bluuebunny/crossref_metadata_2025_split huggingface dataset:
Root economics spectrum and construction costs in Mediterranean woody plants: the role of symbiotic associations and the environment
Authors: de la Riva Enrique G. , Prieto Iván , Marañón Teodoro , Pérez Ramos Ignacio M. , Olmo Manuel , Villar Rafael 
Published: June 2020

AbstractQuantifying the functional variation of fine root traits and their interactions with symbiotic organisms is an uprising research topic to understand the overarching trade-off between maximizing resource acquisition or conservation (root economics spectrum -RES-). The currency of root traits economy is based on the carbon required to construct them; however, we lack a clear understanding of this question.Our main aim was to quantify construction costs (CC) of fine roots (<2 mm) and their underlying components (concentration of carbon, minerals and organic nitrogen) in 60 Mediterranean woody species with contrasting symbiotic association types (ectomycorrhizas, arbuscular and ericoid mycorrhizas and N-Fixing nodules). We examined (1) if the CC depended on the symbiotic type, and if they were associated with morphological traits; (2) the relation of each component of the CC with the root structure for each symbiotic type; and (3) whether soil water and nutrient availability determined differences in CC across sites and symbiotic types.The multivariate analysis of root traits showed a main plane of covariation accordingly to the RES expectations, with contrasting symbiotic types at both ends of the spectrum. We found a significant relationship between root CC and RES; interestingly the slopes of this relationship differed among symbiotic types, which was mainly due to the different role that each specific components of CC plays across them. In addition, independently of the symbiotic type, the CC decreased linearly with the nutrient availability and quadratic with the water availability.Synthesis. Our study demonstrates that woody plants have different strategies in their root carbon investment, which depend on their position along the economics spectrum (RES) and on their main symbiotic association preference. The intrinsic components of the cost of root production varied across species with contrasting symbiotic associations, pointing to a trade-off between structural and metabolic compounds. We also found that root CC are strongly modulated by soil resource availability, following a non-linear pattern with water availability. Thus, CC shifts from high to low at the most arid sites, which points to a strong role of symbiotic associations in this shift.
Understanding pigeon pea (Cajanus cajan) production conditions, stakeholders’ preferences for varietal traits and their implications for breeding programmes in India
Authors: Singh A. , Fromm I. , Jha G. K. , Venkatesh P. , Tewari H. , Padaria R. , Egger U. 
Published: June 2020

AbstractPigeon pea (Cajanus cajan) is an important pulse crop in the Indian diet and one of the most important sources of dietary protein for the population. In the context of the fourth phase of the Indo-Swiss Collaboration in Biotechnology, an assessment how farmers and consumers perceive new pigeon pea cultivars and what are their preferred traits was conducted. This investigation assessed India’s food security implications due to stagnating and low yield of pigeon pea and ascertain farmers’ preferences of pigeon pea varietal traits, production constraints and farmers’ coping strategies in diverse pigeon pea production environments. Results indicated that production constraints in the studied regions were basically similar, with majority of the farmers identifying pod borer & pod fly as the major pest, and wilt as the major disease and drought as a major production constraint. Farmers indicated the use of clean seed, high yielding varieties, inter & mixed cropping, planting density, and manure application as some of the strategies they used to cope with the production constraints. In terms of preference for new cultivars, farmers want high grain yield with drought tolerance, medium to early maturity, pod borer resistance, tolerance to wilt disease, moderate plant height and ease of threshing without compromising other preferred attributes. The analysis of processors’ preference of grain types for dal processing showed that uniform size, oval shape, orange coloured seed and most importantly moderately hard seed coat are highly desirable. Consumers lacked awareness on the varieties, but considered traits like uniform seeds and reduced cooking time traits more desirable.
Nutritional combinatorial impact on the gut microbiota and plasma short-chain fatty acids levels in the prevention of mammary cancer in Her2/neu estrogen receptor-negative transgenic mice
Authors: Sharma Manvi , Arora Itika , Stoll Matthew L. , Li Yuanyuan , Morrow Casey D. , Barnes Stephen , Berryhill Taylor F. , Li Shizhao , Tollefsbol Trygve O. 
Published: June 2020

