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https://www.readbyqxmd.com/read/28107009/nmr-and-computation-reveal-a-pressure-sensitive-folded-conformation-of-trp-cage
#1
Soichiro Kitazawa, Martin J Fossat, Scott A McCallum, Angel E Garcia, Catherine Ann Royer
Beyond defining the structure and stability of folded states of proteins, primary amino acid sequences determine all of the features of their conformational landscapes. Characterizing how sequence modulates the population of protein excited states or folding pathways requires atomic level detailed structural and energetic information. Such insight is essential for improving protein design strategies, as well as for interpreting protein evolution. Here, high pressure NMR and molecular dynamics simulations were combined to probe the conformational landscape of a small model protein, the tryptophan cage variant, Tc5b...
January 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28106288/nuclear-inositide-signaling-via-phospholipase-c
#2
Stefano Ratti, Sara Mongiorgi, Giulia Ramazzotti, Matilde Y Follo, Giulia A Mariani, Pann-Ghill Suh, James A McCubrey, Lucio Cocco, Lucia Manzoli
The existence of an independent nuclear inositide pathway distinct from the cytoplasmic one has been demonstrated in different physiological systems and in diseases. In this prospect we analyze the role of PI-PLCβ1 nuclear isoform in relation to the cell cycle regulation, the cell differentiation and different physiopathological pathways focusing on the importance of the nuclear localization from both molecular and clinical point of view. PI-PLCβ1 is essential for G1/S transition through DAG and Cyclin D3 and plays also a central role in G2/M progression through Cyclin B1 and PKCα...
January 20, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28106190/nonadiabatic-photodynamics-and-uv-absorption-spectrum-of-all-trans-octatetraene
#3
Igor Lyskov, Horst Köppel, Christel M Marian
The short-time molecular quantum dynamics of all-trans-octatetraene after electronic excitation to the first bright valence state is theoretically investigated. A semiempirical approach of a multireference configuration interaction based on density functional theory, the so called hybrid DFT/MRCI, in both its original and redesigned formulations, is used for treating the electronic part of the problem. The nuclear kinetic part is defined with the help of symmetry-adapted internal coordinates also suitable for a large amplitude displacement...
January 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28106042/diverse-feather-shape-evolution-enabled-by-coupling-anisotropic-signalling-modules-with-self-organizing-branching-programme
#4
Ang Li, Seth Figueroa, Ting-Xin Jiang, Ping Wu, Randall Widelitz, Qing Nie, Cheng-Ming Chuong
Adaptation of feathered dinosaurs and Mesozoic birds to new ecological niches was potentiated by rapid diversification of feather vane shapes. The molecular mechanism driving this spectacular process remains unclear. Here, through morphology analysis, transcriptome profiling, functional perturbations and mathematical simulations, we find that mesenchyme-derived GDF10 and GREM1 are major controllers for the topologies of rachidial and barb generative zones (setting vane boundaries), respectively, by tuning the periodic-branching programme of epithelial progenitors...
January 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28104745/molecular-evolution-of-two-distinct-dmrt1-promoters-for-germ-and-somatic-cells-in-vertebrate-gonads
#5
EDITORIAL
Shuuji Mawaribuchi, Masato Musashijima, Mikako Wada, Yumi Izutsu, Erina Kurakata, Min Kyun Park, Nobuhiko Takamatsu, Michihiko Ito
No abstract text is available yet for this article.
January 19, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28103796/phylogenomic-analysis-of-copepoda-arthropoda-crustacea-reveals-unexpected-similarities-with-earlier-proposed-morphological-phylogenies
#6
Seong-Il Eyun
BACKGROUND: Copepods play a critical role in marine ecosystems but have been poorly investigated in phylogenetic studies. Morphological evidence supports the monophyly of copepods, whereas interordinal relationships continue to be debated. In particular, the phylogenetic position of the order Harpacticoida is still ambiguous and inconsistent among studies. Until now, a small number of molecular studies have been done using only a limited number or even partial genes and thus there is so far no consensus at the order-level...
