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Current Issues in Molecular Biology

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https://www.readbyqxmd.com/read/28686571/application-of-omics-approaches-to-studying-methylotrophs-and-methylotroph-comunities
#1
Ludmila Chistoserdova
This review covers some recent advances in application of omics technologies to studying methylotrophs, with special reference to their activities in natural environments. Some of the developments highlighted in this review are the new outlook at the role of the XoxF-type, lanthanum-dependent methanol dehydrogenase in natural habitats, new mechanistic details of methane oxidation through the reverse methanogenesis pathway, propensity of 'aerobic' methanotrophs to thrive in hypoxic environments and potential connection of this process to denitrification, and a novel outlook at methane oxidation as a community function...
July 6, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28686570/using-metagenomics-to-connect-microbial-community-biodiversity-and-functions
#2
Lucas William Mendes, Lucas Peres Palma Braga, Acacio Aparecido Navarrete, Dennis Goss de Souza, Genivaldo Gueiros Zacarias Silva, Siu Mui Tsai
Microbes constitute about a third of the Earth's biomass and are composed by an enormous genetic diversity. In a majority of environments the microbial communities play crucial roles for the ecosystem functioning, where a drastic biodiversity alteration or loss could lead to negative effects on the environment and sustainability. A central goal in microbiome studies is to elucidate the relation between microbial diversity to functions. A better understanding of the relation diversity-function would increase the ability to manipulate that diversity to improve plant and animal health and also setting conservation priorities...
July 6, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28686569/spatio-temporal-variations-in-the-abundance-and-structure-of-denitrifier-communities-in-sediments-differing-in-nitrate-content
#3
David Correa-Galeote, Germán Tortosa, Silvia Moreno, David Bru, Laurent Philippot, Eulogio J Bedmar
Spatial and temporal variations related to hydric seasonality in abundance and diversity of denitrifier communities were examined in sediments taken from two sites differing in nitrate concentration along a stream Doñana National Park during a 3-year study. We found a positive relationship between the relative abundance of denitrifiers, determined as narG, napA, nirK, nirS and nosZ denitrification genes, and sediment nitrate content, with similar spatial and seasonal variations. However, we did not find association between denitrification activity and the community structure of denitrifiers...
July 6, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28686568/comparing-viral-metagenomic-extraction-methods
#4
Jeanette Klenner, Claudia Kohl, Piotr Wojtek Dabrowski, Andreas Nitsche
A crucial step in the molecular detection of viruses in clinical specimens is the efficient extraction of viral nucleic acids. The total yield of viral nucleic acid from a clinical specimen is dependent on the specimen's volume, the initial virus concentration and the effectiveness provided by the extraction method. Recent Next Generation Sequencing (NGS)-based diagnostic approaches (i.e. metagenomics) provide a molecular 'open view' into the sample, as they theoretically generate sequence reads of any nucleic acid present in a specimen in a statistically representative manner...
July 6, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28686567/methods-for-the-metagenomic-data-visualization-and-analysis
#5
Konstantin Sudarikov, Alexander Tyakht, Dmitry Alexeev
Surveys of environmental microbial communities using metagenomic approach produce vast volumes of multidimensional data regarding the phylogenetic and functional composition of the microbiota. Faced with such complex data, a metagenomic researcher needs to select the means for data analysis properly. Data visualization became an indispensable part of the exploratory data analysis and serves a key to the discoveries. While the molecular-genetic analysis of even a single bacterium presents multiple layers of data to be properly displayed and perceived, the studies of microbiota are significantly more challenging...
July 6, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28686566/guidelines-to-statistical-analysis-of-microbial-composition-data-inferred-from-metagenomic-sequencing
#6
Vera Odintsova, Alexander Tyakht, Dmitry Alexeev
Metagenomics, the application of high-throughput DNA sequencing for surveys of environmental samples, has revolutionized our view on the taxonomic and genetic composition of complex microbial communities. An enormous richness of microbiota keeps unfolding in the context of various fields ranging from biomedicine and food industry to geology. Primary analysis of metagenomic reads allows to infer semi-quantitative data describing the community structure. However, such compositional data possess statistical specific properties that are important to be considered during preprocessing, hypothesis testing and interpreting the results of statistical tests...
July 6, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28686565/integration-of-ecology-and-environmental-metagenomics-conceptual-and-methodological-frameworks
#7
Diana Marco
Although from its origin metagenomics was concerned with composition of communities of microbial OTUs (Operational Taxonomic Units) living in a given habitat and their diversity and functional heterogeneity (concepts already well rooted in ecology), the new field was more 'environmentally' than 'ecologically' oriented. Probably by circumstantial reasons, metagenomics and ecology followed rather independent trajectories and conceptual and methodological gaps appeared. Recently, calls for the need of integrating the theoretical basis and methodologies coming from metagenomics (and other meta-omics) and ecology have been made...
