bluuebunny/crossref_metadata_2025_split huggingface dataset:
A gustatory receptor tuned to the steroid plant hormone brassinolide inPlutella xylostella(Lepidoptera: Plutellidae)
Authors: Yang Ke , Gong Xin-Lin , Li Guo-Cheng , Huang Ling-Qiao , Ning Chao , Wang Chen-Zhu 
Published: July 2020

AbstractFeeding and oviposition deterrents help phytophagous insects to identify host plants. The taste organs of phytophagous insects contain bitter gustatory receptors (GRs). To explore their function, we focused on PxylGr34, a bitter GR inPlutella xylostella(L.). We detected abundantPxylGr34transcripts in the larval head and specific expression ofPxylGr34in the antennae of females. Analyses using theXenopusoocyte expression system and two-electrode voltage-clamp recording showed that PxylGr34 is specifically tuned to the plant hormone brassinolide (BL) and its analog 24-epibrassinolide. Electrophysiological analyses revealed that the medial sensilla styloconica on the maxillary galea of the 4thinstar larvae are responsive to BL. Dual-choice bioassays demonstrated that BL inhibits larval feeding and female ovipositing. Knock-down of PxylGr34 by RNAi abolished BL-induced feeding inhibition. These results shed light on gustatory coding mechanisms and deterrence of insect feeding and ovipositing, and may be useful for designing plant hormone-based pest management strategies.
Testing two competing hypotheses for Eurasian jays’ caching for the future: planning versus compensatory caching
Authors: Amodio Piero , Brea Johanni , Farrar Benjamin G. , Ostojic Ljerka , Clayton Nicola S. 
Published: July 2020

AbstractPrevious research reported that corvids preferentially cache food in a location where no food will be available or cache more of a specific food in a location where this food will not be available. Here, we consider possible explanations for these prospective caching behaviours and directly compare two competing hypotheses. The Compensatory Caching Hypothesis suggests that birds learn to cache more of a particular food in places where that food was less frequently available in the past. In contrast, the Future Planning Hypothesis suggests that birds recall what-when-where features of specific past events to predict the future availability of food. We designed a protocol in which the two hypotheses predict different caching patterns across different caching locations such that the two explanations can be disambiguated. We formalised the hypotheses in a Bayesian model comparison and tested this protocol in two experiments with one of the previously tested species, namely Eurasian jays. Consistently across the two experiments, the observed caching pattern did not support either hypothesis; rather it was best explained by a uniform distribution of caches over the different caching locations. Future research is needed to gain more insight into the cognitive mechanism underpinning corvids’ caching for the future.
Extracellular matrix supports excitation-inhibition balance in neuronal networks by stabilizing inhibitory synapses
Authors: Dzyubenko Egor , Fleischer Michael , Manrique-Castano Daniel , Borbor Mina , Kleinschnitz Christoph , Faissner Andreas , Hermann Dirk M 
Published: July 2020

AbstractMaintaining the balance between excitation and inhibition is essential for the appropriate control of neuronal network activity. Sustained excitation-inhibition (E-I) balance relies on the orchestrated adjustment of synaptic strength, neuronal activity and network circuitry. While growing evidence indicates that extracellular matrix (ECM) of the brain is a crucial regulator of neuronal excitability and synaptic plasticity, it remains unclear whether and how ECM contributes to neuronal circuit stability. Here we demonstrate that the integrity of ECM supports the maintenance of E-I balance by retaining inhibitory connectivity. Depletion of ECM in mature neuronal networks preferentially decreases the density of inhibitory synapses and the size of individual inhibitory postsynaptic scaffolds. After ECM depletion, inhibitory synapse strength homeostatically increases via the reduction of presynaptic GABABreceptors. However, the inhibitory connectivity reduces to an extent that inhibitory synapse scaling is no longer efficient in controlling neuronal network activity. Our results indicate that the brain ECM preserves the balanced network state by stabilizing inhibitory synapses.Significance statementThe question how the brain’s extracellular matrix (ECM) controls neuronal plasticity and network activity is key for an appropriate understanding of brain functioning. In this study, we demonstrate that ECM depletion much more strongly affects the integrity of inhibitory than excitatory synapses in vitro and in vivo. We revealed that by retaining inhibitory connectivity, ECM ensures the efficiency of inhibitory control over neuronal network activity. Our work significantly expands our current state of knowledge about the mechanisms of neuronal network activity regulation. Our findings are similarly relevant for researchers working on the physiological regulation of neuronal plasticity in vitro and in vivo and for researchers studying the remodeling of neuronal networks upon brain injury, where prominent ECM alterations occur.
Early Medieval Genetic Data from Ural Region Evaluated in the Light of Archaeological Evidence of Ancient Hungarians
Authors: Csáky Veronika , Gerber Dániel , Szeifert Bea , Egyed Balázs , Stégmár Balázs , Botalov Sergej Gennad’evich , Grudochko Ivan Valer’evich , Matvejeva Natalja Petrovna , Zelenkov Alexander Sergejevich , Slepcova Anastasija Viktorovna , Goldina Rimma D. , Danich Andrey V. , Mende Balázs G. , Türk Attila , Szécsényi-Nagy Anna 
Published: July 2020