AbstractBreast cancer is the second leading cause of cancer-related mortality in women. Various nutritional compounds possess anti-carcinogenic properties which may be mediated through their effects on the gut microbiota and its production of short-chain fatty acids (SCFAs) for the prevention of breast cancer. We evaluated the impact of broccoli sprouts (BSp), green tea polyphenols (GTPs) and their combination on the gut microbiota and SCFAs metabolism from the microbiota in Her2/neu transgenic mice that spontaneously develop estrogen receptor-negative [ER (-)] mammary tumors. The mice were grouped based on the dietary treatment: control, BSp, GTPs or their combination from beginning in early life (BE) or life-long from conception (LC). We found that the combination group showed the strongest inhibiting effect on tumor growth volume and a significant increase in tumor latency. BSp treatment was integrally more efficacious than the GTPs group when compared to the control group. There was similar clustering of microbiota of BSp-fed mice with combination-fed mice, and GTPs-fed mice with control-fed mice at pre-tumor and post-tumor in both BE and LC groups. The mice on all dietary treatment groups incurred a significant increase ofAdlercreutziagenus and S24-7 family in the both BE and LC groups. We found no change in SCFAs levels in the plasma of BSp-fed, GTPs-fed and combination-fed mice of the BE group. Marked changes were observed in the mice of the LC group consisting of significant increases in propionate and isobutyrate in GTPs-fed and combination-fed mice. These studies indicate that nutrients such as BSp and GTPs differentially affect the gut microbial composition in both the BE and LC groups and the key metabolites (SCFAs) levels in the LC group. The findings also suggest that temporal factors related to different time windows of consumption during the life-span can have a promising influence on the gut microbial composition, SCFAs profiles and ER (-) breast cancer prevention.
Structural Motifs, Disorder, and the Efficacy of Viral Vaccines
Authors: Makin Robert A. , Durbin Steven M. 
Published: June 2020

AbstractWe demonstrate that it is possible to draw direct numerical correlations between virus particles and effective virus-like particle (VLP) derived vaccines through extraction of a Bragg-Williams order parameter from electron microscopy. The method has its roots in studies of disorder in metal alloys, and is adapted to describe the type and occurrence of structural motifs within the arrangement of viral coat proteins, captured by the value of the order parameter as a measure of disorder. A conventional approach to viral vaccine design consists of replicating select proteins to create a VLP designed to trigger an immune response while remaining non-infectious. Understanding variations between viruses and vaccine strains therefore tends to focus on differences between proteins, which can be characterized through genetic analysis. While such an approach provides vital information about the functioning and interactions of the proteins, it does not yet yield an early-stage pathway towards predicting the efficacy of a vaccine, and so large-scale clinical trials are required to obtain critical information. With the urgency associated with pandemics, including Coronavirus Disease-2019 (COVID-19) originating from the SARS-CoV-2 virus, there is a need for earlier indications of whether a vaccine has the necessary characteristics. Application of the methodology to Dengue and influenza virus particles indicates that temperature and pH during incubation could potentially be exploited to fine-tune the order parameter of VLP-based vaccines to match the corresponding virus. Additionally, utilization of an Ising model plot reveals a clear relationship between case fatality rate and order parameter for distinct virus families.
Barnacle encrustation on molluscan prey offers associational resistance against drilling predation
Authors: Thangarathinam Vigneshbabu , Chattopadhyay Devapriya 
Published: June 2020

