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https://www.readbyqxmd.com/read/28650586/a-complete-thermodynamic-analysis-of-enzyme-turnover-links-the-free-energy-landscape-to-enzyme-catalysis
#1
Hannah Bl Jones, Stephen A Wells, Erica J Prentice, Anthony Kwok, Liyin L Liang, Vickery L Arcus, Christopher R Pudney
Our understanding of how enzymes work is colored by static structure depictions where the enzyme scaffold is presented as either immobile, or in equilibrium between well-defined static conformations. Proteins however exhibit a large degree of motion over a broad range of timescales and magnitudes and this is defined thermodynamically by the enzyme free energy landscape (FEL). The role and importance of enzyme motion is extremely contentious. Much of the challenge is in the experimental detection of so called 'conformational sampling' involved in enzyme turnover...
June 26, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28650142/conformational-landscapes-of-metal-ii-porphyrinato-chlorinato-and-morpholinochlorinato-complexes
#2
Meenakshi Sharma, Alexander L Ticho, Lalith Samankumara, Matthias Zeller, Christian Brückner
The macrocycle conformation of [meso-tetraarylporphyrinato]metal complexes is metal-dependent. Furthermore, hydroporphyrins and some of their analogues are known to be more conformationally flexible than the parent porphyrins, but the extent to which this is reflected in their metal-dependent conformations was much less studied. meso-Tetraarylmorpholinochlorins are intrinsically nonplanar chlorin analogues in which the five-membered pyrroline moiety was replaced by a six-membered morpholine moiety. The metal complexes (M = Ni(2+), Cu(2+), Zn(2+), Pd(2+), Ag(2+)) of meso-aryl-2,3-dimethoxychlorins and meso-arylmorpholinochlorins were prepared...
June 26, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28650043/heme-containing-enzymes-and-inhibitors-for-tryptophan-metabolism
#3
REVIEW
Daojing Yan, Ying-Wu Lin, Xiangshi Tan
Iron-containing enzymes such as heme enzymes play crucial roles in biological systems. Three distinct heme-containing dioxygenase enzymes, tryptophan 2,3-dioxygenase (TDO), indoleamine 2,3-dioxygenase 1 (IDO1) and indoleamine 2,3-dioxygenase 2 (IDO2) catalyze the initial and rate-limiting step of l-tryptophan catabolism through the kynurenine pathway in mammals. Overexpression of these enzymes causes depletion of tryptophan and the accumulation of metabolic products, which contributes to tumor immune tolerance and immune dysregulation in a variety of disease pathologies...
June 26, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/28649324/conceptualising-the-interactive-effects-of-climate-change-and-biological-invasions-on-subarctic-freshwater-fish
#4
REVIEW
Robert J Rolls, Brian Hayden, Kimmo K Kahilainen
Climate change and species invasions represent key threats to global biodiversity. Subarctic freshwaters are sentinels for understanding both stressors because the effects of climate change are disproportionately strong at high latitudes and invasion of temperate species is prevalent. Here, we summarize the environmental effects of climate change and illustrate the ecological responses of freshwater fishes to these effects, spanning individual, population, community and ecosystem levels. Climate change is modifying hydrological cycles across atmospheric, terrestrial and aquatic components of subarctic ecosystems, causing increases in ambient water temperature and nutrient availability...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28648726/taking-the-measure-of-microed
#5
REVIEW
Jose A Rodriguez, David S Eisenberg, Tamir Gonen
It is now possible to routinely determine atomic resolution structures by electron cryo-microscopy (cryoEM), facilitated in part by the method known as micro electron-diffraction (MicroED). Since its initial demonstration in 2013, MicroED has helped determine a variety of protein structures ranging in molecular weight from a few hundred Daltons to several hundred thousand Daltons. Some of these structures were novel while others were previously known. The resolutions of structures obtained thus far by MicroED range from 3...