July 6, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28561007/application-of-flow-cytometry-to-the-detection-of-pathogenic-bacteria
#8
Deirdre Kennedy, Martin G Wilkinson
Outbreaks of infections have emphasized the necessity for rapid and economic detection methods for pathogens in samples ranging from those of clinical origin to food products during production and retail storage, and increasingly, in environmental samples. Flow cytometry (FCM) allows the rapid acquisition of multi-parametric data regarding cell populations within fluidised samples. However, the application of FCM to pathogen detection depends on the availability of specific fluorescent probes such as antibodies and RNA probes capable of detecting and isolating pathogens from these diverse samples...
May 31, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28504240/maldi-tof-ms-in-the-microbiology-laboratory-current-trends
#9
Sören Schubert, Markus Kostrzewa
Within less than a decade matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has become a gold standard for microbial identification in clinical microbiology laboratories. Besides identification of microorganisms the typing of single strains as well as the antibiotic and antimycotic resistance testing has come into focus in order to speed up the microbiological diagnostic. However, the full potential of MALDI-TOF MS has not been tapped yet and future technological advancements will certainly expedite this method towards novel applications and enhancement of current practice...
May 15, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28154243/plant-immune-system-crosstalk-between-responses-to-biotic-and-abiotic-stresses-the-missing-link-in-understanding-plant-defence
#10
Naghmeh Nejat, Nitin Mantri
Environmental pollution, global warming and climate change exacerbate the impact of biotic and abiotic stresses on plant growth and yield. Plants have evolved sophisticated defence network, also called innate immune system, in response to ever- changing environmental conditions. Significant progress has been made in identifying the key stress-inducible genes associated with defence response to single stressors. However, relatively little information is available on the signaling crosstalk in response to combined biotic/abiotic stresses...
February 3, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/27831541/dna-vaccine-delivery-and-improved-immunogenicity
#11
REVIEW
Kevin R Porter, Kanakatte Raviprakash
The promise of DNA vaccines is as compelling today as it was more than a decade ago. Ease of manufacture, stability at ambient temperatures without the need for a cold chain and its ability to mimic natural infections and elicit appropriate immune responses makes this vaccine platform extremely attractive. Although, human clinical trials of DNA vaccines have yielded less than optimal results, the approval and licensing of a few veterinary vaccines is testimony to the proof-of-concept and the hope that licensed DNA vaccines for human use may not be too far away...
2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/27801664/mrna-a-versatile-molecule-for-cancer-vaccines
#12
REVIEW
Mustafa Diken, Lena M Kranz, Sebastian Kreiter, Ugur Sahin
mRNA vaccines are finally ready to assume their rightful place at the forefront of nucleic acid- based vaccines. Major achievements within the last two decades have turned this highly versatile molecule into a safe and very attractive pharmaceutical platform that combines many positive attributes able to address a broad range of diseases, including cancer. The simplicity of mRNA vaccines greatly reduces complications generally associated with the production of biological vaccines. Intrinsic costimulatory and inflammatory triggers in addition to the provision of the antigenic information makes mRNA an all- in-one molecule that does not need additional adjuvants and that does not pose the risk of genomic integration...
2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/27801354/genomics-a-hallmark-to-monitor-molecular-and-biochemical-processes-leading-toward-a-better-perceptive-of-seed-aging-and-ex-situ-conservation
#13
REVIEW
Zaheer Ahmed, Zahid Hussain Shah, Hafiz Mamoon Rehman, Khurram Shahzad, Ihsanullah Daur, Abdalla Elfeel, Mahmood Ul Hassan, Ali Khalid Elsafori, Seung Hwan Yang, Gyuhwa Chung
For human food security, the preservation of 7.4 million ex-situ germplasm is a global priority. However, ex-situ-conserved seeds are subject to aging, which reduces their viability and ultimately results in the loss of valuable genetic material over long periods. Recent progress in seed biology and genomics has revealed new opportunities to improve the long-term storage of ex-situ seed germplasm. This review summarizes the recent improvements in seed physiology and genomics, with the intention of developing genomic tools for evaluating seed aging...
2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/27705898/dna-vaccines-regulatory-considerations-and-safety-aspects
#14
REVIEW
Anne Ingeborg Myhr
DNA vaccines have great potential as preventive or therapeutic vaccines against viral, bacterial, or parasitic diseases as well as cancer, and may also be used as gene therapy products. Although many human and veterinary DNA vaccines have been investigated in laboratory trials, only four of these have been approved for commercial use. In this paper an overview of the regulatory requirements for the development of DNA vaccines is given. The regulatory process in EU and USA is described. A discussion concerning the relevance of national regulations on gene technology is included...
