bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of food restriction on body mass, energy metabolism and thermogenesis in a tree shrew (Tupaia belangeri)
Authors: Gong Xue-na , Zhang Hao , Zhang Di , Zhu Wan-long 
Published: November 2018

AbstractThis study investigates the energy strategies of a small mammal in response to food shortages as a function of food restriction (FR), metabolic rate and ambient temperature. We subjected tree shrews (Tupaia belangeri) to FR and measured body mass, survival rate, resting metabolic rate (RMR), nonshivering thermogenesis (NST) and cytochromecoxidase (COX) activity of brown adipose tissue (BAT). Cold-exposed animals restricted to 80% ofad libitumfood intake had significantly increased RMR and NST and decreased body mass and survival rates compared with those kept at room temperature on the same FR level. Animals classified has having a high RMR consumed 30.69% more food than those classified as having a low RMR, but showed no differences in body mass or survival when restricted to 80% ofad libitumfood intake. These results indicate that tree shrews, known for their relatively high metabolic rates, are sensitive to periods of FR, which supports the metabolic switch hypothesis. Our findings are also consistent with the prediction that small mammals with food hoarding behaviors, like tree shrews, may have a lower tolerance for food shortages than non-hoarding species.
Dynamic brain interactions during picture naming
Authors: Saravani Aram Giahi , Forseth Kiefer J. , Tandon Nitin , Pitkow Xaq 
Published: November 2018

AbstractBrain computations involve multiple processes by which sensory information is encoded and transformed to drive behavior. These computations are thought to be mediated by dynamic interactions between populations of neurons. Here we demonstrate that human brains exhibit a reliable sequence of neural interactions during speech production. We use an autoregressive hidden Markov model to identify dynamical network states exhibited by electrocorticographic signals recorded from human neurosurgical patients. Our method resolves dynamic latent network states on a trial-by-trial basis. We characterize individual network states according to the patterns of directional information flow between cortical regions of interest. These network states occur consistently and in a specific, interpretable sequence across trials and subjects: a fixed-length visual processing state is followed by a variable-length language state, and then by a terminal articulation state. This empirical evidence validates classical psycholinguistic theories that have posited such intermediate states during speaking. It further reveals these state dynamics are not localized to one brain area or one sequence of areas, but are instead a network phenomenon.
Females facilitate male patch discovery in a wild fish population
Authors: Snijders Lysanne , Kurvers Ralf H. J. M. , Krause Stefan , Tump Alan N. , Ramnarine Indar W. , Krause Jens 
Published: November 2018

AbstractWhen individuals are more socially responsive to one sex than the other, the benefits they get from foraging socially are likely to depend on the sex composition of the social environment. We tested this hypothesis by performing experimental manipulations of guppy,Poecilia reticulata, sex compositions in the wild. Males found fewer novel food patches in the absence of females than in mixed-sex compositions, while female patch discovery did not differ between compositions. We argue that these results were driven by sex-dependent mechanisms of social association: Markov chain-based fission-fusion modeling revealed that males reduced sociality when females were absent, while less social individuals found fewer patches. Females were similarly social with or without males. Finally, males, but not females, preferred to join females over males at patches. Our findings reveal the relevance of considering how individual and population-level traits interact in shaping the adaptive value of social living in the wild.
The effect of chemical distances, physical distances, and the presence of sexuals on aggression inCataglyphisdesert ants
Authors: Inbar Shani , Privman Eyal 
Published: November 2018

AbstractIn social insects, non-nestmates interactions are typically agonistic and many factors may influence the degree of exhibited aggression. Two of these factors are the physical proximity between nests and the chemical dissimilarity between colonies’ chemical signatures. We studied a population sample of 43 colonies ofCataglyphis nigerants distributed along a transect of ∼4KM. This geographic distribution allowed us to examine correlations of aggression levels with physical and chemical distances. Ants were collected before mating season, when sexuals (unmated gynes and drones) could be found in nests. In our sample, colonies had either gynes or drones but never both. The presence of sexuals, therefore, was another factor we took into account in our behavioral analyses. Workers from nests with sexuals were more aggressive towards conspecifics than workers from nests where sexuals were absent. We also found those workers to be more vigorously active towards colonies with greater chemical distances, while workers from nests without sexuals were indifferent to chemical distances. We therefore concluded that ants are able to detect differences in chemical dissimilarity, but their aggression levels are mainly determined by other mechanisms. A possible additional mechanism is associative learning and long term memory of the chemical signatures of neighboring colonies. Such learning is supported by our finding that aggression is higher towards neighboring nests, which is in line with the previously reported ‘nasty neighbour’ effect inCataglyphisants. These results suggest that previous experience and learning of neural templates representing neighbors’ chemical cues is a stronger component than chemical dissimilarity in the mechanisms which determine aggression towards conspecifics in this species. We discuss possible explanations for the observed effect of the presence of sexuals on agonistic behavior and responsiveness to chemical distances.
Gut microbiota features of the geographically diverse Indian population
Authors: Shetty Sudarshan A. 
Published: November 2018

