bluuebunny/crossref_metadata_2025_split huggingface dataset:
A binary effector module secreted by a type VI secretion system
Authors: Dar Yasmin , Jana Biswanath , Bosis Eran , Salomon Dor 
Published: July 2021

ABSTRACTGram-negative bacteria use type VI secretion systems (T6SSs) to deliver toxic effector proteins into neighboring cells. Cargo effectors are secreted by binding non-covalently to the T6SS apparatus. Occasionally, effector secretion is assisted by an adaptor protein, although the adaptor itself is not secreted. Here, we report a new T6SS secretion mechanism, in which an effector and a co-effector are secreted together. Specifically, we identified a novel periplasm-targeting effector that is secreted together with its co-effector, which contains a MIX (marker for type sIX effector) domain previously reported only in polymorphic toxins. The effector and co-effector directly interact, and they are dependent on each other for secretion. We termed this new secretion mechanism “a binary effector module”, and we show that it is widely distributed in marine bacteria.
Deep learning identifies and quantifies recombination hotspot determinants
Authors: Li Yu , Chen Siyuan , Rapakoulia Trisevgeni , Kuwahara Hiroyuki , Yip Kevin Y. , Gao Xin 
Published: July 2021

AbstractRecombination is one of the essential genetic processes for sexually reproducing organisms, which can happen more frequently in some regions, called recombination hotspots. Although several factors, such as PRDM9 binding motifs, are known to be related to the hotspots, their contributions to the recombination hotspots have not been quantified, and other determinants are yet to be elucidated. Here, we develop a computational method, RHSNet, based on deep learning and signal processing, to identify and quantify the hotspot determinants in a purely data-driven manner, utilizing datasets from various studies, populations, sexes, and species. In addition to being able to identify hotspot regions and the well-known determinants accurately, RHSNet is sensitive to the difference between different PRDM9 alleles and different sexes, and can generalize to PRDM9-lacking species. The cross-sex, cross-population, and cross-species studies suggest that the proposed method has the potential to identify and quantify the evolutionary determinant motifs.TeaserRHSNet can accurately identify and quantify recombination hotspot determinants across different studies, sexes, populations, and species.
Quantifying epigenetic modulation of nucleosome breathing by high-throughput AFM imaging
Authors: Konrad Sebastian F. , Vanderlinden Willem , Lipfert Jan 
Published: July 2021

AbstractNucleosomes are the basic units of chromatin and critical to the storage and expression of eukaryotic genomes. Chromatin accessibility and gene readout are heavily regulated by epigenetic marks of which post-translational modifications of histones play a key role. However, the mode of action and the structural implications on the single-molecule level of nucleosomes is often still poorly understood. Here, we apply a high-throughput AFM imaging and analysis pipeline to investigate the conformational landscape of the nucleosome variants H3K36me3, H3S10phos and H4K5/8/12/16ac. Our data set of >25,000 nucleosomes reveals nucleosomal unwrapping steps corresponding to 5 bp DNA. We find that H3K36me3 nucleosomes unwrap significantly more than wild type nucleosomes and additionally unwrap stochastically from both sides similar to CENP-A nucleosomes and in contrast to the highly anti-cooperative unwrapping of wild type nucleosomes. Nucleosomes with H3S10phos or H4K5/8/12/16ac modifications show unwrapping populations similar to wild type nucleosomes and also retain the same level of anti-cooperativity. Our findings help putting the mode of action of these modifications into context: While H3K36me3 likely partially acts by directly affecting nucleosome structure on the single-molecule level, H3S10phos and H4K5/8/12/16ac must predominantly act through higher-order processes. Our analysis pipeline is readily applicable to other nucleosome variants and will facilitate future high-resolution studies of the conformational landscape of nucleoprotein complexes.Statement of SignificanceThe packing and readout of our genome is tightly regulated by post-translational histone modifications (PTMs). While a vast range of PTMs has been studied with respect to their implications for gene activity and replication, a detailed view of the direct effect of PTMs on conformational changes of nucleosomes is still lacking. Here we investigate the structural implications of several key modifications (H3K36me3, H3S10phos and H4K5/8/12/16ac) by high-throughput AFM imaging. Our findings enable a better understanding of the mode of action of these specific modifications and provide an analysis pipeline for the investigation of other epigenetic modifications.
Interfacial tension driven open droplet microfluidics
Authors: Khor Jian Wei , Lee Ulri N. , Berthier Jean , Berthier Erwin , Theberge Ashleigh B. 
Published: July 2021