2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/27698284/far-from-the-madding-crowd-the-molecular-basis-for-immunological-escape-of-plasmodium-falciparum
#15
Manuel E Patarroyo, Jorge Aza-Conde, Armando Moreno-Vranich, Laura Pabón, Yahson Varela, Manuel A Patarroyo
Like Thomas Hardy's famous novel Far from the Madding Crowd, Plasmodium falciparum parasites display their most relevant survival structures (proteins) involved in host cell invasion far away from the immune system's susceptible regions, displaying tremendous genetic variability, to attract the immune response and escape immune pressure. The 3D structure localisation of the conserved amino acid sequences of this deadly parasite's most relevant proteins involved in host cell invasion, as well as the location of the highly polymorphic, highly immunogenic regions, clearly demonstrates that such structures are far apart, sometimes 90° to 180° opposite, thereby rendering the immune response useless...
2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/27669666/liver-x-receptors-and-their-agonists-targeting-for-cholesterol-homeostasis-and-cardiovascular-diseases
#16
REVIEW
Zhiqiang Ma, Chao Deng, Wei Hu, Jie Zhou, Chongxi Fan, Shouyin Di, Dong Liu, Yang Yang, Dongjin Wang
Liver X receptors α (LXRα) and β (LXRβ) are essential for protection against cardiovascular diseases. LXRs are members of the nuclear receptor superfamily of DNA-binding transcription factors and act as sensors of cholesterol homeostasis. In this review, we introduce LXRs and briefly describe the roles of LXRs in reverse cholesterol transport and trans-intestinal cholesterol efflux. We discuss LXR agonists and the downstream genes of LXRs that are involved in the regulation of cholesterol transport. In addition, we describe the cardioprotective effects of LXRs against atherosclerosis, myocardial ischemia/reperfusion injury, diabetic cardiomyopathy, and myocardial hypertrophy...
2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/27648581/molecular-adjuvants-for-dna-vaccines
#17
REVIEW
Lei Li, Nikolai Petrovsky
Poor immunogenicity remains the single biggest obstacle to human DNA vaccines achieving their potential. Strategies to improve DNA vaccine efficacy include codon optimization, transfection reagents, electroporation, vaccine adjuvants or combination with a protein or vector boost. Increased understanding of molecular events driving innate and adaptive immune responses has assisted development of molecular adjuvants for DNA vaccine use. Such adjuvants comprise plasmid-encoded signalling molecules including cytokines, chemokines, immune costimulatory molecules, toll-like receptor agonists or inhibitors of immune suppressive pathways...
2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/27648510/systems-vaccinology-applied-to-dna-vaccines-perspective-and-challenges
#18
REVIEW
Melissa Lever, Eduardo L Silveira, Helder I Nakaya
DNA vaccination represents a new milestone in our technological efforts to avoid infectious diseases. Although this method of vaccination has had success in providing protection in animals, these vaccines suffer from low immunogenicity in humans. Questions remain over the molecular mechanism of DNA vaccination, the best ways in which to safely increase vaccine reactogenecity, and what biomarkers can be used as correlates of protection. Systems vaccinology, which utilizes modern experimental and computational approaches to provide an integrated view of the vaccination process, offers the potential to answer these questions...
2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/27489344/transcriptomics-and-biochemical-profiling-current-dynamics-in-elucidating-the-potential-attributes-of-olive
#19
Zahid Hussain Shah, Bahget T Hamooh, Ihsanullah Daur, Hafiz Mamoon Rehman, Fahad Alghabari
Various transcriptome studies have remained useful in unraveling the complexity of molecular pathways regulating the oil biochemical contents and fruit characteristics of agronomic value in olive. Genes networks associated with plant architect and abiotic stress tolerance have been constructed due to robust genomic data generated by the tools of genomics. This, familiarity will accelerate the breeding programmes in making the selection of high yielding olive genotypes promptly and efficiently. Moreover, comparative transcriptome studies for endogeneous enzymes at different expression sites explicate the contribution of various pathways in phenol and lipid oxidation in olive...
2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/27443861/mycobacteria-and-autophagy-many-questions-and-few-answers
#20
REVIEW
Min Liang, Zeshan Habib, Kaori Sakamoto, Xi Chen, Gang Cao
Tuberculosis (TB) is an ancient disease caused by Mycobacterium tuberculosis (Mtb). TB is one of the world's deadliest diseases, with one-third of infected individuals falling ill each year especially in many developing countries. Upon invading host cells, such as macrophages, Mtb can replicate in infected cells by arresting phagosome maturation and then potentially escaping into the cytosol. Host cells have a mechanism to control intracellular Mtb by inducing autophagy, which is an elaborate cellular process to target intracellular pathogens for degradation in infected cells...
2017: Current Issues in Molecular Biology
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