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https://www.readbyqxmd.com/read/28637301/eden-evolutionary-dynamics-within-environments
#1
Philipp C Münch, Bärbel Stecher, Alice C McHardy
Summary: Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data...
June 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28637253/synthesis-and-secretion-of-isoflavones-by-field-grown-soybean
#2
Akifumi Sugiyama, Yumi Yamazaki, Shoichiro Hamamoto, Hisabumi Takase, Kazufumi Yazaki
Isoflavones play important roles in rhizosphere plant-microbe interactions. Daidzein and genistein secreted by soybean roots induce the symbiotic interaction with rhizobia and may modulate rhizosphere interactions with microbes. Yet despite their important roles, little is known about the biosynthesis, secretion and fate of isoflavones in field-grown soybeans. Here, we analysed isoflavone contents and the expression of isoflavone biosynthesis genes in field-grown soybeans. In roots, isoflavone contents and composition did not change with crop growth, but the expressions of UGT4, an isoflavone-specific 7-O-glucosyltransferase, and of ICHG (Isoflavone conjugates hydrolysing beta-glucosidase) was decreased during the reproductive stages...
June 16, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28637236/the-ribosome-assembly-gene-network-is-controlled-by-the-feedback-regulation-of-transcription-elongation
#3
Fernando Gómez-Herreros, Thanasis Margaritis, Olga Rodríguez-Galán, Vicent Pelechano, Victoria Begley, Gonzalo Millán-Zambrano, Macarena Morillo-Huesca, Mari Cruz Muñoz-Centeno, José E Pérez-Ortín, Jesús de la Cruz, Frank C P Holstege, Sebastián Chávez
Ribosome assembly requires the concerted expression of hundreds of genes, which are transcribed by all three nuclear RNA polymerases. Transcription elongation involves dynamic interactions between RNA polymerases and chromatin. We performed a synthetic lethal screening in Saccharomyces cerevisiae with a conditional allele of SPT6, which encodes one of the factors that facilitates this process. Some of these synthetic mutants corresponded to factors that facilitate pre-rRNA processing and ribosome biogenesis...
June 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28637186/cpg-and-methylation-dependent-dna-binding-and-dynamics-of-the-methylcytosine-binding-domain-2-protein-at-the-single-molecule-level
#4
Hai Pan, Stephanie M Bilinovich, Parminder Kaur, Robert Riehn, Hong Wang, David C Williams
The methylcytosine-binding domain 2 (MBD2) protein recruits the nucleosome remodeling and deacetylase complex (NuRD) to methylated DNA to modify chromatin and regulate transcription. Importantly, MBD2 functions within CpG islands that contain 100s to 1000s of potential binding sites. Since NuRD physically rearranges nucleosomes, the dynamic mobility of this complex is directly related to function. In these studies, we use NMR and single-molecule atomic force microscopy and fluorescence imaging to study DNA binding dynamics of MBD2...
June 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28637183/nuclitrack-an-integrated-nuclei-tracking-application
#5
Sam Cooper, Alexis R Barr, Robert Glen, Chris Bakal
Summary: Live imaging studies give unparalleled insight into dynamic single cell behaviours and fate decisions. However, the challenge of reliably tracking single cells over long periods of time limits both the throughput and ease with which such studies can be performed. Here, we present NucliTrack, a cross platform solution for automatically segmenting, tracking and extracting features from fluorescently-labelled nuclei. NucliTrack performs similarly to other state-of-the-art cell tracking algorithms, but NucliTrack's interactive, graphical interface makes it significantly more user friendly...