AbstractPopulation-level microbial profiling allows for identifying the overarching features of the microbiome. Knowledge of population specific base-line gut microbiome features is important due to the widely reported impact of geography, lifestyle and dietary patterns on the microbiome composition, structure and function. Here, the gut microbiota of more than 1000 subjects across the length and breadth of India is presented. The publicly available 16S rRNA gene profiling data of faecal microbiota from the Landscape Of Gut Microbiome - Pan-India Exploration (LogMPIE) study representing 14 major cities, covering populations from northern, southern, eastern and western part of India analyzed. Majority of the dominant OTUs belonged to the Firmicutes, Bacteroidetes and Proteobacteria phyla. The rarer fraction was comprised of OTUs mainly from the phyla Verrucomicrobia and Spirochaetes. The median core size was estimated to consist of 12 OTUs (>80% prevalence) dominated by representing generaPrevotella,Faecalibacterium, Bacteroides, Roseburia, Megasphaera,EubacteriumandGemmiger. Geographic location explained majority of the variation in the gut microbiota community structure. The observations of the present study support the previous reports ofPrevotelladominance in the Indian population. ThePrevotella/Bacteroidesratio was high for the overall population irrespective of geographic location and did not correlate with BMI or age of the participants. Despite a rapid transition towards a western lifestyle, high prevalence ofTreponemain the Indian gut microbiota suggests that the urban population still harbors signatures of the traditional gut microbiome. The results presented here improve the knowledge of baseline microbiota in the Indian population across the length and breadth of the country. This study provides a base for future studies which need to incorporate numerous other confounding factors and their impact on the observed characteristics of the Indian gut microbiome.
It takes extremes to be robust
Authors: Rocha Felipe Bastos , Vibranovski Maria Dulcetti , Klaczko Louis Bernard 
Published: November 2018

SummaryPhenotypic robustness is a central property of life, manifested in the ability of organisms to endure perturbing conditions throughout their development and often yield rather constant phenotypes. Fundamental questions on robustness (canalization) remain to be answered (see [1]). Do alleles that confer robustness against one perturbation also confer robustness to others? Is the robustness observed in multiple traits/taxa achieved through shared or specific mechanisms? Here, we describe an elementary model of trait development that yields phenotypic robustness without dedicated systems of developmental or transcriptional buffering. Robustness emerges when extremely low or high levels of gene activity lead to either depletion or saturation of the developmental system. We use this model to show that experimental results associating robustness to apparently redundantcis-regulatory sequences (from [2]) probably reflect a similar elementary system of saturation/depletion. We then analyze a large dataset of phenotypic responses of diverse traits of animals, plants and bacteria (from [3]) and show that the amount of response is mostly determined by the distance to the phenotypic extremes. Moreover, the most robust genotypes are often those that yield either extremely low or high phenotypes. Our results help reframing the concepts of canalization and plasticity, suggesting that phenotypic responses are mainly the result of variation in the very systems controlling each trait, rather than being attributable to either “plasticity genes” or “canalization genes”. Furthermore, they provide a hint on the causes of the genomic ubiquity of apparently redundantcis-regulatory sequences [4,5].
Mechanistic origin of cell-size control and homeostasis in bacteria
Authors: Si Fangwei , Treut Guillaume Le , Sauls John T. , Vadia Stephen , Levin Petra Anne , Jun Suckjoon 
Published: November 2018

