bluuebunny/crossref_metadata_2025 huggingface dataset:
Fully Implanted Prostheses for Musculoskeletal Limb Reconstruction after Amputation: AnIn VivoFeasibility Study
Authors: Hall Patrick T. , Bratcher Samantha Z. , Stubbs Caleb , Rifkin Rebecca E. , Grzeskowiak Remi M. , Burton Bryce J. , Greenacre Cheryl B. , Stephenson Stacy M. , Anderson David E. , Crouch Dustin L.
Published: July 2020

Previous prostheses for replacing a missing limb following amputation must be worn externally on the body. This limits the extent to which prostheses could physically interface with biological tissues, such as muscles, to enhance functional recovery. The objectives of our study were to (1) test the feasibility of implanting a limb prosthesis, or endoprosthesis, entirely within living skin at the distal end of a residual limb, and (2) identify effective surgical and post-surgical care approaches for implanting endoprostheses in a rabbit model of hindlimb amputation. We iteratively designed, fabricated, and implanted unjointed endoprosthesis prototypes in six New Zealand White rabbits following amputation. In the first three rabbits, the skin failed to heal due to dehiscence along the sutured incision. The skin of the final three subsequent rabbits successfully healed over the endoprotheses. Factors that contributed to successful outcomes included modifying the surgical incision to preserve vasculature; increasing the radii size on the endoprostheses to reduce skin stress; collecting radiographs pre-surgery to match the bone pin size to the medullary canal size; and ensuring post-operative bandage integrity. These results will support future work to test jointed endoprostheses that can be attached to muscles.
An integrative multi-approach workflow resolves species limits in the southernmost members of theLiolaemus kingiigroup (Squamata: Liolaemini)
Authors: Sánchez Kevin I. , Avila Luciano J. , Sites Jack W. , Morando Mariana
Published: July 2020

Recent conceptual and methodological advances have enabled an increasing number of studies to address the problem of species delimitation in a comprehensive manner. This is of particular interest in cases of species whose divergence times are recent, where the conclusions obtained from a single source of evidence can lead to the incorrect delimitation of entities or assignment of individuals to species. The southernmost species of theLiolaemus kingiigroup (namelyL. baguali, L. escarchadosi, L. sarmientoi, L. tariand the candidate speciesL. sp. A) show widely overlapping distributions as well as recent mitochondrial divergences, thus phylogenetic relationships and species boundaries are ambiguous. Here we use a comprehensive approach to assess species limits and corroborate their status as independent lineages through the use of four sources of molecular and morphological information (mitochondrial cytochrome-b, nuclear sequences collected by ddRADseq, and linear, meristic and landmark-based morphometrics). We found concordance among the different datasets, but signs of admixture were detected between some of the species. Our results indicate that theL. kingiigroup can serve as a model system in studies of diversification accompanied by hybridization in nature. We emphasize the importance of using multiple lines of evidence in order to solve evolutionary stories, and minimizing potential erroneous results that may arise when relying on a single source of information.
ATP Mediates Yeast Cell-Cell Communication
Authors: Caplow Michael
Published: July 2020

Yeast 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

Three-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

Purpose

To 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.

Methods

Phantoms 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.

Results

Segmentation 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%).

Conclusion

3AM 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

In 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

The 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

Most 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

Emerging 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

CRISPR/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

Intracellular 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 STATEMENT

Retromer 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

Acid 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.

IMPORTANCE

Bioremediating 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

Virtually 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

Pentameric 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.
NAD+Redox Imbalance in the Heart Exacerbates Diabetic Cardiomyopathy
Authors: Chiao Ying Ann , Chakraborty Akash Deep , Light Christine M. , Tian Rong , Sadoshima Junichi , Shi Xiaojian , Gu Haiwei , Lee Chi Fung
Published: July 2020

Background

Diabetes is a risk factor of heart failure and promotes cardiac dysfunction. Diabetic tissues are associated with NAD+redox imbalance; however, the hypothesis that NAD+redox imbalance leads to dysfunction of diabetic hearts has not been tested. In this study, we employed mouse models with altered NAD+redox balance to test the hypothesis.

