bluuebunny/crossref_metadata_2025_split huggingface dataset:
Change in protein, oil and fatty acid contents in soybeans (Glycine max (L.) Merr.) of different seed coat colors and seed weight
Authors: Choi Yu-Mi , Yoon Hyemyeong , Shin Myoung-Jae , Lee Yoonjung , Hur On Sook , Lee Bong Choon , Ha Bo-Keun , Wang XiaoHan , Desta Kebede Taye 
Published: February 2021

AbstractSoybean seeds are one of the best sources of plant-based high-quality proteins and oils. The contents of these metabolites are affected by both environmental and genetic factors. In this study, 49 soybean germplasms were cultivated in Korea, the contents of total protein, total oil and five fatty acids were determined, and the influences of seed coat color and seed weight on each were assessed. The total protein and total oil contents were evaluated using Kjeldahl and Soxhlet methods and were in the ranges of 36.28-44.19% and 13.45-19.20%, respectively. Moreover, the contents of individual fatty acids were determined as area percentage from acquired gas-chromatography peaks. The contents of palmitic, stearic, oleic, linoleic and linolenic acids were in the ranges of 9.90-12.55, 2.45-4.00, 14.97-38.74, 43.22-60.26, and 5.37-12.33%, respectively and each significantly varied between the soybean germplasms. Unlike total oil and fatty acid contents, total protein content was not significantly affected by both seed coat color and seed weight. Cluster analysis grouped the soybeans into two classes with notable content differences. Fatty acids were the main factors for the variabilities seen between the soybean germplasms as observed in the principal component analysis. Correlation analysis revealed a significant but negative association between total oil and total protein contents (r = -0.714, p < 0.0001). Besides, a trade-off relationship was observed between oleic acid and linoleic acid (r = -0.936, p < 0.0001) which was reflected with respect to both seed coat color and seed weight. Among all colored soybeans, pale-yellow soybeans had the highest and the lowest levels of oleic acid and linoleic acid, respectively each being significantly different from the rest of colored soybeans (p < 0.05). Likewise, oleic acid content increased with seed weight while that of linoleic acid decreased with seed weight (p < 0.05). In general, this study showed the significance of seed coat color and seed weight to discriminate soybean genotypes, mainly in terms of their fatty acid contents. Moreover, the soybean germplasms with distinct characters and fatty acid contents identified in this study could be important genetic resources for cultivar development.
Electrical Unfolding of Cytochrome c During Translocation Through a Nanopore Constriction
Authors: Tripathi Prabhat , Benabbas Abdelkrim , Mehrafrooz Behzad , Yamazaki Hirohito , Aksimentiev Aleksei , Champion Paul M. , Wanunu Meni 
Published: February 2021

AbstractMany small proteins move across cellular compartments through narrow pores. In order to thread a protein through a constriction, free energy must be overcome to either deform or completely unfold the protein. In principle, the diameter of the pore, along with the effective driving force for unfolding the protein, as well as its barrier to translocation, should be critical factors that govern whether the process proceeds via squeezing, unfolding/threading, or both. To probe this for a well-established protein system, we studied the electric-field-driven translocation behavior of cytochrome c (cyt c) through ultrathin silicon nitride (SiNx) solid-state nanopores of diameters ranging from 1.5 to 5.5 nm. For a 2.5 nm diameter pore we find that, in a threshold electric field regime of ∼30-100 MV/m, cyt c is able to squeeze through the pore. As electric fields inside the pore are increased, the unfolded state of cyt c is thermodynamically stabilized, facilitating its translocation. In contrast, for 1.5 nm and 2.0 nm diameter pores, translocation occurs only by threading of the fully unfolded protein after it transitions through a higher energy unfolding intermediate state at the mouth of the pore. The relative energies between the metastable, intermediate, and unfolded protein states are extracted using a simple thermodynamic model that is dictated by the relatively slow (∼ms) protein translocation times for passing through the nanopore. These experiments map the various modes of protein translocation through a constriction, which opens new avenues for exploring protein folding structures, internal contacts, and electric field-induced deformability.Significance StatementCan localized electric fields drive the complete unfolding of a protein molecule? Protein unfolding prior to its translocation through a nanopore constriction is an important step in protein transport across biological membranes and also an important step in nanopore-based protein sequencing. We studied here the electric-field-driven translocation behavior of a model protein (cyt c) through nanopores of diameters ranging from 1.5 to 5.5 nm. These single molecule measurements show that electric fields at the nanopore constriction can select both partially and fully unfolded protein conformations. Zero-field free energy gaps between these conformations, found using a simple thermodynamic model, are in remarkable agreement with previously reported studies of cyt c unfolding energetics.
Cytogenetic events in the endosperm of amphiploidAvena maroccana×A. longiglumis
Authors: Tomaszewska Paulina , Kosina Romuald 
Published: February 2021

