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https://read.qxmd.com/read/30777051/circadian-oscillator-proteins-across-the-kingdoms-of-life-structural-aspects
#1
REVIEW
Reena Saini, Mariusz Jaskolski, Seth J Davis
Circadian oscillators are networks of biochemical feedback loops that generate 24-hour rhythms in organisms from bacteria to animals. These periodic rhythms result from a complex interplay among clock components that are specific to the organism, but share molecular mechanisms across kingdoms. A full understanding of these processes requires detailed knowledge, not only of the biochemical properties of clock proteins and their interactions, but also of the three-dimensional structure of clockwork components...
February 18, 2019: BMC Biology
https://read.qxmd.com/read/30769793/depletion-of-gram-positive-bacteria-impacts-hepatic-biological-functions-during-the-light-phase
#2
Hui Yun Penny Oh, Sandrine Ellero-Simatos, Ravikumar Manickam, Nguan Soon Tan, Hervé Guillou, Walter Wahli
Living organisms display internal biological rhythms, which are an evolutionarily conserved adaptation to the environment that drives their rhythmic behavioral and physiological activities. The gut microbiota has been proposed, in association with diet, to regulate the intestinal peripheral clock. However, the effect of gut dysbiosis on liver remains elusive, despite that germfree mice show alterations in liver metabolic functions and the hepatic daily rhythm. We analyzed whether the disruption of gut microbial populations with various antibiotics would differentially impact liver functions in mice...
February 14, 2019: International Journal of Molecular Sciences
https://read.qxmd.com/read/30691393/paleozoic-diversification-of-terrestrial-chitin-degrading-bacterial-lineages
#3
Danielle S Gruen, Joanna M Wolfe, Gregory P Fournier
BACKGROUND: Establishing the divergence times of groups of organisms is a major goal of evolutionary biology. This is especially challenging for microbial lineages due to the near-absence of preserved physical evidence (diagnostic body fossils or geochemical biomarkers). Horizontal gene transfer (HGT) can serve as a temporal scaffold between microbial groups and other fossil-calibrated clades, potentially improving these estimates. Specifically, HGT to or from organisms with fossil-calibrated age estimates can propagate these constraints to additional groups that lack fossils...
January 28, 2019: BMC Evolutionary Biology
https://read.qxmd.com/read/30629323/absence-of-biomarker-evidence-for-early-eukaryotic-life-from-the-mesoproterozoic-roper-group-searching-across-a-marine-redox-gradient-in-mid-proterozoic-habitability
#4
Kevin Nguyen, Gordon D Love, J Alex Zumberge, Amy E Kelly, Jeremy D Owens, Megan K Rohrssen, Steven M Bates, Chunfang Cai, Timothy W Lyons
By about 2.0 billion years ago (Ga), there is evidence for a period best known for its extended, apparent geochemical stability expressed famously in the carbonate-carbon isotope data. Despite the first appearance and early innovation among eukaryotic organisms, this period is also known for a rarity of eukaryotic fossils and an absence of organic biomarker fingerprints for those organisms, suggesting low diversity and relatively small populations compared to the Neoproterozoic era. Nevertheless, the search for diagnostic biomarkers has not been performed with guidance from paleoenvironmental redox constrains from inorganic geochemistry that should reveal the facies that were most likely hospitable to these organisms...
January 10, 2019: Geobiology
https://read.qxmd.com/read/30616504/chronic-circadian-misalignment-results-in-reduced-longevity-and-large-scale-changes-in-gene-expression-in-drosophila
#5
Alex C Boomgarden, Gabriel D Sagewalker, Aashaka C Shah, Sarah D Haider, Pramathini Patel, Heather E Wheeler, Christine M Dubowy, Daniel J Cavanaugh
BACKGROUND: Circadian clocks are found in nearly all organisms, from bacteria to mammals, and ensure that behavioral and physiological processes occur at optimal times of day and in the correct temporal order. It is becoming increasingly clear that chronic circadian misalignment (CCM), such as occurs in shift workers or as a result of aberrant sleeping and eating schedules common to modern society, has profound metabolic and cognitive consequences, but the proximate mechanisms connecting CCM with reduced organismal health are unknown...
