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https://www.readbyqxmd.com/read/28822939/short-term-effects-of-spring-prescribed-burning-on-the-understory-vegetation-of-a-pinushalepensis-forest-in-northeastern-spain
#1
Laura Fuentes, Beatriz Duguy, Daniel Nadal-Sala
Since the 1970s, fire regimes have been modified in the Northern Mediterranean region due to profound landscape changes mostly driven by socioeconomic factors, such as rural abandonment and large-scale plantations. Both fuel accumulation and the increasing vegetation spatial continuity, combined with the expansion of the wildland-urban interface, have enhanced fire risk and the occurrence of large wildfires. This situation will likely worsen under the projected aridity increase resulting from climate change...
August 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28822924/local-and-landscape-scale-land-cover-affects-microclimate-and-water-use-in-urban-gardens
#2
Brenda B Lin, Monika H Egerer, Heidi Liere, Shalene Jha, Peter Bichier, Stacy M Philpott
Urban gardens in Central California are highly vulnerable to the effects of climate change, experiencing both extended high heat periods as well as water restrictions because of severe drought conditions. This puts these critical community-based food production systems at risk as California is expected to experience increasing weather extremes. In agricultural systems, increased vegetation complexity, such as greater structure or biodiversity, can increase the resilience of food production systems from climate fluctuations...
August 16, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28821847/overcoming-the-plasticity-of-plant-specialized-metabolism-for-selective-diterpene-production-in-yeast
#3
Codruta Ignea, Anastasia Athanasakoglou, Aggeliki Andreadelli, Maria Apostolaki, Minas Iakovides, Euripides G Stephanou, Antonios M Makris, Sotirios C Kampranis
Plants synthesize numerous specialized metabolites (also termed natural products) to mediate dynamic interactions with their surroundings. The complexity of plant specialized metabolism is the result of an inherent biosynthetic plasticity rooted in the substrate and product promiscuity of the enzymes involved. The pathway of carnosic acid-related diterpenes in rosemary and sage involves promiscuous cytochrome P450s whose combined activity results in a multitude of structurally related compounds. Some of these minor products, such as pisiferic acid and salviol, have established bioactivity, but their limited availability prevents further evaluation...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821787/analysis-of-spatial-genetic-variation-reveals-genetic-divergence-among-populations-of-primula-veris-associated-to-contrasting-habitats
#4
Pablo Deschepper, Rein Brys, Miguel A Fortuna, Hans Jacquemyn
Genetic divergence by environment is a process whereby selection causes the formation of gene flow barriers between populations adapting to contrasting environments and is often considered to be the onset of speciation. Nevertheless, the extent to which genetic differentiation by environment on small spatial scales can be detected by means of neutral markers is still subject to debate. Previous research on the perennial herb Primula veris has shown that plants from grassland and forest habitats showed pronounced differences in phenology and flower morphology, suggesting limited gene flow between habitats...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28820298/surveillance-for-hemorrhagic-septicemia-in-buffalo-bubalus-bubalis-as-an-aid-to-range-expansion-of-the-javan-rhinoceros-rhinoceros-sondaicus-in-ujung-kulon-national-park-indonesia
#5
Kurnia Oktavia Khairani, Daryl Nydam, M Julia Felippe, Pat McDonough, Jason Barry, Rois Mahmud, M Haryono, Robin W Radcliffe
The Javan rhinoceros (Rhinoceros sondaicus) of Ujung Kulon National Park (UKNP) is the crown jewel of Indonesia's rich natural history. The park lies on a peninsula surrounded by coastline and agriculture-dominated landscapes. The invasion of water buffalo (Bubalus bubalis) into the park carries a substantial health risk to the Javan rhinoceros and threatens plans to establish a new population outside of its only current range in UKNP. Hemorrhagic septicemia (HS), known locally as septicemia epizootica and caused by Pasteurella multocida B:2, could thwart Indonesia's efforts to expand the range of the Javan rhinoceros...