AbstractThis study analysed cytogenetic events occurring in the syncytial endosperm of theAvena maroccanaGand. ×Avena longiglumisDur. amphiploid, which is a product of two wild species having different genomes. Selection through the elimination of chromosomes and their fragments, including those translocated, decreased the level of ploidy in the endosperm below the expected 3n, leading to the modal number close to 2n. During intergenomic translocations, fragments of the heterochromatin-rich C-genome were transferred to the A and Al genomes. Terminal and non-reciprocal exchanges dominated, whereas other types of translocations, including microexchanges, were less common. Using two probes and by counterstaining with DAPI, theA. longiglumisand the rare exchanges between the A and Al genomes were detected by GISH. The large discontinuity in the probe labelling in the C chromosomes demonstrated inequality in the distribution of repetitive sequences along the chromosome and probable intragenomic rearrangements. In the nucleus, the spatial arrangement of genomes was non-random and showed a sectorial-concentric pattern, which can vary during the cell cycle, especially in the less stable tissue like the hybrid endosperm.
Fixational drift is driven by diffusive dynamics in central neural circuitry
Authors: Ben-Shushan Nadav , Shaham Nimrod , Joshua Mati , Burak Yoram 
Published: February 2021

AbstractDuring fixation and between saccades, our eyes undergo diffusive random motion called fixational drift [1]. The role of fixational drift in visual coding and inference has been debated in the past few decades, but the mechanisms that underlie this motion remained unknown. In particular, it has been unclear whether fixational drift arises from peripheral sources, or from central sources within the brain. Here we show that fixational drift is correlated with neural activity, and identify its origin in central neural circuitry within the oculomotor system. We analyzed a large data set of ocular motoneuron (OMN) recordings in the rhesus monkey, alongside precise measurements of eye position [2, 3], and found that most of the variance of fixational eye drifts must arise upstream of the OMNs. The diffusive statistics of the motion points to the oculomotor integrator, a memory circuit responsible for holding the eyes still between saccades, as a likely source of the motion. Theoretical modeling, constrained by the parameters of the primate oculomotor system, supports this hypothesis by accounting for the amplitude as well as the statistics of the motion. Thus, we propose that fixational ocular drift provides a direct observation of diffusive dynamics in a neural circuit responsible for storage of continuous parameter memory in persistent neural activity. The identification of a mechanistic origin for fixational drift is likely to advance the understanding of its role in visual processing and inference.
Computational Simulations of the 4-D Micro-Circulatory Network in Zebrafish Tail Amputation and Regeneration
Authors: Roustaei Mehrdad , Baek Kyung In , Wang Zhaoqiang , Cavallero Susana , Satta Sandro , Lai Angela , O’Donnell Ryan , Vedula Vijay , Ding Yichen , Marsden Alison Lesley , Hsiai Tzung 
Published: February 2021

AbstractWall shear stress (WSS) in the micro-vasculature contributes to biomechanical cues that regulate mechanotransduction underlying vascular development, regeneration, and homeostasis. We hereby elucidate the interplay between hemodynamic shear forces and luminal remodeling in response to vascular injury and regeneration in the zebrafish model of tail amputation. Using the transgenicTg(fli1:eGFP; Gata1:ds-red) line, we were able to track the enhanced green-fluorescent protein (eGFP)-labeled endothelial lining of the 3-D microvasculature for post-image segmentation and reconstruction of fluid domain for computational fluid dynamics (CFD) simulation. At 1 day post amputation (dpa), dorsal aorta (DA) and posterior cardinal vein (PCV) were severed, and vasoconstriction developed in the dorsal longitudinal anastomotic vessel (DLAV) with a concomitant increase in WSS in the segmental vessels (SV) proximal to the amputation site and a decrease in WSS in SVs distal to amputation. Simultaneously, we observed angiogenesis commencing at the tips of the amputated DLAV and PCV where WSS was minimal in the absence of blood flow. At 2 dpa, vasodilation occurred in a pair of SVs proximal to amputation, resulting in increased flow rate and WSS, whereas in the SVs distal to amputation, WSS normalized to the baseline. At 3 dpa, the flow rate in the arterial SV proximal to amputation continued to rise and merged with DLAV that formed a new loop with PCV. Thus, our CFD modeling uncovered a well-coordinated micro-vascular adaptation process following tail amputation, accompanied by the rise and fall of WSS and dynamic changes in flow rate during vascular regeneration.
Relatively Shorter Muscle Lengths Increase the Metabolic Rate of Cyclic Force Production
Authors: Beck Owen N. , Schroeder Jordyn N. , Trejo. Lindsey H. , Franz Jason R. , Sawicki Gregory S. 
Published: February 2021