AbstractWe developed an open channel droplet microfluidic system that autonomously generates droplets at low Ca (~10-4-10-3) by leveraging competing hydrostatic and capillary pressure. With only our open channel polytetrafluoroethylene (PTFE) device, pipettes, and commercially available carrier fluid, we produce hundreds of microliter droplets; tubing, electronics, or pumps are not required, making droplet technology feasible for research labs without external flow generators. Furthermore, we demonstrated conceptual applications that showcase the process of droplet generation, splitting, transport, incubation, mixing, and sorting in our system. Unlike conventional droplet microfluidics, the open nature of the device enables the use of physical tools such as tweezers and styli to directly access the system; with this, we developed a new method of droplet sorting and transfer that capitalizes on the Cheerios effect, the aggregation of buoyant objects along a liquid interface. Our platform offers enhanced usability, direct access to the droplet contents, easy manufacturability, compact footprint, and high customizability. This design is a first step in exploring the space of power-free open droplet microfluidic systems and provide design rules for similar channel designs.
Functional Coupling of TRPM2 and NMDARs exacerbates excitotoxicity in ischemic brain injury
Authors: Zong Pengyu , Feng Jianlin , Yue Zhichao , Wu Gongxiong , Sun Baonan , He Yanlin , Miller Barbara , Yu Albert S. , Su Zhongping , Mori Yasuo , Xie Jia , Yue Lixia 
Published: July 2021

SUMMARYExcitotoxicity caused by NMDA receptors (NMDARs) is a major cause of neuronal death in ischemic stroke. However, past efforts of directly targeting NMDARs have unfortunately failed in clinical ischemic stroke trials. Here we reveal an unexpected mechanism underlying NMDARs-mediated neurotoxicity, which leads to identification of a novel target and development of an effective therapeutic peptide for ischemic stroke. We show that NMDAR’s excitotoxicity upon ischemic insults is mediated by physical and functional coupling to TRPM2. The physical interaction of TRPM2 with NMDARs results in markedly increase in the surface expression of NMDARs, leading to enhanced NMDAR function and increased neuronal death. We identified a specific NMDAR-interacting domain on TRPM2, and developed a cell-permeable peptide to uncouple TRPM2-NMDARs. The disrupting-peptide protects neurons against ischemic injury in vitro and protects mice against ischemic stroke in vivo. These findings provide an unconventional strategy to eliminate excitotoxic neuronal death without directly targeting NMDARs.HIGHLIGHTSTRPM2 physically and functionally interacts with NMDARsInteraction of TRPM2 with NMDARs exacerbates NMDAR’s extrasynaptic excitotoxicity by increasing NMDAR’s surface expression during ischemic injuryTRPM2 recruits PKCγ to the interacting complexes to increase NMDAR’s surface expressionUncoupling the interaction between TRPM2 and NMDARs with a disrupting peptide (TAT-EE3) protects neurons against ischemic stroke in vitro and in vivoGRAPHIC ABSTRACTTRPM2 excerbates NMDAR’s excitotoxicity by physically and functionally interacting with NMDARs. The disrupting pipette TAT-EE3 protects neurons against ischemic injury in vitro and in vivo.
A phylotranscriptome study using silica gel-dried leaf tissues produces an updated robust phylogeny of Ranunculaceae
Authors: He Jian , Lyu Rudan , Luo Yike , Xiao Jiamin , Xie Lei , Wen Jun , Li Wenhe , Pei Linying , Cheng Jin 
Published: July 2021

