bluuebunny/crossref_metadata_2025_split huggingface dataset:
The fluoride permeation pathway and anion recognition in Fluc family fluoride channels
Authors: McIlwain Benjamin C. , Gundepudi Roja , Koff B. Ben , Stockbridge Randy B. 
Published: April 2021

AbstractFluc family fluoride channels protect microbes against ambient environmental fluoride by undermining the cytoplasmic accumulation of this toxic halide. These proteins are structurally idiosyncratic, and thus the permeation pathway and mechanism have no analogy in other known ion channels. Although fluoride binding sites were identified in previous structural studies, it was not evident how these ions access aqueous solution, and the molecular determinants of anion recognition and selectivity have not been elucidated. Using x-ray crystallography, planar bilayer electrophysiology and liposome-based assays, we identify additional binding sites along the permeation pathway. We use this information to develop an oriented system for planar lipid bilayer electrophysiology and observe anion block at one of these sites, revealing insights into the mechanism of anion recognition. We propose a permeation mechanism involving alternating occupancy of anion binding sites that are fully assembled only as the substrate approaches.
Agronomic behavior of four cultivars and 56 F1 tomato populations
Authors: Choque Gonzalo Quispe 
Published: April 2021

AbstractThis research was conducted under a greenhouse at the National Vegetable Seed Production Center located in the municipality of Sipe Sipe, Quillacollo province with the aim of analyzing agronomic behavior in 56 F1 progenies and four hybrid tomato cultivars. The research consisted of 60 genotypes as treatments. Each experimental unit was made up of 6 plants. The variables evaluated were: number of flowers per inflorescence, number of fruits per cluster, weight of fruit, equatorial diameter, polar diameter, heart diameter, thickness of pericarp, number of fruits per plant, weight of fruit per plant, hardness and solids soluble . The data obtained were analyzed with descriptive statistics, correlation, cluster and principal component analysis. Significant correlations were found for the number of fruits per plant and number of flowers per inflorescence with the weight of fruit per plant. The polar dendogram identified four distant groups in the performance and quality components. The principal component analysis identified the degree of association between variables and genotypes, identifying groups correlated to components of fruit yield and quality.
From treadmill to trails: predicting performance of runners
Authors: Crowell B. 
Published: April 2021

AbstractPrevious laboratory studies have measured the energetic costs to humans of running at uphill and downhill slopes on a treadmill. This work investigates the extension of those results to the prediction of relative performance of athletes running on flat, hilly, or very mountainous outdoor courses. Publicly available race results in the Los Angeles area provided a set of 109,000 times, with 2200 runners participating in more than one race, so that their times could be compared under different conditions. I compare with the results of a traditional model in which the only parameters considered are total distance and elevation gain. Both the treadmill-based model and the gain-based model have some shortcomings, leading to the creation of a hybrid model that combines the best features of each.Author summaryRunning a race on a road allows absolute measures of performance. Trail running, however, has traditionally been thought of as a sport in which the only valid comparison is between different runners competing on the same course on the same day. Even the exact measurement of distance is considered to be unimportant, since courses and conditions vary so much.An extreme example is the relatively new genre of “vertical” races, in which runners race up a mountain. In a typical example, the competitors cover a horizontal distance of 5 km, while climbing about 1000 m. The winner in one such race had a time almost triple that expected for a state-champion high school runner in a 5k road race. Clearly no comparison can be made here without taking into account the amount of climbing.In noncompetitive contexts, many runners venture onto mountain trails, lightly dressed and with little equipment, so that it becomes important to be able to anticipate whether they will have the endurance needed to be able to safely complete a planned route. Again, this is impossible without some model of the effect of hill climbing.
Deacetylation of IFIT2 mediated by HDAC5 promotes the stemness and progression of glioma
Authors: Liu Ying , Zhang Kun , Peng Xingzhi , Zhou Zhuan , Zhou Peijun , Tang Siyuan , Li Dan , Shen Liangfang , Feng Deyun , Yang Lifang 
Published: April 2021