June 22, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28648362/formation-of-an-international-intergroup-to-coordinate-clinical-trials-in-head-and-neck-cancers-hncig
#6
Quynh Thu Le, John J Welch, Jan B Vermorken, Danny Rischin, Hisham Mehanna
Clinical trials in head and neck cancer (HNC) face multiple challenges including low global incidence, excessive patient comorbidity rate, high treatment-related toxicity and more recently a changing tumor biology landscape. As clinical trials evolve to address new knowledge about HNC biology, the overall pool of eligible patients for each trial becomes smaller, leading to more accrual challenges. These challenges have led to the formation of the Head and Neck Cancer Intergroup (HNCIG) comprised of large HNC international and national cooperative groups and sites with the goal of facilitating the conduct of high quality clinical trials in a timely manner to improve outcomes in HNC...
June 22, 2017: Oral Oncology
https://www.readbyqxmd.com/read/28646471/decoding-early-myelopoiesis-from-dynamics-of-core-endogenous-network
#7
Hang Su, Gaowei Wang, Ruoshi Yuan, Junqiang Wang, Ying Tang, Ping Ao, Xiaomei Zhu
A decade ago mainstream molecular biologists regarded it impossible or biologically ill-motivated to understand the dynamics of complex biological phenomena, such as cancer genesis and progression, from a network perspective. Indeed, there are numerical difficulties even for those who were determined to explore along this direction. Undeterred, seven years ago a group of Chinese scientists started a program aiming to obtain quantitative connections between tumors and network dynamics. Many interesting results have been obtained...
May 29, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28645947/role-structure-and-effects-of-medical-tourism-in-africa-a-systematic-scoping-review-protocol
#8
John Jo Mogaka, Joyce M Tsoka-Gwegweni, Lucia M Mupara, Tivani Mashamba-Thompson
INTRODUCTION: Some patients travel out of, while others come into Africa for medical care through a growing global phenomenon referred to as medical tourism (MT): the travel in search of medical care that is either unavailable, unaffordable or proscribed at home healthcare systems. While some castigate MT as promoting healthcare inequity, others endorse it as a revenue generator, promising local healthcare system strengthening. Currently, however, the understanding of this component of healthcare in Africa is inadequate...
June 23, 2017: BMJ Open
https://www.readbyqxmd.com/read/28645716/guide-to-active-vaccine-safety-surveillance-report-of-cioms-working-group-on-vaccine-safety-executive-summary
#9
U Heininger, K Holm, I Caplanusi, S R Bailey
In 2013, the Council for International Organizations of Medical Sciences (CIOMS) created a Working Group on Vaccine Safety (WG) to address unmet needs in the area of vaccine pharmacovigilance. Generating reliable data about specific vaccine safety concerns is becoming a priority due to recent progress in the development and deployment of new vaccines of global importance, as well as novel vaccines targeting diseases specifically endemic to many resource-limited countries (RLCs), e.g. malaria, dengue. The WG created a Guide to Active Vaccine Safety Surveillance (AVSS) to assist national regulatory authorities and national immunization program officers in RLCs in determining the best course of action with regards to non-routine pharmacovigilance activities, when confronted with a launch of a new vaccine or a vaccine that is new to their country...
June 20, 2017: Vaccine
https://www.readbyqxmd.com/read/28645141/does-the-seed-bank-contribute-to-the-build-up-of-a-genetic-extinction-debt-in-the-grassland-perennial-campanula-rotundifolia
#10
Jan Plue, Katrien Vandepitte, Olivier Honnay, Sara A O Cousins
Background and Aims: Habitat fragmentation threatens global biodiversity. Many plant species persist in habitat fragments via persistent life cycle stages such as seed banks, generating a species extinction debt. Here, seed banks are hypothesized to cause a temporal delay in the expected loss of genetic variation, which can be referred to as a genetic extinction debt, as a possible mechanism behind species extinction debts. Methods: Fragmented grassland populations of Campanula rotundifolia were examined for evidence of a genetic extinction debt, investigating if the seed bank contributed to the extinction debt build-up...
