bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural and functional evaluation ofde novo-designed, two-component nanoparticle carriers for HIV Env trimer immunogens
Authors: Antanasijevic Aleksandar , Ueda George , Brouwer Philip JM , Copps Jeffrey , Huang Deli , Allen Joel D , Cottrell Christopher A , Yasmeen Anila , Sewall Leigh M , Bontjer Ilja , Ketas Thomas J , Turner Hannah L , Berndsen Zachary T , Klasse Per Johan , Crispin Max , Nemazee David , Moore John P , Sanders Rogier W , King Neil P , Baker David , Ward Andrew B 
Published: February 2020

AbstractTwo-component, self-assembling nanoparticles represent a versatile platform for multivalent presentation of viral antigens. Nanoparticles of different sizes and geometries can be designed and combined with appropriate antigens to fit the requirements of different immunization strategies. Here, we describe detailed antigenic, structural, and functional characterization of computationally designed tetrahedral, octahedral, and icosahedral nanoparticle immunogens displaying trimeric HIV envelope glycoprotein (Env) ectodomains. Env trimers, based on subtype A (BG505) or consensus group M (ConM) sequences and engineered with SOSIP stabilizing mutations, were fused to the underlying trimeric building block of each nanoparticle. Initial screening yielded one icosahedral and two tetrahedral nanoparticle candidates, capable of presenting twenty or four copies of the Env trimer. A number of analyses, including detailed structural characterization by cryo-EM, demonstrated that the nanoparticle immunogens possessed the intended structural and antigenic properties. Comparing the humoral responses elicited by ConM-SOSIP trimers presented on a two-component tetrahedral nanoparticle to the corresponding soluble protein revealed that multivalent presentation increased the proportion of the overall antibody response directed against autologous neutralizing Ab epitopes present on the ConM-SOSIP trimers.Author SummaryProtein constructs based on soluble ectodomains of HIV glycoprotein (Env) trimers are the basis of many current HIV vaccine platforms. Multivalent antigen display is one strategy applied to improve the immunogenicity of different subunit vaccine candidates. Here, we describe and comprehensively evaluate a library ofde novodesigned, protein nanoparticles of different geometries for their ability to present trimeric Env antigens. We found three nanoparticle candidates that can stably incorporate model Env trimer on their surface while maintaining its structure and antigenicity. Immunogenicity of the designed nanoparticles is assessedin vitroandin vivo. In addition to introducing a novel set of reagents for multivalent display of Env trimers, this work provides both guiding principles and a detailed experimental roadmap for the generation, characterization, and optimization of Env-presenting, self-assembling nanoparticle immunogens.
Evolution of sperm morphology in a crustacean genus with fertilization inside an open brood pouch
Authors: Duneau David , Möst Markus , Ebert Dieter 
Published: February 2020

AbstractSperm is the most fundamental male reproductive feature. It serves the fertilization of eggs and evolves under sexual selection. Two components of sperm are of particular interest, their number and their morphology. Mode of fertilization is believed to be a key determinant of sperm length across the animal kingdom. External fertilization, unlike internal, favors small and numerous sperm, since sperm density is thinned out in the environment. Here, we study the evolution of sperm morphology in the genusDaphnia, where fertilization occurs in a receptacle, the brood pouch, where sperm can constantly be flushed out by a water current. Based on microscopic observations of sperm morphologies mapped on a phylogeny with 15Daphniaand 2 outgroup species, we found that despite the internal fertilization mode,Daphniahave among the smallest sperm recorded, as would be expected with external fertilization. Despite being all relatively small compared to other arthropods, sperm length diverged at least twice, once within each of theDaphniasubgeneraCtenodaphniaandDaphnia.Furthermore, species in the latter subgenus also lost the ability of cell compaction by extracellular encapsulation and have very polymorphic sperm with long, and often numerous, filopodia. We discuss the different strategies thatDaphniaevolved to achieve fertilization success in the females’ brood pouch.
Microbial community assembly in a multi-layer dendritic metacommunity
Authors: Wisnoski Nathan I. , Lennon Jay T. 
Published: February 2020

