bluuebunny/crossref_metadata_2025_split huggingface dataset:
ATP Mediates Yeast Cell-Cell Communication
Authors: Caplow Michael 
Published: July 2020

AbstractYeast secrete ATP in response to glucose, a property with previously unknown functional consequence. In this report, we show that extracellular ATP is a signal for growth of surrounding cells. The ATP signaling behavior was serendipitously uncovered by finding reduced toxicity of an inducible, dominant-lethal form of alpha tubulin (tub1-828); lethality was dramatically reduced in cultures grown at high, compared to low cell density. Reduced cell death at high cell density occurred because the mutant tubulin’s deleterious effect of mitosis was reduced such that the rate of chromosome loss/cell division was lower (18-fold) in cultures inoculated with a high density (75,000/ml) compared to a low density (1,000/ml) of cells. The sparing effect of growth at high cell density could be replicated by co-culturing a low number of cells (3440/5 ml) that expressed tub1-828, with a high number of cells (2.3 E6/5 ml) that did not express the mutant protein. In this condition toxicity was reduced at high cell density apparently because it produced a sufficient concentration of a secreted growth substance, such that the mutant protein was rapidly diluted by synthesis of wild-type alpha tubulin (TUB1). Enhanced growth at high cell density was confirmed by fluorescence-activated cell sorting (FACS) analysis after DNA staining, which showed that the rate of the G1-G2 transition was faster for cells at high density. ATP replaced the need for high cell density for resistance to tub1-828, and stimulated the transition from G1 to G2 in cells at low density. This newly discovered quorum sensing response in yeast, mediated by ATP, indicates that yeast decision-making is not entirely autonomous.
Loop competition and extrusion model predicts CTCF interaction specificity
Authors: Xi Wang , Beer Michael A. 
Published: July 2020

AbstractThree-dimensional chromatin looping interactions play an important role in constraining enhancer-promoter interactions and mediating transcriptional gene regulation. CTCF is thought to play a critical role in the formation of these loops, but the specificity of which CTCF binding events form loops and which do not is difficult to predict. Loops often have convergent CTCF binding site motif orientation, but this constraint alone is only weakly predictive of genome-wide interaction data. Here we present an easily interpretable and simple mathematical model of CTCF mediated loop formation which is consistent with Cohesin extrusion and can predict ChIA-PET CTCF looping interaction measurements with high accuracy. Competition between overlapping loops is a critical determinant of loop specificity. We show that this model is consistent with observed chromatin interaction frequency changes induced by CTCF binding site deletion, inversion, and mutation, and is also consistent with observed constraints on validated enhancer-promoter interactions.
Microstructural characterization and validation of a 3D printed axon-mimetic phantom for diffusion MRI
Authors: Mushtaha Farah N. , Kuehn Tristan K. , El-Deeb Omar , Rohani Seyed A. , Helpard Luke W. , Moore John , Ladak Hanif , Moehring Amanda , Baron Corey A. , Khan Ali R. 
Published: July 2020

AbstractPurposeTo introduce and characterize inexpensive and easily produced 3D-printed axon-mimetic (3AM) diffusion MRI (dMRI) phantoms in terms of pore geometry and diffusion kurtosis imaging (DKI) metrics.MethodsPhantoms were 3D-printed with a composite printing material that, after dissolution of the PVA, exhibits microscopic fibrous pores. Confocal microscopy and synchrotron phase contrast micro-CT imaging were performed to visualize and assess the pore sizes. dMRI scans of four identical phantoms and phantoms with varying print parameters in water were performed at 9.4T. DKI was fit to both datasets and used to assess the reproducibility between phantoms and effects of print parameters on DKI metrics. Identical scans were performed 25 and 76 days later to test their stability.ResultsSegmentation of pores in three microscopy images yielded a mean, median, and standard deviation of equivalent pore diameters of 7.57 μm, 3.51 μm, and 12.13 μm, respectively. Phantoms with identical parameters showed a low coefficient of variation (∼10%) in DKI metrics (D=1.38 ×10−3mm2/s and K=0.52, T1= 3960 ms and T2=119 ms). Printing temperature and speed had a small effect on DKI metrics (<16%) while infill density had a larger and more variable effect (>16%). The stability analysis showed small changes over 2.5 months (<7%).Conclusion3AM phantoms can mimic the fibrous structure of axon bundles on a microscopic scale, serving as complex, anisotropic dMRI phantoms.
On the origin of photoperiod non-responsiveness in barley
Authors: Sharma Rajiv , Shaaf Salar , Neumann Kerstin , Go Yu , Mascher Martin , David Michal , Al-Yassin Adnan , Özkan Hakan , Blake Tom , Hübner Sariel , Castañeda-Álvarez Nora P. , Grando Stefania , Ceccarelli Salvatore , Baum Michael , Graner Andreas , Coupland George , Pillen Klaus , Weiss Ehud , Mackay Ian J , Powell Wayne , Kilian Benjamin 
Published: July 2020

