bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity-induced plant history and soil history effects modulate plant responses to global change
Authors: Dietrich Peter , Schumacher Jens , Eisenhauer Nico , Roscher Christiane 
Published: October 2021

AbstractGlobal change has dramatic impacts on grassland diversity. However, little is known about how fast species can adapt to these changes and how this affects their responses to global change. To close this gap, we performed a common garden experiment testing whether plant responses to global change are influenced by the selection history of the plants and the conditioning history of soil at different levels of plant diversity. Therefore, we collected seeds and took soil samples from 14-year old plant communities of a biodiversity experiment. Offspring of plants from low- and high-diversity communities were either grown in their own soil or in soil of a different community, and were either exposed to drought, increased nitrogen input, or a combination of both. Results show that, under nitrogen addition, offspring of plants selected at high diversity produced more biomass than those selected at low diversity, while drought neutralized differences in biomass production. Moreover, under the influence of global change drivers, mainly soil, and to a lesser extent plant history, influenced the expression of plant traits. Our results show that plant diversity modulates plant-soil interactions and growth strategies of plants, which feedback on the eco-evolutionary pathways of the plants and thus their responses to global change.
Quantitative live-imaging of Aquilegia floral meristems reveals distinct patterns of floral organ initiation and cell-level dynamics of floral meristem termination
Authors: Min Ya , Conway Stephanie J. , Kramer Elena M. 
Published: October 2021

ABSTRACTIn-depth investigation of any developmental process in plants requires knowledge of both the underpinning molecular networks and how they directly determine patterns of cell division and expansion over time. Floral meristems (FM) produce floral organs, after which they undergo floral meristem termination (FMT), and precise control of organ initiation and FMT is crucial to reproductive success of any flowering plant. Using a live confocal imaging, we characterized developmental dynamics during floral organ primordia initiation and FMT in Aquilegia coerulea (Ranunculaceae). Our results have uncovered distinct patterns of primordium initiation between stamens and staminodes compared to carpels, and provided insight into the process of FMT, which is discernable based on cell division dynamics preceding carpel initiation. To our knowledge, this is the first quantitative live imaging of meristem development in a system with numerous whorls of floral organs as well as an apocarpous gynoecium. This study provides crucial information for our understanding of how the spatial-temporal regulation of floral meristem behavior is achieved in both an evolutionary and developmental context.
In silico discovery of small molecules for efficient stem cell differentiation into definitive endoderm
Authors: Novakovsky Gherman , Sasaki Shugo , Fornes Oriol , Omur Meltem E. , Huang Helen , Lim Nathaniel , Cherkasov Artem , Pavlidis Paul , Mostafavi Sara , Lynn Francis C. , Wasserman Wyeth W. 
Published: October 2021

SummaryImproving methods for human embryonic stem cell differentiation represents a challenge in modern regenerative medicine research. Using drug repurposing approaches, we discover small molecules that regulate the formation of definitive endoderm. Among them are inhibitors of known processes involved in endoderm differentiation (mTOR, PI3K, and JNK pathways) and a new compound, with an unknown mechanism of action, capable of inducing endoderm formation in the absence of growth factors in the media. Optimization of the classical protocol by including this compound achieves the same differentiation efficiency with a 90% cost reduction. The gene expression profile induced by the compound suggests that it is an inhibitor of the MYC pathway. The proposed in silico procedure for candidate molecule selection has broad potential for improving stem cell differentiation protocols.
StarBeast3: Adaptive Parallelised Bayesian Inference of the Multispecies Coalescent
Authors: Douglas Jordan , Jiménez-Silva Cinthy L. , Bouckaert Remco 
Published: October 2021