AbstractBackgroundGlioma is the most common primary brain tumor, and the tumor stemness is a major regulatory factor affecting the progression, metastasis and recurrence of glioma. Recent research has shown that, nonhistone acetylation is widely involved in key cellular processes, including stemness regulation. The deacetylase inhibitors are promising new drugs, but their application and molecular mechanism in glioma have not been elucidated.MethodsCCK8 and colony formation assay were used to detect cell proliferation, transwell assay was used to detect cell migration, flow cytometry was used to analyze cell apoptosis, sphere formation assay and western blot were used to detect the status of stemness. RNA-sequence, quantitative PCR and western blot were performed to screen the key molecules mediating LBH589 function. Immunoprecipitation (IP) and western blot were used to analyze the acetylation level of IFIT2. The SiRNA target HDAC4 or HDAC5, overexpression plasmids of acetyltransferases were used to identify the acetyltransferase and deacetylase regulating IFIT2. The regulatory mechanism was explored by IP and ubiquitination analysis. Finally, the xenograft tumor model in nude mice was constructed and further analyzed in vivo.ResultsThe data showed that IFIT2 mediates the HDACi LBH589 inhibition on cell proliferation, migration and stemness, and contribution to autophagy and apoptosis in glioma. And the down-regulation of IFIT2 in glioma was confirmed to be related to its deacetylation by overexpression HDAC5, which promotes the stemness and progression of glioma. Further, deacetylation of IFIT2 by HDAC5 was demonstrated to induce its ubiquitination and subsequent protein instability, which led to loss of anti-tumor activity for IFIT2, and acceleration to glioma stemness and progression. In addition, the results indicated that IFIT2 inhibits PKC pathway, and suppressing of IFIT2 promotes tumor growth in vivo.ConclusionsThese results not only clarify a novel post-transcriptional regulatory mode of IFIT2, but also provide a new sight of molecular mechanism for HDACi in glioma.
Directional reorientation of migrating neutrophils is limited by suppression of receptor input signaling at the cell rear through myosin II activity
Authors: Hadjitheodorou Amalia , Bell George R. R. , Ellett Felix , Shastry Shashank , Irimia Daniel , Collins Sean R. , Theriot Julie A. 
Published: April 2021

ABSTRACTTo migrate efficiently to target locations, cells must integrate receptor inputs while maintaining polarity: a distinct front that leads and a rear that follows. Here we investigate what is necessary to overwrite pre-existing front/rear polarity in neutrophil-like HL60 cells migrating inside straight microfluidic channels. Using subcellular optogenetic receptor activation, we show that receptor inputs can reorient weakly polarized cells, but the rear of strongly polarized cells is refractory to new inputs. Transient stimulation reveals a multi-step repolarization process, confirming that cell rear sensitivity to receptor input is the primary determinant of large-scale directional reversal. We demonstrate that the RhoA/ROCK/myosin II pathway limits the ability of receptor inputs to signal to Cdc42 and reorient migrating neutrophils. We discover that by tuning the phosphorylation of myosin regulatory light chain we can modulate the activity and localization of myosin II and thus the amenability of the cell rear to ‘listen’ to receptor inputs and respond to directional reprogramming.
Computational and Image Processing Methods for Analysis and Automation of Anatomical Alignment and Joint Spacing in Reconstructive Surgery
Authors: Chaudhary Usamah N. , Kelly Cambre N. , Wesorick Benjamin R. , Reese Cameron M. , Gall Ken , Adams Samuel B. , Sapiro Guillermo , Di Martino J. Matias 
Published: April 2021

