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Biology Dark Matter

Matthew A Knox, Kristene R Gedye, David T S Hayman
The reliable identification and classification of infectious diseases is critical for understanding their biology and controlling their impact. Recent advances in sequencing technology have allowed insight into the remarkable diversity of the virosphere, of which a large component remains undiscovered. For these emerging or undescribed viruses, the process of classifying unknown sequences is heavily reliant on existing nucleotide sequence information in public databases. However, due to the enormous diversity of viruses, and past focus on the most prevalent and impactful virus types, databases are often incomplete...
December 3, 2018: Viruses
Ricardo Parreira
Viruses, which are the most abundant biological entities on the planet, have been regarded as the "dark matter" of biology in the sense that despite their ubiquity and frequent presence in large numbers, their detection and analysis are not always straightforward. The majority of them are very small (falling under the limit of 0.5 μm), and collectively, they are extraordinarily diverse. In fact, the majority of the genetic diversity on the planet is found in the so-called virosphere, or the world of viruses...
November 2018: Microbiology Spectrum
Vladimir N Uversky
Articles assembled to this Special Issue use the perspective of protein intrinsic disorder to highlight different aspects of the dark proteome (i.e., a part of protein universe that includes proteins, which are not amenable to experimental structure determination by existing means and inaccessible to homology modeling) and some of its components. They illustrate that IDPs/IDPRs do not only serve as important constituents of the biological dark matter, but clearly act as the dark horse of the protein universe, being almost completely unknown or at least very little known in a recent past, but suddenly emerging to prominence...
October 18, 2018: Proteomics
Xing Chen, Ya-Zhou Sun, Na-Na Guan, Jia Qu, Zhi-An Huang, Ze-Xuan Zhu, Jian-Qiang Li
From transcriptional noise to dark matter of biology, the rapidly changing view of long non-coding RNA (lncRNA) leads to deep understanding of human complex diseases induced by abnormal expression of lncRNAs. There is urgent need to discern potential functional roles of lncRNAs for further study of pathology, diagnosis, therapy, prognosis, prevention of human complex disease and disease biomarker detection at lncRNA level. Computational models are anticipated to be an effective way to combine current related databases for predicting most potential lncRNA functions and calculating lncRNA functional similarity on the large scale...
September 21, 2018: Briefings in Functional Genomics
Prakash Kulkarni, Vladimir N Uversky
A good portion of the 'protein universe' embodies the 'dark proteome'. The latter comprises proteins not amenable to experimental structure determination by existing means and inaccessible to homology modeling. Hence, the dark proteome has remained largely unappreciated. Intrinsically disordered proteins (IDPs) that lack rigid 3D structure are a major component of this dark proteome across all three kingdoms of life. Despite lack of structure, IDPs play critical roles in numerous important biological processes...
September 14, 2018: Proteomics
Kosti Tapio, Dongkai Shao, Sanna Auer, Jussipekka Tuppurainen, Markus Ahlskog, Vesa P Hytönen, J Jussi Toppari
Merging biological and non-biological matter to fabricate nanoscale assemblies with controllable motion and function is of great interest due to its potential application, for example, in diagnostics and biosensing. Here, we have constructed a DNA-based bionanoactuator that interfaces with biological and non-biological matter via an electric field in a reversibly controllable fashion. The read-out of the actuator is based on motion-induced changes in the plasmon resonance of a gold nanoparticle immobilized to a gold surface by single stranded DNA...
November 7, 2018: Nanoscale
Marootpong Pooam, Louis-David Arthaut, Derek Burdick, Justin Link, Carlos F Martino, Margaret Ahmad
Arabidopsis cryptochrome mediates responses to magnetic fields that have been applied in the absence of light, consistent with flavin reoxidation as the primary detection mechanism. Cryptochromes are highly conserved blue-light-absorbing flavoproteins which have been linked to the perception of electromagnetic stimuli in numerous organisms. These include sensing the direction of the earth's magnetic field in migratory birds and the intensity of magnetic fields in insects and plants. When exposed to light, cryptochromes undergo flavin reduction/reoxidation redox cycles leading to biological activation which generate radical pairs thought to be the basis for magnetic sensitivity...
September 7, 2018: Planta
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
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...
November 2018: Environment International
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
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
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
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
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
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
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
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
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
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
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
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