bluuebunny/crossref_metadata_2025_split huggingface dataset:
The direct and indirect effects of environmental toxicants on the health of bumble bees and their microbiomes
Authors: Rothman Jason A. , Russell Kaleigh A. , Leger Laura , McFrederick Quinn S. , Graystock Peter 
Published: April 2020

AbstractBumble bees (Bombusspp.) are important and widespread insect pollinators, but the act of foraging on flowers can expose them to harmful pesticides and environmental chemicals such as oxidizers and heavy metals. How these compounds directly influence bee survival and indirectly affect bee health via the gut microbiome is largely unknown. As the toxins and toxicants in floral nectar and pollen take many forms, we explored the genomes of core bumblebee microbes (Using RAST) for their potential to detoxify cadmium, copper, selenium, the neonicotinoid pesticide imidacloprid, and hydrogen peroxide - which have all been identified in floral nectar and pollen. We then exposedBombus impatiensworkers to varying concentrations of these chemicals spiked into their diet and identified the direct effects on bee survival. Using field realistic doses, we further explored indirect effects on bee microbiomes. We found multiple genes in core gut microbes that have the potential to aid in detoxifying harmful chemicals. We also found that while the chemicals are largely toxic at levels within and above field-realistic concentrations, the field-realistic concentrations - except for imidacloprid - altered the composition of the bee microbiome, potentially causing gut dysbiosis. Overall, our study shows that environmental chemicals found in floral nectar and pollen can directly cause bee mortality, and at field-realistic levels, likely have indirect, deleterious effects on bee health via their influence on the bee microbiome.
Control of ribosomal protein synthesis by Microprocessor complex
Authors: Jiang Xuan , Prabhakar Amit , Van der Voorn Stephanie M. , Ghatpande Prajakta , Celona Barbara , Venkataramanan Srivats , Calviello Lorenzo , Lin Chuwen , Wang Wanpeng , Black Brian L. , Floor Stephen N. , Lagna Giorgio , Hata Akiko 
Published: April 2020

AbstractRibosome biogenesis in eukaryotes requires stoichiometric production and assembly of 80 ribosomal proteins (RPs) and 4 ribosomal RNAs, and its rate must be coordinated with cellular growth. The indispensable regulator of RP biosynthesis is the 5’-terminal oligopyrimidine (TOP) motif, spanning the transcription start site of all RP genes. Here we show that the Microprocessor complex, previously linked to the first step of processing microRNAs (miRNAs), coregulates RP expression by binding the TOP motif of nascent RP mRNAs and stimulating transcription elongation via resolution of DNA/RNA hybrids. Cell growth arrest triggers nuclear export and degradation of the Microprocessor protein Drosha by the E3 ubiquitin ligase Nedd4, accumulation of DNA/RNA hybrids at RP gene loci, decreased RP synthesis, and ribosome deficiency, hence synchronizing ribosome production with cell growth. Conditional deletion ofDroshain erythroid progenitors phenocopies human ribosomopathies, in which ribosomal insufficiency leads to anemia. Outlining a miRNA-independent role of the Microprocessor complex at the interphase between cell growth and ribosome biogenesis offers a new paradigm by which cells alter their protein biosynthetic capacity and cellular metabolism.
Enhanced differentiation of functional human T cells in NSGW41 mice with tissue-specific expression of human interleukin-7
Authors: Coppin Emilie , Sundarasetty Bala Sai , Rahmig Susann , Blume Jonas , Verheyden Nikita A. , Bahlmann Franz , Ravens Sarina , Schubert Undine , Schmid Janine , Ludwig Stefan , von Kaisenberg Constantin , Platz Alexander , Naumann Ronald , Ludwig Barbara , Prinz Immo , Waskow Claudia , Krueger Andreas 
Published: April 2020