January 19, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28102938/low-energy-catalytic-electrolysis-for-simultaneously-hydrogen-evolution-and-lignin-depolymerization
#7
Xu Du, Wei Liu, Zhe Zhang, Arie Mulyadi, Alex Brittain, Jian Gong, Yulin Deng
Hereby we present a novel proton exchange membrane (PEM) electrolysis process in which lignin was used as the hydrogen source at anode for hydrogen production. Either polyoxometalate (POM) or FeCl3 was used as the catalysts and charge transfer agents in anode. Over 90% Faraday efficiency was achieved. In a thermal insulation reactor, the heat energy can be maintained at a very low stage for continuous operation. Compared to the best alkaline water electrolysis reported in literature, the electrical energy consumption could be 40% lower with novel lignin electrolysis method...
January 19, 2017: ChemSusChem
https://www.readbyqxmd.com/read/28101895/on-the-rarity-of-dioecy-in-flowering-plants
#8
Jos Käfer, Gabriel A B Marais, John R Pannell
Dioecy, the co-existence of separate male and female individuals in a population, is a rare but phylogenetically widespread sexual system in flowering plants. While research has concentrated on why and how dioecy evolves from hermaphroditism, the question of why dioecy is rare, despite repeated transitions to it, has received much less attention. Previous phylogenetic and theoretical studies have suggested that dioecy might be an evolutionary dead end. However, recent research indicates that the phylogenetic support for this hypothesis is attributable to a methodological bias, and that there is no evidence for reduced diversification in dioecious angiosperms...
January 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28100614/human-rhinovirus-diversity-and-evolution-how-strange-the-change-from-major-to-minor
#9
Nicole Lewis-Rogers, Jon Seger, Frederick R Adler
: Rhinoviruses are the most common cause of the common cold. Their many distinct lineages fall into "major" and "minor" groups that use different cell-surface receptors to enter host cells. Minor-group rhinoviruses are more immunogenic in laboratory studies, although their patterns of transmission and their cold symptoms are broadly similar to those of the major group. Here we present evolutionary evidence that minor-group viruses are also more immunogenic in humans. A key finding is that rates of amino-acid substitution at exposed sites in the capsid proteins VP2, VP3 and VP1 tend to be elevated in minor-group relative to major-group viruses, while rates at buried sites show no consistent differences...
January 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28100385/-phylogenetic-analysis-of-envelope-gene-of-dengue-virus-serotype-2-in-guangzhou-2001-2015
#10
Y Liu, L Y Jiang, L Luo, Y M Cao, Q L Jing, Z C Yang
Objective: To investigate the molecular characteristics of dengue virus serotype 2 (DENV2) in Guangzhou during 2001-2015, and analyze the E gene of the strains isolated, the phylogenetic tree and molecular clock were constructed to know about the evolution of the strains. Methods: The serum samples of the patients were detected by real time PCR, and positive samples were used to isolate dengue virus by using C6/36 cells. The E gene of the isolated strains were sequenced. The phylogenetic tree was constructed by using software Mega 4...
January 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28099022/molecular-weight-dependence-of-interdiffusion-and-adhesion-of-polymers-at-short-contact-times
#11
Robert Gurney, Anastase Henry, Regis Schach, Anke Lindner, Costantino Creton
The self-adhesion and subsequent debonding of thin layers of three linear and monodisperse random copolymers of styrene-butadiene (SBR) with molecular weights varying between 30 and 75 times the average molecular weight between entanglements Me was investigated using a carefully controlled tack adhesion testing device in conjunction with a fast camera setup over a range of contact times tc (10 ms to 10 s) much shorter in comparison to the terminal relaxation times of the polymers. The evolution of the stress-strain curves and debonding mechanisms with increasing contact time was examined, and the work required to debond the layers was found to be strongly dependent on molecular weight at long contact times, but not at short contact times...