AbstractIn barley, the transition from the vegetative to reproductive phase is complex and under the control of photoperiodic and temperature conditions. One major gene involved isPPD-H1, aPSEUDO-RESPONSE REGULATOR 7(PRR7) that encodes a component of the circadian clock. Mutation atPPD-H1resulted in the photoperiod non-responsiveppd-H1alleles that are beneficial under high latitudinal environments as they allow vegetative growth during the long-day summer conditions whereby higher yields are harvested by farmers. Utilizing a diverse GWAS panel of world-wide origin and a genome-wide gene-based set of 50K SNP markers, a strong association of days to heading with thePPD-H1gene was detected in multi-location field trials. Re-sequencing of the gene spanning putative causative SNPs, SNP22 (Turner et al. 2005) and SNP48 (Jones et al. 2008), detected recombination between the two, previously reported to be in complete LD. Phenotyping of the recombinants and phylogenetic relationships among haplotypes supported the original conclusion of Turner et al. (2005) that SNP22, present in the CCT domain, is the most likely causative SNP. To infer the origin of non-responsiveness, thePPD-H1gene was re-sequenced in a geo-referenced collection of 2057 wild and domesticated barleys and compared with the allelic status of the 6000-year-old barley sample from the Yoram cave in the Masada cliff. A monophyletic and post-domestication origin in the Fertile Crescent was found in contrast to the pre-domestication origin proposed by Jones et al. (2008). We show that the photoperiod non-responsiveness originated from Desert type wild barley in the Southern Levant.
Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions
Authors: Bayer Barbara , Saito Mak A. , McIlvin Matthew R. , Lücker Sebastian , Moran Dawn M. , Lankiewicz Thomas S. , Dupont Christopher L. , Santoro Alyson E. 
Published: July 2020

AbstractThe genus Nitrospira is the most widespread group of chemolithoautotrophic nitrite-oxidizing bacteria that thrive in diverse natural and engineered ecosystems. Nitrospira marina Nb-295T represents the type genus and was isolated from the oceanic water column over 30 years ago, however, its genome has not yet been analyzed. Here, we analyzed the complete genome sequence of N. marina and performed select physiological experiments to test genome-derived hypotheses. Our data confirm that N. marina benefits from additions of undefined organic carbon substrates, has adaptations to combat oxidative, osmotic and UV-light induced stress and low dissolved pCO2, and is able to grow chemoorganotrophically on formate. We further investigated the metabolic response of N. marina to low (∼5.6 µM) O2 concentrations commonly encountered in marine environments with high nitrite concentrations. In response to O2-limited conditions, the abundance of a potentially more efficient CO2-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high affinity cbb3-type terminal oxidase increased, suggesting a role in sustaining nitrite oxidation-driven autotrophy under O2 limitation. Additionally, a Cu/Zn-binding superoxide dismutase increased in abundance potentially protecting this putatively more O2-sensitive POR complex from oxidative damage. An increase in abundance of proteins involved in alternative energy metabolisms, including type 3b [NiFe] hydrogenase and formate dehydrogenase, indicate a high metabolic versatility to survive conditions unfavorable for aerobic nitrite oxidation. In summary, the genome and proteome of the first marine Nitrospira isolate identifies adaptations to life in the oxic ocean and provides important insights into the metabolic diversity and niche differentiation of NOB in marine environments.
The Roles of Space and Stochasticity in Computational Simulations of Cellular Biochemistry: Quantitative Analysis and Qualitative Insights
Authors: Johnson M. E. , Chen A. , Faeder J. R. , Henning P. , Moraru I. I. , Meier-Schellersheim M. , Murphy R. F. , Prüstel T. , Theriot J. A. , Uhrmacher A. M. 
Published: July 2020

