used for NGS data analysis...
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28885172/status-and-prospects-of-next-generation-sequencing-technologies-in-crop-plants
#19
T R Sharma, B N Devanna, Kanti Kiran, Pankaj K Singh, Kirti Arora, Priyanka Jain, Ila M Tiwari, Himanshu Dubey, Banita Saklani, Mandeep Kumari, Jyoti Singh, Rajdeep Jaswal, Ritu Kapoor, Deepak V Pawar, Shruti Sinha, Deepak Singh Bisht, A U Solanke, T K Mondal
The history of DNA sequencing dates back to 1970s. During this period the two first generation nucleotide sequencing techniques were developed. Subsequently the Sanger's dideoxy method of sequencing gained popularity over Maxam and Gilbert's chemical method of sequencing. However, in the last decade, we have observed revolutionary changes in DNA sequencing technologies leading to the emergence of next-generation sequencing (NGS) techniques. NGS technologies have enhanced the throughput and speed of sequencing combined with bringing down the overall cost of the process over a time...
September 8, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28879860/ethical-issues-regarding-crispr-mediated-genome-editing
#20
Zabta Khan Shinwari, Faouzia Tanveer, Ali Talha Khalil
CRISPR-Cas9 has emerged as a simple, precise and most rapid genome editing technology. With a number of promising applications ranging from agriculture and environment to clinical therapeutics, it is greatly transforming the field of molecular biology. However, there are certain ethical, moral and safety concerns related to the attractive applications of this technique. The most contentious issues concerning human germline modifications are the challenges to human safety and morality such as risk of unforeseen, undesirable effects in clinical applications particularly to correct or prevent genetic diseases, matter of informed consent and the risk of exploitation for eugenics...
September 7, 2017: Current Issues in Molecular Biology
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