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Biology Dark Matter

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https://www.readbyqxmd.com/read/30108727/dark-chemical-matter-in-public-screening-assays-and-derivation-of-target-hypotheses
#1
Swarit Jasial, Jürgen Bajorath
Compounds that are consistently inactive in many screening assays, so-called dark chemical matter (DCM), have recently experienced increasing attention. One of the reasons is that many DCM compounds may not be fully inert biologically, but may provide interesting leads for obtaining compounds that are highly selective or active against unusual targets. In this study, we have systematically identified DCM among extensively assayed screening compounds and searched for analogs of these compounds that have known bioactivities...
November 1, 2017: MedChemComm
https://www.readbyqxmd.com/read/30098554/history-advancements-and-perspective-of-biological-research-in-deep-underground-laboratories-a-brief-review
#2
REVIEW
Jifeng Liu, Tengfei Ma, Yilin Liu, Jian Zou, Mingzhong Gao, Ru Zhang, Jiang Wu, Shixi Liu, Heping Xie
The world is entering a new era of exploring and exploiting the deep-underground space. With humans poised to reach historical depths in the use of the deep Earth, it is essential to understand the effect of the deep-underground environment on the health of humans and other living organisms. This article outlines the history and development of biological research conducted in deep-underground laboratories and provides insight into future areas of investigation. Many deep-underground laboratories have investigated the effects of reduced cosmic ray muons flux, searching for rare events such as proton decay, dark matter particles, or neutrino interactions, but few have focused on the influence of the environmental factors in the deep-underground on living organisms...
August 8, 2018: Environment International
https://www.readbyqxmd.com/read/30037084/rna-phage-biology-in-a-metagenomic-era
#3
REVIEW
Julie Callanan, Stephen R Stockdale, Andrey Shkoporov, Lorraine A Draper, R Paul Ross, Colin Hill
The number of novel bacteriophage sequences has expanded significantly as a result of many metagenomic studies of phage populations in diverse environments. Most of these novel sequences bear little or no homology to existing databases (referred to as the "viral dark matter"). Also, these sequences are primarily derived from DNA-encoded bacteriophages (phages) with few RNA phages included. Despite the rapid advancements in high-throughput sequencing, few studies enrich for RNA viruses, i.e., target viral rather than cellular fraction and/or RNA rather than DNA via a reverse transcriptase step, in an attempt to capture the RNA viruses present in a microbial communities...
July 21, 2018: Viruses
https://www.readbyqxmd.com/read/30018188/the-nefarious-nexus-of-noncoding-rnas-in-cancer
#4
REVIEW
Eleni Anastasiadou, Alberto Faggioni, Pankaj Trivedi, Frank J Slack
The past decade has witnessed enormous progress, and has seen the noncoding RNAs (ncRNAs) turn from the so-called dark matter RNA to critical functional molecules, influencing most physiological processes in development and disease contexts. Many ncRNAs interact with each other and are part of networks that influence the cell transcriptome and proteome and consequently the outcome of biological processes. The regulatory circuits controlled by ncRNAs have become increasingly more relevant in cancer. Further understanding of these complex network interactions and how ncRNAs are regulated, is paving the way for the identification of better therapeutic strategies in cancer...
July 17, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29968336/identifying-labile-dom-components-in-a-coastal-ocean-through-depleted-bacterial-transcripts-and-chemical-signals
#5
Alexey Vorobev, Shalabh Sharma, Mengyun Yu, Juhyung Lee, Benjamin J Washington, William B Whitman, Ford Ballantyne, Patricia M Medeiros, Mary Ann Moran
Understanding which compounds comprising the complex and dynamic marine dissolved organic matter (DOM) pool are important in supporting heterotrophic bacterial production remains a major challenge. We eliminated sources of labile phytoplankton products, advected terrestrial material and photodegradation products to coastal microbial communities by enclosing water samples in situ for 24 h in the dark. Bacterial genes for which expression decreased between the beginning and end of the incubation and chemical formulae that were depleted over this same time frame were used as indicators of bioavailable compounds, an approach that avoids augmenting or modifying the natural DOM pool...
July 2, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29780404/intrinsic-disorder-and-posttranslational-modifications-the-darker-side-of-the-biological-dark-matter
#6
REVIEW
April L Darling, Vladimir N Uversky
Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs) are functional proteins and domains that devoid stable secondary and/or tertiary structure. IDPs/IDPRs are abundantly present in various proteomes, where they are involved in regulation, signaling, and control, thereby serving as crucial regulators of various cellular processes. Various mechanisms are utilized to tightly regulate and modulate biological functions, structural properties, cellular levels, and localization of these important controllers...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29755206/epilithic-chamaesiphon-synechococcales-cyanobacteria-species-in-mountain-streams-of-the-alps-interspecific-differences-in-photo-physiological-traits
#7
Siegfried Aigner, Klaus Herburger, Andreas Holzinger, Ulf Karsten
Many alpine streams inhabit conspicuous epilithic biofilms on pebbles and rocks that are formed by members of the cyanobacterial genus Chamaesiphon (Synechococcales). In the Austrian Alps, some Chamaesiphon species can even overgrow up to 70% of the surface of river rocks, and hence they must play an important but still unstudied ecological role in the organic matter flux. Since photo-biological traits have not been investigated so far, photosynthetic features, pigments, and UV-sunscreen compounds were studied in three Chamaesiphon morphospecies ( C...