January 18, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28098598/science-of-intracrinology-in-postmenopausal-women
#12
Fernand Labrie, Alain Bélanger, Georges Pelletier, Céline Martel, David F Archer, Wulf H Utian
OBJECTIVE: To illustrate the marked differences between classical endocrinology that distributes hormones to all tissues of the body through the bloodstream and the science of intracrinology, whereby each cell of each peripheral tissue makes a small and appropriate amount of estrogens and androgens from the inactive precursor dehydroepiandrosterone (DHEA), DHEA being mainly of adrenal origin. Because only the inactivated sex steroids are released in the blood, influence in the other tissues is avoided...
January 16, 2017: Menopause: the Journal of the North American Menopause Society
https://www.readbyqxmd.com/read/28098528/spread-and-evolution-of-respiratory-syncytial-virus-a-genotype-on1-coastal-kenya-2010-2015
#13
James R Otieno, Everlyn M Kamau, Charles N Agoti, Clement Lewa, Grieven Otieno, Ann Bett, Mwanajuma Ngama, Patricia A Cane, D James Nokes
In February 2012, the novel respiratory syncytial virus (RSV) group A, genotype ON1, was detected in Kilifi County, coastal Kenya. ON1 is characterized by a 72-nt duplication within the highly variable G gene (encoding the immunogenic attachment surface protein). Cases were diagnosed through surveillance of pneumonia in children at the county hospital. Analysis of epidemiologic, clinical, and sequence data of RSV-A viruses detected over 5 RSV seasons (2010/2011 to 2014/2015) indicated the following: 1) replacement of previously circulating genotype GA2 ON1, 2) an abrupt expansion in the number of ON1 variants detected in the 2014/2015 epidemic, 3) recently accumulation of amino acid substitutions within the ON1 duplicated sequence, and 4) no clear evidence of altered pathogenicity relative to GA2...
February 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28098444/a-heterogeneous-electrocatalyst-with-molecular-cobalt-ions-serving-as-the-center-of-active-sites
#14
Jiong Wang, Xiaoming Ge, Zhaolin Liu, Larissa Thia, Ya Yan, Wei Xiao, Xin Wang
Molecular Co2+ ions were grafted onto doped graphene in a coordination environment, resulting in the formation of molecularly well-defined, highly active electrocatalytic sites at a heterogeneous interface for the oxygen evolution reaction (OER). The S dopants of graphene are suggested to be one of the binding sites and to be responsible for improving the intrinsic activity of the Co sites. The turnover frequency of such Co sites is greater than that of many Co-based nanostructures and IrO2 catalysts. Through a series of carefully designed experiments, the pathway for the evolution of the Co cation-based molecular catalyst for the OER was further demonstrated on such a single Co-ion site for the first time...
January 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28098347/evolutionary-origin-of-phytochrome-responses-and-signaling-in-land-plants
#15
REVIEW
Keisuke Inoue, Ryuichi Nishihama, Takayuki Kohchi
Phytochromes comprise one of the major photoreceptor families in plants, and they regulate many aspects of plant growth and development throughout the plant life cycle. A canonical land plant phytochrome originated in the common ancestor of streptophytes. Phytochromes have diversified in seed plants and some basal land plants due to lineage-specific gene duplications that occurred during the course of land plant evolution. Molecular genetic analyses using Arabidopsis thaliana suggested that there are two types of phytochromes in angiosperms, light-labile type I and light-stable type II, which have different signaling mechanisms and which regulate distinct responses...