AbstractThe ancient Hungarians originated from the Ural region of Russia, and migrated through the Middle-Volga region and the Eastern European steppe into the Carpathian Basin during the 9th century AD. Their Homeland was probably in the southern Trans-Ural region, where the Kushnarenkovo culture disseminated. In the Cis-Ural region Lomovatovo and Nevolino cultures are archaeologically related to ancient Hungarians. In this study we describe maternal and paternal lineages of 36 individuals from these regions and nine Hungarian Conquest period individuals from today’s Hungary, as well as shallow shotgun genome data from the Trans-Uralic Uyelgi cemetery. We point out the genetic continuity between the three chronological horizons of Uyelgi cemetery, which was a burial place of a rather endogamous population. Using phylogenetic and population genetic analyses we demonstrate the genetic connection between Trans-, Cis-Ural and the Carpathian Basin on various levels. The analyses of this new Uralic dataset fill a gap of population genetic research of Eurasia, and reshape the conclusions previously drawn from 10-11th century ancient mitogenomes and Y-chromosomes from Hungary.
Divergence and Remarkable Diversity of the Y Chromosome in Guppies
Authors: Almeida Pedro , Sandkam Benjamin A. , Morris Jake , Darolti Iulia , Breden Felix , Mank Judith E. 
Published: July 2020

AbstractThe guppy sex chromosomes show an extraordinary diversity in divergence across populations and closely related species. In order to understand the dynamics of the guppy Y chromosome, we used linked-read sequencing to assess Y chromosome evolution and diversity across upstream and downstream population pairs that vary in predator and food abundance in three replicate watersheds. Based on our population-specific genome assemblies, we first confirmed and extended earlier reports of two strata on the guppy sex chromosomes. Stratum I shows significant accumulation of male-specific sequence, consistent with Y divergence, and predates the colonization of Trinidad. In contrast, Stratum II shows divergence from the X, but no Y-specific sequence, and this divergence is greater in three replicate upstream populations compared to their downstream pair. Despite longstanding assumptions that sex chromosome recombination suppression is achieved through inversions, we find no evidence of inversions associated with either Stratum I or Stratum II. Instead, we observe a remarkable diversity in Y chromosome haplotypes within each population, even in the ancestral Stratum I. This diversity is likely due to gradual mechanisms of recombination suppression, which, unlike an inversion, allow for the maintenance of multiple haplotypes. In addition, we show that this Y diversity is dominated by low-frequency haplotypes segregating in the population, suggesting a link between haplotype diversity and female-preference for rare Y-linked colour variation. Our results reveal the complex interplay between recombination suppression and Y chromosome divergence at the earliest stages of sex chromosome divergence.
Pan-genome analyses of peach and its wild relatives provide insights into the genetics of disease resistance and species adaptation
Authors: Cao Ke , Peng Zhen , Zhao Xing , Li Yong , Liu Kuozhan , Arus Pere , Zhu Gengrui , Deng Shuhan , Fang Weichao , Chen Changwen , Wang Xinwei , Wu Jinlong , Fei Zhangjun , Wang Lirong 
Published: July 2020