June 20, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28637181/crosstalk-between-histone-modifications-indicates-that-inhibition-of-arginine-methyltransferase-carm1-activity-reverses-hiv-latency
#6
Zheng Zhang, Bryan C Nikolai, Leah A Gates, Sung Yun Jung, Edward B Siwak, Bin He, Andrew P Rice, Bert W O'Malley, Qin Feng
In eukaryotic cells, the gene expression status is strictly controlled by epigenetic modifications on chromatin. The repressive status of chromatin largely contributes to HIV latency. Studies have shown that modification of histone H3K27 acts as a key molecular switch for activation or suppression of many cellular genes. In this study, we found that K27-acetylated histone H3 specifically recruited Super Elongation Complex (SEC), the transcriptional elongation complex essential for HIV-1 long terminal repeat (LTR)-mediated and general cellular transcription...
June 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28637161/sequential-batch-thermophilic-solid-state-anaerobic-digestion-of-lignocellulosic-biomass-via-recirculating-digestate-as-inoculum-part-ii-microbial-diversity-and-succession
#7
Long Lin, Zhongtang Yu, Yebo Li
This study aimed to investigate the effect of recirculation of digestate as inoculum on the microbial communities in thermophilic solid-state anaerobic digestion (SS-AD) of yard trimmings. The SS-AD consisted of 4 consecutive runs (30days/run), with digestate from the previous run being used as the inoculum of the subsequent run. Bacterial and archaeal communities (day 0, 4, 8, 12, 20, and 30) were examined using Illumina sequencing of 16S rRNA genes. The results revealed substantial microbial succession toward increased diversity until run 3...
June 9, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28637126/ecological-momentary-assessment-for-rehabilitation-of-chronic-illness-and-disability
#8
Ashlee McKeon, Michael McCue, Elizabeth Skidmore, Michelle Schein, Jamie Kulzer
PURPOSE: The main objectives of this manuscript were to provide a theoretical perspective on naturalistic delivery in rehabilitation based upon a literature review and establish a rationale for using ecological momentary assessment (EMA) for naturalistic assessment for chronic illness and disability (CID) in rehabilitation. METHOD: Existing literature on EMA use across CID cohorts was gathered and analyzed to form a theoretical overview of implementation of this method in research...
February 7, 2017: Disability and Rehabilitation
https://www.readbyqxmd.com/read/28637098/uncovering-the-contribution-of-epigenetics-to-plant-phenotypic-variation-in-mediterranean-ecosystems
#9
REVIEW
F Balao, O Paun, C Alonso
Epigenetic signals can affect plant phenotype and fitness and be stably inherited across multiple generations. Epigenetic regulation plays a key role in the mechanisms of plant response to the environment without altering DNA sequence. As plants cannot adapt behaviourally or migrate instantly, such dynamic epigenetic responses may be particularly crucial for survival of plants within changing and challenging environments, such as the Mediterranean-Type Ecosystems (MTEs). These ecosystems suffer recurrent stressful events (warm and dry summers with associated fire regimes) that have selected for plants with similar phenotypic complex traits, resulting in similar vegetation growth forms...
June 21, 2017: Plant Biology
https://www.readbyqxmd.com/read/28637006/the-effect-of-ca125-on-metastasis-of-ovarian-cancer-old-marker-new-function
#10
Qin Yuan, Jiayin Song, Weiwei Yang, Hongyan Wang, Qianyu Huo, Jie Yang, Xiaoxu Yu, Yunde Liu, Chen Xu, Huijing Bao
CA125 has been used extensively to screen for neoplasms, especially in ovarian cancer. The serum CA125 level can be used as a better prognosis evaluation and it may dynamic monitoring the disease progression. We explored the effect of CA125 on ovarian cancer cell migration and its underlying mechanism. Transwell assays showed that exposure to 0.2 μg/ml or 0.4 μg/ml CA125 for 48 h increased migration of A2780 and OVCAR-3 ovarian cancer cells. This effect of CA125 was blocked addition of 200 ng/ml DKK-1, a Wnt pathway inhibitor...
