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https://www.readbyqxmd.com/read/29927110/recording-and-analyzing-nucleic-acid-distance-distributions-with-x-ray-scattering-interferometry-xsi
#1
Thomas Zettl, Rhiju Das, Pehr A B Harbury, Daniel Herschlag, Jan Lipfert, Rebecca S Mathew, Xuesong Shi
Most structural techniques provide averaged information or information about a single predominant conformational state. However, biological macromolecules typically function through series of conformations. Therefore, a complete understanding of macromolecular structures requires knowledge of the ensembles that represent probabilities on a conformational free energy landscape. Here we describe an emerging approach, X-ray scattering interferometry (XSI), a method that provides instantaneous distance distributions for molecules in solution...
June 2018: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/29926462/constructing-free-energy-landscapes-of-nucleic-acid-hairpin-unfolding
#2
Micah J McCauley, Ioulia Rouzina, Mark C Williams
Single nucleic acid molecules form hairpins that may stabilize secondary and tertiary structures as well as perform enzymatic and other chemical functions. Considerable progress has been made in the effort to understand the contributions of various factors to the stability of a given hairpin sequence. For a given sequence, it is possible to compute both the most likely structural arrangements and their associated free energies over a range of experimental conditions. However, there are many observed hairpin irregularities for which the energies and function are not well understood...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29925055/temporal-dynamics-of-phosphorus-during-aquatic-and-terrestrial-litter-decomposition-in-an-alpine-forest
#3
Yan Peng, Wanqin Yang, Kai Yue, Bo Tan, Chunping Huang, Zhenfeng Xu, Xiangyin Ni, Li Zhang, Fuzhong Wu
Plant litter decomposition in forested soil and watershed is an important source of phosphorus (P) for plants in forest ecosystems. Understanding P dynamics during litter decomposition in forested aquatic and terrestrial ecosystems will be of great importance for better understanding nutrient cycling across forest landscape. However, despite massive studies addressing litter decomposition have been carried out, generalizations across aquatic and terrestrial ecosystems regarding the temporal dynamics of P loss during litter decomposition remain elusive...
June 17, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29920553/diverse-effects-of-degree-of-urbanisation-and-forest-size-on-species-richness-and-functional-diversity-of-plants-and-ground-surface-active-ants-and-spiders
#4
Ramona Laila Melliger, Brigitte Braschler, Hans-Peter Rusterholz, Bruno Baur
Urbanisation is increasing worldwide and is regarded a major driver of environmental change altering local species assemblages in urban green areas. Forests are one of the most frequent habitat types in urban landscapes harbouring many native species and providing important ecosystem services. By using a multi-taxa approach covering a range of trophic ranks, we examined the influence of degree of urbanisation and forest size on the species richness and functional diversity of plants, and ground surface-active ants and spiders...
2018: PloS One
https://www.readbyqxmd.com/read/29915689/genetic-differentiation-local-adaptation-and-phenotypic-plasticity-in-fragmented-populations-of-a-rare-forest-herb
#5
Rodolfo Gentili, Aldo Solari, Martin Diekmann, Cecilia Duprè, Gianna Serafina Monti, Stefano Armiraglio, Silvia Assini, Sandra Citterio
Background: Due to habitat loss and fragmentation, numerous forest species are subject to severe population decline. Investigating variation in genetic diversity, phenotypic plasticity and local adaptation should be a prerequisite for implementing conservation actions. This study aimed to explore these aspects in ten fragmented populations of Physospermum cornubiense in view of translocation measures across its Italian range. Methods: For each population we collected environmental data on landscape (habitat size, quality and fragmentation) and local conditions (slope, presence of alien species, incidence of the herbivorous insect Metcalfa pruinosa and soil parameters)...