January 7, 2019: BMC Genomics
https://read.qxmd.com/read/30411862/early-archean-origin-of-photosystem-ii
#6
Tanai Cardona, Patricia Sánchez-Baracaldo, A William Rutherford, Anthony W Larkum
Photosystem II is a photochemical reaction center that catalyzes the light-driven oxidation of water to molecular oxygen. Water oxidation is the distinctive photochemical reaction that permitted the evolution of oxygenic photosynthesis and the eventual rise of eukaryotes. At what point during the history of life an ancestral photosystem evolved the capacity to oxidize water still remains unknown. Here, we study the evolution of the core reaction center proteins of Photosystem II using sequence and structural comparisons in combination with Bayesian relaxed molecular clocks...
November 9, 2018: Geobiology
https://read.qxmd.com/read/30169070/robustness-of-clocks-to-input-noise
#7
Michele Monti, David K Lubensky, Pieter Rein Ten Wolde
To estimate the time, many organisms, ranging from cyanobacteria to animals, employ a circadian clock which is based on a limit-cycle oscillator that can tick autonomously with a nearly 24 h period. Yet, a limit-cycle oscillator is not essential for knowing the time, as exemplified by bacteria that possess an "hourglass": a system that when forced by an oscillatory light input exhibits robust oscillations from which the organism can infer the time, but that in the absence of driving relaxes to a stable fixed point...
August 17, 2018: Physical Review Letters
https://read.qxmd.com/read/30093890/low-affinity-dnaa-atp-recognition-sites-in-e-coli-oric-make-non-equivalent-and-growth-rate-dependent-contributions-to-the-regulated-timing-of-chromosome-replication
#8
Prassanna Rao, Tania A Rozgaja, Abdulaziz Alqahtani, Julia E Grimwade, Alan C Leonard
Although the mechanisms that precisely time initiation of chromosome replication in bacteria remain unclear, most clock models are based on accumulation of the active initiator protein, DnaA-ATP. During each cell division cycle, sufficient DnaA-ATP must become available to interact with a distinct set of low affinity recognition sites in the unique chromosomal replication origin, oriC , and assemble the pre-replicative complex (orisome) that unwinds origin DNA and helps load the replicative helicase. The low affinity oriC -DnaA-ATP interactions are required for the orisome's mechanical functions, and may also play a role in timing of new rounds of DNA synthesis...
2018: Frontiers in Microbiology
https://read.qxmd.com/read/29723738/soil-metabarcoding-identifies-season-indicators-and-differentiators-of-pig-and-agrostis-festuca-spp-decomposition
#9
Ayodeji O Olakanye, T Komang Ralebitso-Senior
To gain a better understanding of how environmental microbiota respond to cadaver decomposition, a forensic ecogenomic study was made with soil only control and 4g each of Sus scrofa domesticus and plant litter (Agrostis/Festuca spp.) buried individually in a sandy clay loam (80g) in sealed but perforated triplicate microcosms. The next-generation sequencing (Illumina Miseq) of the soil bacteria (16S rRNA gene) clade revealed seasonal taxomonic shifts at genus-level for the pig and plant litter microcosms compared to the non-burial controls...
July 2018: Forensic Science International
https://read.qxmd.com/read/29610471/gene-transfers-can-date-the-tree-of-life
#10
Adrián A Davín, Eric Tannier, Tom A Williams, Bastien Boussau, Vincent Daubin, Gergely J Szöllősi
Biodiversity has always been predominantly microbial, and the scarcity of fossils from bacteria, archaea and microbial eukaryotes has prevented a comprehensive dating of the tree of life. Here, we show that patterns of lateral gene transfer deduced from an analysis of modern genomes encode a novel and abundant source of information about the temporal coexistence of lineages throughout the history of life. We use state-of-the-art species tree-aware phylogenetic methods to reconstruct the history of thousands of gene families and demonstrate that dates implied by gene transfers are consistent with estimates from relaxed molecular clocks in Bacteria, Archaea and Eukarya...