AbstractDuring animal locomotion, force-producing leg muscles are almost exclusively responsible for the whole-body’s metabolic energy expenditure. Animals can change the length of these leg muscles by altering body posture (e.g.,joint angles), kinetics (e.g.,body weight), or the structural properties of their biological tissues (e.g.,tendon stiffness). Currently, it is uncertain whether relative muscle fascicle operating length has a measurable effect on the metabolic energy expenditure of cyclic locomotion-like contractions. To address this uncertainty, we measured the metabolic energy expenditure of human participants as they cyclically produce two distinct ankle moments at three separate ankle angles (90°, 105°, 120°) on a fixed-position dynamometer exclusively using their soleus. Overall, increasing participant ankle angle from 90° to 120° (more plantar flexion) reduced minimum soleus fascicle length by 17% (both moment levels, p<0.001) and increased metabolic energy expenditure by an average of 208% (both p<0.001). Across both moment levels, the increased metabolic energy expenditure was not driven by greater fascicle positive mechanical work (higher moment level, p=0.591), fascicle force rate (both p≥0.235), or active muscle volume (both p≥0.122); but it was correlated with average relative soleus fascicle length (r=-179, p=0.002) and activation (r=0.51, p<0.001). Therefore, the metabolic energy expended during locomotion can likely be reduced by lengthening active muscles that operate on the ascending-limb of their force-length relationship.
Cued Naming and the left inferior frontal cortex
Authors: Holland Rachel , Crinion Jennifer T. 
Published: February 2021

AbstractClinical studies have shown that naming can be behaviorally facilitated by priming, e.g., phonemic cues reduce anomia. Rehabilitation of language is argued to rely upon the same processes of priming in healthy speakers. Here we show, in healthy older adults, the immediate facilitatory behavioral and neural priming elicited by phonemic cues presented during an fMRI experiment of overt naming; thus, bridging the gap between lesion and neuroimaging studies. Four types of auditory cues were presented concurrently with an object picture (e.g., cat): (i) word (i.e., the target name (/kat/), (ii) initial phoneme segment (e.g., /ka/), (iii) final phoneme segment (/at/), or (iv) acoustic (noise) control cue. Naming was significantly faster with word, initial and final phonemic cues compared to noise; and word and initial cues compared to final cues, with no difference between word and initial cues. A neural priming effect – a significant decrease in neural activity – was observed in the left inferior frontal cortex (LIFC, pars triangularis, BA45) and the anterior insula bilaterally consistent with theories of primed articulatory encoding and post-lexical selection. The reverse contrast revealed increased activation in left posterior dorsal supramarginal gyrus for word cues that, we argue, may reflect integration of semantic and phonology processing during word rather than phonemic conditions. Taken together, these data from unimpaired speakers identified nodes within the naming network affected by phonemic cues. Activity within these regions may act as a possible biomarker to index anomic individuals’ responsiveness to phonemically cued anomia treatment.
Differential roles of RIG-I-like receptors in SARS-CoV-2 infection
Authors: Yang Duomeng , Geng Tingting , Harrison Andrew G. , Wang Penghua 
Published: February 2021