AbstractThe utility of transcriptome data in plant phylogenetics has gained popularity in recent years. However, because RNA degrades much more easily than DNA, the logistics of obtaining fresh tissues has become a major limiting factor for widely applying this method. Here, we used Ranunculaceae to test whether silica-dried plant tissues could be used for RNA extraction and subsequent phylogenomic studies. We sequenced 27 transcriptomes, 21 from silica gel-dried (SD-samples) and six from liquid nitrogen-preserved (LN-samples) leaf tissues, and downloaded 27 additional transcriptomes from GenBank. Our results showed that although the LN-samples produced slightly better reads than the SD-samples, there were no significant differences in RNA quality and quantity, assembled contig lengths and numbers, and BUSCO comparisons between two treatments. Using this data, we conducted phylogenomic analyses, including concatenated- and coalescent-based phylogenetic reconstruction, molecular dating, coalescent simulation, phylogenetic network estimation, and whole genome duplication (WGD) inference. The resulting phylogeny was consistent with previous studies with higher resolution and statistical support. The 11 core Ranunculaceae tribes grouped into two chromosome type clades (T- and R-types), with high support. Discordance among gene trees is likely due to hybridization and introgression, ancient genetic polymorphism and incomplete lineage sorting. Our results strongly support one ancient hybridization event within the R-type clade and three WGD events in Ranunculales. Evolution of the three Ranunculaceae chromosome types is likely not directly related to WGD events. By clearly resolving the Ranunculaceae phylogeny, we demonstrated that SD-samples can be used for RNA-seq and phylotranscriptomic studies of angiosperms.
Systemic antibody-oligonucleotide delivery to the central nervous system ameliorates mouse models of spinal muscular atrophy
Authors: Hammond Suzan M , Abendroth Frank , Goli Larissa , Burrell Matthew , Thom George , Gurrell Ian , Stoodley Jessica , Ahlskog Nina , Gait Michael J , Wood Matthew J A , Webster Carl 
Published: July 2021

AbstractAntisense oligonucleotides (ASOs) have emerged as one of the most innovative new genetic drug modalities, however, the high molecular weight limits their bioavailability for otherwise treatable neurological disorders. We investigated conjugation of ASOs to an antibody against the murine transferrin receptor (TfR), 8D3130, and evaluated it via systemic administration in mouse models of the neurodegenerative disease, spinal muscular atrophy (SMA). SMA like several other neurological and neuromuscular diseases, is treatable with single-stranded ASOs, inducing splice modulation of the survival motor neuron 2 (SMN2) gene. Administration of 8D3130-ASO conjugate resulted in bioavailability of 2.7% of the injected dose in brain. Additionally, 8D3130-ASO yielded therapeutically high levels ofSMN2splicing in the central nervous system of mildly affected adult SMA mice and resulted in extended survival of severe SMA mice. Systemic delivery of nucleic acid therapies with brain targeting antibodies offers powerful translational potential for future treatments of neuromuscular and neurodegenerative diseases.
WAPO-A1 is the causal gene of the 7AL QTL for spikelet number per spike in wheat
Authors: Kuzay Saarah , Lin Huiqiong , Li Chengxia , Chen Shisheng , Woods Daniel , Zhang Junli , Dubcovsky Jorge 
Published: July 2021

AbstractImproving our understanding of the genes regulating grain yield can contribute to the development of more productive wheat varieties. Previously, a highly significant QTL affecting spikelet number per spike (SNS), grain number per spike (GNS) and grain yield was detected on chromosome arm 7AL in multiple genome-wide association studies. Using a high-resolution genetic map, we established that the A-genome homeolog of WHEAT ORTHOLOG OF APO1 (WAPO-A1) was a leading candidate gene for this QTL. Using mutants and transgenic plants, we demonstrate in this study that WAPO-A1 is the causal gene underpinning this QTL. Loss-of-function mutants wapo-A1 and wapo-B1 showed reduced SNS in tetraploid wheat, and the effect was exacerbated in wapo1 combining both mutations. By contrast, spikes of transgenic wheat plants carrying extra copies of WAPO-A1 driven by its native promoter had higher SNS, a more compact spike apical region and a smaller terminal spikelet than the wild type. Taken together, these results indicate that WAPO1 affects SNS by regulating the timing of terminal spikelet formation. Both transgenic and wapo1 mutant plants showed a wide range of floral abnormalities, indicating additional roles of WAPO1 on wheat floral development. Previously, we found three widespread haplotypes in the QTL region (H1, H2 and H3), each associated with particular WAPO-A1 alleles. Integrating results from this study and previous findings, we show that the WAPO-A1 allele in the H1 haplotype (115-bp deletion in the promoter) is expressed at significantly lower levels in the developing spikes than the alleles in the H2 and H3 haplotypes, resulting in reduced SNS. Field experiments also showed that the H2 haplotype is associated with the strongest effects in increasing SNS and GNS (H2>H3>H1). The H2 haplotype is already present in most modern common wheats, so it might be particularly useful in durum wheat where H2 is rare.AUTHOR SUMMARYA region on wheat chromosome 7A has been previously shown to affect the number of spikelets and grains per spike as well as total grain yield in multiple breeding programs. In this study, we show that loss-of-function mutations in the WAPO1 gene located within this region reduce the number of spikelets per spike and that additional transgenic copies of this gene increase this number. These results demonstrate that WAPO1 is the gene responsible for the differences in grain number and yield associated with the 7A chromosome region. Among the three main variants identified for this gene, we demonstrate in field experiments that the H2 variant is associated with the largest increases in number of spikelets and grains per spike. The H2 WAPO1 variant is frequent in bread wheat breeding programs but is almost absent in modern pasta wheat varieties. Therefore, the introgression of the H2 represents a promising opportunity to improve grain yield in pasta wheat breeding programs.
A Non-Canonical Raf Function Is Required for Dorsal-Ventral Patterning During Drosophila Embryogenesis
Authors: Lusk Jay B. , Zhen Chua Ellora Hui , Kaur Prameet , Han Sung Isabelle Chiao , Lim Wen Kin , Man Lam Vanessa Yuk , Harmston Nathan , Tolwinski Nicholas S. 
Published: July 2021