May 2018: Nature Ecology & Evolution
https://read.qxmd.com/read/29556218/multiparametric-profiling-for-identification-of-chemosensitizers-against-gram-negative-bacteria
#11
Vincent Lôme, Jean-Michel Brunel, Jean-Marie Pagès, Jean-Michel Bolla
Antibiotic resistance is now a worldwide therapeutic problem. Since the beginning of anti-infectious treatment bacteria have rapidly shown an incredible ability to develop and transfer resistance mechanisms. In the last decades, the design variation of pioneer bioactive molecules has strongly improved their activity and the pharmaceutical companies partly won the race against the clock. Since the 1980s, the new classes of antibiotics that emerged were mainly directed to Gram-positive bacteria. Thus, we are now facing to multidrug-resistant Gram-negative bacteria, with no therapeutic options to deal with them...
2018: Frontiers in Microbiology
https://read.qxmd.com/read/29434506/parameter-robustness-analysis-for-a-biochemical-oscillator-model-describing-the-social-behaviour-transition-phase-of-myxobacteria
#12
Hadi Taghvafard, Hildeberto Jardón-Kojakhmetov, Ming Cao
We develop a tool based on bifurcation analysis for parameter-robustness analysis for a class of oscillators and, in particular, examine a biochemical oscillator that describes the transition phase between social behaviours of myxobacteria. Myxobacteria are a particular group of soil bacteria that have two dogmatically different types of social behaviour: when food is abundant they live fairly isolated forming swarms, but when food is scarce, they aggregate into a multicellular organism. In the transition between the two types of behaviours, spatial wave patterns are produced, which is generally believed to be regulated by a certain biochemical clock that controls the direction of myxobacteria's motion...
January 2018: Proceedings. Mathematical, Physical, and Engineering Sciences
https://read.qxmd.com/read/29384268/dating-phototrophic-microbial-lineages-with-reticulate-gene-histories
#13
C Magnabosco, K R Moore, J M Wolfe, G P Fournier
Phototrophic bacteria are among the most biogeochemically significant organisms on Earth and are physiologically related through the use of reaction centers to collect photons for energy metabolism. However, the major phototrophic lineages are not closely related to one another in bacterial phylogeny, and the origins of their respective photosynthetic machinery remain obscured by time and low sequence similarity. To better understand the co-evolution of Cyanobacteria and other ancient anoxygenic phototrophic lineages with respect to geologic time, we designed and implemented a variety of molecular clocks that use horizontal gene transfer (HGT) as additional, relative constraints...
March 2018: Geobiology
https://read.qxmd.com/read/29305511/a-cytoplasmic-antiholin-is-embedded-in-frame-with-the-holin-in-a-lactobacillus-fermentum-bacteriophage
#14
Tingting Guo, Yongping Xin, Chenchen Zhang, Jian Kong
In double-stranded DNA bacteriophages, infection cycles are ended by host cell lysis through the action of phage-encoded endolysins and holins. The precise timing of lysis is regulated by the holin inhibitors, named antiholins. Sequence analysis has revealed that holins with a single transmembrane domain (TMD) are prevalent in Lactobacillus bacteriophages. A temperate bacteriophage of Lactobacillus fermentum , ϕPYB5, has a two-component lysis cassette containing endolysin Lyb5 and holin Hyb5. The hyb5 gene is 465 bp long, encoding 154 amino acid residues with an N-terminal TMD and a large cytoplasmic C-terminal domain...
March 15, 2018: Applied and Environmental Microbiology
https://read.qxmd.com/read/29208747/proposed-role-for-kaic-like-atpases-as-major-signal-transduction-hubs-in-archaea
#15
Kira S Makarova, Michael Y Galperin, Eugene V Koonin
All organisms must adapt to ever-changing environmental conditions and accordingly have evolved diverse signal transduction systems. In bacteria, the most abundant networks are built around the two-component signal transduction systems that include histidine kinases and receiver domains. In contrast, eukaryotic signal transduction is dominated by serine/threonine/tyrosine protein kinases. Both of these systems are also found in archaea, but they are not as common and diversified as their bacterial and eukaryotic counterparts, suggesting the possibility that archaea have evolved other, still uncharacterized signal transduction networks...