June 21, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28644577/evidence-of-fuels-management-and-fire-weather-influencing-fire-severity-in-an-extreme-fire-event
#11
Jamie M Lydersen, Brandon M Collins, Matthew L Brooks, John R Matchett, Kristen L Shive, Nicholas A Povak, Van R Kane, Douglas F Smith
Following changes in vegetation structure and pattern, along with a changing climate, large wildfire incidence has increased in forests throughout the western U.S. Given this increase there is great interest in whether fuels treatments and previous wildfire can alter fire severity patterns in large wildfires. We assessed the relative influence of previous fuels treatments (including wildfire), fire weather, vegetation and water balance on fire severity in the Rim Fire of 2013. We did this at three different spatial scales to investigate whether the influences on fire severity changed across scales...
June 23, 2017: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/28644475/post-translational-modification-of-ribosomally-synthesized-peptides-by-a-radical-sam-epimerase-in-bacillus-subtilis
#12
Alhosna Benjdia, Alain Guillot, Pauline Ruffié, Jérôme Leprince, Olivier Berteau
Ribosomally synthesized peptides are built out of L-amino acids, whereas D-amino acids are generally the hallmark of non-ribosomal synthetic processes. Here we show that the model bacterium Bacillus subtilis is able to produce a novel type of ribosomally synthesized and post-translationally modified peptide that contains D-amino acids, and which we propose to call epipeptides. We demonstrate that a two [4Fe-4S]-cluster radical S-adenosyl-L-methionine (SAM) enzyme converts L-amino acids into their D-counterparts by catalysing Cα-hydrogen-atom abstraction and using a critical cysteine residue as the hydrogen-atom donor...
July 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28642863/friends-enemies-endogenous-retroviruses-are-major-transcriptional-regulators-of-human-dna
#13
REVIEW
Anton A Buzdin, Vladimir Prassolov, Andrew V Garazha
Endogenous retroviruses are mobile genetic elements hardly distinguishable from infectious, or "exogenous," retroviruses at the time of insertion in the host DNA. Human endogenous retroviruses (HERVs) are not rare. They gave rise to multiple families of closely related mobile elements that occupy ~8% of the human genome. Together, they shape genomic regulatory landscape by providing at least ~320,000 human transcription factor binding sites (TFBS) located on ~110,000 individual HERV elements. The HERVs host as many as 155,000 mapped DNaseI hypersensitivity sites, which denote loci active in the regulation of gene expression or chromatin structure...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/28640634/structure-prediction-for-surface-induced-phases-of-organic-monolayers-overcoming-the-combinatorial-bottleneck
#14
Veronika Obersteiner, Michael Scherbela, Lukas Hörmann, Daniel Wegner, Oliver T Hofmann
Structure determination and prediction pose a major challenge to computational material science, demanding efficient global structure search techniques tailored to identify promising and relevant candidates. A major bottleneck is the fact that, due to the many combinatorial possibilities, there are too many possible geometries to be sampled exhaustively. Here, an innovative computational approach to overcome this problem is presented, that explores the potential energy landscape of commensurate organic/inorganic interfaces where the orientation and conformation of the molecules in the tightly packed layer is close to a favorable geometry adopted by isolated molecules on the surface...
June 22, 2017: Nano Letters
https://www.readbyqxmd.com/read/28640496/distance-decay-relationships-in-foliar-fungal-endophytes-are-driven-by-rare-taxa
#15
Ryoko Oono, Anna Rasmussen, Emilie Lefèvre
Foliar fungal endophytes represent a diverse and species-rich plant microbiome. Their biogeography provides essential clues to their cryptic relationship with hosts and the environment in which they disperse. We present species composition, diversity, and dispersal patterns of endophytic fungi associated with needles of Pinus taeda trees across regional scales in the absence of strong environmental gradients as well as within individual trees. An empirical designation of rare and abundant taxa enlightens us on the structure of endophyte communities...