Methods and Results

Diabetes was induced in C57BL/6 mice by streptozotocin injections, and diabetic cardiomyopathy (DCM) was allowed to develop for 16 weeks. Diabetic stress led to cardiac dysfunction and lowered NAD+/NADH ratio. This diabetogenic regimen was administered to cardiac-specific knockout mice of complex I subunit Ndufs4 (cKO), a model with lowered cardiac NAD+/NADH ratio without baseline dysfunction. Cardiac NAD+redox imbalance in cKO hearts exacerbated systolic and diastolic dysfunction of diabetic mice in both sexes. Collagen levels and transcript analyses of fibrosis and extracellular matrix-dependent pathways did not show change in diabetic cKO hearts, suggesting that the exacerbated cardiac dysfunction was likely due to cardiomyocyte dysfunction. We found that cardiac NAD+redox imbalance promoted superoxide dismutase 2 (SOD2) acetylation, protein oxidation, induced troponin I S150 phosphorylation and impaired energetics in diabetic cKO hearts. Importantly, elevation of cardiac NAD+levels by nicotinamide phosphoribosyltransferase (NAMPT) normalized NAD+redox balance, over-expression alleviated cardiac dysfunction and reversed pathogenic mechanisms in diabetic mice.

Conclusion

Our results show that NAD+redox imbalance to regulate protein acetylation and phosphorylation is a critical mediator of the progression of DCM, and suggest the therapeutic potential of harnessing NAD+metabolism in DCM.
Primate heart regenerationviamigration and fibroblast repulsion by human heart progenitors
Authors: Schneider Christine , Foo Kylie S. , De Angelis Maria Teresa , Santamaria Gianluca , Reiter Franziska , Dorn Tatjana , Bähr Andrea , Tsoi Yat Long , Hoppmann Petra , My Ilaria , Meier Anna , Jurisch Victoria , Hornaschewitz Nadja , Schwarz Sascha , Lu Kun , Tomasi Roland , Sudhop Stefanie , Parrotta Elvira , Gaspari Marco , Cuda Giovanni , Klymiuk Nikolai , Dendorfer Andreas , Krane Markus , Kupatt Christian , Sinnecker Daniel , Moretti Alessandra , Chien Kenneth R. , Laugwitz Karl-Ludwig
Published: July 2020

Human heart regeneration is one of the most critical unmet clinical needs at a global level1. Muscular regeneration is hampered both by the limited renewing capacity of adult cardiomyocytes2-4and the onset of cardiac fibrosis5,6, resulting in reduced compliance of the tissue. Primate have proven to be ideal models for pluripotent stem cell strategies for heart regeneration, but unravelling specific approaches to drive cell migration to the site of injury and inhibition of subsequent fibrosis have been elusive. Herein, by combining human cardiac progenitor lineage tracing and single-cell transcriptomics in injured non-human primate heart bio-mimics, we uncover the coordinated muscular regeneration of the primate heartviadirected migration of human ventricular progenitors to sites of injury, subsequent fibroblast repulsion targeting fibrosis, and ultimate functional replacement of damaged cardiac muscle by differentiation and electromechanical integration. Single-cell RNAseq captured distinct modes of action, uncovering chemoattraction mediated by CXCL12/CXCR4 signalling and fibroblast repulsion regulated by SLIT2/ROBO1 guidance in organizing cytoskeletal dynamics. Moreover, transplantation of human cardiac progenitors into hypo-immunogenic CAG-LEA29Y transgenic porcine hearts following injury proved their chemotactic response and their ability to generate a remuscularized scar without the risk of arrhythmogenesisin vivo. Our study demonstrates that inherent developmental programs within cardiac progenitors are sequentially activated in the context of disease, allowing the cells to sense and counteract injury. As such, they may represent an ideal bio-therapeutic for functional heart rejuvenation.
Genomic resources and toolkits for developmental study of whip spiders (Amblypygi) provide insights into arachnid genome evolution and antenniform leg patterning
Authors: Gainett Guilherme , Sharma Prashant P.
Published: July 2020

Background

The resurgence of interest in the comparative developmental study of chelicerates has led to important insights, such as the discovery of a genome duplication shared by spiders and scorpions, inferred to have occurred at the most recent common ancestor of Arachnopulmonata (a clade comprised of the five book lung-bearing arachnid orders). Nonetheless, several arachnid groups remain understudied in the context of development and genomics, such as the order Amblypygi (whip spiders). The phylogenetic position of Amblypygi in Arachnopulmonata posits them as an interesting group to test the incidence of the proposed genome duplication in the common ancestor of Arachnopulmonata, as well as the degree of retention of duplicates over 450 Myr. Moreover, whip spiders have their first pair of walking legs elongated and modified into sensory appendages (a convergence with the antenna of mandibulates), but the genetic patterning of these antenniform legs has never been investigated.