AbstractProper embryonic development requires directional axes to pattern cells into embryonic structures. In Drosophila, spatially discrete expression of transcription factors determines the anterior to posterior organization of the early embryo, while the Toll and TGFβ signalling pathways determine the early dorsal to ventral pattern. Embryonic MAPK/ERK signaling contributes to both anterior to posterior patterning in the terminal regions and to dorsal to ventral patterning during oogenesis and embryonic stages. Here we describe a novel loss of function mutation in the Raf kinase gene, which leads to loss of ventral cell fates as seen through the loss of the ventral furrow, the absence of Dorsal/NFκB nuclear localization, the absence of mesoderm determinants Twist and Snail, and the expansion of TGFβ. Gene expression analysis showed cells adopting ectodermal fates much like loss of Toll signaling. Our results combine novel mutants, live imaging, optogenetics and transcriptomics to establish a novel role for Raf, that appears to be independent of the MAPK cascade, in embryonic patterning.
Automatic calibration of a functional-structural wheat model using an adaptive design and a metamodelling approach
Authors: Blanc Emmanuelle , Enjalbert Jérôme , Barbillon Pierre 
Published: July 2021

AbstractBackground and AimsFunctional-structural plant models are increasingly being used by plant scientists to address a wide variety of questions. However, the calibration of these complex models is often challenging, mainly because of their high computational cost. In this paper, we applied an automatic method to the calibration of WALTer: a functional-structural wheat model that simulates the plasticity of tillering in response to competition for light.MethodsWe used a Bayesian calibration method to estimate the values of 5 parameters of the WALTer model by fitting the model outputs to tillering dynamics data. The method presented in this paper is based on the Efficient Global Optimisation algorithm. It involves the use of Gaussian process metamodels to generate fast approximations of the model outputs. To account for the uncertainty associated with the metamodels approximations, an adaptive design was used. The efficacy of the method was first assessed using simulated data. The calibration was then applied to experimental data.Key ResultsThe method presented here performed well on both simulated and experimental data. In particular, the use of an adaptive design proved to be a very efficient method to improve the quality of the metamodels predictions, especially by reducing the uncertainty in areas of the parameter space that were of interest for the fitting. Moreover, we showed the necessity to have a diversity of field data in order to be able to calibrate the parameters.ConclusionsThe method presented in this paper, based on an adaptive design and Gaussian process metamodels, is an efficient approach for the calibration of WALTer and could be of interest for the calibration of other functional-structural plant models.
Vergence accuracy in an autostereoscopic display
Authors: Lo Verde Luca , Norcia Anthony M. 
Published: July 2021