AbstractAs genomic sequence data becomes increasingly available, inferring the phylogeny of the species as that of concatenated genomic data can be enticing. However, this approach makes for a biased estimator of branch lengths and substitution rates and an inconsistent estimator of tree topology. Bayesian multispecies coalescent methods address these issues. This is achieved by embedding a set of gene trees within a species tree and jointly inferring both under a Bayesian framework. However, this approach comes at the cost of increased computational demand. Here, we introduce StarBeast3 – a software package for efficient Bayesian inference of the multispecies coalescent model via Markov chain Monte Carlo. We gain efficiency by introducing cutting-edge proposal kernels and adaptive operators, and StarBeast3 is particularly efficient when a relaxed clock model is applied. Furthermore, gene tree inference is parallelised, allowing the software to scale with the size of the problem. We validated our software and benchmarked its performance using three real and two synthetic datasets. Our results indicate that StarBeast3 is up to one-and-a-half orders of magnitude faster than StarBeast2, and therefore more than two orders faster than *BEAST, depending on the dataset and on the parameter, and is suitable for multispecies coalescent inference on large datasets (100+ genes). StarBeast3 is open-source and is easy to set up with a friendly graphical user interface.
Higher education responses to COVID-19 in the United States: Evidence for the impacts of university policy
Authors: Klein Brennan , Generous Nicholas , Chinazzi Matteo , Bhadricha Zarana , Gunashekar Rishab , Kori Preeti , Li Bodian , McCabe Stefan , Green Jon , Lazer David , Marsicano Christopher R. , Scarpino Samuel V. , Vespignani Alessandro 
Published: October 2021

AbstractWith a dataset of testing and case counts from over 1,400 institutions of higher education (IHEs) in the United States, we analyze the number of infections and deaths from SARS-CoV-2 in the counties surrounding these IHEs during the Fall 2020 semester (August to December, 2020). We used a matching procedure designed to create groups of counties that are aligned along age, race, income, population, and urban/rural categories—socio-demographic variables that have been shown to be correlated with COVID-19 outcomes. We find that counties with IHEs that remained primarily online experienced fewer cases and deaths during the Fall 2020 semester; whereas before and after the semester, these two groups had almost identical COVID-19 incidence. Additionally, we see fewer deaths in counties with IHEs that reported conducting any on-campus testing compared to those that reported none. We complement the statistical analysis with a case study of IHEs in Massachusetts—a rich data state in our dataset—which further highlights the importance of IHE-affiliated testing for the broader community. The results in this work suggest that campus testing can itself be thought of as a mitigation policy and that allocating additional resources to IHEs to support efforts to regularly test students and staff would be beneficial to mitigating the spread of COVID-19 in the general population.
3D imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa
Authors: Mondragón-Palomino Octavio , Poceviciute Roberta , Lignell Antti , Griffiths Jessica A. , Takko Heli , Ismagilov Rustem F. 
Published: October 2021

AbstractImproving our understanding of host-microbe relationships in the gut requires the ability to both visualize and quantify the spatial organization of microbial communities in their native orientation with the host tissue. We developed a systematic procedure to quantify the 3D spatial structure of the native mucosal microbiota in any part of the intestines with taxonomic and high spatial resolution. We performed a 3D biogeographical analysis of the microbiota of mouse cecal crypts at different stages of antibiotic exposure. By tracking eubacteria and four dominant bacterial taxa, we found that the colonization of crypts by native bacteria is a dynamic and spatially organized process. Ciprofloxacin treatment drastically reduced bacterial loads and eliminated Muribaculaceae (or all Bacteroidetes entirely) even 10 days after recovery when overall bacterial loads returned to pre-antibiotic levels. Our 3D quantitative imaging approach revealed that the bacterial colonization of crypts is organized in a spatial pattern that consists of clusters of adjacent colonized crypts that are surrounded by unoccupied crypts, and that this spatial pattern was resistant to the elimination of Muribaculaceae or of all Bacteroidetes by ciprofloxacin. Our approach also revealed that the composition of cecal crypt communities is diverse and that bacterial taxa are distributed differently within crypts, with Lactobacilli laying closer to the lumen than Bacteroidetes, Ruminococcaceae, and Lachnospiraceae. Finally, we found that crypts communities with similar taxonomic composition were physically closer to each other than communities that were taxonomically different.Significance StatementMany human diseases are causally linked to the gut microbiota, yet the field still lacks mechanistic understanding of the underlying complex interactions because existing tools cannot simultaneously quantify microbial communities and their intact native context. In this work, we provide a new approach to tissue clearing and preservation that enables visualization, in 3D and at scales ranging from centimeters to micrometers, of the complete biogeography of the host-microbiota interface. We combine this new tool with sequencing and multiplexed labelling of the microbiota to provide the field with a platform on which to discover patterns in the spatial distribution of microbes. We validated this platform by quantifying the distribution of bacteria in the cecal mucosa at different stages of antibiotic exposure. This approach will enable researchers to formulate and test new hypotheses about host-microbe and microbe-microbe interactions.
A Systematic Interrogation of MHC Class I Peptide Presentation Identifies Constitutive and Compensatory Protein Degradation Pathways
Authors: Mamrosh Jennifer L. , Sherman David J. , Cohen Joseph R. , Johnston James A. , Joubert Marisa K. , Li Jing , Lipford J. Russell , Lomenick Brett , Moradian Annie , Prabhu Siddharth , Sweredoski Michael J. , Lugt Bryan Vander , Verma Rati , Deshaies Raymond J. 
Published: October 2021