AbstractPurposeReconstructive surgeries to treat a number of musculoskeletal conditions, from arthritis to severe trauma, involve implant placement and reconstructive planning components. Anatomically matched 3D printed implants are becoming increasingly patient-specific; however the preoperative planning and design process requires several hours of manual effort from highly trained engineers and clinicians. Our work mitigates this problem by proposing algorithms for the automatic re-alignment of unhealthy anatomies, leading to more efficient, affordable, and scalable treatment solutions.MethodsOur solution combines global alignment techniques such as iterative closest points (ICP) with novel joint space refinement algorithms. The latter is achieved by a low dimensional characterization of the joint space, computed from the distribution of the distance between adjacent points in a joint.ResultsExperimental validation is presented on real clinical data from human subjects. Compared with ground truth healthy anatomies, our algorithms can reduce misalignment errors by 22% in translation and 19% in rotation for the full foot-and-ankle and 37% in translation and 39% in rotation for the hind-foot only, achieving a performance comparable to expert technicians.ConclusionOur methods and histogram-based metric allow for automatic and unsupervised alignment of anatomies, a major step toward a fully automated and data driven re-positioning, designing, and diagnosing tool.
Analysis of variability of functionals of recombinant protein production trajectories based on limited data
Authors: Liao Shuting , Macharoen Kantharakorn , McDonald Karen A. , Nandi Somen , Paul Debashis 
Published: April 2021

AbstractWe propose a method for analyzing the variability in smooth, possibly nonlinear, functionals associated with a set of product production trajectories measured under different experimental conditions. The key challenge is to make meaningful inference on these parameters across different experimental conditions when only a limited number of measurements in time are collected for each treatment, and when there are only a few, or no, replicates available. For this purpose we adopt a modeling approach by representing the production trajectories in a B-spline basis, and develop a bootstrap-based inference procedure for the parameters of interest, also accounting for multiple comparisons. The methodology is applied to study two types of quantities of interest – “time to harvest” and “maximal productivity” in the context of an experiment on the production of certain recombinant proteins under laboratory conditions. We complement the findings by extensive numerical experiments that look into the effects of different types of bootstrap procedures and associated schemes for computingp-values for tests of hypotheses.
The response of desert biocrust bacterial communities to hydration-desiccation cycles
Authors: Baubin Capucine , Ran Noya , Siebner Hagar , Gillor Osnat 
Published: April 2021

ABSTRACTRain events in arid environments are highly unpredictable, interspersing extended periods of drought. Therefore, following changes in desert soil bacterial communities during hydration-desiccation cycles in the field, was seldom attempted. Here, we assessed rain-mediated dynamics of active community in the Negev Desert biological soil crust (biocrust), and evaluated the changes in bacterial composition, potential function, and photosynthetic activity. We predicted that increased biocrust moisture would resuscitate the phototrophs, while desiccation would inhibit their activity. Our results show that hydration increased chlorophyll content, resuscitated the biocrustCyanobacteria,and induced potential phototrophic functions. However, decrease in the soil water content did not immediately decrease the phototrophs activity, though chlorophyll levels decreased. Moreover, while theCyanobacteriarelative abundance significantly increased,Actinobacteria, the former dominant taxa, significantly decreased in abundance. We propose that, following a rain event biocrust moisture significantly decreased, almost to drought levels, yet the response of the active bacterial community lagged, in contrast to topsoil. Possible explanations to the described rain-mediated bacteria dynamics are discussed.
Ozone Stress Responsive Gene Database (OSRGD ver. 1.1): a literature curated database for crop improvement
Authors: Prachi Yadav , Mina Usha 
Published: April 2021

AbstractOzone (O3) is a major abiotic stress which severely affects the growth and development of plants. In order to cope up with ozone stress, plants exhibit a plethora of morphological, physiological and molecular changes. Various molecular studies have been performed and a variety of genes exhibiting expression in response to ozone stress have been identified. However, no existing database has been designed yet to present information on ozone stress responsive genes differentially expressed across different plant species. The lack of a curated database limits the research potential in the area and therefore a cohesive database should be designed as a data repository of the ozone responsive genes. OSRGD ver. 1.1 is a user friendly web interface to explore ozone stress specific transcriptome dataset of different plant species. It allows users to retrieve the ozone stress responsive gene data by keyword based search. Each entry upon keyword query contains detailed information about the specific species, its foliar injury symptoms, pattern of gene expression, and platform used for gene expression analysis with reference literature. This comprehensive biocuration will offer researchers a better biological insight into plants’ response to ozone stress which will focus on development of climate smart crops through crop breeding.
Visual orientation discrimination skills are tightly linked with specific aspects of human intelligence
Authors: Mikellidou Kyriaki , Lambrou Nefeli , Georgiou Ellada , Avraamides Marios 
Published: April 2021