ABSTRACTMost of the fascinating phenomena studied in cell biology emerge from interactions among highly organized multi-molecular structures and rapidly propagating molecular signals embedded into complex and frequently dynamic cellular morphologies. For the exploration of such systems, computational simulation has proved to be an invaluable tool, and many researchers in this field have developed sophisticated computational models for application to specific cell biological questions. However it is often difficult to reconcile conflicting computational results that use different simulation approaches (for example partial differential equations versus particle-based stochastic methods) to describe the same phenomenon. Moreover, the details of the computational implementation of any particular algorithm may give rise to quantitatively or even qualitatively different results for the same set of starting assumptions and parameters. In an effort to address this issue systematically, we have defined a series of computational test cases ranging from very simple (bimolecular binding in solution) to moderately complex (spatial and temporal oscillations generated by proteins binding to membranes) that represent building blocks for comprehensive three-dimensional models of cellular function. Having used two or more distinct computational approaches to solve each of these test cases with consistent parameter sets, we generally find modest but measurable differences in the solutions of the same problem, and a few cases where significant deviations arise. We discuss the strengths and limitations of commonly used computational approaches for exploring cell biological questions and provide a framework for decision-making by researchers wishing to develop new models for cell biology. As computational power and speed continue to increase at a remarkable rate, the dream of a fully comprehensive computational model of a living cell may be drawing closer to reality, but our analysis demonstrates that it will be crucial to evaluate the accuracy of such models critically and systematically.
SPRDA: a matrix completion approach based on the structural perturbation to infer disease-associated Piwi-Interacting RNAs
Authors: Zheng Kai , You Zhu-Hong , Wang Lei , Wong Leon , Zhan Zhao-hui 
Published: July 2020

AbstractEmerging evidence suggests that PIWI-interacting RNAs (piRNAs) are one of the most influential small non-coding RNAs (ncRNAs) that regulate RNA silencing. piRNA and PIWI proteins have been confirmed for disease diagnosis and treatment as novel biomarkers due to its abnormal expression in various cancers. However, the current research is not strong enough to further clarify the functions of piRNA in cancer and its underlying mechanism. Therefore, how to provide large-scale and serious piRNA candidates for biological research has grown up to be a pressing issue. The main motivation of this work is tantamount to fill the gap in research on large-scale prediction of disease-related piRNAs. In this study, a novel computational model based on the structural perturbation method is proposed, called SPRDA. In detail, the duplex network is constructed based on the piRNA similarity network and disease similarity network extracted from piRNA sequence information, Gaussian interaction profile kernel similarity information and gene-disease association information. The structural perturbation method is then used to predict the potential associations on the duplex network, which is more predictive than other network structures in terms of structural consistency. In the five-fold cross-validation, SPRDA shows high performance on the benchmark dataset piRDisease, with an AUC of 0.9529. Furthermore, the predictive performance of SPRDA for 10 diseases shows the robustness of the proposed method. Overall, the proposed approach can provide unique insights into the pathogenesis of the disease and will advance the field of oncology diagnosis and treatment.
Upgraded CRISPR/Cas9 Tools for Tissue-Specific Mutagenesis inDrosophila
Authors: Koreman Gabriel T. , Hu Qinan , Xu Yineng , Zhang Zijing , Allen Sarah E. , Wolfner Mariana F. , Wang Bei , Han Chun 
Published: July 2020

