915 research outputs found
Seasonality and predictability shape temporal species diversity
Temporal environmental fluctuations, such as seasonality, exert strong controls on biodiversity. While the effects of seasonality are well known, the predictability of fluctuations across years may influence seasonality in ways that are less well understood. The ability of a habitat to support unique, nonânested assemblages of species at different times of the year should depend on both seasonality (occurrence of events at specific periods of the year) and predictability (the reliability of event recurrence) of characteristic ecological conditions. Drawing on tools from wavelet analysis and information theory, we developed a framework for quantifying both seasonality and predictability of habitats, and applied this using global longâterm rainfall data. Our analysis predicted that temporal beta diversity should be maximized in highly predictable and highly seasonal climates, and that low degrees of seasonality, predictability, or both would lower diversity in characteristic ways. Using stream invertebrate communities as a case study, we demonstrated that temporal species diversity, as exhibited by community turnover, was determined by a balance between temporal environmental variability (seasonality) and the reliability of this variability (predictability). Communities in highly seasonal mediterranean environments exhibited strong oscillations in community structure, with turnover from one unique community type to another across seasons, whereas communities in aseasonal New Zealand environments fluctuated randomly. Understanding the influence of seasonal and other temporal scales of environmental oscillations on diversity is not complete without a clear understanding of their predictability, and our framework provides tools for examining these trends at a variety of temporal scales, seasonal and beyond. Given the uncertainty of future climates, seasonality and predictability are critical considerations for both basic science and management of ecosystems (e.g., dam operations, bioassessment) spanning gradients of climatic variability
A Comparison of Noninvasive Techniques to Survey Carnivore Communities in Northeastern North America
GEO 600 and the GEO-HF upgrade program: successes and challenges
The German-British laser-interferometric gravitational wave detector GEO 600
is in its 14th year of operation since its first lock in 2001. After GEO 600
participated in science runs with other first-generation detectors, a program
known as GEO-HF began in 2009. The goal was to improve the detector sensitivity
at high frequencies, around 1 kHz and above, with technologically advanced yet
minimally invasive upgrades. Simultaneously, the detector would record science
quality data in between commissioning activities. As of early 2014, all of the
planned upgrades have been carried out and sensitivity improvements of up to a
factor of four at the high-frequency end of the observation band have been
achieved. Besides science data collection, an experimental program is ongoing
with the goal to further improve the sensitivity and evaluate future detector
technologies. We summarize the results of the GEO-HF program to date and
discuss its successes and challenges
Cryptotomography: reconstructing 3D Fourier intensities from randomly oriented single-shot diffraction patterns
We reconstructed the 3D Fourier intensity distribution of mono-disperse
prolate nano-particles using single-shot 2D coherent diffraction patterns
collected at DESY's FLASH facility when a bright, coherent, ultrafast X-ray
pulse intercepted individual particles of random, unmeasured orientations. This
first experimental demonstration of cryptotomography extended the
Expansion-Maximization-Compression (EMC) framework to accommodate unmeasured
fluctuations in photon fluence and loss of data due to saturation or background
scatter. This work is an important step towards realizing single-shot
diffraction imaging of single biomolecules.Comment: 4 pages, 4 figure
Microcondylaea bonellii as a new host for the European bitterling Rhodeus amarus
We report for the first time that the freshwater mussel Microcondylaea bonellii (Ferussac, 1827) functions as a suitable host for the European bitterling Rhodeus amarus (Bloch, 1782). Given the recent expansion of R. amarus in Europe, the possible physiological cost (e.g. competition for oxygen, reduction in water circulation, and consequent impairment of filter-feeding) of this interaction may further affect the already poor conservation status of M. bonellii populations.We acknowledge the two anonymous referees for the helpful suggestions that improve the clarity of our manuscript. This research was funded by FCT under project ConBiomics No NORTE-01-0145-FEDER-030286, cofinanced by COMPETE 2020, Portugal 2020 and the European Union through the ERDF
The conservation status of the worldâs freshwater molluscs
With the biodiversity crisis continuing unchecked, we need to establish levels and drivers of extinction risk, and reassessments over time, to effectively allocate conservation resources and track progress towards global conservation targets. Given that threat appears particularly high in freshwaters, we assessed the extinction risk of 1428 randomly selected freshwater molluscs using the IUCN Red List Categories and Criteria, as part of the Sampled Red List Index project. We show that close to one-third of species in our sample are estimated to be threatened with extinction, with highest levels of threat in the Nearctic, Palearctic and Australasia and among gastropods. Threat levels were higher in lotic than lentic systems. Pollution (chemical and physical) and the modification of natural systems (e.g. through damming and water abstraction) were the most frequently reported threats to freshwater molluscs, with some regional variation. Given that we found little spatial congruence between species richness patterns of freshwater molluscs and other freshwater taxa, apart from crayfish, new additional conservation priority areas emerged from our study. We discuss the implications of our findings for freshwater mollusc conservation, the adequacy of a sampled approach and important next steps to estimate trends in freshwater mollusc extinction risk over time