2018: PeerJ
https://www.readbyqxmd.com/read/29915518/conformational-landscapes-of-ubiquitin-cytochrome-c-and-myoglobin-uniform-field-ion-mobility-measurements-in-helium-and-nitrogen-drift-gas
#6
Jody C May, Ewa Jurneczko, Sarah M Stow, Isabel Kratochvil, Stefan Kalkhof, John A McLean
In this study, a commercial uniform field drift tube ion mobility-mass spectrometer (IM-MS) was utilized to measure the gas-phase conformational populations of three well-studied proteins: ubiquitin (8566 Da), cytochrome c (12,359 Da), and myoglobin in both apo and holo forms (16,951 and 17,567 Da, respectively) in order to evaluate the use of this technology for broadscale structural proteomics applications. Proteins were electrosprayed from either acidic organic (pH ~3) or aqueous buffered (pH ~6.6) solution phase conditions, which generated a wide range of cation charge states corresponding to both extended (unfolded) and compact (folded) gas-phase conformational populations...
April 2018: International Journal of Mass Spectrometry
https://www.readbyqxmd.com/read/29915302/high-resolution-crossover-mapping-reveals-similarities-and-differences-of-male-and-female-recombination-in-maize
#7
Penny M A Kianian, Minghui Wang, Kristin Simons, Farhad Ghavami, Yan He, Stefanie Dukowic-Schulze, Anitha Sundararajan, Qi Sun, Jaroslaw Pillardy, Joann Mudge, Changbin Chen, Shahryar F Kianian, Wojciech P Pawlowski
Meiotic crossovers (COs) are not uniformly distributed across the genome. Factors affecting this phenomenon are not well understood. Although many species exhibit large differences in CO numbers between sexes, sex-specific aspects of CO landscape are particularly poorly elucidated. Here, we conduct high-resolution CO mapping in maize. Our results show that CO numbers as well as their overall distribution are similar in male and female meioses. There are, nevertheless, dissimilarities at local scale. Male and female COs differ in their locations relative to transcription start sites in gene promoters and chromatin marks, including nucleosome occupancy and tri-methylation of lysine 4 of histone H3 (H3K4me3)...
June 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29914971/epigenetic-maintenance-of-topological-domains-in-the-highly-rearranged-gibbon-genome
#8
Nathan H Lazar, Kimberly A Nevonen, Brendan O'Connell, Christine McCann, Rachel J O'Neill, Richard E Green, Thomas J Meyer, Mariam Okhovat, Lucia Carbone
The relationship between evolutionary genome remodeling and the three-dimensional structure of the genome remain largely unexplored. Here, we use the heavily rearranged gibbon genome to examine how evolutionary chromosomal rearrangements impact genome-wide chromatin interactions, topologically associating domains (TADs), and their epigenetic landscape. We use high-resolution maps of gibbon-human breaks of synteny (BOS), apply Hi-C in gibbon, measure an array of epigenetic features, and perform cross-species comparisons...
June 18, 2018: Genome Research
https://www.readbyqxmd.com/read/29914800/the-respiratory-syncytial-virus-vaccine-landscape-lessons-from-the-graveyard-and-promising-candidates
#9
REVIEW
Natalie I Mazur, Deborah Higgins, Marta C Nunes, José A Melero, Annefleur C Langedijk, Nicole Horsley, Ursula J Buchholz, Peter J Openshaw, Jason S McLellan, Janet A Englund, Asuncion Mejias, Ruth A Karron, Eric Af Simões, Ivana Knezevic, Octavio Ramilo, Pedro A Piedra, Helen Y Chu, Ann R Falsey, Harish Nair, Leyla Kragten-Tabatabaie, Anne Greenough, Eugenio Baraldi, Nikolaos G Papadopoulos, Johan Vekemans, Fernando P Polack, Mair Powell, Ashish Satav, Edward E Walsh, Renato T Stein, Barney S Graham, Louis J Bont
The global burden of disease caused by respiratory syncytial virus (RSV) is increasingly recognised, not only in infants, but also in older adults (aged ≥65 years). Advances in knowledge of the structural biology of the RSV surface fusion glycoprotein have revolutionised RSV vaccine development by providing a new target for preventive interventions. The RSV vaccine landscape has rapidly expanded to include 19 vaccine candidates and monoclonal antibodies (mAbs) in clinical trials, reflecting the urgency of reducing this global health problem and hence the prioritisation of RSV vaccine development...