ABSTRACTEvolutionarily divergent bacteria share a common phenomenological strategy for cell-size homeostasis under steady-state conditions. In the presence of inherent physiological stochasticity, cells following this “adder” principle gradually return to their steady-state size by adding a constant volume between birth and division regardless of their size at birth. However, the mechanism of the adder has been unknown despite intense efforts. In this work, we show that the adder is a direct consequence of two general processes in biology: (1) threshold -- accumulation of initiators and precursors required for cell division to a respective fixed number, and (2) balanced biosynthesis -- maintenance of their production proportional to volume growth. This mechanism is naturally robust to static growth inhibition, but also allows us to “reprogram” cell-size homeostasis in a quantitatively predictive manner in both Gram-negativeEscherichia coliand Gram-positiveBacillus subtilis. By generating dynamic oscillations in the concentration of the division protein FtsZ, we were able to oscillate cell size at division and systematically break the adder. In contrast, periodic induction of replication initiator protein DnaA caused oscillations in cell size at initiation, but did not alter division size or the adder. Finally, we were able to restore the adder phenotype in slow-growingE. coli, the only known steady-state growth condition whereinE. colisignificantly deviates from the adder, by repressing active degradation of division proteins. Together these results show that cell division and replication initiation are independently controlled at the gene-expression level, and that division processes exclusively drive cell-size homeostasis in bacteria.HIGHLIGHTSThe adder requires accumulation of division proteins to a threshold for division.The adder requires constant production of division proteins during cell elongation.InE. coliandB. subtilis, initiation and division are independently controlled.InE. coliandB. subtilis, cell division exclusively drives size homeostasis.GRAPHICAL ABSTRACTeTOC BlurbSi and Le Treutet al. show that cell-size homeostasis in bacteria is exclusively driven by accumulation of division proteins to a threshold and their balanced biosynthesis during cell elongation. This mechanistic insight allowed them to reprogram cell-size homeostasis in bothE. coliandB. subtilis. Evolutionary implications are discussed.
Deep-learning-based label-free segmentation of cell nuclei in time-lapse refractive index tomograms
Authors: Lee Jimin , Kim Hyejin , Cho Hyungjoo , Jo YoungJu , Song Yujin , Ahn Daewoong , Lee Kangwon , Park YongKeun , Ye Sung-Joon 
Published: November 2018

AbstractIn order to identify cell nuclei, fluorescent proteins or staining agents has been widely used. However, use of exogenous agents inevitably prevents from long-term imaging of live cells and rapid analysis, and even interferes with intrinsic physiological conditions. In this work, we proposed a method of label-free segmentation of cell nuclei in optical diffraction tomography images by exploiting a deep learning framework. The proposed method was applied for precise cell nucleus segmentation in two, three, and four-dimensional label-free imaging. A novel architecture with optimised training strategies was validated through cross-modality and cross-laboratory experiments. The proposed method would bring out broad and immediate biomedical applications with our framework publicly available.
Identification of large-scale genomic rearrangements during wheat evolution and the underlying mechanisms
Authors: Bariah Inbar , Keidar-Friedman Danielle , Kashkush Khalil 
Published: November 2018

AbstractFollowing allopolyploidization, nascent polyploid wheat species react with massive genomic rearrangements, including deletion of transposable element-containing sequences. While such massive rearrangements are considered to be a prominent process in wheat genome evolution and speciation, their structure, extent, and underlying mechanisms remain poorly understood. In this study, we retrieved ~3500 insertions of a specific variant ofFatima, one of the most dynamic long-terminal repeat retrotransposons in wheat from the recently available high-quality genome drafts ofTriticum aestivum(bread wheat) andTriticum turgidum ssp. dicoccoidesor wild emmer, the allotetraploid mother of all modern wheats. The dynamic nature ofFatimafacilitated the identification of large (i.e., up to ~ 1 million bases)Fatima-containing insertions/deletions (InDels) upon comparison of bread wheat and wild emmer genomes. We characterized 11 such InDels using computer-assisted analysis followed by PCR validation, and found that they occurred via unequal intra-strand recombination or double-strand break events. In most cases, InDels breakpoints were located within transposable element sequences. Additionally, we observed one case of introgression of novel DNA fragments from an unknown source into the wheat genome. Our data thus indicate that massive large-scale DNA rearrangements might play a prominent role in wheat speciation.
The evolutionary advantage of condition-dependent recombination in a Red Queen model with diploid antagonists
Authors: Rybnikov Sviatoslav R. , Frenkel Zeev M. , Fahima Tzion , Korol Abraham B. 
Published: November 2018

AbstractAntagonistic interaction, like those between a host and its parasite, are known to cause oscillations in genetic structure of both species, usually referred to as Red Queen dynamics (RQD). The RQD is believed to be a plausible explanation for the evolution of sex/recombination, although numerous theoretical models showed that this may happen only under rather restricted parameter values (selection intensity, epistasis, etc.). Here, we consider two diploid antagonists, each with either two or three selected loci; the interaction is based on matching phenotypes model. We use the RQD, whenever it emerges in this system, as a substrate to examine the evolution of one recombination feature, condition dependence in diploids, which still remains an underexplored question. We consider several forms of condition-dependent recombination, with recombination rates in the host being sensitive either to the parasite’s mean fitness, or to the host’s infection status, or to the host’s genotype fitness. We show that all form of condition-dependent recombination can be favored over the corresponding optimal constant recombination rate, even including situations in which the optimal constant recombination rate is zero.
HNI9 and HY5 maintain ROS homeostasis under high nitrogen provision in Arabidopsis
Authors: Bellegarde Fanny , Maghiaoui Amel , Boucherez Jossia , Krouk Gabriel , Lejay Laurence , Bach Liên , Gojon Alain , Martin Antoine 
Published: November 2018