AbstractPredation is one of the driving forces that shaped the marine ecosystems through time. Apart from the anti-predatory strategies adopted by the prey, the predatory outcome is often indirectly influenced by the other members of the ecological community. Association between organisms are often found to influence the outcome and the evolution of such association may have been guided by such interactions. Mollusc-burnacle association, although common, is not explored to assess if the epibiont offers the molluscs any protection against predation (associational resistance) or increases the risk by attracting predators (shared doom). Using a series of controlled experiments with a drilling predator (Paratectonatica tigrina), its prey (Pirenella cingulata) and an epibiont (Amphibalanus amphitrite), we evaluated the effect of epibionts on the drilling behavior of the predator by documenting the successful attack (Drilling frequency, DF), and handling time. Our results show that the prey with epibionts are significantly less likely to be drilled when the predator has sufficient choice of prey, consistent with the tenets of the associational resistance. The preference of choosing the non-encrusted prey, however, diminishes with fewer available prey. The handling time is significantly higher in the attacks on the encrusted prey than non-encrusted prey, even though the barnacles are not drilled. Although the proximity of the drilling site to encrustation tends to increase the handling time, the size of encrustation does not have any effect. Because the profitability of prey largely depends on the ratio of handling time and the energetic yield from consuming the prey, the increase in handling time due to encrustation makes it less profitable for the predator. The role of encrustation as a deterrent to predation might also explain the complex shell architecture in some prey gastropods that increases the likelihood of encrustation besides providing direct resistance against predation.
FasR regulates fatty acid biosynthesis and is essential for virulence ofMycobacterium tuberculosis
Authors: Mondino Sonia , Vázquez Cristina L. , Cabruja Matías , Sala Claudia , Cazenave-Gassiot Amaury , Blanco Federico C. , Wenk Markus R. , Bigi Fabiana , Cole Stewart T. , Gramajo Hugo , Gago Gabriela 
Published: June 2020

AbstractMycobacterium tuberculosis, the etiologic agent of human tuberculosis, is the world’s leading cause of death from an infectious disease. One of the main features of this pathogen is the complex and dynamic lipid composition of the cell envelope, which adapts to the variable host environment and defines the fate of infection by actively interacting with and modulating immune responses. However, while much has been learned about the enzymes of the numerous lipid pathways, little knowledge is available regarding the proteins and metabolic signals regulating lipid metabolism duringM. tuberculosisinfection. In this work, we constructed and characterized a FasR-deficient mutant inM. tuberculosisand demonstrated that FasR positively regulatesfasandacpSexpression. Lipidomic analysis of the wild type and mutant strains revealed complete rearrangement of most lipid components of the cell envelope, with phospholipids, mycolic acids, sulfolipids and phthiocerol dimycocerosates relative abundance severely altered. As a consequence, replication of the mutant strain was impaired in macrophages leading to reduced virulence in a mouse model of infection. Moreover, we show that thefasRmutant resides in acidified cellular compartments, suggesting that the lipid perturbation caused by the mutation preventedM. tuberculosisinhibition of phagolysosome maturation. This study identified FasR as a novel factor involved in regulation of mycobacterial virulence and provides evidence for the essential role that modulation of lipid homeostasis plays in the outcome ofM. tuberculosisinfection.
Quantifying the contribution of Neanderthal introgression to the heritability of complex traits
Authors: McArthur Evonne , Rinker David , Capra John A. 
Published: June 2020

ABSTRACTBackgroundNearly all Eurasians have ∼2% Neanderthal ancestry due to several events of inbreeding between anatomically modern humans and archaic hominins. Previous studies characterizing the legacy of Neanderthal ancestry in modern Eurasians have identified examples of both adaptive and deleterious effects of admixture. However, we lack a comprehensive understanding of the genome-wide influence of Neanderthal introgression on modern human diseases and traits.ResultsWe integrate recent maps of Neanderthal ancestry with well-powered association studies for more than 400 diverse traits to estimate heritability enrichment patterns in regions of the human genome tolerant of Neanderthal ancestry and in introgressed Neanderthal variants themselves. First, we find that variants in regions tolerant of Neanderthal ancestry are depleted of heritability for all traits considered, except skin and hair-related traits. Second, the introgressed variants remaining in modern Europeans are depleted of heritability for most traits; however, we discover that they are enriched for heritability of several traits with potential relevance to human adaptation to non-African environments, including hair and skin traits, autoimmunity, chronotype, bone density, lung capacity, and menopause age. To better understand the phenotypic consequences of these enrichments, we adapt recent methods to test for consistent directional effects of introgressed alleles, and we find directionality for several traits. Finally, we use a direction-of-effect-aware approach to highlight novel candidate introgressed variants that influence risk for disease.ConclusionOur results demonstrate that genomic regions retaining Neanderthal ancestry are not only less functional at the molecular-level, but are also depleted for variation influencing a diverse array of complex traits in modern humans. In spite of this depletion, we identify traits where introgression has an outsized effect. Integrating our results, we propose a framework for using quantification of trait heritability and direction of effect in introgressed regions to understand how Neanderthals were different from modern humans, how selection acted on different traits, and how introgression may have facilitated adaptation to non-African environments.
Wiring Up Vision: Minimizing Supervised Synaptic Updates Needed to Produce a Primate Ventral Stream
Authors: Geiger Franziska , Schrimpf Martin , Marques Tiago , DiCarlo James J. 
Published: June 2020