AbstractAs a foundation to understand the molecular mechanisms of peach evolution and high-altitude adaptation, we performedde novogenome assembling of four wild relatives ofP. persica, P. mira, P. kansuensis, P. davidianaandP. ferganensis. Through comparative genomic analysis, abundant genetic variations were identified in four wild species when compared toP. persica. Among them, a deletion, located at the promoter ofPrupe.2G053600inP. kansuensis, was validated to regulate the resistance to nematode. Next, a pan-genome was constructed which comprised 15,216 core gene families among four wild peaches andP. perisca. We identified the expanded and contracted gene families in different species and investigated their roles during peach evolution. Our results indicated thatP. mirawas the primitive ancestor of cultivated peach, and peach evolution was non-linear and a cross event might have occurred betweenP. miraandP. dulcisduring the process. Combined with the selective sweeps identified using accessions ofP. miraoriginating from different altitude regions, we proposed that nitrogen recovery was essential for high-altitude adaptation ofP. mirathrough increasing its resistance to low temperature. The pan-genome constructed in our study provides a valuable resource for developing elite cultivars, studying the peach evolution, and characterizing the high-altitude adaptation in perennial crops.
Differential transcriptional reprogramming by wild type and lymphoma-associated mutant MYC proteins as B-cells convert to lymphoma-like cells
Authors: Mahani Amir , Arvidsson Gustav , Sadeghi Laia , Grandien Alf , Wright Anthony P. 
Published: July 2020

AbstractThe transcription factor MYC regulates the expression of a vast number of genes and is implicated in various human malignancies, for which it’s deregulation by genomic events such as translocation or amplification can be either disease-defining or associated with poor prognosis. In hematological malignancies MYC is frequently subject to missense mutations and one such hot spot where mutations have led to increased protein stability and elevated transformation activity exists within its transactivation domain. Here we present and characterize a model system for studying the effects of gradually increasing MYC levels as B-cells progress to lymphoma-like cells. Inclusion of two frequent lymphoma-associated MYC mutants (T58A and T58I) allowed for discrimination of changes in the MYC regulatory program according to mutation status. Progressive increase in MYC levels significantly altered the transcript levels of 7569 genes and subsets of these were regulated differently in mutant MYC proteins compared to WT MYC or between the mutant MYC proteins. Functional classification of the differentially regulated genes based on expression levels across different MYC levels confirmed previously found MYC regulated functions such as ribosome biogenesis and purine metabolism while other functional groups such as the downregulation of genes involved in B-cell differentiation and chemotaxis were novel. Gene sets that were differently regulated in cells overexpressing mutant MYC proteins contained an over-representation of genes involved in DNA Replication and transition from the G2 phase to mitosis. The cell model presented here mimics changes seen during lymphoma development in the Eμ-Myc mouse model as well as MYC-dependent events associated with poor prognosis in a wide range of human cancer types and therefore constitutes a relevant cell model forin vitromechanistic studies of wild type and mutant MYC proteins in relation to lymphoma development.
A quantised cyclin-based cell cycle model
Authors: Emerson Chris , Bennie Lindsey , Green Dermot , Currell Fred , Coulter Jonathan A. 
Published: July 2020