June 15, 2018: Lancet Infectious Diseases
https://www.readbyqxmd.com/read/29912933/assessing-the-multi-scale-predictive-ability-of-ecosystem-functional-attributes-for-species-distribution-modelling
#10
Salvador Arenas-Castro, João Gonçalves, Paulo Alves, Domingo Alcaraz-Segura, João P Honrado
Global environmental changes are rapidly affecting species' distributions and habitat suitability worldwide, requiring a continuous update of biodiversity status to support effective decisions on conservation policy and management. In this regard, satellite-derived Ecosystem Functional Attributes (EFAs) offer a more integrative and quicker evaluation of ecosystem responses to environmental drivers and changes than climate and structural or compositional landscape attributes. Thus, EFAs may hold advantages as predictors in Species Distribution Models (SDMs) and for implementing multi-scale species monitoring programs...
2018: PloS One
https://www.readbyqxmd.com/read/29912326/soils-associated-to-different-tree-communities-do-not-elicit-predictable-responses-in-lake-bacterial-community-structure-and-function
#11
Clara Ruiz-González, Esther Archambault, Isabelle Laforest-Lapointe, Paul A Del Giorgio, Steven W Kembel, Christian Messier, Charles A Nock, Beatrix E Beisner
Freshwater bacterioplankton communities are influenced by the inputs of material and bacteria from the surrounding landscape, yet few studies have investigated how different terrestrial inputs affect bacterioplankton. We examined whether the addition of soils collected under various tree species combinations differentially influences lake bacterial communities. Lake water was incubated for 6 days following addition of five different soils. We assessed the taxonomic composition (16S rRNA gene sequencing) and metabolic activity (Biolog Ecoplates) of lake bacteria with and without soil addition, and compared these to initial soil communities...
June 14, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29912311/dispersal-limitation-and-thermodynamic-constraints-govern-spatial-structure-of-permafrost-microbial-communities
#12
Eric M Bottos, David W Kennedy, Elvira B Romero, Sarah J Fansler, Joseph M Brown, Lisa M Bramer, Rosalie K Chu, Malak M Tfaily, Janet K Jansson, James C Stegen
Understanding drivers of permafrost microbial community composition is critical for understanding permafrost microbiology and predicting ecosystem responses to thaw. We hypothesize that permafrost communities are shaped by physical constraints imposed by prolonged freezing, and exhibit spatial distributions that reflect dispersal limitation and selective pressures associated these physical constraints. To test this, we characterized patterns of environmental variation and microbial community composition in permafrost across an Alaskan boreal forest landscape...
June 14, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29911719/two-wavelength-wrinkling-patterns-in-helicoidal-plywood-surfaces-imprinting-energy-landscapes-onto-geometric-landscapes
#13
P Rofouie, Z Wang, A D Rey
We present a model to investigate the formation of two-length scale surface patterns in biological and synthetic anisotropic soft matter materials through the high order interaction of anisotropic interfacial tension and capillarity at their free surfaces. The unique pattern-formation mechanism emerging from the presented model is based on the interaction between lower and higher order anchoring modes. Analytical and numerical solutions are used to shed light on why and how simple anisotropic anchoring generates two-lengthscale wrinkles whose amplitudes are given in terms of anchoring coefficients...
June 18, 2018: Soft Matter
https://www.readbyqxmd.com/read/29911198/comprehensive-relative-quantitative-metabolomics-analysis-of-lycopodium-alkaloids-in-different-tissues-of-huperzia-serrata
#14
Shiwen Wu, Zhen Fan, Youli Xiao
Qian ceng Ta , the whole plant of Huperzia serrata , is an important landscape and medicinal herbs and contains abundant bioactive lycopodium alkaloids. Although the structures of more than 100 lycopodium alkaloids in Huperzia serrata have been isolated and identified, the content and distribution of these alkaloids in different tissues are still unclear. In current study, an ultra-performance liquid chromatography-mass spectrometry based comprehensive metabolomics strategy was developed, including the extraction, separation, identification, and statistical analysis...
March 2018: Synthetic and Systems Biotechnology
https://www.readbyqxmd.com/read/29910537/disentangling-the-pathways-of-land-use-impacts-on-the-functional-structure-of-fish-assemblages-in-amazon-streams
#15
Rafael P Leitão, Jansen Zuanon, David Mouillot, Cecília G Leal, Robert M Hughes, Philip R Kaufmann, Sébastien Villéger, Paulo S Pompeu, Daniele Kasper, Felipe R de Paula, Silvio F B Ferraz, Toby A Gardner
Agricultural land use is a primary driver of environmental impacts on streams. However, the causal processes that shape these impacts operate through multiple pathways and at several spatial scales. This complexity undermines the development of more effective management approaches, and illustrates the need for more in-depth studies to assess the mechanisms that determine changes in stream biodiversity. Here we present results of the most comprehensive multi-scale assessment of the biological condition of streams in the Amazon to date, examining functional responses of fish assemblages to land use...