AbstractWe investigate the notion that basic visual information is acting as a building block for more complex cognitive processes in humans. Specifically, we measured individual visual orientation discrimination thresholds to report significant correlations against the total standardised intelligence quotient (IQ), verbal-IQ and non-verbal IQ scores evaluated using the Wechsler Abbreviated Scale of Intelligence Second Edition (WASI-II) test battery comprising Verbal Reasoning, Block Design, Similarities and Matrix Reasoning subtests (N=92). A multiple linear regression analysis showed that participants’ performance in our visual discrimination task, could be explained only by individual scores in Verbal Reasoning which quantifies the ability to comprehend and describe words and Matrix Reasoning, which evaluates general visual processing skills including abstract and spatial perception. Our results demonstrate that low-level visual abilities and high-level cognitive processes are more tightly interwoven together than previously thought and this result could pave the way for further research on how cognition can be defined by basic sensory processes.
An extended admixture pulse model reveals the limitations to Human-Neandertal introgression dating
Authors: Iasi Leonardo N. M. , Ringbauer Harald , Peter Benjamin M. 
Published: April 2021

AbstractNeandertal DNA makes up 2-3% of the genomes of all non-African individuals. The patterns of Neandertal ancestry in modern humans have been used to estimate that this is the result of gene flow that occurred during the expansion of modern humans into Eurasia, but the precise dates of this event remain largely unknown. Here, we introduce an extended admixture pulse model that allows joint estimation of the timing and duration of gene flow. This model leads to simple expressions for both the admixture segment distribution and the decay curve of ancestry linkage disequilibrium, and we show that these two statistics are closely related. In simulations, we find that estimates of the mean time of admixture are largely robust to details in gene flow models, but that the duration of the gene flow can only be recovered if gene flow is very recent and the exact recombination map is known. These results imply that gene flow from Neandertals into modern humans could have happened over hundreds of generations. Ancient genomes from the time around the admixture event are thus likely required to resolve the question when, where, and for how long humans and Neandertals interacted.
Genetic diversity in facultatively sexual populations and its implications for the origins of self-incompatibility in algae and fungi
Authors: Smith A.S.A. , Penington S. , Letter I. , Wilson D.B. , Constable G.W.A. 
Published: April 2021

AbstractThe evolutionary mechanism that drove the establishment of self-incompatibility in early sexual eukaryotes is still a debated topic. While a number of competing hypotheses have been proposed, many have not received detailed theoretical attention. In particular, the hypothesis that self-incompatibility increases the benefits of genetic recombination in sexual haploids has been comparatively understudied. In this paper we address this topic by mathematically deriving how the probability of mating with a genetically distinct individual changes as a function of the presence or absence of self-incompatible mating type classes. We find that although populations with mating types successfully engage in sexual reproduction less frequently than their self-compatible competitors, they can nevertheless engage in useful sex with genetically distinct partnersmorefrequently. This conclusion holds when the number of sexual reproductive events per generation is low (i.e. in small populations with low rates of facultative sexual reproduction). Finally we demonstrate the potential for frequency-dependent selection in competitive dynamics between self-compatible and self-incompatible types. These analytic results provide a baseline for studying the sex advantage enhancer model for the evolutionary origin of mating types within each specific hypothesis for the evolution of recombination.PACS87.23.-n Ecology and evolution, 87.23.Kg Dynamics of evolution, 02.50.Ey Stochastic processes2000 MSC37N25: Dynamical systems in biology, 60J70: Applications of diffusion theory (population genetics, absorption problems, etc.)
Heterogeneous non-canonical nucleosomes predominate in yeast cellsin situ
Authors: Tan Zhi Yang , Cai Shujun , Noble Alex J. , Chen Jon K. , Shi Jian , Gan Lu 
Published: April 2021