AbstractAfter training on large datasets, certain deep neural networks are surprisingly good models of the neural mechanisms of adult primate visual object recognition. Nevertheless, these models are poor models of the development of the visual system because they posit millions of sequential, precisely coordinated synaptic updates, each based on a labeled image. While ongoing research is pursuing the use of unsupervised proxies for labels, we here explore a complementary strategy of reducing the required number of supervised synaptic updates to produce an adult-like ventral visual stream (as judged by the match to V1, V2, V4, IT, and behavior). Such models might require less precise machinery and energy expenditure to coordinate these updates and would thus move us closer to viable neuroscientific hypotheses about how the visual system wires itself up. Relative to the current leading model of the adult ventral stream, we here demonstrate that the total number of supervised weight updates can be substantially reduced using three complementary strategies: First, we find that only 2% of supervised updates (epochs and images) are needed to achieve ~80% of the match to adult ventral stream. Second, by improving the random distribution of synaptic connectivity, we find that 54% of the brain match can already be achieved “at birth” (i.e. no training at all). Third, we find that, by training only ~5% of model synapses, we can still achieve nearly 80% of the match to the ventral stream. When these three strategies are applied in combination, we find that these new models achieve ~80% of a fully trained model’s match to the brain, while using two orders of magnitude fewer supervisedsynapticupdates. These results reflect first steps in modeling not just primate adult visual processing during inference, but also how the ventral visual stream might be “wired up” by evolution (a model’s “birth” state) and by developmental learning (a model’s updates based on visual experience).
Molecular species selectivity of lipid transport creates a mitochondrial sink for di-unsaturated phospholipids
Authors: Renne Mike F. , Bao Xue , Hokken Margriet W.J. , Bierhuizen Adolf S. , Hermansson Martin , Ewing Tom A. , Ma Xiao , Cox Ruud C. , Brouwers Jos F. , De Smet Cedric H. , Ejsing Christer S. , de Kroon Anton I.P.M. 
Published: June 2020

AbstractMitochondria depend on the import of phospholipid precursors for the biosynthesis of the non-bilayer lipids phosphatidylethanolamine (PE) and cardiolipin required for proper function, yet the mechanism of lipid import remains elusive. Pulse labeling yeast with stable isotope-labeled serine followed by mass spectrometry analysis revealed that mitochondria preferentially import di-unsaturated phosphatidylserine (PS) for conversion to PE by the mitochondrial PS decarboxylase Psd1p. Several protein complexes tethering mitochondria to the endomembrane system have been implicated in lipid transport in yeast, including the endoplasmic reticulum (ER)-mitochondrial encounter structure (ERMES), ER-mitochondria complex (EMC) and the vacuole and mitochondria patch (vCLAMP). By limiting the availability of unsaturated phospholipids through overexpression of the glycerol-3-phosphate acyltransferase Sct1p, conditions were created to investigate the mechanism of lipid transfer and the contribution of the tethering complexesin vivo. Under these conditions, inactivation of ERMES components or the vCLAMP component Vps39p exacerbated the lipid phenotype, indicating that ERMES and Vps39 contribute to the mitochondrial sink for unsaturated acyl chains by mediating transfer of di-unsaturated phospholipids. The results support the concept that intermembrane lipid flow is rate-limited by molecular species-dependent lipid efflux from the donor membrane and driven by the lipid species’ concentration gradient between donor and acceptor membrane.
Development of a Nested-MultiLocus Sequence Typing approach for a highly sensitive and specific identification ofXylella fastidiosasubspecies directly from plant samples
Authors: Cesbron Sophie , Dupas Enora , Beaurepère Quentin , Briand Martial , Borrego Miguel Montes , Velasco Amo Maria del Pilar , Landa Blanca B. , Jacques Marie-Agnès 
Published: June 2020