Results

We established genomic resources and protocols for cultivation of embryos and gene expression assays by in situ hybridization to study the development of the whip spiderPhrynus marginemaculatus. Using embryonic transcriptomes from three species of Amblypygi, we show that the ancestral whip spider exhibited duplications of all ten Hox genes. We deploy these resources to show that paralogs of the leg gap genesdachshundandhomothoraxretain arachnopulmonate-specific expression patterns inP. marginemaculatus. We characterize the expression of leg gap genesDistal-less, dachshund-1/2andhomothorax-1/2in the embryonic antenniform leg and other appendages, and provide evidence that allometry, and by extension the antenniform leg fate, is specified early in embryogenesis.

Conclusion

This study is the first step in establishingP. marginemaculatusas a model for modern chelicerate evolutionary developmental study, and provides the first resources sampling whip spiders for comparative genomics. Our results suggest that Amblypygi share a genome duplication with spiders and scorpions, and set up a framework to study the genetic specification of antenniform legs. Future efforts to study whip spider development must emphasize the development of tools for functional experiments inP. marginemaculatus.
A CRISPR-based SARS-CoV-2 diagnostic assay that is robust against viral evolution and RNA editing
Authors: Ooi Kean Hean , Tay Jie Wen Douglas , Teo Seok Yee , Liu Mengying Mandy , Kaewsapsak Pornchai , Jin Shengyang , Gao Yong-Gui , Tan Meng How
Published: July 2020

Extensive testing is essential to break the transmission of the new coronavirus SARS-CoV-2, which causes the ongoing COVID-19 pandemic. Recently, CRISPR-based diagnostics have emerged as attractive alternatives to quantitative real-time PCR due to their faster turnaround time and their potential to be used in point-of-care testing scenarios. However, existing CRISPR-based assays for COVID-19 have not considered viral genome mutations and RNA editing in human cells. Here, we present the VaNGuard (Variant Nucleotide Guard) test that is not only specific and sensitive for SARS-CoV-2, but can also detect the virus when its genome or transcriptome has evolved or has been edited by deaminases in infected human cells. We show that an engineered AsCas12a enzyme is more tolerant of mismatches than wildtype LbCas12a and that multiplexed Cas12a targeting can overcome the presence of single nucleotide variations. Our assay can be completed in 30 minutes with a dipstick for a rapid point-of-care test.
Viability and mitochondrial bioenergetic functions in human colon cancer cells are not affected by treatment with peptides mtCPP1, UPF25, mtgCPP, and mtCPP1gHO
Authors: Timohhina Natalja , Cerrato Carmine Pasquale , Kurrikoff Kaido , Chekulayev Vladimir , Aid-Vanakova Jekaterina , Puurand Marju , Tepp Kersti , Shevchuk Igor , Langel Ulo , Kaambre Tuuli
Published: July 2020

The popularity of the specially synthesized cell-penetrating peptides (CPPs) in cancer treatment has grown recently. The main aim of this study was to investigate the effects of four mitochondrially targeted antioxidant CPPs on the viability and bioenergetic function of mitochondria in human adenocarcinoma Caco-2 cells. The number of viable cells was measured by MTT and trypan blue assays. Respirometry and the permeabilized cell technique were applied to measure the mitochondrial function in this cell line. We did not observe any significant effect of CPPs on the mitochondrial reserve respiratory capacity, the function of respiratory chain complexes, and the inclination of these cancer cells to aerobic glycolysis. mtgCPP peptide with the highest antioxidant activity demonstrated improved mitochondrial coupling efficiency. CPPs do not affect mitochondrial function directly but can be considered in therapeutics as a drug-delivery molecule
Rhizobium desertarenaesp. nov., isolated from the Saline Desert Soil from the Rann of Kachchh, India
Authors: Khairnar Mitesh , Hagir Ashwini , Narayan Avinash , Jain Kunal , Madamwar Datta , Shouche Yogesh , Rahi Praveen
Published: July 2020