AbstractThe retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated protein 5 (MDA5) are the major viral RNA sensors that are essential for activation of antiviral immune responses. However, their roles in severe acute respiratory syndrome (SARS)-causing coronavirus (CoV) infection are largely unknown. Herein we investigate their functions in human epithelial cells, the primary and initial target of SARS-CoV-2, and the first line of host defense. A deficiency in MDA5 (MDA5−/−), RIG-I or mitochondrial antiviral signaling protein (MAVS) greatly enhanced viral replication. Expression of the type I/III interferons (IFN) was upregulated following infection in wild-type cells, while this upregulation was severely abolished inMDA5−/−andMAVS−/−, but not inRIG-I−/−cells. Of note, ACE2 expression was ~2.5 fold higher inRIG-I−/−than WT cells. These data demonstrate a dominant role of MDA5 in activating the type I/III IFN response to SARS-CoV-2, and an IFN-independent anti-SARS-CoV-2 role of RIG-I.
Human retinal organoids release extracellular vesicles that regulate gene expression in target human retinal progenitor cells
Authors: Zhou Jing , Flores-Bellver Miguel , Pan Jianbo , Benito-Martin Alberto , Shi Cui , Onwumere Onyekwere , Mighty Jason , Qian Jiang , Zhong Xiufeng , Hogue Tasmim , Amponsah-Antwi Baffour , Einbond Linda , Gharbaran Rajendra , Wu Hao , Chen Bo-Juen , Zheng Zhiliang , Tchaikovskaya Tatyana , Zhang Xusheng , Peinado Hector , Canto-Soler Maria Valeria , Redenti Stephen 
Published: February 2021

AbstractThe mechanisms underlying retinal development have not been completely elucidated. Extracellular vesicles (EVs) are novel essential mediators of cell-to-cell communication with emerging roles in developmental processes. Nevertheless, the identification of EVs in human retinal tissue, characterization of their cargo, and analysis of their potential role in retina development has not been accomplished. Three-dimensional retinal tissue derived from human induced pluripotent stem cells (hiPSC) provide an ideal developmental system to achieve this goal. Here we report that hiPSC-derived retinal organoids release exosomes and microvesicles with small noncoding RNA cargo. EV miRNA cargo-predicted targetome correlates with GO pathways involved in mechanisms of retinogenesis relevant to specific developmental stages corresponding to hallmarks of native human retina development. Furthermore, uptake of EVs by human retinal progenitor cells leads to changes in gene expression correlated with EV miRNA cargo predicted gene targets, and mechanisms involved in retinal development, ganglion cell and photoreceptor differentiation and function.
Expression of a tetracycline-controlled transactivator (Tet-On/Off system) in beta cells reduces insulin expression and secretion in mice
Authors: Jouvet Nathalie , Bouyakdan Khalil , Baldwin Cindy , Marcinkiewicz Jadwiga , Alquier Thierry , Estall Jennifer L. 
Published: February 2021

ABSTRACTControllable genetic manipulation is an indispensable tool in research, greatly advancing our understanding of cell biology and physiology. However, in beta cells, transgene silencing, low inducibility, ectopic expression and off-targets effects on cell function and glucose homeostasis are a persistent challenge. In this study, we investigated whether an inducible, Tet-Off system with beta-cell specific MIP-itTA driven expression of TetO-CreJaw/Jcould circumvent previous issues of specificity, efficacy and toxicity. Following assessment of tissue-specific gene recombination; beta cell architecture;in vitroandin vivoglucose-stimulated insulin secretion (GSIS); and whole-body glucose homeostasis, we discovered that expression of any tetracycline-controlled transactivator (e.g. itTA, rtTA or tTA) in beta cells significantly reducedInsulingene expression and decreased insulin content. This translated into lower pancreatic insulin levels and reduced insulin secretion in mice carrying a MIP-itTA transgene, independent of Cre-recombinase expression or doxycycline treatment. These results raise significant concern regarding the use of Tet-On or Tet-Off systems for genome editing in beta cells and emphasize the need to control for effects of transactivator expression. Our study echoes ongoing challenges faced by fundamental researchers focused on beta cells and highlights the need for consistent and careful control of experiments using these research tools.
A system for continuous and automated measurement of mouse home-cage drinking with automated control of liquid access
Authors: Bagley Jared R. , Kashinsky Wayne M. , Jentsch James D. 
Published: February 2021