One sentence summaryExcessive N nutrition leads to ROS accumulation, and requires the function of major transcriptional regulators to maintain plants under physiological conditions.Author contributionsAn.M. and A.G. conceived research plans and supervised the experiments; F.B, Am.M., J.B., L.L., L.B. and An.M performed most of the experiments; F.B, Am.M., J.B., G.K., L.L., L.B. and An.M analyzed the data; An.M. wrote the article with contributions of all the authors.Competing interestsThe authors declare no competing financial interests.SummaryReactive Oxygen Species (ROS) can accumulate in cells at excessive levels, leading to unbalanced redox status and to a potential oxidative stress, which can have damaging effects to the molecular components of plant cells. Several environmental conditions have been described as causing an elevation of ROS production in plants. Consequently, this requires the expression of detoxification responses in order to maintain ROS homeostasis at physiological levels. In case of mis-regulation of the detoxification systems, oxidative stress can lead ultimately to growth retardation and developmental defects. Here, we demonstrate that Arabidopsis plants growing under high nitrogen environment have to express a set of genes involved in detoxification of ROS in order to maintain ROS at physiological levels. We show that the chromatin factor HNI9 is an important actor of this response, required for the expression of these detoxification genes. Mutation in HNI9 leads to elevated ROS levels, and to ROS-dependent phenotypic defects under high but not low N provision. In addition, we identify HY5 as one of the major transcription factors also required for the expression of this detoxification program under high N condition. Our results demonstrate the requirement of a balance between N nutrition and ROS production, and identified the first major regulators required to control ROS homeostasis under excessive N nutrition.
Choice of assembly software has a critical impact on virome characterisation
Authors: Sutton Thomas D.S. , Clooney Adam G. , Ryan Feargal J. , Ross R. Paul , Hill Colin 
Published: November 2018

AbstractBackgroundThe viral component of microbial communities play a vital role in driving bacterial diversity, facilitating nutrient turnover and shaping community composition. Despite their importance, the vast majority of viral sequences are poorly annotated and share little or no homology to reference databases. As a result, investigation of the viral metagenome (virome) relies heavily on de novo assembly of short sequencing reads to recover compositional and functional information. Metagenomic assembly is particularly challenging for virome data, often resulting in fragmented assemblies and poor recovery of viral community members. Despite the essential role of assembly in virome analysis and difficulties posed by these data, current assembly comparisons have been limited to subsections of virome studies or bacterial datasets.DesignThis study presents the most comprehensive virome assembly comparison to date, featuring 16 metagenomic assembly approaches which have featured in human virome studies. Assemblers were assessed using four independent virome datasets, namely; simulated reads, two mock communities, viromes spiked with a known phage and human gut viromes.ResultsAssembly performance varied significantly across all test datasets, with SPAdes (meta) performing consistently well. Performance of MIRA and VICUNA varied, highlighting the importance of using a range of datasets when comparing assembly programs. It was also found that while some assemblers addressed the challenges of virome data better than others, all assemblers had limitations. Low read coverage and genomic repeats resulted in assemblies with poor genome recovery, high degrees of fragmentation and low accuracy contigs across all assemblers. These limitations must be considered when setting thresholds for downstream analysis and when drawing conclusions from virome data.
Nuclear arms races: experimental evolution for mating success in the mushroom-forming fungus Schizophyllum commune
Authors: Nieuwenhuis Bart P. S. , Aanen Duur K. 
Published: November 2018

SummaryWhen many gametes compete to fertilize a limited number of compatible gametes, sexual selection will favour traits that increase competitive success during mating. In animals and plants, sperm and pollen competition have yielded many interesting adaptations for improved mating success. In fungi, similar processes have not been shown directly yet. We test the hypothesis that sexual selection can increase competitive fitness during mating, using experimental evolution in the mushroom-forming fungus Schizophyllum commune (Basidiomycota). Mating in mushroom fungi occurs by donation of nuclei to a mycelium. These fertilizing ‘male’ nuclei migrate through the receiving ‘female’ mycelium. In our setup, an evolving population of nuclei was serially mated with a non-evolving female mycelium for 20 sexual generations. From the twelve tested evolved lines, four had increased and one had decreased fitness relative to an unevolved competitor. Even though only two of those five remained significant after correcting for multiple comparisons, for all five lines we found a correlation between the efficiency with which the female mycelium is accessed and fitness, providing additional circumstantial evidence for fitness change in those five lines. In two lines, fitness change was also accompanied by increased spore production. The one line with net reduced competitive fitness had increased spore production, but reduced fertilisation efficiency. We did not find trade-offs between male reproductive success and other fitness components. We compare these findings with examples of sperm and pollen competition and show that many similarities between these systems and nuclear competition in mushrooms exist.