AbstractHumanized mouse models have become increasingly valuable tools to study human hematopoiesis and infectious diseases. However, human T cell differentiation remains inefficient. We generated mice expressing human interleukin (IL-7), a critical growth and survival factor for T cells, under the control of murine IL-7 regulatory elements. After transfer of human cord blood-derived hematopoietic stem and progenitor cells, transgenic mice on the NSGW41 background, termed NSGW41hIL7, showed elevated and prolonged human cellularity in the thymus while maintaining physiological ratios of thymocyte subsets. As a consequence, numbers of functional human T cells in the periphery were increased without evidence for pathological lymphoproliferation or aberrant expansion of effector or memory-like T cells. We conclude that the novel NSGW41hIL7 strain represents an optimized mouse model for humanization to better understand human T cell differentiationin vivoand to generate a human immune system with a better approximation of human lymphocyte ratios.
Coupling spectral and resource-use complementarity in experimental grassland and forest communities
Authors: Schweiger Anna K. , Cavender-Bares Jeannine , Kothari Shan , Townsend Philip A. , Madritch Michael D. , Grossman Jake J. , Gholizadeh Hamed , Wang Ran , Gamon John A. 
Published: April 2020

AbstractReflectance spectra provide integrative measures of plant phenotypes by capturing chemical, morphological, anatomical and architectural trait information. Here we investigate the linkages between plant spectral variation, spectral and resource-use complementarity that contribute to ecosystem productivity. In both a prairie grassland and a forest diversity experiment, we delineated N-dimensional hypervolumes using either wavelength-bands of reflectance spectra or foliar traits. First, we compared the hypervolume fraction unique to each species in either spectral or trait space with increasing dimensionality. Then, we investigated the association between the spectral space occupied by individual plants and their growth, as well as the spectral space occupied by plant communities and ecosystem productivity. We show that species are better distinguished in spectral space than in trait space, providing a conceptual basis for identifying plant taxa spectrally. In addition, the spectral space occupied by individuals increased with plant growth, and the spectral space occupied by plant communities increased with ecosystem productivity. Furthermore, ecosystem productivity was better explained by inter-individual spectral complementarity than by the large spectral space occupied by productive individuals. Our results indicate that spectral hypervolumes of plants can reflect ecological strategies that shape community composition and ecosystem function, and that spectral complementarity can reveal resource-use complementarity.
The Role of Rif1 in telomere length regulation is separable from its role in origin firing
Authors: Shubin Calla B. , Greider Carol W. 
Published: April 2020

AbstractTo examine the established link between DNA replication and telomere length, we tested whether firing of telomeric origins would cause telomere lengthening. We found thatRIF1mutants that block Protein Phosphatase 1 (PP1) binding activated telomeric origins but did not elongate telomeres. In a second approach, we found overexpression of ΔN-Dbf4 and Cdc7 increased DDK activity and activated telomeric origins, yet telomere length was unchanged. We tested a third mechanism to activate origins using thesld3-A mcm5-bob1mutant that deregulates the pre-replication complex, and again saw no change in telomere length. Finally, we tested whether mutations inRIF1that cause telomere elongation would affect origin firing. We found that neitherrif1-Δ1322norrif1HOOKaffected firing of telomeric origins. We conclude that telomeric origin firing does not cause telomere elongation, and the role of Rif1 in regulating origin firing is separable from its role in regulating telomere length.
Quantification of Mouse Reach Kinematics as a Foundation for Mechanistic Interrogation of Motor Control
Authors: Becker Matthew I. , Calame Dylan , Wrobel Julia , Person Abigail L. 
Published: April 2020

AbstractMice use reaching movements to grasp and manipulate objects in their environment, similar to primates. Thus, many recent studies use mouse reach to uncover neural control mechanisms, but quantification of mouse reach kinematics remains lacking, limiting understanding. Here we implement several analytical frameworks, from basic kinematic relationships to statistical machine learning, to quantify mouse reach kinematics across freely-behaving and head-fixed conditions. Overall, we find that many canonical features of primate reaches are conserved in mice, with some notable differences. Our results highlight the decelerative phase of reach as important in driving successful outcome. Late-phase kinematic adjustments are yoked to mid-flight position and velocity of the limb, allowing dynamic correction of initial variability, with head-fixed reaches being less dependent on position. Furthermore, consecutive reaches exhibit positional error-correction but not hot-handedness, implying opponent regulation of motor variability. Overall, our results establish foundational mouse reach kinematics in the context of neuroscientific investigation.
Sex-Specific Cross Tissue Meta-Analysis Identifies Immune Dysregulation in Women with Alzheimer’s Disease
Authors: Paranjpe Manish D , Belonwu Stella , Wang Jason K , Oskotsky Tomiko , Gupta Aarzu , Taubes Alice , Zalokusky Kelly , Paranjpe Ishan , Glicksberg Benjamin S , Huang Yadong , Sirota Marina ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: April 2020