AbstractComputational modelling is an important research tool, helping predict the outcome of proposed treatment plans or to illuminate the mechanics of tumour growth.In silicomodelling has been used in every aspect of cancer research from DNA damage and repair, tumour growth, drug/tumour interactions, and mutational status. Indeed, modelling even holds potential in understanding the interactions between individual proteins on a single cell basis. Here, we present a computational model of the cell cycle network of the cyclin family of proteins (cyclin A, B, D and E). This model has been quantised using western blot and flow cytometry data from a synchronised HUVEC line to enable the determination of the absolute number of cyclin protein molecules per cell. This quantification allows the model to have stringent controls over the thresholds between transitions. The results show that the peak values obtained for the four cyclins are similar with cyclin B having a peak values of 5×106to 9×106molecules per cell. Comparing this value with the number of actin proteins, 5E8, shows that despite their importance, the level of cyclin family proteins are approximately 2 orders of magnitude lower. The efficiency of the model presented would also allow for its use as an internal component in more complex models such as a tumour growth model, in which each individual cell would have its own cell cycle calculated independently from neighbouring cells. Additionally, the model can also be used to help understand the impact of novel therapeutic interventions on cell cycle progression.Author SummaryProtein and gene networks control every physiological behaviour of cells, with the cell cycle being controlled by the network of genes that promote the cyclin family of proteins. These networks hold the key to creating accurate and relevant biological models. Normally these models are presented with relative protein concentrations without any real world counterpart to their outputs. The model presented within shows and advancement of this approach by calculating the absolute concentration of each cyclin protein in one cell as it progresses through the cell cycle. This model employs Boolean variables to represent the genetic network, either the gene is active or not, and continuous variables to represent the concentrations of the proteins. This hybridised approach allows for rapid calculations of the protein concentrations and of the cell cycle progression allowing for a model that could be easily incorporated into larger tumour models, allowing for the tracking of discrete cells within the tumour.
Resolving phylogeny and polyploid parentage using genus-wide genome-wide sequence data from birch trees
Authors: Wang Nian , Kelly Laura J. , McAllister Hugh A. , Zohren Jasmin , Buggs Richard J. A. 
Published: July 2020

AbstractNumerous plant genera have a history including frequent hybridisation and polyploidisation, which often means that their phylogenies are not yet fully resolved. The genusBetula, which contains many ecologically important allopolyploid tree species, is a case in point. We generated genome-wide sequence data for 27 diploid and 31 polyploidBetulaspecies or subspecies using restriction site associated DNA (RAD) sequences assembled into contigs with a mean length of 675 bp. We reconstructed the evolutionary relationships among diploidBetulaspecies using both supermatrix and species tree methods. We identified progenitors of the polyploids according to the relative rates at which their reads mapped to contigs from different diploid species. We sorted the polyploid reads into different putative sub-genomes and used the extracted contigs, along with the diploid sequences, to build new phylogenies that included the polyploid sub-genomes. This approach yielded a highly evidenced phylogenetic hypothesis for the genusBetula, including the complex reticulate origins of the majority of its polyploid taxa. The genus was split into two well supported clades, which differ in their seed-wing morphology. We propose a new taxonomy forBetula, splitting it into two subgenera. We have resolved the parentage of many widespread and economically important polyploid tree species, opening the way for their population genomic study.
A cell non-autonomous mechanism of yeast chronological aging regulated by caloric restriction and one-carbon metabolism
Authors: Enriquez-Hesles Elisa , Smith Daniel L. , Maqani Nazif , Wierman Margaret B. , Sutcliffe Matthew , Fine Ryan D. , Kalita Agata , Santos Sean M. , Muehlbauer Michael J. , Bain James R. , Janes Kevin A. , Hartman John L. , Hirschey Matthew D. , Smith Jeffrey S. 
Published: July 2020

AbstractCaloric restriction (CR) improves healthspan and lifespan of organisms ranging from yeast to mammals. Understanding the mechanisms involved will uncover future interventions for aging associated diseases. In budding yeast,Saccharomyces cerevisiae, CR is commonly defined by reduced glucose in the growth medium, which extends both replicative and chronological lifespan (CLS). We found that conditioned media collected from stationary phase CR cultures extended CLS when supplemented into non-restricted (NR) cultures, suggesting a potential cell non-autonomous mechanism of CR-induced lifespan regulation. Chromatography and untargeted metabolomics of the conditioned media, as well as transcriptional responses associated with the longevity effect, pointed to specific amino acids enriched in the CR conditioned media (CRCM) as functional molecules, with L-serine being a particularly strong candidate. Indeed, supplementing L-serine into NR cultures extended CLS through a mechanism dependent on the one-carbon metabolism pathway, thus implicating this conserved and central metabolic hub in lifespan regulation.
Multi-Task Learning based 3-Dimensional Striatal Segmentation of MRI – a Multi-modal Objective Assessment
Authors: Serrano-Sosa Mario , Van Snellenberg Jared X. , Meng Jiayan , Spuhler Karl , Weinstein Jodi J. , Abi-Dargham Anissa , Slifstein Mark , Huang Chuan 
Published: July 2020