June 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28636959/the-enteric-network-interactions-between-the-immune-and-nervous-systems-of-the-gut
#11
REVIEW
Bryan B Yoo, Sarkis K Mazmanian
Interactions between the nervous and immune systems enable the gut to respond to the variety of dietary products that it absorbs, the broad spectrum of pathogens that it encounters, and the diverse microbiome that it harbors. The enteric nervous system (ENS) senses and reacts to the dynamic ecosystem of the gastrointestinal (GI) tract by translating chemical cues from the environment into neuronal impulses that propagate throughout the gut and into other organs in the body, including the central nervous system (CNS)...
June 20, 2017: Immunity
https://www.readbyqxmd.com/read/28636954/germinal-center-selection-and-affinity-maturation-require-dynamic-regulation-of-mtorc1-kinase
#12
Jonatan Ersching, Alejo Efeyan, Luka Mesin, Johanne T Jacobsen, Giulia Pasqual, Brian C Grabiner, David Dominguez-Sola, David M Sabatini, Gabriel D Victora
During antibody affinity maturation, germinal center (GC) B cells cycle between affinity-driven selection in the light zone (LZ) and proliferation and somatic hypermutation in the dark zone (DZ). Although selection of GC B cells is triggered by antigen-dependent signals delivered in the LZ, DZ proliferation occurs in the absence of such signals. We show that positive selection triggered by T cell help activates the mechanistic target of rapamycin complex 1 (mTORC1), which promotes the anabolic program that supports DZ proliferation...
June 20, 2017: Immunity
https://www.readbyqxmd.com/read/28636949/cloning-expression-and-nutritional-regulation-of-the-glutamine-synthetase-gene-in-ctenopharyngodon-idellus
#13
Rong Hu, Fufa Qu, Jianzhou Tang, Qiong Zhao, Jinpeng Yan, Zhigang Zhou, Yi Zhou, Zhen Liu
Glutamine synthetase (GS) is considered a master enzyme that catalyses ATP-dependent biosynthesis of glutamine from glutamate. In the present study, the GS gene was cloned from the intestine of grass carp, (Ctenopharyngodon idellus). The full-length cDNA sequence of GS encodes a 371-amino-acid polypetide. Phylogenetic analysis of the C. idellus GS sequence reveals common carp (Cyprinus carpio) as its closest neighbor. GS mRNA was differentially expressed in different tissues, with high to low gradient expression the intestine, brain, muscle, heart, gill, liver, pituitary gland, and spleen...
June 18, 2017: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/28636943/opa1-isoforms-in-the-hierarchical-organization-of-mitochondrial-functions
#14
Valentina Del Dotto, Prashant Mishra, Sara Vidoni, Mario Fogazza, Alessandra Maresca, Leonardo Caporali, J Michael McCaffery, Martina Cappelletti, Enrico Baruffini, Guy Lenaers, David Chan, Michela Rugolo, Valerio Carelli, Claudia Zanna
OPA1 is a GTPase that controls mitochondrial fusion, cristae integrity, and mtDNA maintenance. In humans, eight isoforms are expressed as combinations of long and short forms, but it is unclear whether OPA1 functions are associated with specific isoforms and/or domains. To address this, we expressed each of the eight isoforms or different constructs of isoform 1 in Opa1(-/-) MEFs. We observed that any isoform could restore cristae structure, mtDNA abundance, and energetic efficiency independently of mitochondrial network morphology...