ABSTRACTCRISPR/Cas9 has emerged as a powerful technology for tissue-specific mutagenesis. However, tissue-specific CRISPR/Cas9 tools currently available inDrosophilaremain deficient in three significant ways. First, many existing gRNAs are inefficient, such that further improvements of gRNA expression constructs are needed for more efficient and predictable mutagenesis in both somatic and germline tissues. Second, it has been difficult to label mutant cells in target tissues with current methods. Lastly, application of tissue-specific mutagenesis at present often relies on Gal4-driven Cas9, which hampers the flexibility and effectiveness of the system. Here we tackle these deficiencies by building upon our previous CRISPR-mediated tissue restricted mutagenesis (CRISPR-TRiM) tools. First, we significantly improved gRNA efficiency in somatic tissues by optimizing multiplexed gRNA design. Similarly, we also designed efficient dual-gRNA vectors for the germline. Second, we developed methods to positively and negatively label mutant cells in tissue-specific mutagenesis by incorporating co-CRISPR reporters into gRNA expression vectors. Lastly, we generated genetic reagents for convenient conversion of existing Gal4 drivers into tissue-specific Cas9 lines based on homology-assisted CRISPR knock-in (HACK). In this way, we expand the choices of Cas9 for CRISPR-TRiM analysis to broader tissues and developmental stages. Overall, our upgraded CRISPR/Cas9 tools make tissue-specific mutagenesis more versatile, reliable, and effective inDrosophila. These improvements may be also applied to other model systems.
Mistargeting of secretory cargo in retromer-deficient cells
Authors: Neuman Sarah D. , Terry Erica L. , Selegue Jane E. , Cavanagh Amy T. , Bashirullah Arash 
Published: July 2020

ABSTRACTIntracellular trafficking is a basic and essential cellular function required for delivery of proteins to the appropriate subcellular destination; this process is especially demanding in professional secretory cells, which synthesize and secrete massive quantities of cargo proteins via regulated exocytosis. TheDrosophilalarval salivary glands are professional secretory cells that synthesize and secrete mucin proteins at the onset of metamorphosis. Using the larval salivary glands as a model system, we have identified a role for the highly conserved retromer complex in trafficking of secretory granule membrane proteins. We demonstrate that retromer-dependent trafficking via endosomal tubules is induced at the onset of secretory granule biogenesis, and that recycling via endosomal tubules is required for delivery of essential secretory granule membrane proteins to nascent granules. Without retromer function, nascent granules do not contain the proper membrane proteins; as a result, cargo from these defective granules is mistargeted to Rab7-positive endosomes, where it progressively accumulates to generate dramatically enlarged endosomes. Retromer complex dysfunction is strongly associated with Alzheimer’s disease, characterized by accumulation of amyloid β (Aβ). We show that amyloid precursor protein (APP) undergoes regulated exocytosis and accumulates within enlarged endosomes in retromer-deficient cells. These results highlight recycling of secretory granule membrane proteins as a critical step during secretory granule maturation and provide new insights into our understanding of retromer complex function in secretory cells. Our data also suggests that misrouting of secretory cargo, including APP, may contribute to the progressive nature of neurodegenerative disease.SUMMARY STATEMENTRetromer complex dysfunction is implicated in neurodegeneration. Here the authors show a new role for the retromer complex in recycling of secretory membrane and cargo proteins during regulated exocytosis.
Metagenome assembled genomes of novel taxa from an acid mine drainage environment
Authors: Grettenberger Christen L. , Hamilton Trinity L. 
Published: July 2020

ABSTRACTAcid mine drainage (AMD) is a global problem in which iron sulfide minerals oxidize and generate acidic, metal-rich water. Bioremediation relies on understanding how microbial communities inhabiting an AMD site contribute to biogeochemical cycling. A number of studies have reported community composition in AMD sites from16S rRNA gene amplicons but it remains difficult to link taxa to function, especially in the absence of closely related cultured species or those with published genomes. Unfortunately, there is a paucity of genomes and cultured taxa from AMD environments. Here, we report 29 novel metagenome assembled genomes from Cabin Branch, an AMD site in the Daniel Boone National Forest, KY, USA. The genomes span 11 bacterial phyla and include one Archaea and include taxa that contribute to carbon, nitrogen, sulfur, and iron cycling. These data reveal overlooked taxa that contribute to carbon fixation in AMD sites as well as uncharacterized Fe(II)-oxidizing bacteria. These data provide additional context for 16S rRNA gene studies, add to our understanding of the taxa involved in biogeochemical cycling in AMD environments, and can inform bioremediation strategies.IMPORTANCEBioremediating acid mine drainage requires understanding how microbial communities influence geochemical cycling of iron and sulfur and biologically important elements like carbon and nitrogen. Research in this area has provided an abundance of 16S rRNA gene amplicon data. However, linking these data to metabolisms is difficult because many AMD taxa are uncultured or lack published genomes. Here, we present metagenome assembled genomes from 29 novel AMD taxa and detail their metabolic potential. These data provide information on AMD taxa that could be important for bioremediation strategies including taxa that are involved in cycling iron, sulfur, carbon, and nitrogen.
Expectations and blind spots for structural variation detection from short-read alignment and long-read assembly
Authors: Zhao Xuefang , Collins Ryan L. , Lee Wan-Ping , Weber Alexandra M. , Jun Yukyung , Zhu Qihui , Weisburd Ben , Huang Yongqing , Audano Peter A. , Wang Harold , Walker Mark , Lowther Chelsea , Fu Jack ,   Human Genome Structural Variation Consortium, Gerstein Mark B. , Devine Scott E. , Marschall Tobias , Korbel Jan O. , Eichler Evan E. , Chaisson Mark J. P. , Lee Charles , Mills Ryan E. , Brand Harrison , Talkowski Michael E. 
Published: July 2020