January 1, 2018: Ecography
https://www.readbyqxmd.com/read/29906880/multiple-scales-and-phases-in-discrete-chains-with-application-to-folded-proteins
#16
A Sinelnikova, A J Niemi, Johan Nilsson, M Ulybyshev
Chiral heteropolymers such as large globular proteins can simultaneously support multiple length scales. The interplay between the different scales brings about conformational diversity, determines the phase properties of the polymer chain, and governs the structure of the energy landscape. Most importantly, multiple scales produce complex dynamics that enable proteins to sustain live matter. However, at the moment there is incomplete understanding of how to identify and distinguish the various scales that determine the structure and dynamics of a complex protein...
May 2018: Physical Review. E
https://www.readbyqxmd.com/read/29900620/habitat-loss-and-fragmentation-reduce-effective-gene-flow-by-disrupting-seed-dispersal-in-a-neotropical-palm
#17
Luke Browne, Jordan Karubian
Habitat loss and fragmentation often reduce gene flow and genetic diversity in plants by disrupting the movement of pollen and seed. However, direct comparisons of the contributions of pollen vs. seed dispersal to genetic variation in fragmented landscapes are lacking. To address this knowledge gap, we partitioned the genetic diversity contributed by male gametes from pollen sources and female gametes from seed sources within established seedlings of the palm Oenocarpus bataua in forest fragments and continuous forest in northwest Ecuador...
June 13, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29900297/in-silico-data-analyses-of-the-hotspot-mutations-of-chm-gene-in-choroideremia-disease
#18
Saber Imani, Iqra Ijaz, Marzieh Dehghan Shasaltaneh, Shangyi Fu, Jingliang Cheng, Junjiang Fu
This data article provides compelling computational analysis of the hotspot CHM gene mutations that contribute to the progressive causativeness and susceptibility of Choroideremia in patients. We performed structural and molecular dynamics (MD) simulation analysis on abnormal states of the CHM protein caused by deleterious and disease-causing hotspot mutant forms of CHM: S89C, E177K, and V529H. Within 40 ns, MD simulation time composed of the E177K mutant shows conformational alteration especially in several parts of the variant...
June 2018: Data in Brief
https://www.readbyqxmd.com/read/29898720/landscape-reveals-critical-network-structures-for-sharpening-gene-expression-boundaries
#19
Chunhe Li, Lei Zhang, Qing Nie
BACKGROUND: Spatial pattern formation is a critical issue in developmental biology. Gene expression boundary sharpening has been observed from both experiments and modeling simulations. However, the mechanism to determine the sharpness of the boundary is not fully elucidated. RESULTS: We investigated the boundary sharpening resulted by three biological motifs, interacting with morphogens, and uncovered their probabilistic landscapes. The landscape view, along with calculated average switching time between attractors, provides a natural explanation for the boundary sharpening behavior relying on the noise induced gene state switchings...
June 13, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29898559/rare-flash-floods-and-debris-flows-in-southern-germany
#20
Ugur Ozturk, Dadiyorto Wendi, Irene Crisologo, Adrian Riemer, Ankit Agarwal, Kristin Vogel, José Andrés López-Tarazón, Oliver Korup
Flash floods and debris flows are iconic hazards in mountainous regions with steep relief, high rainfall intensities, rapid snowmelt events, and abundant sediments. The cuesta landscapes of southern Germany hardly come to mind when dealing with such hazards. A series of heavy rainstorms dumping up to 140 mm in 2 h caused destructive flash floods and debris flows in May 2016. The most severe damage occurred in the Braunsbach municipality, which was partly buried by 42,000 m3 of boulders, gravel, mud, and anthropogenic debris from the small catchment of Orlacher Bach (~6 km2 )...
June 1, 2018: Science of the Total Environment
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