ABSTRACTThe adaptive immune system distinguishes self from non-self by surveying peptides generated from degradation of intracellular proteins that are loaded onto MHC Class I molecules for display on the cell surface. While early studies reported that the bulk of cell surface MHC Class I complexes require the ubiquitin-proteasome system (UPS) for their generation, this conclusion has been challenged. To better understand MHC Class I peptide origins, we sought to carry out a comprehensive, quantitative census of the MHC Class I peptide repertoire in the presence and absence of UPS activity. We introduce optimized methodology to enrich for authentic Class I-bound peptides in silico and then quantify by mass spectrometry their relative amounts upon perturbation of the ubiquitin-proteasome system. Whereas most peptides are dependent on the proteasome and ubiquitination for their generation, a surprising 30% of the MHC Class I repertoire, enriched in peptides of mitochondrial origin, appears independent of these pathways. A further ∼10% of Class I-bound peptides were found to be dependent on the proteasome but independent of ubiquitination for their generation. Notably, clinically achievable partial inhibition of the proteasome resulted in display of novel peptides antigens, at least one of which promotes immune system activation. Our results suggest that generation of MHC Class I•peptide complexes is more complex than previously recognized and also provide evidence for compensatory peptide-generating pathways when canonical pathways are impaired.
A Snapshot of the Global Drinking Water Virome: Diversity and Metabolic Potential Vary with Residual Disinfectant Use
Authors: Hegarty Bridget , Dai Zihan , Raskin Lutgarde , Pinto Ameet , Wigginton Krista , Duhaime Melissa 
Published: October 2021

AbstractViruses are important drivers of microbial community ecology and evolution, influencing microbial mortality, metabolism, and horizontal gene transfer. However, the effects of viruses remain largely unknown in many environments, including in drinking water systems. Drinking water metagenomic studies have offered a whole community perspective of bacterial impacts on water quality, but have not yet considered the influences of viruses. In this study, we address this gap by mining viral DNA sequences from publicly available drinking water metagenomes from distribution systems in six countries around the world. These datasets provide a snapshot of the taxonomic diversity and metabolic potential of the global drinking water virome; and provide an opportunity to investigate the effects of geography, climate, and drinking water treatment practices on viral diversity. Both environmental conditions and differences in sample processing were found to influence the viral composition. Using free chlorine as the residual disinfectant was associated with clear differences in viral taxonomic diversity and metabolic potential, with significantly fewer viral populations and less even viral community structures than observed in distribution systems without residual disinfectant. Additionally, drinking water viruses carry antibiotic resistance genes (ARGs), as well as genes to survive oxidative stress and nitrogen limitation. Through this study, we have demonstrated that viral communities are diverse across drinking water systems and vary with the use of residual disinfectant. Our findings offer directions for future research to develop a more robust understanding of how virus-bacteria interactions in drinking water distribution systems affect water quality.
A sensitive and specific genetically encodable biosensor for potassium ions
Authors: Wu Sheng-Yi , Wen Yurong , Serre Nelson Bernard Calixte , Laursen Cathrine Charlotte Heiede , Dietz Andrea Grostøl , Taylor Brian R. , Aggarwal Abhi , Rancic Vladimir , Becker Michael , Ballanyi Klaus , Podgorski Kaspar , Hirase Hajime , Nedergaard Maiken , Fendrych Matyáš , Lemieux M. Joanne , Eberl Daniel F. , Kay Alan R. , Campbell Robert E. , Shen Yi 
Published: October 2021