December 5, 2017: MBio
https://read.qxmd.com/read/29203514/time-restricted-feeding-alters-the-innate-immune-response-to-bacterial-endotoxin
#16
Yasmine M Cissé, Jeremy C Borniger, Elise Lemanski, William H Walker, Randy J Nelson
An important entraining signal for the endogenous circadian clock, independent of light, is food intake. The circadian and immune systems are linked; forced desynchrony of the circadian clock via nighttime light exposure or genetic ablation of core clock components impairs immune function. The timing of food intake affects various aspects of the circadian clock, but its effects on immune function are unknown. We tested the hypothesis that temporal desynchrony of food intake alters innate immune responses. Adult male Swiss Webster mice were provided with food during the night, the day, or ad libitum for 4 wk, followed by administration of LPS prior to the onset of either the active phase (zeitgeber time [ZT]12: Experiment 1) or the inactive phase (ZT0: Experiment 2)...
January 15, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
https://read.qxmd.com/read/29092409/dissipative-structures-and-biological-rhythms
#17
Albert Goldbeter
Sustained oscillations abound in biological systems. They occur at all levels of biological organization over a wide range of periods, from a fraction of a second to years, and with a variety of underlying mechanisms. They control major physiological functions, and their dysfunction is associated with a variety of physiological disorders. The goal of this review is (i) to give an overview of the main rhythms observed at the cellular and supracellular levels, (ii) to briefly describe how the study of biological rhythms unfolded in the course of time, in parallel with studies on chemical oscillations, (iii) to present the major roles of biological rhythms in the control of physiological functions, and (iv) the pathologies associated with the alteration, disappearance, or spurious occurrence of biological rhythms...
October 2017: Chaos
https://read.qxmd.com/read/29080415/successive-bacterial-colonisation-of-pork-and-its-implications-for-forensic-investigations
#18
Jessica Handke, Noemi Procopio, Michael Buckley, Dieudonne van der Meer, Graham Williams, Martin Carr, Anna Williams
AIMS: Bacteria are considered one of the major driving forces of the mammalian decomposition process and have only recently been recognised as forensic tools. At this point, little is known about their potential use as 'post-mortem clocks'. This study aimed to establish the proof of concept for using bacterial identification as post-mortem interval (PMI) indicators, using a multi-omics approach. METHODS AND RESULTS: Pieces of pork were placed in the University's outdoor facility and surface swabs were taken at regular intervals up to 60 days...
December 2017: Forensic Science International
https://read.qxmd.com/read/28970536/hsf1-dependent-and-independent-regulation-of-the-mammalian-in-vivo-heat-shock-response-and-its-impairment-in-huntington-s-disease-mouse-models
#19
Andreas Neueder, Theresa A Gipson, Sophie Batterton, Hayley J Lazell, Pamela P Farshim, Paolo Paganetti, David E Housman, Gillian P Bates
The heat shock response (HSR) is a mechanism to cope with proteotoxic stress by inducing the expression of molecular chaperones and other heat shock response genes. The HSR is evolutionarily well conserved and has been widely studied in bacteria, cell lines and lower eukaryotic model organisms. However, mechanistic insights into the HSR in higher eukaryotes, in particular in mammals, are limited. We have developed an in vivo heat shock protocol to analyze the HSR in mice and dissected heat shock factor 1 (HSF1)-dependent and -independent pathways...
October 2, 2017: Scientific Reports
https://read.qxmd.com/read/28732467/minimal-tool-set-for-a-prokaryotic-circadian-clock
#20
Nicolas M Schmelling, Robert Lehmann, Paushali Chaudhury, Christian Beck, Sonja-Verena Albers, Ilka M Axmann, Anika Wiegard
BACKGROUND: Circadian clocks are found in organisms of almost all domains including photosynthetic Cyanobacteria, whereby large diversity exists within the protein components involved. In the model cyanobacterium Synechococcus elongatus PCC 7942 circadian rhythms are driven by a unique KaiABC protein clock, which is embedded in a network of input and output factors. Homologous proteins to the KaiABC clock have been observed in Bacteria and Archaea, where evidence for circadian behavior in these domains is accumulating...
July 21, 2017: BMC Evolutionary Biology
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