SUMMARYNuclear processes depend on the organization of chromatin, whose basic units are cylinder-shaped complexes called nucleosomes. A subset of mammalian nucleosomesin situ(inside cells) resembles the canonical structure determinedin vitro25 years ago. Nucleosome structurein situis otherwise poorly understood. Using cryo-ET and 3-D classification analysis of budding yeast cells, here we find that canonical nucleosomes account for less than 10% of total nucleosomes expectedin situ. In a strain in which H2A-GFP is the sole source of histone H2A, class averages that resemble canonical nucleosomes both with and without GFP densities are foundex vivo(in nuclear lysates), but notin situ. These data suggest that the budding yeast intranuclear environment favors multiple non-canonical nucleosome conformations. Using the structural observations here and the results of previous genomics and biochemical studies, we propose a model in which the average budding yeast nucleosome’s DNA is partially detachedin situ.
ANP32A represses Wnt signaling across tissues tissues thereby protecting against joint and heart disease
Authors: Monteagudo Silvia , Cornelis Frederique M. F. , Wang Xiangdong , de Roover Astrid , Peeters Tine , Quintiens Jolien , Sermon An , de Almeida Rodrigo C. , Meulenbelt Ingrid , Lories Rik J. 
Published: April 2021

AbstractWnt signaling is key to diverse homeostatic and pathological processes. This cascade is hyper-activated in osteoarthritis, the most common joint disease. Yet, fundamental aspects of Wnt signaling remain undiscovered. Here, we report that ANP32A negatively regulates Wnt signaling across tissues. In cartilage, loss ofAnp32atriggered Wnt hyper-activation. Mechanistically, ANP32A directly interacted with Wnt pathway components and inhibited Wnt target genes via histone acetylation masking. Wnt antagonist treatment reduced severity of osteoarthritis inAnp32a-deficient mice preventing osteophyte formation, contrasting with cartilage-protective effects of ANP32A on oxidative stress. Hence, dual therapy targeting Wnt signaling and oxidative stress inAnp32a-deficient mice ameliorated more osteoarthritis features than individual treatments.Anp32aloss also resulted in Wnt hyper-activation in the heart with cardiac hypertrophy, and in the hippocampus, shedding light on mechanisms for reported links between ANP32A and Alzheimer’s disease. Collectively, this work reveals that ANP32A is a translationally relevant repressor of Wnt signaling, impacting homeostasis and disease across tissues.
A translation control module coordinates germline stem cell differentiation with ribosome biogenesis duringDrosophilaoogenesis
Authors: Martin Elliot T. , Blatt Patrick , Ngyuen Elaine , Lahr Roni , Selvam Sangeetha , Yoon Hyun Ah M. , Pocchiari Tyler , Emtenani Shamsi , Siekhaus Daria E. , Berman Andrea , Fuchs Gabriele , Rangan Prashanth 
Published: April 2021

SummaryRibosomal defects perturb stem cell differentiation, causing diseases called ribosomopathies. How ribosome levels control stem cell differentiation is not fully known. Here, we discovered three RNA helicases are required for ribosome biogenesis and forDrosophilaoogenesis. Loss of these helicases, which we named Aramis, Athos and Porthos, lead to aberrant stabilization of p53, cell cycle arrest and stalled GSC differentiation. Unexpectedly, Aramis is required for efficient translation of a cohort of mRNAs containing a 5’-Terminal-Oligo-Pyrimidine (TOP)-motif, including mRNAs that encode ribosomal proteins and a conserved p53 inhibitor,NovelNucleolar protein 1 (Non1). The TOP-motif co-regulates the translation of growth-related mRNAs in mammals. As in mammals, the La-related protein co-regulates the translation of TOP-motif containing RNAs duringDrosophilaoogenesis. Thus, a previously unappreciated TOP-motif inDrosophilaresponds to reduced ribosome biogenesis to co-regulate the translation of ribosomal proteins and a p53 repressor, thus coupling ribosome biogenesis to GSC differentiation.