ABSTRACTA major goal of metacommunity ecology is to infer the local- and regional-scale processes that underlie community assembly. In dendritic ecological networks (e.g., stream metacommunities), branching and directional dispersal connectivity can alter the balance between local and regional factors during assembly. However, the implications of vertical habitat structure (e.g., planktonic versus benthic sediments) in dendritic metacommunities remain unclear. In this study, we analyzed the bacterial metacommunity of a fifth-order mountain stream network to assess habitat differences in the (1) dominant community assembly processes, (2) spatial scaling of community assembly processes, and (3) longitudinal variation in community assembly. Using taxonomic and phylogenetic null modeling approaches, we found habitat-specific spatial patterns of community assembly across the dendritic network. Compositional differences between planktonic and benthic communities were maintained by divergent species sorting, but stochasticity influenced assembly at local scales. Planktonic communities showed scale-dependent assembly, transitioning from convergent sorting at local scales to divergent sorting at regional scales, while sediment community assembly was less scale dependent (convergent sorting remained important across all scales). While divergent sorting structured headwaters in both habitat types, sediment communities converged in structure downstream. Taken together, our results show that vertical habitat structure regulates the scale-dependent processes of community assembly across the dendritic metacommunity.
Metagenomic Insights into Microbial Metabolisms of a Sulfur-Influenced Glacial Ecosystem
Authors: Trivedi Christopher B. , Stamps Blake W. , Lau Graham E. , Grasby Stephen E. , Templeton Alexis S. , Spear John R. 
Published: February 2020

AbstractBiological sulfur cycling in polar, low-temperature ecosystems is an understudied phenomenon in part due to difficulty of access and the ephemeral nature of such environments. One such environment where sulfur cycling plays an important role in microbial metabolisms is located at Borup Fiord Pass (BFP) in the Canadian High Arctic. Here, transient springs emerge from the toe of a glacier creating a large proglacial aufeis (spring-derived ices) that are often covered in bright yellow/white sulfur, sulfate, and carbonate mineral precipitates that are accompanied by a strong odor of hydrogen sulfide. Metagenomic sequencing from multiple sample types at sites across the BFP glacial system produced 31 highly complete metagenome assembled genomes (MAGs) that were queried for sulfur-, nitrogen- and carbon-cycling/metabolism genes. Sulfur cycling, especially within the Sox complex of enzymes, was widespread across the isolated MAGs and taxonomically associated with the bacterial classesAlpha-, Beta-, Gamma-, andEpsilon- Proteobacteria. While this does agree with previous research from BFP implicating organisms within theGamma-andEpsilon- Proteobacteriaas the primary classes responsible for sulfur oxidation, our new data suggests putative sulfur oxidation by organisms withinAlpha-andBeta- Proteobacterialclasses which was not predicted. These findings indicate that in a low-temperature, ephemeral sulfur-based environment such as this, functional redundancy may be a key mechanism that microorganisms use to co-exist whenever energy is limited and/or focused by redox chemistry.ImportanceBorup Fiord Pass is a unique environment characterized by a sulfur-enriched glacial ecosystem, in the low-temperature environment of the Canadian High Arctic. This unique combination makes BFP one of the best analog sites for studying icy, sulfur-rich worlds outside of our own, such as Europa and Mars. The site also allows investigation of sulfur-based microbial metabolisms in cold environments here on Earth. Herein, we report whole genome sequencing data that suggests sulfur cycling metabolisms at BFP are more widely used across bacterial taxa than predicted. From our data, the metabolic capability of sulfur oxidation among multiple community members appears likely due to functional redundancy within their genomes. Functional redundancy, with respect to sulfur-oxidation at BFP, may indicate that this dynamic ecosystem hosts microorganisms that are able to use multiple sulfur electron donors alongside other important metabolic pathways, including those for carbon and nitrogen.
The branched chain aminotransferase IlvE promotes growth, stress resistance and pathogenesis ofListeria monocytogenes
Authors: Passalacqua Karla D. , Zhou Tianhui , Washington Tracy A. , Abuaita Basel H. , Sonenshein Abraham L. , O’Riordan Mary X.D. 
Published: February 2020