A novel bacterial strain designated ADMK78Twas isolated from the saline desert soil. The cells were rod-shaped, Gram-negative, and non-motile. The strain ADMK78Tgrows best at 28°C and pH 7.0 and can tolerate up to 2% (w/v) NaCl. Based on 16S rRNA gene phylogeny, the strain ADMK78Tbelongs to the genusRhizobium, with the highest similarity toRhizobium wuzhouenseW44T(98.7%) andRhizobium ipomoeaeshin9-1T(97.9%). Core-genes based phylogenetic analysis revealed that the strain ADMK78Tforms a distinct branch in betweenRhizobium ipomoeaeshin9-1TandRhizobium selenitireducensBAA-1503T. The average nucleotide identity of ADMK78Twas less than 82%, to members of the familyRhizobiaceae. The genomic DNA G+C content of strain ADMK78Tis 58.6 mol%. The major fatty acids of strain ADMK78Twere C18:0and C18:1 ω7c. The strain ADMK78Tshowed differences in physiological, phenotypic, and protein profiles estimated by MALDI-TOF MS to its closest relatives. Based on the phenotypic, chemotaxonomic properties, and phylogenetic analyses, the strain ADMK78Tcould be distinguished from the recognized species of the genusRhizobium. It is suggested to represent a novel species of this genus, for which the nameRhizobium desertarenaesp. nov. is proposed. The type strain is ADMK78T(=MCC 3400T; KACC 21383T; JCM 33657T).
Dissimilar conservation pattern in hepatitis C virus mutant spectra, consensus sequences, and data banks
Authors: García-Crespo Carlos , Soria María Eugenia , Gallego Isabel , de Ávila Ana Isabel , Martínez-González Brenda , Vázquez-Sirvent Lucía , Gómez Jordi , Briones Carlos , Gregori Josep , Quer Josep , Perales Celia , Domingo Esteban
Published: July 2020

The influence of quasispecies dynamics on long-term virus diversification in nature is a largely unexplored question. Specifically, whether intra-host nucleotide and amino acid variation in quasispecies fits variation observed in consensus sequences or data bank alignments is unknown. Genome conservation and dynamics simulations are used for the computational design of universal vaccines, therapeutic antibodies and pan-genomic antiviral agents. The expectation is that selection of escape mutants will be limited when mutations at conserved residues are required. This strategy assumes long-term (epidemiologically relevant) conservation but, critically, does not consider short-term (quasispecies-dictated) residue conservation. We have calculated mutant frequencies of individual loci from mutant spectra of hepatitis C virus (HCV) populations passaged in cell culture and from infected patients. Nucleotide or amino acid conservation in consensus sequences of the same populations, or in the Los Alamos HCV data bank did not match residue conservation in mutant spectra. The results relativize the concept of sequence conservation in viral genetics, and suggest that residue invariance in data banks is an insufficient basis for the design of universal viral ligands for clinical purposes. Our calculations suggest relaxed mutational restrictions during quasispecies dynamics, which may contribute to higher calculated short-term than long-term viral evolutionary rates.
IPANEMAP: Integrative Probing Analysis of Nucleic Acids Empowered by Multiple Accessibility Profiles
Authors: Saaidi Afaf , Allouche Delphine , Regnier Mireille , Sargueil Bruno , Ponty Yann
Published: July 2020

The manual production of reliable RNA structure models from chemical probing experiments benefits from the integration of information derived from multiple protocols and reagents. However, the interpretation of multiple probing profiles remains a complex task, hindering the quality and reproducibility of modeling efforts.

We introduceIPANEMAP, the first automated method for the modeling of RNA structure from multiple probing reactivity profiles. Input profiles can result from experiments based on diverse protocols, reagents, or collection of variants, and are jointly analyzed to predict the dominant conformations of an RNA.

IPANEMAPcombines sampling, clustering, and multi-optimization, to produce secondary structure models that are both stable and well-supported by experimental evidences. The analysis of multiple reactivity profiles, both publicly available and produced in our study, demonstrates the good performances ofIPANEMAP, even in a mono probing setting. It confirms the potential of integrating multiple sources of probing data, informing the design of informative probing assays.

Availability

IPANEMAPis freely downloadable athttps://github.com/afafbioinfo/IPANEMAP

Contact

yann.ponty@lix.polytechnique.fr

Supplementary information available at NAR online.
A calcineurin-mediated scaling mechanism that controls a K+-leak channel to regulate morphogen and growth factor transcription
Authors: Yi Chao , Spitters Tim WGM , Al-Far Ezz Al-Din Ahmed , Wang Sen , Xiong Tian Long , Cai Simian , Yan Xin , Guan Kaomei , Wagner Michael , El-Armouche Ali , Antos Christopher L.
Published: July 2020

The increase in activity of the two-pore potassium-leak channel Kcnk5b maintains allometric juvenile growth of adult zebrafish appendages. However, it remains unknown how this channel maintains allometric growth and how its bioelectric activity is regulated to scale these anatomical structures. We show the activation of Kcnk5b is sufficient to activate several genes that are part of important development programs. We providein vivotransplantation evidence that the activation of gene transcription is cell autonomous. We also show that Kcnk5b will induce the expression of different subsets of the tested developmental genes in different cultured mammalian cell lines, which may explain how one electrophysiological stimulus can coordinately regulate the allometric growth of diverse populations of cells in the fin that use different developmental signals. We also provide evidence that the post-translational modification of serine 345 in Kcnk5b by calcineurin regulates channel activity to scale the fin. Thus, we show how an endogenous bioelectric mechanism can be regulated to promote coordinated developmental signaling to generate and scale a vertebrate appendage.
Replication dynamics of recombination-dependent replication forks
Authors: Naiman Karel , Campillo-Funollet Eduard , Watson Adam T. , Budden Alice , Miyabe Izumi , Carr Antony M.
Published: July 2020