2018: Journal of Applied Phycology
https://www.readbyqxmd.com/read/29672703/phylogenomic-analysis-of-%C3%AE-lactamase-in-archaea-and-bacteria-enables-the-identification-of-putative-new-members
#8
Vivek Keshri, Arup Panda, Anthony Levasseur, Jean-Marc Rolain, Pierre Pontarotti, Didier Raoult
β-lactamases are enzymes which are commonly produced by bacteria and which degrade the β-lactam ring of β-lactam antibiotics, namely penicillins, cephalosporins, carbapenems, and monobactams, and inactivate these antibiotics. We performed a rational and comprehensive investigation of β-lactamases in different biological databases. In this study, we constructed hidden Markov model profiles as well as the ancestral sequence of four classes of β-lactamases (A, B, C, and D), which were used to identify potential β-lactamases from environmental metagenomic (1206), human microbiome metagenomic (6417), human microbiome reference genome (1310), and NCBI's nonredundant databases (44101)...
April 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29504575/the-dark-matter-of-dna-and-the-regulation-of-bone-metabolism-the-role-of-non-coding-rnas
#9
Maria P Yavropoulou, John G Yovos
Epigenetics, present a new discipline that attempts to explain significant differences in phenotypes among patients with the same disease. In contrast to the other epigenetic mechanisms that modulate gene transcription, non-coding RNAs act at the post-transcriptional level. They directly modulate the gene expression of mRNA genes leading to mRNA target cleavage and degradation and translation repression. Bioinformatic predictions indicate that non coding RNAs may be involved in the regulation of 60% of the coding genes and each non-coding RNA can have multiple target genes, and each gene may be regulated by more than one non-coding RNAs...
March 1, 2018: Journal of Musculoskeletal & Neuronal Interactions
https://www.readbyqxmd.com/read/29498880/-long-non-coding-rnas-in-the-pathophysiology-of-atherosclerosis
#10
Jan Novak, Julie Bienertová Vašků, Miroslav Souček
The human genome contains about 22 000 protein-coding genes that are transcribed to an even larger amount of messenger RNAs (mRNA). Interestingly, the results of the project ENCODE from 2012 show, that despite up to 90 % of our genome being actively transcribed, protein-coding mRNAs make up only 2-3 % of the total amount of the transcribed RNA. The rest of RNA transcripts is not translated to proteins and that is why they are referred to as "non-coding RNAs". Earlier the non-coding RNA was considered "the dark matter of genome", or "the junk", whose genes has accumulated in our DNA during the course of evolution...
2018: Vnitr̆ní Lékar̆ství
https://www.readbyqxmd.com/read/29472151/evaluation-of-the-biodegradability-and-toxicity-of-landfill-leachates-after-pretreatment-using-advanced-oxidative-processes
#11
Fabio Moraes da Costa, Sarah Dario Alves Daflon, Daniele Maia Bila, Fabiana Valeria da Fonseca, Juacyara Carbonelli Campos
Leachate from urban solid waste landfills is a complex mixture of organic and inorganic substances that cause damage to the environment, due to the high concentration of recalcitrant organic matter and toxicity. The objective of this study was to apply advanced oxidation processes (AOP), namely the dark Fenton and solar photo-Fenton processes, to young and old landfill leachates prior to biological treatment. The leachates were obtained from the Seropedica and Gramacho landfill sites, respectively, located in Rio de Janeiro State, Brazil...
June 2018: Waste Management
https://www.readbyqxmd.com/read/29420719/microbial-dark-matter-investigations-how-microbial-studies-transform-biological-knowledge-and-empirically-sketch-a-logic-of-scientific-discovery
#12
Guillaume Bernard, Jananan S Pathmanathan, Romain Lannes, Philippe Lopez, Eric Bapteste
Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics data sets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists...
March 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29380028/influence-of-darkness-and-aging-on-marine-and-freshwater-biofilm-microbial-communities-using-microcosm-experiments
#13
Niyati Hede, Lidita Khandeparker
Ballast tank biofilms pose an additional risk of microbial invasion if sloughed off during ballasting operations, yet their significance and invasion biology is poorly understood. In this study, biofilms developed in marine and freshwater locations were exposed to prolonged darkness and aging by mimicking ballast water conditions in the laboratory. Upon prolonged darkness, the decay of phytoplankton, as indicated by the decrease in chlorophyll a in marine biofilms, led to remineralization and enhanced bacterial and protist populations...