Exploring Protein-Protein Interactions as Drug Targets for Anti-cancer Therapy with In Silico Workflows
We describe a computational protocol to aid the design of small molecule and peptide drugs that target protein-protein interactions, particularly for anti-cancer therapy. To achieve this goal, we explore multiple strategies, including finding binding hot spots, incorporating chemical similarity and bioactivity data, and sampling similar binding sites from homologous protein complexes. We demonstrate how to combine existing interdisciplinary resources with examples of semi-automated workflows. Finally, we discuss several major problems, including the occurrence of drug-resistant mutations, drug promiscuity, and the design of dual-effect inhibitors.Fil: Goncearenco, Alexander. National Institutes of Health; Estados UnidosFil: Li, Minghui. Soochow University; China. National Institutes of Health; Estados UnidosFil: Simonetti, Franco Lucio. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Oficina de CoordinaciĂłn Administrativa Parque Centenario. Instituto de Investigaciones BioquĂmicas de Buenos Aires. FundaciĂłn Instituto Leloir. Instituto de Investigaciones BioquĂmicas de Buenos Aires; ArgentinaFil: Shoemaker, Benjamin A. National Institutes of Health; Estados UnidosFil: Panchenko, Anna R. National Institutes of Health; Estados Unido
Nrt1 and Tna1-Independent Export of NAD+ Precursor Vitamins Promotes NAD+ Homeostasis and Allows Engineering of Vitamin Production
NAD+ is both a co-enzyme for hydride transfer enzymes and a
substrate of sirtuins and other NAD+ consuming enzymes.
NAD+ biosynthesis is required for two different regimens
that extend lifespan in yeast. NAD+ is synthesized from
tryptophan and the three vitamin precursors of NAD+: nicotinic
acid, nicotinamide and nicotinamide riboside. Supplementation of yeast cells
with NAD+ precursors increases intracellular
NAD+ levels and extends replicative lifespan. Here we show
that both nicotinamide riboside and nicotinic acid are not only vitamins but are
also exported metabolites. We found that the deletion of the nicotinamide
riboside transporter, Nrt1, leads to increased export of nicotinamide riboside.
This discovery was exploited to engineer a strain to produce high levels of
extracellular nicotinamide riboside, which was recovered in purified form. We
further demonstrate that extracellular nicotinamide is readily converted to
extracellular nicotinic acid in a manner that requires intracellular
nicotinamidase activity. Like nicotinamide riboside, export of nicotinic acid is
elevated by the deletion of the nicotinic acid transporter, Tna1. The data
indicate that NAD+ metabolism has a critical extracellular
element in the yeast system and suggest that cells regulate intracellular
NAD+ metabolism by balancing import and export of
NAD+ precursor vitamins
Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensembles
The ability to interact with different partners is one of the most important features in proteins. Proteins that bind a large number of partners (hubs) have been often associated with intrinsic disorder. However, many examples exist of hubs with an ordered structure, and evidence of a general mechanism promoting promiscuity in ordered proteins is still elusive. An intriguing hypothesis is that promiscuous binding sites have specific dynamical properties, distinct from the rest of the interface and pre-existing in the protein isolated state. Here, we present the first comprehensive study of the intrinsic dynamics of promiscuous residues in a large protein data set. Different computational methods, from coarse-grained elastic models to geometry-based sampling methods and to full-atom Molecular Dynamics simulations, were used to generate conformational ensembles for the isolated proteins. The flexibility and dynamic correlations of interface residues with a different degree of binding promiscuity were calculated and compared considering side chain and backbone motions, the latter both on a local and on a global scale. The study revealed that (a) promiscuous residues tend to be more flexible than nonpromiscuous ones, (b) this additional flexibility has a higher degree of organization, and (c) evolutionary conservation and binding promiscuity have opposite effects on intrinsic dynamics. Findings on simulated ensembles were also validated on ensembles of experimental structures extracted from the Protein Data Bank (PDB). Additionally, the low occurrence of single nucleotide polymorphisms observed for promiscuous residues indicated a tendency to preserve binding diversity at these positions. A case study on two ubiquitin-like proteins exemplifies how binding promiscuity in evolutionary related proteins can be modulated by the fine-tuning of the interface dynamics. The interplay between promiscuity and flexibility highlighted here can inspire new directions in protein-protein interaction prediction and design methods. © 2013 American Chemical Society
- âŠ