August 18, 2017: Journal of Wildlife Diseases
https://www.readbyqxmd.com/read/28816457/a-coupled-cluster-investigation-of-sno-radical-isomers-and-their-reactions-with-hydrogen-atom-insight-into-structures-conformers-barriers-and-energetics
#6
Manoj Kumar, Joseph S Francisco
High-level coupled cluster theory with single and double excitation, and including a perturbative triples correction (CCSD(T)) method and a series of Dunning's augmented correlation consistent basis sets, aug-cc-pVXZ (X=D, T, Q and 5) was applied to examine the conformational landscape of SNO radical system. The basis set has an important effect on the relative stability of SNO radical isomers, and the NSO radical is the most stable member of SNO radical family. This is in contrast to previous density functional theory prediction suggesting SNO radical is the most stable isomer...
August 17, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28816453/modeling-of-oligosaccharides-within-glycoproteins-from-free-energy-landscapes
#7
Aysegül Turupcu, Chris Oostenbrink
In spite of the abundance of glycoproteins in biological processes, relatively little three-dimensional structural data is available for glycan structures. Here, we study the structure and flexibility of the vast majority of mammalian oligosaccharides appearing in N- and O- glycosylated proteins using a bottom up approach. We report the conformational free-energy landscapes of all relevant glycosidic linkages as obtained from local elevation simulations and subsequent umbrella sampling. To the best of our knowledge, this represents the first complete conformational library for the construction of N- and O-glycan structures...
August 17, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28816066/stressing-the-epi-genome-dealing-with-ros-in-cancer
#8
Akshay V Bhat, Shainan Hora, Ananya Pal, Sudhakar Jha, Reshma Taneja
SIGNIFICANCE: Growing evidence indicates cross-talk between Reactive oxygen species (ROS) and several key epigenetic processes like DNA methylation, histone modifications and miRNAs in normal physiology and human pathologies including cancer. This review focuses on how ROS-induced oxidative stress, metabolic intermediates and epigenetic processes influence each other in various cancers. Recent Advances: ROS alters chromatin structure and metabolism which impact the epigenetic landscape in cancer cells...
August 17, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28815237/induced-polarization-restricts-the-conformational-distribution-of-a-light-harvesting-molecular-triad-in-the-ground-state
#9
Oleg N Starovoytov, Pengzhi Zhang, Piotr Cieplak, Margaret S Cheung
The light-harvesting molecular triad consisting of carotenoid polyene (C), diaryl-porphyrin (P) and pyrrole-fullerene (C60) is a donor-acceptor molecule capable of absorbing incident light in the visible range. Its ability to convert solar energy to electrical excitation and charge separation energy suggests a great potential in real-world applications. The ensemble of its conformations under ambient conditions varies widely according to its electronic state. In previous work, we applied a non-polarizable model to study the conformational distribution of the molecular triad in the ground and charge separated states...
August 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28812724/the-genomic-landscape-of-evolutionary-convergence-in-mammals-birds-and-reptiles
#10
Liron Levin, Dan Mishmar
Many lineage-defining (nodal) mutations possess high functionality. However, differentiating adaptive nodal mutations from those that are functionally compensated remains challenging. To address this challenge, we identified functional nodal mutations (fNMs) in ~3,400 nuclear DNA (nDNA) and 4 mitochondrial DNA (mtDNA) protein structures from 91 and 1,003 species, respectively, representing the entire mammalian, bird and reptile phylogeny. A screen for candidate compensatory mutations among co-occurring amino acid changes in close structural proximity revealed that such compensated fNMs encompass 37% and 27% of the mtDNA and nDNA datasets, respectively...