DNA replication fidelity is essential for maintaining genetic stability. Forks arrested at replication fork barriers can be stabilised by the intra-S phase checkpoint, subsequently being rescued by a converging fork, or resuming when the barrier is removed. However, some arrested forks cannot be stabilised and fork convergence cannot rescue in all situations. Thus, cells have developed homologous recombination-dependent mechanisms to restart persistently inactive forks. To understand HR-restart we use polymerase usage sequencing to visualizein vivoreplication dynamics at anS. pombereplication barrier,RTS1, and model replication by Monte Carlo simulation. We show that HR-restarted forks synthesise both strands with Pol δ for up to 30 kb without maturing to a δ/ε configuration and that Pol α is not used significantly on either strand, suggesting the lagging strand template remains as a gap that is filled in by Pol δ later. We further demonstrate that HR-restarted forks progress uninterrupted through a fork barrier that arrests canonical forks. Finally, by manipulating lagging strand resection during HR-restart by deletingpku70, we show that the leading strand initiates replication at the same position, signifying the stability of the 3’ single strand in the context of increased resection.
Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence
Authors: Murray Gemma G. R. , Charlesworth Jane , Miller Eric L. , Casey Michael J. , Lloyd Catrin T. , Gottschalk Marcelo , Tucker A. W. (Dan) , Welch John J. , Weinert Lucy A.
Published: July 2020

Emerging bacterial pathogens threaten global health and food security, and so it is important to ask whether these transitions to pathogenicity have any common features. We present a systematic study of the claim that pathogenicity is associated with genome reduction and gene loss. We compare broad-scale patterns across all bacteria, with detailed analyses ofStreptococcus suis,a zoonotic pathogen of pigs, which has undergone multiple transitions between disease and carriage forms. We find that pathogenicity is consistently associated with reduced genome size across three scales of divergence (between species within genera, and between and within genetic clusters ofS. suis). While genome reduction is most often associated with bacterial endosymbionts, other correlates of symbiosis (reduced metabolic capacity, GC content, and the expansion of non-coding elements) are not found consistently in pathogens, and genome reduction in pathogens cannot be attributed to changes in intracellularity or host restriction. Together, our results indicate that genome reduction is a predictive marker of pathogenicity in bacteria, and that the causes and consequences of genome reduction in pathogens are sometimes distinct from those in endosymbionts.
AE-LGBM: Sequence-Based Novel Approach To Detect Interacting Protein PairsviaEnsemble of Autoencoder and LightGBM
Authors: Sharma Abhibhav , Singh Buddha
Published: July 2020

1.

Protein-protein interactions (PPIs) are a vital phenomenon for every biological process. Prediction of PPI can be very helpful in the probing of protein functions which can further help in the development of new and powerful therapy designs for disease prevention. A lot of experimental studies have been done previously to study PPIs. However, lab-based experimental studies of PPI prediction are resource-extensive and time-consuming. In recent years, several high throughput, computational approaches to predict PPI have been developed but they could be fallible in terms of accuracy and false-positive rate. To overcome these shortcomings, we propose a novel approach AE-LGBM to predict the PPI more accurately. This method is based on the LightGBM classifier and utilizes the Autoencoder, which is an artificial neural network, to efficiently produce lower-dimensional, discriminative, and noise-free features. We incorporate conjoint triad (CT) features along with Composition-Transition-Distribution (CTD) features into the model and obtained promising results. The ten-fold cross-validation results indicate that the prediction accuracies obtained for Human and Yeast datasets are 98.7% and 95.4% respectively. This method was further evaluated on other datasets and has achieved excellent accuracies of 100%, 100%, 99.9%, 99.2% on E.coli, M.musculus, C.elegans, and H.sapiens respectively. We also executed AE-LGBM over three important PPI networks namely, single-core network (CD9), the multiple-core network (The Ras/Raf/MEK/ERK pathway), and the cross-connection network (Wnt Network). The method was successful in predicting the pathway with an impressive accuracy of 100%, 100%, and 98.9% respectively. These figures are significantly higher than previous methods that are based on state-of-the-art models and models including LightGBM or Autoencoder, proving AE-LGBM to be highly versatile, efficient, and robust.