ABSTRACTThe bacterial plasma membrane is a key interface during pathogen-host interactions, and membrane composition enhances resistance against host antimicrobial defenses. Branched chain fatty acids (BCFAs) are the major plasma membrane component in the intracellular Gram-positive pathogenListeria monocytogenes(Lm) and BCFA metabolism is essential for Lm growth and virulence. BCFA synthesis requires branched chain amino acids (BCAAs), and the BCAA Isoleucine (Ile) is a necessary substrate for the predominant membrane anteiso-BCFAs (ai-BCFAs) as well as an environmental signal for virulence regulation in Lm. In this study, we explored how two proteins that metabolize or sense Ile contribute to Lm growth, BCFA metabolism, and virulence. The IlvE aminotransferase incorporates Ile into ai-BCFAs, while CodY is an Ile-sensing regulator that coordinates BCAA synthesis and virulence gene expression. Analysis of deletion mutants lacking IlvE (ΔilvE) or CodY (ΔcodY) revealed a major role for IlvE under nutrient restriction and stress conditions. Cultures of the ΔilvEmutant contained proportionally less ai-BCFAs relative to wild type, while of the ΔcodYmutant had a lower proportion of ai-BCFAs in stationary phase, despite containing more cell-associated Ile. Both ΔilvEand ΔcodYmutants required exogenous Ile for optimal growth, but the ΔilvEmutant had an absolute requirement for Valine and Leucine when Ile was absent. IlvE was also necessary for resistance to membrane stress, cell-to-cell spread, infection of primary macrophages, and virulence in mice. Our findings implicate IlvE as an integral aspect of Lm stress resistance and emphasize the central importance of Ile in Lm growth and virulence.
An allometric scaling approach to estimate epiphytic bryophyte biomass in tropical montane cloud forests
Authors: Lai Guan-Yu , Liu Hung-Chi , Kuo Ariel J. , Huang Cho-ying 
Published: February 2020

AbstractEpiphytic bryophytes (EB) are some of the most commonly found plant species in tropical montane cloud forests, and they play a disproportionate role in influencing the terrestrial hydrological and nutrient cycles. However, it is difficult to estimate the abundance of EB due to the nature of their “epiphytic” habitat. This study proposes an allometric scaling approach to measure EB biomass, implemented in 16,773 ha tropical montane cloud forests of northeastern Taiwan. A general allometry was developed to estimate EB biomass of 100 cm2circular-shaped mats (n = 131) and their central depths. A point-intercept instrument was invented to measure the depths of EB along tree trunks (n = 210) below 3-m from the ground level (sampled stem surface area [SSA]) in twenty-one 30 × 30 m plots. Biomass of EB of each point measure was derived using the general allometry and was aggregated across each SSA, and its performance was evaluated. Total EB biomass of a tree was estimated by referring to anin-situconversion model and was interpolated for all trees in the plots (n = 1451). Finally, we assessed EB biomass density at the plot scale and preliminarily estimated EB biomass of the study region. The general EB biomass-depth allometry showed that the depth of an EB mat was a salient variable for biomass estimation (R2= 0.72,p< 0.001). The performance of upscaling from mats to SSA was satisfactory, which allowed us to further estimate mean (± standard deviation) EB biomass of the 21 plots (272 ± 104 kg ha-1) and to provide preliminary estimation of the total EB biomass of 4562 Mg for the study region. Since a significant relationship between tree size and EB abundance is commonly found, regional EB biomass may be mapped by integrating our method and three-dimensional airborne data.
Epigenetic mediation of the onset of reproduction in a songbird
Authors: Lindner Melanie , Laine Veronika N. , Verhagen Irene , Viitaniemi Heidi M. , Visser Marcel E. , van Oers Kees , Husby Arild 
Published: February 2020