January 18, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28097160/contribution-to-the-molecular-systematics-of-the-genus-capoeta-from-the-south-caspian-sea-basin-using-mitochondrial-cytochrome-b-sequences-teleostei-cyprinidae
#16
Halimeh Zareian, Hamid Reza Esmaeili, Adeleh Heidari, Majid Reza Khoshkholgh, Hamed Mousavi-Sabet
Traditionally, Capoeta populations from the southern Caspian Sea basin have been considered as Capoeta capoeta gracilis. Study on the phylogenetic relationship of Capoeta species using mitochondrial cytochrome b gene sequences show that Capoeta population from the southern Caspian Sea basin is distinct species and receive well support (posterior probability of 100%). Based on the tree topologies obtained from Bayesian and Maximum Likelihood methods, three main groups for the studied Capoeta were detected: Clade I) Capoeta trutta group (the Mesopotamian Capoeta group) including closely related taxa (e...
June 2016: Molecular Biology Research Communications
https://www.readbyqxmd.com/read/28097046/molecular-classification-of-tissue-from-a-transformed-non-hogkin-s-lymphoma-case-with-unexpected-long-time-remission
#17
Julie Støve Bødker, Marianne Tang Severinsen, Tarec Christoffer El-Galaly, Rasmus Froberg Brøndum, Maria Bach Laursen, Steffen Falgreen, Mette Nyegaard, Alexander Schmitz, Lasse Hjort Jakobsen, Anna Amanda Schönherz, Hanne Due, Linn Reinholdt, Martin Bøgsted, Karen Dybkær, Hans Erik Johnsen
BACKGROUND: The concept of precision medicine in cancer includes individual molecular studies to predict clinical outcomes. In the present N = 1 case we retrospectively have analysed lymphoma tissue by exome sequencing and global gene expression in a patient with unexpected long-term remission following relaps. The goals were to phenotype the diagnostic and relapsed lymphoma tissue and evaluate its pattern. Furthermore, to identify mutations available for targeted therapy and expression of genes to predict specific drug effects by resistance gene signatures (REGS) for R-CHOP as described at http://www...
2017: Experimental Hematology & Oncology
https://www.readbyqxmd.com/read/28096374/phylogenetic-analysis-of-the-human-antibody-repertoire-reveals-quantitative-signatures-of-immune-senescence-and-aging
#18
Charles F A de Bourcy, Cesar J Lopez Angel, Christopher Vollmers, Cornelia L Dekker, Mark M Davis, Stephen R Quake
The elderly have reduced humoral immunity, as manifested by increased susceptibility to infections and impaired vaccine responses. To investigate the effects of aging on B-cell receptor (BCR) repertoire evolution during an immunological challenge, we used a phylogenetic distance metric to analyze Ig heavy-chain transcript sequences in both young and elderly individuals before and after influenza vaccination. We determined that BCR repertoires become increasingly specialized over a span of decades, but less plastic...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28096304/antibiotic-cycling-and-antibiotic-mixing-which-one-best-mitigates-antibiotic-resistance
#19
R E Beardmore, R Pena-Miller, F Gori, J Iredell
Can we exploit our burgeoning understanding of molecular evolution to slow the progress of drug resistance? One role of an infection clinician is exactly that: to foresee trajectories to resistance during antibiotic treatment and to hinder that evolutionary course. But can this be done at a hospital-wide scale? Clinicians and theoreticians tried to when they proposed two conicting behavioural strategies that are expected to curb resistance evolution in the clinic, these are known as 'antibiotic cycling' and 'antibiotic mixing'...
January 17, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28096247/order-matters-the-order-of-somatic-mutations-influences-cancer-evolution
#20
David G Kent, Anthony R Green
Cancers evolve as a consequence of multiple somatic lesions, with competition between subclones and sequential subclonal evolution. Some driver mutations arise either early or late in the evolution of different individual tumors, suggesting that the final malignant properties of a subclone reflect the sum of mutations acquired rather than the order in which they arose. However, very little is known about the cellular consequences of altering the order in which mutations are acquired. Recent studies of human myeloproliferative neoplasms show that the order in which individual mutations are acquired has a dramatic impact on the cell biological and molecular properties of tumor-initiating cells...
January 17, 2017: Cold Spring Harbor Perspectives in Medicine
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