February 13, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812622/species-rich-networks-and-eco-evolutionary-synthesis-at-the-metacommunity-level
#11
Hirokazu Toju, Masato Yamamichi, Paulo R Guimarães, Jens M Olesen, Akihiko Mougi, Takehito Yoshida, John N Thompson
Understanding how ecological and evolutionary processes interdependently structure biosphere dynamics is a major challenge in the era of worldwide ecosystem degradation. However, our knowledge of 'eco-evolutionary feedbacks' depends largely on findings from simple systems representing limited spatial scales and involving few species. Here we review recent conceptual developments for the understanding of multispecies coevolutionary processes and then discuss how new lines of concepts and methods will accelerate the integration of ecology and evolutionary biology...
January 24, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812092/effect-of-ligand-structure-on-the-size-control-of-mono-and-bi-thiolate-protected-silver-nanoclusters
#12
Kaiyuan Zheng, Xun Yuan, Jianping Xie
Ligand structure could control the size and structure of thiolate-protected silver nanoclusters (Ag NCs) in water. Small alkane-thiols, medium-sized aromatic-thiols, and bulky thiol-containing tri-peptides direct the formation of Ag25(SR)18, Ag44(SR)30, and Ag9-15(SR)5-10, respectively. In addition, small alkane-thiol collocates well with other types of thiolate ligand to generate bi-thiolate-protected Ag25 NCs with controlled ligand landscapes on their surfaces.
August 16, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28812069/the-sensitivity-of-folding-free-energy-landscapes-of-trpzips-to-mutations-in-the-hydrophobic-core
#13
Madhulika Gupta, Prabir Khatua, Charusita Chakravarty, Sanjoy Bandyopadhyay
The sensitivity of the stability of folded states and free energy landscapes to the differences in the hydrophobic content of the core residues has been studied for the set of 16-residue trpzips, namely, Trpzip4, Trpzip5 and Trpzip6. The combination of principal component analysis and different secondary structure order metrics as reaction coordinates has been used to characterize and identify all the underlying attractive basins corresponding to the folded and the unfolded states for each trpzip at 300 K. Our results reveal that even a single mutation in the hydrophobic core perturbs the stability of the folded peptide and the conformational preferences for the partially folded and unfolded states significantly, leading to concomitant alterations in the free energy landscape of trpzips...
August 16, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28811339/heritable-bovine-rumen-bacteria-are-phylogenetically-related-and-correlated-with-the-cow-s-capacity-to-harvest-energy-from-its-feed
#14
Goor Sasson, Sheerli Kruger Ben-Shabat, Eyal Seroussi, Adi Doron-Faigenboim, Naama Shterzer, Shamay Yaacoby, Margret E Berg Miller, Bryan A White, Eran Halperin, Itzhak Mizrahi
Ruminants sustain a long-lasting obligatory relationship with their rumen microbiome dating back 50 million years. In this unique host-microbiome relationship, the host's ability to digest its feed is completely dependent on its coevolved microbiome. This extraordinary alliance raises questions regarding the dependent relationship between ruminants' genetics and physiology and the rumen microbiome structure, composition, and metabolism. To elucidate this relationship, we examined the association of host genetics with the phylogenetic and functional composition of the rumen microbiome...
August 15, 2017: MBio
https://www.readbyqxmd.com/read/28808053/navigating-the-conformational-landscape-of-g-protein-coupled-receptor-kinases-during-allosteric-activation
#15
Xin-Qiu Yao, M Claire Cato, Emily Labudde, Tyler S Beyett, John J G Tesmer, Barry J Grant
G protein-coupled receptors (GPCRs) are essential for transferring extracellular signals into carefully choreographed intracellular responses controlling diverse aspects of cell physiology. The duration of GPCR mediated signaling is primarily regulated via GPCR kinase (GRK)-mediated phosphorylation of activated receptors. Although many GRK structures have been reported, the mechanisms underlying GRK activation are not well understood, in part because it is unknown how these structures map to the conformational landscape available to this enzyme family...