AbstractVirtually all genome sequencing efforts in national biobanks, complex and Mendelian disease programs, and emerging clinical diagnostic approaches utilize short-reads (srWGS), which present constraints for genome-wide discovery of structural variants (SVs). Alternative long-read single molecule technologies (lrWGS) offer significant advantages for genome assembly and SV detection, while these technologies are currently cost prohibitive for large-scale disease studies and clinical diagnostics (∼5-12X higher cost than comparable coverage srWGS). Moreover, only dozens of such genomes are currently publicly accessible by comparison to millions of srWGS genomes that have been commissioned for international initiatives. Given this ubiquitous reliance on srWGS in human genetics and genomics, we sought to characterize and quantify the properties of SVs accessible to both srWGS and lrWGS to establish benchmarks and expectations in ongoing medical and population genetic studies, and to project the added value of SVs uniquely accessible to each technology. In analyses of three trios with matched srWGS and lrWGS from the Human Genome Structural Variation Consortium (HGSVC), srWGS captured ∼11,000 SVs per genome using reference-based algorithms, while haplotype-resolved assembly from lrWGS identified ∼25,000 SVs per genome. Detection power and precision for SV discovery varied dramatically by genomic context and variant class: 9.7% of the current GRCh38 reference is defined by segmental duplications (SD) and simple repeats (SR), yet 91.4% of deletions that were specifically discovered by lrWGS localized to these regions. Across the remaining 90.3% of the human reference, we observed extremely high concordance (93.8%) for deletions discovered by srWGS and lrWGS after error correction using the raw lrWGS reads. Conversely, lrWGS was superior for detection of insertions across all genomic contexts. Given that the non-SD/SR sequences span 90.3% of the GRCh38 reference, and encompass 95.9% of coding exons in currently annotated disease associated genes, improved sensitivity from lrWGS to discover novel and interpretable pathogenic deletions not already accessible to srWGS is likely to be incremental. However, these analyses highlight the added value of assembly-based lrWGS to create new catalogues of functional insertions and transposable elements, as well as disease associated repeat expansions in genomic regions previously recalcitrant to routine assessment.
Mutational analysis to explore long-range allosteric coupling and decoupling in a pentameric channel receptor
Authors: Lefebvre Solène N. , Taly Antoine , Menny Anaïs , Medjebeur Karima , Corringer Pierre-Jean 
Published: July 2020

AbstractPentameric ligand-gated ion channels (pLGICs) mediate chemical signaling through a succession of allosteric transitions that are yet not completely understood. On the prototypic bacterial channel GLIC, we explored the conformational landscape of the protein during pH-gating. To this aim, we introduced a series of allosteric mutations, and characterized the protein conformation over a broad pH range. We combined electrophysiological recordings, fluorescence quenching experiments monitoring key quaternary reorganizations, and simulations by normal mode analysis. Moderate loss-of-function mutations and the allosteric modulator propofol displace allosteric equilibria involved in pre-activation and pore opening processes, highlighting long-range allosteric coupling between distant regions of the protein. In contrast, total loss-of-function mutations stabilize the protein in unique intermediate conformations where motions are decoupled. Altogether, our data show that the protein can access a wide conformational landscape, raising the possibility of multiple conformational pathways during gating.