AbstractPotassium ions (K+) play a critical role as an essential electrolyte in all biological systems. Here we report the crystal structure-guided optimization and directed evolution of an improved genetically encoded fluorescent K+ biosensor, GINKO2. GINKO2 is highly sensitive and specific for K+ and enables in vivo detection of K+ dynamics in multiple species.
Vernalization-triggered expression of the antisense transcriptCOOLAIRis mediated byCBFgenes
Authors: Jeon Myeongjune , Jeong Goowon , Yang Yupeng , Luo Xiao , Jeong Daesong , Kyung Jinseul , Hyun Youbong , He Yuehui , Lee Ilha 
Published: October 2021

AbstractTo synchronize flowering time with spring, many plants undergo vernalization, a floral-promotion process triggered by exposure to long-term winter cold. InArabidopsis thaliana, this is achieved through cold-mediated epigenetic silencing of the floral repressor,FLOWERING LOCUS C(FLC).COOLAIR, a cold-induced antisense RNA transcribed from theFLClocus, has been proposed to facilitateFLCsilencing. Here, we show that C-repeat (CRT)/dehydration-responsive elements (DREs) at the 3′-end ofFLCand CRT/DRE-binding factors (CBFs) are required for cold-mediated expression ofCOOLAIR. CBFs bind to CRT/DREs at the 3′-end ofFLC, bothin vitroandin vivo, and CBF levels increase gradually during vernalization. Cold-inducedCOOLAIRexpression is severely impaired incbfsmutants in which allCBFgenes are knocked-out. Conversely,CBF-overexpressing plants show increasedCOOLAIRlevels even at warm temperatures. We show thatCOOLAIRis induced by CBFs during early stages of vernalization but COOLAIR levels decrease in later phases asFLCchromatin transitions to an inactive state to which CBFs can no longer bind. We also demonstrate thatcbfsandFLCΔCOOLAIRmutants exhibit a normal vernalization response despite their inability to activateCOOLAIRexpression during cold, revealing thatCOOLAIRis not required for the vernalization process.
Can DNA help trace the local trade of pangolins? A genetic assessment of white-bellied pangolins from the Dahomey Gap (West Africa)
Authors: Zanvo Stanislas , Djagoun Sylvestre C.A.M. , Azihou Akomian F. , Djossa Bruno , Afiademanyo Komlan , Olayemi Ayodedji , Agbangla Clément , Sinsin Brice , Gaubert Philippe 
Published: October 2021

AbstractWe conducted in the Dahomey Gap (DG) a pioneer study on the genetic tracing of the African pangolin trade. We sequenced and genotyped 189 white-bellied pangolins from 18 forests and 12 wildlife markets using one mitochondrial fragment and 20 microsatellites loci. Tree-based assignment procedure showed the ‘endemicity’ of the pangolin trade, as strictly fed by the lineage endemic to the DG (DGL). DGL populations were characterized by low levels of genetic diversity, an overall absence of equilibrium, inbreeding depression and lack of geographic structure. We identified a 92-98% decline in DGL effective population size 200-500 ya –concomitant with major political transformations along the ‘Slave Coast’– leading to contemporaneous estimates inferior to minimum viable population size. Genetic tracing suggested that wildlife markets from the DG sourced through the entire DGL range. Our loci provided the necessary power to distinguish among all the genotyped pangolins, tracing the dispatch of same individuals on the markets and within local communities. We developed an approach combining rarefaction analysis of private allele frequencies and cross-validation with observed data that could trace five traded pangolins to their forest origin, c. 200-300 km away from the markets. Although the genetic toolkit that we designed from traditional markers can prove helpful to trace the pangolin trade, our tracing ability was limited by the lack of population structure within DGL. Given the deleterious combination of genetic, demographic and trade-related factors affecting DGL populations, the conservation status of white-bellied pangolins in the DG should be urgently re-evaluated.
Self-regulation of the brain’s right frontal Beta rhythm using a brain-computer interface
Authors: Enz Nadja , Schmidt Jemima , Nolan Kate , Mitchell Matthew , Gomez Sandra Alvarez , Alkayyali Miryam , Cambay Pierce , Gippert Magdalena , Whelan Robert , Ruddy Kathy L. 
Published: October 2021