August 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28808004/critical-structural-fluctuations-of-proteins-upon-thermal-unfolding-challenge-the-lindemann-criterion
#16
Marina Katava, Guillaume Stirnemann, Marco Zanatta, Simone Capaccioli, Maria Pachetti, K L Ngai, Fabio Sterpone, Alessandro Paciaroni
Internal subnanosecond timescale motions are key for the function of proteins, and are coupled to the surrounding solvent environment. These fast fluctuations guide protein conformational changes, yet their role for protein stability, and for unfolding, remains elusive. Here, in analogy with the Lindemann criterion for the melting of solids, we demonstrate a common scaling of structural fluctuations of lysozyme protein embedded in different environments as the thermal unfolding transition is approached. By combining elastic incoherent neutron scattering and advanced molecular simulations, we show that, although different solvents modify the protein melting temperature, a unique dynamical regime is attained in proximity of thermal unfolding in all solvents that we tested...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28807238/unravelling-the-complexity-of-signalling-networks-in-cancer-a-review-of-the-increasing-role-for-computational-modelling
#17
REVIEW
John Garland
Cancer induction is a highly complex process involving hundreds of different inducers but whose eventual outcome is the same. Clearly, it is essential to understand how signalling pathways and networks generated by these inducers interact to regulate cell behaviour and create the cancer phenotype. While enormous strides have been made in identifying key networking profiles, the amount of data generated far exceeds our ability to understand how it all "fits together". The number of potential interactions is astronomically large and requires novel approaches and extreme computation methods to dissect them out...
September 2017: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/28806978/transcriptome-sequencing-in-pediatric-acute-lymphoblastic-leukemia-identifies-fusion-genes-associated-with-distinct-dna-methylation-profiles
#18
Yanara Marincevic-Zuniga, Johan Dahlberg, Sara Nilsson, Amanda Raine, Sara Nystedt, Carl Mårten Lindqvist, Eva C Berglund, Jonas Abrahamsson, Lucia Cavelier, Erik Forestier, Mats Heyman, Gudmar Lönnerholm, Jessica Nordlund, Ann-Christine Syvänen
BACKGROUND: Structural chromosomal rearrangements that lead to expressed fusion genes are a hallmark of acute lymphoblastic leukemia (ALL). In this study, we performed transcriptome sequencing of 134 primary ALL patient samples to comprehensively detect fusion transcripts. METHODS: We combined fusion gene detection with genome-wide DNA methylation analysis, gene expression profiling, and targeted sequencing to determine molecular signatures of emerging ALL subtypes...
August 14, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28805793/conformational-landscape-of-a-virus-by-single-particle-x-ray-scattering
#19
Ahmad Hosseinizadeh, Ghoncheh Mashayekhi, Jeremy Copperman, Peter Schwander, Ali Dashti, Reyhaneh Sepehr, Russell Fung, Marius Schmidt, Chun Hong Yoon, Brenda G Hogue, Garth J Williams, Andrew Aquila, Abbas Ourmazd
Using a manifold-based analysis of experimental diffraction snapshots from an X-ray free electron laser, we determine the three-dimensional structure and conformational landscape of the PR772 virus to a detector-limited resolution of 9 nm. Our results indicate that a single conformational coordinate controls reorganization of the genome, growth of a tubular structure from a portal vertex and release of the genome. These results demonstrate that single-particle X-ray scattering has the potential to shed light on key biological processes...
August 14, 2017: Nature Methods
https://www.readbyqxmd.com/read/28805227/landscape-of-the-structure-o-h-bond-dissociation-energy-relationship-of-oximes-and-hydroxylamines
#20
Rina Dao, Xinyu Wang, Kexian Chen, Chenxuan Zhao, Jia Yao, Haoran Li
The relationship between the homolytic O-H bond dissociation enthalpies (BDEs) and the structures of N-oxyl radical precursors (i.e. hydroxylamines and oximes) is important to predict their reactivity. Yet several crucial facts remain hidden to complete the picture such as the substituent electronic effects on the BDEs of oximes. In this work, the O-H BDEs of 120 hydroxylamines and 120 oximes have been calculated. It was found that the majority of the iminoxyl radicals are σ radicals, except for some π radicals...
August 14, 2017: Physical Chemistry Chemical Physics: PCCP
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