ABSTRACTClimate change significantly impacts natural populations, particularly phenology traits, like the seasonal onset of reproduction in birds. This impact is mainly via plastic responses in phenology traits to changes in the environment, but the molecular mechanism mediating this plasticity remains elusive. Epigenetic modifications can mediate plasticity and consequently constitute promising candidates for mediating phenology traits. Here, we used genome-wide DNA methylation profiles of individual great tit (Parus major) females that we blood sampled repeatedly throughout the breeding season. We demonstrate rapid and directional variation in DNA methylation within the regulatory region of genes known to play key roles in avian reproduction that are in line with observed changes in gene expression in chickens. Our findings provide an important step towards unraveling the molecular mechanism mediating a key life history trait, an essential knowledge-gap for understanding how natural populations may cope with future climate change.IMPACT SUMMARYNatural populations are increasingly challenged by changing environmental conditions like global increases in temperature. A key way for species to adapt to global warming is via phenotypic plasticity, i.e. the ability to adjust the expression of traits to the environment. We, however, know little about how the environment can interact with an organism’s genetic make-up to shape its trait value. Epigenetic marks are known to vary with the environment and can modulate the expression of traits without any change in the genetic make-up and therefore have the potential to mediate phenotypic plasticity.To study the role of epigenetics for phenotypic plasticity, we here focus on the great tit (Parus major), a species that is strongly affected by global warming and plastic for temperature in an essential phenology trait, the seasonal onset of egg laying. As a first step, we investigated whether great tit females show within-individual and short-term variation in DNA methylation that corresponds to changes in the reproductive state of females. We therefore housed breeding pairs in climate-controlled aviaries to blood sample each female repeatedly throughout the breeding season and used these repeated samples for methylation profiling.We found rapid and directional variation in DNA methylation at the time females prepared to initiate egg laying that is located within the regulatory region of genes that have previously described functions for avian reproduction. Although future work is needed to establish a causal link between the observed temporal variation in DNA methylation and the onset of reproduction in female great tits, our work highlights the potential role for epigenetic modifications in mediating an essential phenology trait that is sensitive to temperatures.
Improving multi-site autism classification based on site-dependence minimisation and second-order functional connectivity
Authors: Kunda Mwiza , Zhou Shuo , Gong Gaolang , Lu Haiping 
Published: February 2020

AbstractAutism spectrum disorder (ASD) has no objective diagnosis method despite having a high prevalence. Machine learning has been widely used to develop classification models for ASD using neuroimaging data. Recently, studies have shifted towards using large multi-site neuroimaging datasets to boost the clinical applicability and statistical power of results. However, the classification performance is hindered by the heterogeneous nature of agglomerative datasets. In this paper, we propose new methods for multi-site autism classification using the Autism Brain Imaging Data Exchange (ABIDE) dataset. We firstly propose a new second-order measure of functional connectivity (FC) named as Tangent Pearson embedding to extract better features for classification. Then we assess the statistical dependence between acquisition sites and FC features, and apply a domain adaptation approach to minimise the site dependence of FC features to improve classification. Our analysis shows that 1) statistical dependence between site and FC features is statistically significant at the 5% level, and 2) extracting second-order features from neuroimaging data and minimising their site dependence can improve over state-of-the-art classification results on the ABIDE dataset, achieving a classification accuracy of 73%.
TRIM67 Regulates Exocytic Mode and Neuronal Morphogenesis via SNAP47
Authors: Urbina Fabio L. , Menon Shalini , Goldfarb Dennis , Edwards Reginald , Major M. Ben , Brennwald Patrick , Gupton Stephanie L. 
Published: February 2020

AbstractNeuronal morphogenesis involves dramatic plasma membrane expansion, likely fueled by SNARE-mediated exocytosis. Distinct fusion modes described at neuronal synapses include full-vesicle-fusion (FVF) and kiss-and-run fusion (KNR). During FVF, lumenal cargo is secreted and vesicle membrane incorporates into the plasma membrane. During KNR a transient fusion pore secretes cargo, but closes without membrane addition. In contrast, fusion modes are not described in developing neurons where plasma membrane expansion is significant. Here, we resolve individual exocytic events in developing murine cortical neurons and use new classification tools to identify four distinguishable fusion modes: two FVF-like modes that insert membrane material and two KNR-like modes that do not. Discrete fluorescence profiles suggest distinct behavior of the fusion pore with each mode. Simulations and experiments agree that FVF-like exocytosis provides sufficient membrane material for morphogenesis. We find the E3 ubiquitin ligase TRIM67 promotes FVF-like exocytosis. Our data suggest this is accomplished in part by limiting incorporation of the Qb/Qc SNARE SNAP47 into SNARE complexes and thus, SNAP47 involvement in exocytosis.
A wireless, implantable optoelectrochemical probe for optogenetic stimulation and dopamine detection
Authors: Liu Changbo , Zhao Yu , Cai Xue , Xie Yang , Wang Taoyi , Cheng Dali , Li Lizhu , Li Rongfeng , Deng Yuping , Ding He , Lv Guoqing , Zhao Guanlei , Liu Lei , Zou Guisheng , Feng Meixin , Sun Qian , Yin Lan , Sheng Xing 
Published: February 2020