AbstractWhen fixating an object, observers typically under or over-converge by a small amount, a phenomenon known as “fixation disparity”. Fixation disparity is typically measured with physical fixation targets and dichotically presented nonius lines. Here we made fixation disparity measurements with an autostereoscopic display, varying the retinal eccentricity and disparity of the fixation targets. Measurements were made in a group of four practiced observers and in a group of thirteen experimentally naïve observers. Fixation disparities with a zero-disparity target were in the direction of fixation behind the plane of the screen and the magnitude of the fixation disparity grew with the eccentricity of the fixation targets (1-5 deg in the practiced observers and 1 – 10 deg in the naïve observers). Fixation disparity also increased with increasing disparity of the targets, especially when they were presented at crossed disparities. Fixation disparities were larger overall for naïve observers who additionally did not converge in front of the screen when vergence demand was created by crossed disparity fusion locks presented at 5 and 10 deg eccentricities.
Large-scale dendritic spine extraction and analysis through petascale computing
Authors: Wildenberg Gregg , Li Hanyu , Badalamente Griffin , Uram Thomas D. , Ferrier Nicola J. , Kasthuri Narayanan 
Published: July 2021

ABSTRACTThe synapse is a central player in the nervous system serving as the key structure that permits the relay of electrical and chemical signals from one neuron to another. The anatomy of the synapse contains important information about the signals and the strength of signal it transmits. Because of their small size, however, electron microscopy (EM) is the only method capable of directly visualizing synapse morphology and remains the gold standard for studying synapse morphology. Historically, EM has been limited to small fields of view and often only in 2D, but recent advances in automated serial EM (“connectomics”) have enabled collecting large EM volumes that capture significant fractions of neurons and the different classes of synapses they receive (i.e. shaft, spine, soma, axon). However, even with recent advances in automatic segmentation methods, extracting neuronal and synaptic profiles from these connectomics datasets are difficult to scale over large EM volumes. Without methods that speed up automatic segmentation over large volumes, the full potential of utilizing these new EM methods to advance studies related to synapse morphologies will never be fully realized. To solve this problem, we describe our work to leverage Argonne leadership-scale supercomputers for segmentation of a 0.6 terabyte dataset using state of the art machine learning-based segmentation methods on a significant fraction of the 11.69 petaFLOPs supercomputer Theta at Argonne National Laboratory. We describe an iterative pipeline that couples human and machine feedback to produce accurate segmentation results in time frames that will make connectomics a more routine method for exploring how synapse biology changes across a number of biological conditions. Finally, we demonstrate how dendritic spines can be algorithmically extracted from the segmentation dataset for analysis of spine morphologies. Advancing this effort at large compute scale is expected to yield benefits in turnaround time for segmentation of individual datasets, accelerating the path to biology results and providing population-level insight into how thousands of synapses originate from different neurons; we expect to also reap benefits in terms of greater accuracy from the more compute-intensive algorithms these systems enable.
A cationic motif in Engrailed-2 homeoprotein controls its internalization via selective cell-surface glycosaminoglycans interactions
Authors: Cardon Sébastien , Bolbach Gérard , Hervis Yadira P. , Lopin-Bon Chrystel , Jacquinet Jean-Claude , Illien Françoise , Walrant Astrid , Ravault Delphine , He Bingwei , Molina Laura , Burlina Fabienne , Lequin Olivier , Joliot Alain , Carlier Ludovic , Sagan Sandrine 
Published: July 2021

AbstractEngrailed-2 (En2) is a transcription factor that possesses as most homeoproteins the unique and intriguing property to transfer from cell to cell through unconventional pathways. The internalization mechanism of this cationic protein is far from being fully understood and is proposed to require an initial interaction with cell-surface glycosaminoglycans (GAGs). To decipher the role of GAGs in the recognition of En2 at the cell surface, we have quantified the internalization of the homeodomain region in cell lines that differ in their content in cell-surface GAGs. The binding specificity to GAGs and the influence of this interaction on the structure and dynamics of En2 was also investigated at the amino acid level. Our results show that a high-affinity GAG-binding hexadecapeptide (RKPKKKNPNKEDKRPR) located upstream of the homeodomain controls internalization efficiency of En2 through selective interactions with highly-sulfated GAGs of heparan sulfate type. Our data underline the functional importance of the intrinsically disordered basic region that precedes the prominent internalization domain in En2, and demonstrate the critical role of GAGs as an entry gate for En2, finely tuning its capacity to internalize into cells.