May 18, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28639666/conformational-landscape-of-the-sf6-dimer-as-revealed-by-high-resolution-infrared-spectroscopy-and-complexation-with-rare-gas-atoms
#16
Pierre Asselin, Alexey Potapov, Andrew C Turner, Vincent Boudon, Laurent Bruel, Marc-André Gaveau, Michel Mons
Taking advantage of a versatile set-up, combining pulsed pin hole or slit nozzle supersonic expansion with an external cavity quantum cascade laser, the rovibrational absorption spectrum of the SF6 dimer in the ν3 mode region has been revisited at high resolution under various experimental conditions in SF6:He mixtures. Two new rotationally resolved spectral bands have been identified in the range of the parallel band of the dimer spectrum in addition to that previously reported. Among these three spectral features, two of them are assigned to conformations of the dimer (noted #1 and #2), clearly distinguished from their different S-S interatomic distances, i...
June 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28639623/imaging-quasiperiodic-electronic-states-in-a-synthetic-penrose-tiling
#17
Laura C Collins, Thomas G Witte, Rochelle Silverman, David B Green, Kenjiro K Gomes
Quasicrystals possess long-range order but lack the translational symmetry of crystalline solids. In solid state physics, periodicity is one of the fundamental properties that prescribes the electronic band structure in crystals. In the absence of periodicity and the presence of quasicrystalline order, the ways that electronic states change remain a mystery. Scanning tunnelling microscopy and atomic manipulation can be used to assemble a two-dimensional quasicrystalline structure mapped upon the Penrose tiling...
June 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28638402/dna-methylation-nuclear-organization-and-cancer
#18
REVIEW
Bhavani P Madakashira, Kirsten C Sadler
The dramatic re-organization of the cancer cell nucleus creates telltale morphological features critical for pathological staging of tumors. In addition, the changes to the mutational and epigenetic landscape in cancer cells alter the structure and stability of the genome and directly contribute to malignancy. DNA methylation is one of the best studied epigenetic changes in cancer, as nearly every type of cancer studied shows a loss of DNA methylation spread across most of the genome. This global hypomethylation is accompanied by hypermethylation at distinct loci, and much of the work on DNA methylation in cancer has focused on how local changes contribute to gene expression...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28637304/effects-of-alternative-electron-acceptors-on-the-activity-and-community-structure-of-methane-producing-and-consuming-microbes-in-the-sediments-of-two-shallow-boreal-lakes
#19
Antti J Rissanen, Anu Karvinen, Hannu Nykänen, Sari Peura, Marja Tiirola, Anita Mäki, Paula Kankaala
The role of anaerobic CH4 oxidation in controlling lake sediment CH4 emissions remains unclear. Therefore, we tested how relevant EAs (SO42-, NO3-, Fe3+, Mn4+, O2) affect CH4 production and oxidation in the sediments of two shallow boreal lakes. The changes induced to microbial communities by the addition of Fe3+ and Mn4+ were studied using next-generation sequencing targeting the 16S rRNA and methyl-coenzyme M reductase (mcrA) genes and mcrA transcripts. Putative anaerobic CH4 oxidizing archaea (ANME-2D) and bacteria (NC 10) were scarce (up to 3...
June 15, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28632790/diversity-structure-of-culturable-bacteria-isolated-from-the-fildes-peninsula-king-george-island-antarctica-a-phylogenetic-analysis-perspective
#20
Gerardo González-Rocha, Gabriel Muñoz-Cartes, Cristian B Canales-Aguirre, Celia A Lima, Mariana Domínguez-Yévenes, Helia Bello-Toledo, Cristián E Hernández
It has been proposed that Antarctic environments select microorganisms with unique biochemical adaptations, based on the tenet 'Everything is everywhere, but, the environment selects' by Baas-Becking. However, this is a hypothesis that has not been extensively evaluated. This study evaluated the fundamental prediction contained in this hypothesis-in the sense that species are structured in the landscape according to their local habitats-, using as study model the phylogenetic diversity of the culturable bacteria of Fildes Peninsula (King George Island, Antarctica)...
2017: PloS One
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