ABSTRACTIn spite of evidence of females having a greater lifetime risk of developing Alzheimer’s Disease (AD) and greater apolipoprotein E4-related (apoE4) AD risk compared to males, molecular signatures underlying these findings remain elusive. We took a meta-analysis approach to study gene expression in the brains of 1,084 AD patients and age-matched controls and whole blood from 645 AD patients and age-matched controls. Gene-expression, network-based analysis and cell type deconvolution approaches revealed a consistent immune signature in the brain and blood of female AD patients that was absent in males. Machine learning-based classification of AD using gene expression from whole blood in addition to clinical features revealed an improvement in classification accuracy upon stratifying by sex, achieving an AUROC of 0.91 for females and 0.80 for males. These results help identify sex and apoE4 genotype-specific transcriptomic signatures of AD and underscore the importance of considering sex in the development of biomarkers and therapeutic strategies for AD.
The genomes of invasive coral Tubastraea spp. (Dendrophylliidae) as tool for the development of biotechnological solutions
Authors: Soares-Souza Giordano Bruno , Amaral Danielle , Batista Daniela , Torres André Q. , Silva Serra Anna Carolini , Uliano-Silva Marcela , Leomil Luciana , Reis Aryane Camos , de Matos Elyabe Monteiro , Calderon Emiliano , Yu Vriko , Dondero Francesco , de Sousa Saulo Marçal , Baker David , Dumaresq Aline , Rebelo Mauro F. 
Published: April 2020

AbstractCorals have been attracting huge attention due to the impact of climate change and ocean acidification on reef formation and resilience. Nevertheless, some species like Tubastraea coccinea and T. tagusensis have been spreading very fast replacing the native ones which affect the local environment and decrease biodiversity of corals and other organisms associated with them. Despite some focal efforts to understand the biology of these organisms, they remain understudied at the molecular level. This knowledge gap hinders the development of cost-effective strategies for both conservation and management of invasive species. In this circumstance, it is expected that genome sequencing would provide powerful insights that could lead to better strategies for prevention, management, and control of this and other invasive species. Here, we present three genomes of Tubastraea spp. in one of the most comprehensive biological studies of corals, that includes flow cytometry, karyotyping, transcriptomics, genomics, and phylogeny. The genome of T. tagusensis is organized in 23 chromosomes pairs and has 1.1 Gb, the T. coccinea genome is organized in 22 chromosome pairs and has 806 Mb, and the Tubastraea sp. genome is organized in 21 chromosome pairs and has 795 Mb. The hybrid assembly of T. tagusensis using short and long-reads has a N50 of 227,978 bp, 7,996 contigs and high completeness estimated as 91.6% of BUSCO complete genes, of T. coccinea has a N50 of 66,396 bp, 17,214 contigs and 88.1% of completeness, and of Tubastraea sp. has a N50 of 82,672 bp, 12,922 contigs and also 88.1% of completeness. We inferred that almost half of the genome consists of repetitive elements, mostly interspersed repeats. We provide evidence for exclusive Scleractinia and Tubastraea gene content related to adhesion and immunity. The Tubastraea spp. genomes are a fundamental study which promises to provide insights not only about the genetic basis for the extreme invasiveness of this particular coral genus, but to understand the adaptation flaws of some reef corals in the face of anthropic-induced environmental disturbances. We expect the data generated in this study will foster the development of efficient technologies for the management of coral species, whether invasive or threatened.
Functional Annotation of Human Cognitive States using Deep Graph Convolution
Authors: Zhang Yu , Tetrel Loïc , Thirion Bertrand , Bellec Pierre 
Published: April 2020