AbstractMeasurement of drinking behavior in laboratory animals is an often utilized method in many areas of scientific research, including the study of ingestive behaviors and addictions. We have designed a system that measures drinking by continuously tracking fluid-filled bottle weights with load cells and calculating change in fluid weight per drinking bout. The load cells serve both as a contact sensor that detects mouse-spout contact, as well as a monitor of fluid weight change per contact bout. The design described here fulfills several key criteria, including automated and continuous recording of drinking in the home-cage, automated control of liquid access, and inexpensive/reproducible fabrication. These features may allow researchers to generate high-resolution, detailed information on drinking behavior in high-throughput experimental designs. Here, we provide an overview of the design and present results from tests to validate the system. C57BL/6J mice were offered water and ethanol concurrently, using this system. Consumption weights were determined by the system and independently by conventional approaches. The results indicated a near-perfect correlation between the two methods, indicating the system returned valid consumption weights. This system functions as a valid drinking monitor that provides temporally precise data with a low cost design.
The role of gene segment interactions in driving the emergence of dominant gene constellations during influenza virus reassortment
Authors: Trifkovic Sanja , Gilbertson Brad , Fairmaid Emily , Cobbin Joanna , Rockman Steven , Brown Lorena E. 
Published: February 2021

AbstractA segmented genome enables influenza virus to undergo reassortment when two viruses infect the same cell. Resulting reassorted progeny have a spectrum of gene constellations and potentially different phenotypes. Although reassortment is involved in the creation of pandemic influenza strains and is routinely used to produce influenza vaccines, our understanding of the factors that drive the emergence of dominant gene constellations during this process is incomplete. Using an influenza vaccine seed production model, reassortant genotypes were tracked through the reassortment process under antibody selective pressure. We discovered that certain gene constellations conferring low replicative fitness were selected at the expense of more fit progeny. Nevertheless, relatively unfit reassortants likely provide high hemagglutinin antigen yields through co-production of non-infectious particles and/or by more hemagglutinin molecules per virion. Our data illustrate the dynamics and complexity of reassortment and highlight how gene segment interactions formed during packaging, in addition to antibody pressure, restrict the final viruses that dominate.
VIA: Generalized and scalable trajectory inference in single-cell omics data
Authors: Stassen Shobana V. , Yip Gwinky G. K. , Wong Kenneth K. Y. , Ho Joshua W. K. , Tsia Kevin K. 
Published: February 2021

AbstractInferring cellular trajectories using a variety of omic data is a critical task in single-cell data science. However, accurate prediction of cell fates, and thereby biologically meaningful discovery, is challenged by the sheer size of single-cell data, the diversity of omic data types, and the complexity of their topologies. We present VIA, a scalable trajectory inference algorithm that overcomes these limitations by using lazy-teleporting random walks to accurately reconstruct complex cellular trajectories beyond tree-like pathways (e.g. cyclic or disconnected structures). We show that VIA robustly and efficiently unravels the fine-grained sub-trajectories in a 1.3-million-cell transcriptomic mouse atlas without losing the global connectivity at such a high cell count. We further apply VIA to discovering elusive lineages and less populous cell fates missed by other methods across a variety of data types, including single-cell proteomic, epigenomic, multi-omics datasets, and a new in-house single-cell morphological dataset.
A strategy to address dissociation-induced compositional and transcriptional bias for single-cell analysis of the human mammary gland
Authors: Engelbrecht Lisa K. , Twigger Alecia-Jane , Ganz Hilary M. , Gabka Christian J. , Bausch Andreas R. , Lickert Heiko , Sterr Michael , Kunze Ines , Khaled Walid T. , Scheel Christina H. 
Published: February 2021

SummarySingle-cell transcriptomics provide insights into cellular heterogeneity and lineage dynamics that are key to better understanding normal mammary gland function as well as breast cancer initiation and progression. In contrast to murine tissue, human mammary glands require laborious dissociation protocols to isolate single cells. This leads to unavoidable procedure-induced compositional and transcriptional bias. Here, we present a new strategy on how to identify and minimize systematic error by combining different tissue dissociation strategies and then directly comparing composition and transcriptome of isolated cells using single-cell RNA sequencing and flow cytometry. Depending on the tissue isolation strategy, we found dramatic differences in abundance and heterogeneity of certain stromal cells types. Moreover, we identified lineage-specific dissociation-induced gene expression changes that, if left unchecked, could lead to misinterpretation of cellular heterogeneity and, since the basal epithelial population is particularly affected by this, wrongful assignment of putative stem cell populations.