August 2018: Microbial Ecology
https://www.readbyqxmd.com/read/29335452/chaotic-universe-model
#14
Ekrem Aydiner
In this study, we consider nonlinear interactions between components such as dark energy, dark matter, matter and radiation in the framework of the Friedman-Robertson-Walker space-time and propose a simple interaction model based on the time evolution of the densities of these components. By using this model we show that these interactions can be given by Lotka-Volterra type equations. We numerically solve these coupling equations and show that interaction dynamics between dark energy-dark matter-matter or dark energy-dark matter-matter-radiation has a strange attractor for 0 > w de  >-1, w dm  ≥ 0, w m  ≥ 0 and w r  ≥ 0 values...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29240300/genomic-origin-and-nuclear-localization-of-terra-telomeric-repeat-containing-rna-from-darkness-to-dawn
#15
REVIEW
Aurélie Diman, Anabelle Decottignies
Long noncoding RNAs, produced from distinct regions of the chromosomes, are emerging as new key players in several important biological processes. The long noncoding RNAs add a new layer of complexity to cellular regulatory pathways, from transcription to cellular trafficking or chromatin remodeling. More than 25 years ago, the discovery of a transcriptional activity at telomeres of protozoa ended the long-lasting belief that telomeres were transcriptionally silent. Since then, progressively accumulating evidences established that production of TElomeric Repeat-containing RNA (TERRA) was a general feature of eukaryotic cells...
April 2018: FEBS Journal
https://www.readbyqxmd.com/read/29154906/increase-in-taxonomic-assignment-efficiency-of-viral-reads-in-metagenomic-studies
#16
S François, D Filloux, M Frayssinet, P Roumagnac, D P Martin, M Ogliastro, R Froissart
Metagenomics studies have revolutionized the field of biology by revealing the presence of many previously unisolated and uncultured micro-organisms. However, one of the main problems encountered in metagenomic studies is the high percentage of sequences that cannot be assigned taxonomically using commonly used similarity-based approaches (e.g. BLAST or HMM). These unassigned sequences are allegorically called « dark matter » in the metagenomic literature and are often referred to as being derived from new or unknown organisms...
January 15, 2018: Virus Research
https://www.readbyqxmd.com/read/29054012/the-role-of-long-noncoding-rnas-in-cancer-the-dark-matter-matters
#17
REVIEW
Xiaowen Hu, Anil K Sood, Chi V Dang, Lin Zhang
Sequencing technology has facilitated a new era of cancer research, especially in cancer genomics. Using next-generation sequencing, thousands of long noncoding RNAs (lncRNAs) have been identified as abnormally altered in the cancer genome or differentially expressed in tumor tissues. These lncRNAs are associated with imbalanced gene regulation and aberrant biological processes that contribute to malignant transformation. The functions and therapeutic potential of cancer-related lncRNAs have attracted considerable interest in the past few years...
February 2018: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/29048608/zebrafish-locomotor-responses-reveal-irritant-effects-of-fine-particulate-matter-extracts-and-a-role-for-trpa1
#18
Joey S Stevens, Stephanie Padilla, David M DeMarini, Deborah L Hunter, W Kyle Martin, Leslie C Thompson, M Ian Gilmour, Mehdi S Hazari, Aimen K Farraj
Exposure to fine particulate matter (PM) air pollution causes adverse cardiopulmonary outcomes. Yet, the limited capacity to readily identify contributing PM sources and associated PM constituents in any given ambient air shed impedes risk assessment efforts. The health effects of PM have been attributed in part to its capacity to elicit irritant responses. A variety of chemicals trigger irritant behavior responses in zebrafish that can be easily measured. The purposes of this study were to examine the utility of zebrafish locomotor responses in the toxicity assessment of fine PM and its chemical fractions and uncover mechanisms of action...
February 1, 2018: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29026445/viral-communities-of-the-human-gut-metagenomic-analysis-of-composition-and-dynamics
#19
REVIEW
Varun Aggarwala, Guanxiang Liang, Frederic D Bushman
BACKGROUND: The numerically most abundant biological entities on Earth are viruses. Vast populations prey on the cellular microbiota in all habitats, including the human gut. MAIN BODY: Here we review approaches for studying the human virome, and some recent results on movement of viral sequences between bacterial cells and eukaryotic hosts. We first overview biochemical and bioinformatic methods, emphasizing that specific choices in the methods used can have strong effects on the results obtained...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28727425/database-and-bioinformatics-studies-of-probiotics
#20
REVIEW
Lin Tao, Bohua Wang, Yafen Zhong, Siok Hoon Pow, Xian Zeng, Chu Qin, Peng Zhang, Shangying Chen, Weidong He, Ying Tan, Hongxia Liu, Yuyang Jiang, Weiping Chen, Yu Zong Chen
Probiotics have been widely explored for health benefits, animal cares, and agricultural applications. Recent advances in microbiome, microbiota, and microbial dark matter research have fueled greater interests in and paved ways for the study of the mechanisms of probiotics and the discovery of new probiotics from uncharacterized microbial sources. A probiotics database named PROBIO was developed to facilitate these efforts and the need for the information on the known probiotics, which provides the comprehensive information about the probiotic functions of 448 marketed, 167 clinical trial/field trial, and 382 research probiotics for use or being studied for use in humans, animals, and plants...
September 6, 2017: Journal of Agricultural and Food Chemistry
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