AbstractA key goal in neuroscience is to understand brain mechanisms of cognitive functions. An emerging approach is “brain decoding”, which consists of inferring a set of experimental conditions performed by a participant, using pattern classification of brain activity. Few works so far have attempted to train a brain decoding model that would generalize across many different cognitive tasks drawn from multiple cognitive domains. To tackle this problem, we proposed amultidomainbrain decoder that automatically learns the spatiotemporal dynamics of brain response within a short time window using a deep learning approach. We evaluated the decoding model on a large population of 1200 participants, under 21 different experimental conditions spanning six different cognitive domains, acquired from the Human Connectome Project task-fMRI database. Using a 10s window of fMRI response, the 21 cognitive states were identified with a test accuracy of 90% (chance level 4.8%). Performance remained good when using a 6s window (82%). It was even feasible to decode cognitive states from a single fMRI volume (720ms), with the performance following the shape of the hemodynamic response. Moreover, a saliency map analysis demonstrated that the high decoding performance was driven by the response of biologically meaningful brain regions. Together, we provide an automated tool to annotate human brain activity with fine temporal resolution and fine cognitive granularity. Our model shows potential applications as a reference model for domain adaptation, possibly making contributions in a variety of domains, including neurological and psychiatric disorders.
Enhancer Remodeling Promotes Tumor-Initiating Activity in NRF2-Activated Non-Small Cell Lung Cancers
Authors: Okazaki Keito , Anzawa Hayato , Liu Zun , Ota Nao , Kitamura Hiroshi , Onodera Yoshiaki , Alam Md. Morshedul , Matsumaru Daisuke , Suzuki Takuma , Katsuoka Fumiki , Tadaka Shu , Motoike Ikuko , Watanabe Mika , Sakurada Akira , Okada Yoshinori , Yamamoto Masayuki , Suzuki Takashi , Kinoshita Kengo , Sekine Hiroki , Motohashi Hozumi 
Published: April 2020

SummaryTranscriptional dysregulation, which can be caused by genetic and epigenetic alterations, is a fundamental feature of many cancers. A key cytoprotective transcriptional activator, NRF2, is often aberrantly activated in non-small cell lung cancers (NSCLCs) and supports both aggressive tumorigenesis and therapeutic resistance. Herein, we found that persistently activated NRF2 in NSCLCs generates enhancers at gene loci that are not normally regulated by transiently activated NRF2 under physiological conditions. Elevated accumulation of CEBPB in NRF2-activated NSCLCs was found to be one of the prerequisites for establishment of the unique NRF2-dependent enhancers, among whichNOTCH3enhancer was shown to be critical for the promotion of tumor-initiating activity. Enhancer remodeling mediated by NRF2-CEBPB cooperativity promotes tumor-initiating activity and drives malignancy of NRF2-activated NSCLCs via establishment of the NRF2-NOTCH3 regulatory axis.
Advanced computational and statistical multiparametric analysis of Susceptibility-Weighted Imaging to characterize gliomas and brain metastases
Authors: Ieva Antonio Di , Russo Carlo , Le Reste Pierre-Jean , Magnussen John S. , Heller Gillian 
Published: April 2020

AbstractSusceptibility-weighted imaging (SWI) is a technique useful for evaluation of the internal structures of brain tumors, including microvasculature and microbleeds. Intratumoral patterns of magnetic susceptibility can be quantified by means of fractal analysis. Here, we propose a radiomics methodological pipeline to merge advanced fractal-based computational modelling with statistical analysis to objectively characterize the fingerprint of gliomas and brain metastases. Forty-seven patients with glioma (grades II-IV, according to the WHO 2016 classification system) and fourteen with brain metastases underwent 3 Tesla MRI using a SWI protocol. All images underwent computational analysis aimed to quantify three Euclidean parameters (related to tumor and SWI volume) and five fractal-based parameters (related to the pixel distribution and geometrical complexity of the SWI patterns). Principal components analysis, linear and quadratic discriminant analysis, K-nearest neighbor and support vector machine methods were used to discriminate between tumor types. The combination of parameters offered an objective evaluation of the SWI pattern in gliomas and brain metastases. The model accurately predicted 88% of glioblastoma, according to the quantification of intratumoral SWI features, failing to discriminate the other types. SWI is not normally used to classify brain tumors, however fractal-based multi-parametric computational analysis can be used to characterize intratumoral SWI patterns to objectively quantify tumors-related features. Specific parameters still have to be identified to provide completely automatic computerized differential diagnosis.
Chromosome-scale de novo diploid assembly of the apple cultivar ‘Gala Galaxy’
Authors: Broggini Giovanni A.L. , Schlathölter Ina , Russo Giancarlo , Copetti Dario , Yates Steven A. , Studer Bruno , Patocchi Andrea 
Published: April 2020