ABSTRACTPhysical and chemical technologies have been continuously progressing advances of neuroscience research. The development of research tools for closed-loop control and monitoring neural activities in behaving animals is highly desirable. In this paper, we introduce a wirelessly operated, miniaturized microprobe system for optical interrogation and neurochemical sensing in the deep brain. Via epitaxial liftoff and transfer printing, microscale light emitting diodes (micro-LEDs) as light sources, and poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) coated diamond films as electrochemical sensors are vertically assembled to form implantable optoelectrochemical probes, for real-time optogenetic stimulation and dopamine detection capabilities. A customized, lightweight circuit module is employed for untethered, remote signal control and data acquisition. Injected into the ventral tegmental area (VTA) of freely behaving mice,in vivoexperiments clearly demonstrate the utilities of the multifunctional optoelectrochemical microprobe system for optogenetic interference of place preferences and detection of dopamine release. The presented options for material and device integrations provide a practical route to simultaneous optical control and electrochemical sensing of complex nervous systems.
Thermogenic hydrocarbons fuel a redox stratified subseafloor microbiome in deep sea cold seep sediments
Authors: Dong Xiyang , Rattray Jayne E. , Campbell D. Calvin , Webb Jamie , Chakraborty Anirban , Adebayo Oyeboade , Matthews Stuart , Li Carmen , Fowler Martin , Macdonald Adam , Groves Ryan A. , Lewis Ian A. , Wang Scott H. , Mayumi Daisuke , Greening Chris , Hubert Casey R.J. 
Published: February 2020

AbstractAt marine cold seeps, gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface. Cold seep sediments are known to host taxonomically diverse microorganisms, but little is known about their metabolic potential and depth distribution in relation to hydrocarbon and electron acceptor availability. In this work, we combined geochemical, metagenomic and metabolomic measurements in distinct sediment redox regimes to profile microbial activities within the uppermost 350 cm of a newly discovered cold seep in the NW Atlantic deep sea (2.3 km water depth). Depth-resolved metagenomic profiling revealed compositional and functional differentiation between near-surface sediments (dominated by Proteobacteria) and deeper subsurface layers (dominated by Atribacteria, Chloroflexi, Euryarchaeota and Lokiarchaeota). Metabolic capabilities of community members were inferred from 376 metagenome-assembled genomes spanning 46 phyla (including five novel candidate phyla). In deeper sulfate-reducing and methanogenic sediments, various community members are capable of anaerobically oxidizing short-chain alkanes (alkyl-CoM reductase pathway), longer-chain alkanes (fumarate addition pathway), and aromatic hydrocarbons (fumarate addition and subsequent benzoyl-CoA pathways). Geochemical profiling demonstrated that hydrocarbon substrates are abundant in this location, thermogenic in origin, and subject to biodegradation. The detection of alkyl-/arylalkylsuccinate metabolites, together with carbon isotopic signatures of ethane, propane and carbon dioxide, support that microorganisms are actively degrading hydrocarbons in these sediments. Hydrocarbon oxidation pathways operate alongside other deep seabed metabolisms such as sulfide oxidation, hydrogen oxidation, carbon fixation, fermentation and reductive dehalogenation. Upward migrated thermogenic hydrocarbons thus sustain diverse microbial communities with activities that affect subseafloor biogeochemical processes across the redox spectrum in deep sea cold seeps.