June 20, 2017: Cell Reports
https://www.readbyqxmd.com/read/28636923/mechanosensitive-adhesion-explains-stepping-motility-in-amoeboid-cells
#15
Calina A Copos, Sam Walcott, Juan C Del Álamo, Effie Bastounis, Alex Mogilner, Robert D Guy
Cells employing amoeboid motility exhibit repetitive cycles of rapid expansion and contraction and apply coordinated traction forces to their environment. Although aspects of this process are well studied, it is unclear how the cell controls the coordination of cell length changes with adhesion to the surface. Here, we develop a simple model to mechanistically explain the emergence of periodic changes in length and spatiotemporal dynamics of traction forces measured in chemotaxing unicellular amoeba, Dictyostelium discoideum...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636920/nanog-fluctuations-in-embryonic-stem-cells-highlight-the-problem-of-measurement-in-cell-biology
#16
Rosanna C G Smith, Patrick S Stumpf, Sonya J Ridden, Aaron Sim, Sarah Filippi, Heather A Harrington, Ben D MacArthur
A number of important pluripotency regulators, including the transcription factor Nanog, are observed to fluctuate stochastically in individual embryonic stem cells. By transiently priming cells for commitment to different lineages, these fluctuations are thought to be important to the maintenance of, and exit from, pluripotency. However, because temporal changes in intracellular protein abundances cannot be measured directly in live cells, fluctuations are typically assessed using genetically engineered reporter cell lines that produce a fluorescent signal as a proxy for protein expression...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636918/actin-filament-strain-promotes-severing-and-cofilin-dissociation
#17
Anthony C Schramm, Glen M Hocky, Gregory A Voth, Laurent Blanchoin, Jean-Louis Martiel, Enrique M De La Cruz
Computational and structural studies have been indispensable in investigating the molecular origins of actin filament mechanical properties and modulation by the regulatory severing protein cofilin. All-atom molecular dynamics simulations of cofilactin filament structures determined by electron cryomicroscopy reveal how cofilin enhances the bending and twisting compliance of actin filaments. Continuum mechanics models suggest that buckled cofilactin filaments localize elastic energy at boundaries between bare and cofilin-decorated segments because of their nonuniform elasticity, thereby accelerating filament severing...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636916/structural-behavior-of-the-peptaibol-harzianin-hk-vi-in-a-dmpc-bilayer-insights-from-md-simulations
#18
Marina Putzu, Sezgin Kara, Sergii Afonin, Stephan L Grage, Andrea Bordessa, Grégory Chaume, Thierry Brigaud, Anne S Ulrich, Tomáš Kubař
Microsecond molecular dynamics simulations of harzianin HK VI (HZ) interacting with a dimyristoylphosphatidylcholine bilayer were performed at the condition of low peptide-to-lipid ratio. Two orientations of HZ molecule in the bilayer were found and characterized. In the orientation perpendicular to the bilayer surface, HZ induces a local thinning of the bilayer. When inserted into the bilayer parallel to its surface, HZ is located nearly completely within the hydrophobic region of the bilayer. A combination of solid-state NMR and circular dichroism experiments found the latter orientation to be dominant...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636915/probing-the-structural-dynamics-of-the-nmda-receptor-activation-by-coarse-grained-modeling
#19
Wenjun Zheng, Han Wen, Gary J Iacobucci, Gabriela K Popescu
N-Methyl-D-aspartate (NMDA) receptors are glutamate-gated excitatory channels that play essential roles in brain functions. High-resolution structures have been solved for an allosterically inhibited and agonist-bound form of a functional NMDA receptor; however, other key functional states (particularly the active open-channel state) were only resolved at moderate resolutions by cryo-electron microscopy (cryo-EM). To decrypt the mechanism of the NMDA receptor activation, structural modeling is essential to provide presently missing information about structural dynamics...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636914/peptide-protein-binding-investigated-by-far-ir-spectroscopy-and-molecular-dynamics-simulations
#20
Yoann Cote, Yves Nominé, Juan Ramirez, Petra Hellwig, Roland H Stote
Molecular dynamics (MD) simulations and far-infrared (far-IR) spectroscopy were combined to study peptide binding by the second PDZ domain (PDZ1) of MAGI1, which has been identified as an important target for the Human Papilloma Virus. PDZ1 recognizes and binds to the C-terminal end of the E6 protein from high-risk Human Papilloma Virus. The far-IR spectra of two forms of the protein, an unbound APO form and a HOLO form (where the PDZ1 is bound to an 11-residue peptide derived from the C terminus of HPV16 E6), were obtained...
June 20, 2017: Biophysical Journal
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