AbstractApple (Malus × domestica) is one of the most important fruit crops in terms of worldwide production. Due to its self-incompatibility system and the long juvenile period, breeding of new apple cultivars combining traits desired by growers (e.g. yield, pest and disease resistance) and consumers (e.g. fruit size, color, and flavor) is a long and complex process. Genomics-assisted breeding strategies can facilitate the selection of germplasm leading to new cultivars. While the most complete apple genome assemblies available to date are from anther-derived homozygous lines, de novo assembly of apple genomes encompassing the natural heterozygosity remains challenging. Using long- and short-read sequencing technologies in combination with optical mapping, we de novo assembled a diploid and heterozygous genome of the apple cultivar ‘Gala Galaxy’. This approach resulted in 154 hybrid scaffolds (N50 = 34.3 Mb) spanning 999.9 Mb and in 414.7 Mb of unscaffolded sequences. Anchoring 31 scaffolds with a genetic map was sufficient to represent an entire haploid genome of 17 pseudomolecules (719.4 Mb). The remaining sequences were assembled in a second set of 17 pseudomolecules, which spanned 601 Mb, leaving 80.6 Mb of unplaced sequences. A total of 41,264 genes were annotated using 74,900 transcripts derived from RNA sequencing of pooled leaf tissue samples. This study provides a high-quality diploid reference genome sequence encompassing the natural heterozygosity of the widely popular cultivar ‘Gala Galaxy’. The DNA sequence resources and the assembly described here will serve as a solid foundation for fundamental and applied apple breeding research.
Genome sequence of the banana aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae) and its symbionts
Authors: Mathers Thomas C. , Mugford Sam T. , Hogenhout Saskia A. , Tripathi Leena 
Published: April 2020

AbstractThe banana aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae), is a major pest of cultivated bananas (Musa spp., order Zingiberales), primarily due to its role as a vector of Banana bunchy top virus (BBTV), the most severe viral disease of banana worldwide. Here, we generated a highly complete genome assembly of P. nigronervosa using a single PCR-free Illumina sequencing library. Using the same sequence data, we also generated complete genome assemblies of the P. nigronervosa symbiotic bacteria Buchnera aphidicola and Wolbachia. To improve our initial assembly of P. nigronervos a we developed a k-mer based deduplication pipeline to remove genomic scaffolds derived from the assembly of haplotigs (allelic variants assembled as separate scaffolds). To demonstrate the usefulness of this pipeline, we applied it to the recently generated assembly of the aphid Myzus cerasi, reducing the duplication of conserved BUSCO genes by 25%. Phylogenomic analysis of P. nigronervos a, our improved M. cerasi assembly, and seven previously published aphid genomes, spanning three aphid tribes and two subfamilies, reveals that P. nigronervos a falls within the tribe Macrosiphini, but is an outgroup to other Macrosiphini sequenced so far. As such, the genomic resources reported here will be useful for understanding both the evolution of Macrosphini and for the study of P. nigronervosa. Furthermore, our approach using low cost, high-quality, Illumina short-reads to generate complete genome assemblies of understudied aphid species will help to fill in genomic black spots in the diverse aphid tree of life.
Genome-wide chromatin binding of transcriptional corepressor Topless-related 1 inArabidopsis
Authors: Griebel Thomas , Lapin Dmitry , Kracher Barbara , Concia Lorenzo , Benhamed Moussa , Parker Jane E. 
Published: April 2020

AbstractTimely and specific regulation of gene expression is critical for plant responses to environmental and developmental cues. Transcriptional coregulators have emerged as important factors in gene expression control, although they lack DNA-binding domains and the mechanisms by which they are recruited to and function at the chromatin are poorly understood. Plant Topless-related 1 (TPR1), belonging to a family of transcriptional corepressors found across eukaryotes, contributes to immunity signaling inArabidopsis thalianaand wild tobacco. We performed chromatin immunoprecipitation and sequencing (ChIP-seq) on anArabidopsis TPR1-GFPexpressing transgenic line to characterize genome-wide TPR1-chromatin associations. The analysis revealed ∼1400 genes bound by TPR1, with the majority of binding sites located at gene upstream regions. Among the TPR1 bound genes, we find not only regulators of immunity but also genes controlling growth and development. To support further analysis of TPR1-chromatin complexes and other transcriptional corepressors in plants, we provide two ways to access the processed ChIP-seq data and enable their broader use by the research community.