AbstractDifferent sequence types (ST) ofXylella fastidiosawere already identified in France and Spain based on direct MultiLocus Sequence Typing (MLST) of plant DNA samples. However, direct typing of plant DNA is partly efficient. In order to improve the sensitivity ofX. fastidiosaidentification, we developed a direct nested-MLST assay on plant extracted DNA. This method was performed based on a largely used scheme targeting seven housekeeping gene (HKG) loci (cysG, gltT, holC, leuA, malF, nuoL, petC). Nested primers were designed from multi-sequence alignments of 38 genomes representing all subspecies and one genome ofXylella taiwanensis. Sequences obtained were long enough to be used for BLAST comparison in PubMLST database. No nonspecific amplification products were observed in these samples. Efficiency of the nested-MLST was tested on extracted DNA from 106 samples proven positive (Cq<35) or equivocal (35≤Cq≤40) using the Harper’s qPCR test. Samples analyzed included 49 plant species and two insect species (Philaenus spumarius, Neophilaenus campestris) that were collected in 2017 (106 plant samples in France), in 2018 (162 plant samples in France, 40 plant samples and 26 insect samples in Spain), and in 2019 (30 plant samples in Spain). With the conventional-MLST assay, no complete MLST profile was obtained for any of the samples from France and for most samples (59/66) from Spain. Conversely, with the nested approach, complete profiles were obtained for six French plant samples, 55 Spanish plant samples and nine Spanish insect samples. The threshold was improved by 100 to 1000 times compared to conventional PCR and was between 22 pg.mL−1to 2.2 pg.mL−1depending on the HKG. Using nested-MLST assay, plants that were not yet considered hosts tested positive and revealed novel alleles in France, whereas for Spanish samples it was possible to assign the subspecies or ST to samples considered as new hosts in Europe. Direct typing by nested-MLST from plant material has an increased sensitivity and may be useful for epidemiological purposes.
Evidence of progenitor cell lineage rerouting in the adult mouse hippocampus
Authors: Moura Daniela M.S. , Brandão Juliana Alves , Lentini Celia , Heinrich Christophe , Queiroz Claudio M. , Costa Marcos R. 
Published: June 2020

SummaryCell lineage in the adult hippocampus comprises multipotent and neuron-committed progenitors. In the present work, we fate-mapped neuronal progenitors using Dcx-CreERT2 and CAG-CAT-EGFP double-transgenic mice (cDCX/EGFP). We show that three days after tamoxifen-mediated recombination in cDCX/EGFP adult mice, GFP+ cells in the dentate gyrus co-expresses DCX and about 6% of these cells are proliferative neuronal progenitors. After 30 days, 20% of GFP+ generated from these progenitors differentiate into GFAP+ astrocytes. Administration of the chemoconvulsants kainic acid (KA) or pilocarpine (PL) led to a significant increase in the number of GFP+ cells in both ipsi and contralateral dentate gyrus. However, while PL favored the differentiation of neurons in both ipsi- and contralateral sides, KA stimulated neurogenesis only in the contralateral side. In the ipsilateral side, KA injection led to an unexpected increase of astrogliogenesis in the Dcx-lineage. These different effects of KA and PL in the Dcx-lineage are associated with distinct alterations of the parvalbuminergic plexus and inflammatory responses in the hippocampi. Finally, we also observed a small number of GFP+/GFAP+ cells displaying radial-glia morphology ipsilaterally 3 days after KA administration, indicating that Dcx-progenitors could regress to a multipotent stage. Altogether, our data suggest that cell lineage in the adult hippocampus is not unidirectional and can be modulated by environmental signals.