AbstractThe human striatum is a collection of subcortical nuclei that serves as a critical node in an information processing network. Recent studies have established a clear topographical and functional organization of projections to and from striatal regions that involves detailed and complex subdivisions of the striatum. Manual segmentation of these functional subdivisions is labor-intensive and time-consuming, yet automated methods have also been a challenging computational problem. Recently, deep learning has emerged as a powerful tool for various tasks, including semantic segmentation. Multi-Task Learning (MTL) is a machine learning technique that allows latent representations between related tasks to be shared during model prediction of multiple tasks with better accuracy. We utilized MTL to segment subregions of the striatum consisting of pre-commissural putamen (prePU), pre-commissural caudate (preCA), post-commissural putamen (postPU), post-commissural caudate (postCA), and ventral striatum (VST). Dice similarity coefficients (DSC) demonstrate excellent spatial agreement between manual and MTL-generated segmentations (≥ 0.72 across all striatal subregions). Further quantitative task-based analysis was also conducted. Binding potential values, BPND, of [11C]raclopride PET, and ROI time-series and whole-brain connectivity using fMRI images were compared between results generated from manual segmentations and MTL-generated segmentations. BPNDvalues from MTL-generated segmentations were shown to correlate well with manual segmentations with R2≥ 0.91 in all caudate and putamen subregions, and R2=0.69 in VST. Mean Pearson correlation coefficients of the fMRI data between MTL-generated and manual segmentations were also high in time-series (≥0.86) and whole-brain connectivity (≥0.89) across all subregions. We conclude that the MTL approach is a fast, robust and reliable method for 3D striatal subregion segmentation with results comparable to manually segmented ROIs.
The impact of dominance on adaptation in changing environments
Authors: Devi Archana , Jain Kavita 
Published: July 2020

AbstractNatural environments are seldom static and therefore it is important to ask how a population adapts in a changing environment. We consider a finite, diploid population evolving in a periodically changing environment and study how the fixation probability of a rare mutant depends on its dominance coefficient and the rate of environmental change. We find that in slowly changing environments, the effect of dominance is the same as in the static environment, that is, if a mutant is beneficial (deleterious) when it appears, it is more (less) likely to fix if it is dominant. But in fast changing environments, the effect of dominance can be different from that in the static environment and is determined by the mutant’s fitness at the time of appearance as well as that in the time-averaged environment. We find that in a rapidly varying environment which is neutral on average, an initially beneficial (deleterious) mutant that arises while selection is decreasing (increasing) has a fixation probability lower (higher) than that for a neutral mutant as a result of which the recessive (dominant) mutant is favored. If the environment is beneficial (deleterious) on average but the mutant is deleterious (beneficial) when it appears in the population, the dominant (recessive) mutant is favored in a fast changing environment. We also find that when recurrent mutations occur, dominance does not have a strong influence on evolutionary dynamics.
Causal inference in environmental sound recognition
Authors: Traer James , Norman-Haignere Sam V. , McDermott Josh H. 
Published: July 2020

AbstractSound is caused by physical events in the world. Do humans infer these causes when recognizing sound sources? We tested whether the recognition of common environmental sounds depends on the inference of a basic physical variable – the source intensity (i.e., the power that produces a sound). A source’s intensity can be inferred from the intensity it produces at the ear and its distance, which is normally conveyed by reverberation. Listeners could thus use intensity at the ear and reverberation to constrain recognition by inferring the underlying source intensity. Alternatively, listeners might separate these acoustic cues from their representation of a sound’s identity in the interest of invariant recognition. We compared these two hypotheses by measuring recognition accuracy for sounds with typically low or high source intensity (e.g., pepper grinders vs. trucks) that were presented across a range of intensities at the ear or with reverberation cues to distance. The recognition of low-intensity sources (e.g., pepper grinders) was impaired by high presentation intensities or reverberation that conveyed distance, either of which imply high source intensity. Neither effect occurred for high-intensity sources. The results suggest that listeners implicitly use the intensity at the ear along with distance cues to infer a source’s power and constrain its identity. The recognition of real-world sounds thus appears to depend upon the inference of their physical generative parameters, even generative parameters whose cues might otherwise be separated from the representation of a sound’s identity.