AbstractNeural oscillations, or brain rhythms, fluctuate in a manner reflecting ongoing behavior. Whether these fluctuations are instrumental or epiphenomenal to the behavior remains elusive. Attempts to experimentally manipulate neural oscillations exogenously using non-invasive brain stimulation have shown some promise, but difficulty with tailoring stimulation parameters to individuals has hindered progress in this field. We demonstrate here using electroencephalography (EEG) neurofeedback in a brain-computer interface that human participants (n=44) learned over multiple sessions across a 6-day period to self-regulate their Beta rhythm (13-20 Hz) over the right inferior frontal cortex (rIFC). The modulation was evident only during neurofeedback task performance but did not lead to offline alteration of Beta rhythm characteristics at rest, nor to changes in subsequent cognitive behavior. Likewise, a control group (n=38) who underwent training of the Alpha rhythm (8-12 Hz) did not exhibit behavioral changes. Although the right frontal Beta rhythm has been repeatedly implicated as a key component of the brain’s inhibitory control system, the present data suggest that its manipulation offline prior to cognitive task performance does not result in behavioral change. Thus, this form of neurofeedback training of the tonic Beta rhythm would not serve as a useful therapeutic target for disorders with dysfunctional inhibitory control as their basis.
Shiitake mycelium fermentation improves digestibility, nutritional value, flavor and functionality of plant proteins
Authors: Clark Anthony , Soni Bhupendra K , Sharkey Brendan , Acree Terry , Lavin Edward , Bailey Hannah M. , Stein Hans H. , Han Ashley , Elie Marc , Nadal Marina 
Published: October 2021

ABSTRACTPlant proteins can serve as inexpensive and environmentally friendly meat-replacements. However, poor taste characteristics and relatively low nutritional value prevent their full acceptance as meat substitutes. Fermentation of food has been historically used to improve the quality of foods. In this work we describe the improvement in digestibility, nutritional value, physical properties, and organoleptic characteristics, of a pea and rice protein concentrate blend through fermentation with shiitake mushroom mycelium. Ileal digestibility pig studies show increases in the DIAAS for the shiitake fermented pea and rice protein blend turning the blend into an “excellent source” of protein for humans. The fermentation also increases the solubility of the protein blend and reduces the content of the antinutrient compounds phytates and protease inhibitor. Mass spectrometry and sensory analyses of fermented protein blend indicates that fermentation leads to a reduction in off-note compounds substantially improving its organoleptic performance.
Cytoplasmic dynein-1 cargo diversity is mediated by the combinatorial assembly of FTS-Hook-FHIP complexes
Authors: Christensen Jenna R. , Kendrick Agnieszka A. , Truong Joey B. , Aguilar-Maldonado Adriana , Adani Vinit , Dzieciatkowska Monika , Reck-Peterson Samara L. 
Published: October 2021

AbstractIn eukaryotic cells, intracellular components are organized by the microtubule motors cytoplasmic dynein-1 (dynein) and kinesins, which are linked to cargos via adaptor proteins. While ∼40 kinesins transport cargo toward the plus end of microtubules, a single dynein moves cargo in the opposite direction. How dynein transports a wide variety of cargos remains an open question. The FTS-Hook-FHIP (“FHF”) cargo adaptor complex links dynein to cargo in mammals and fungi. As human cells have three Hooks and four FHIP proteins, we hypothesized that the combinatorial assembly of different Hook and FHIP proteins could underlie dynein cargo diversity. Using proteomic approaches, we determine the protein ‘interactome’ of each FHIP protein. Live-cell imaging and biochemical approaches show that different FHF complexes associate with distinct motile cargos. These complexes also move with dynein and its cofactor dynactin in single-molecule in vitro reconstitution assays. Complexes composed of FTS, FHIP1B, and Hook1/Hook3 co-localize with Rab5-tagged early endosomes via a direct interaction between FHIP1B and GTP-bound Rab5. In contrast, complexes composed of FTS, FHIP2A and Hook2 colocalize with Rab1A-tagged ER-to-Golgi cargos and FHIP2A is involved in the motility of Rab1A tubules. Our findings suggest that combinatorial assembly of different FTS-Hook-FHIP complexes is one mechanism dynein uses to achieve cargo specificity.