bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery of EMRE in fungi resolves the true evolutionary history of the mitochondrial calcium uniporter
Authors: Pittis Alexandros A. , Goh Valerie , Cebrian-Serrano Alberto , Wettmarshausen Jennifer , Perocchi Fabiana , Gabaldón Toni 
Published: March 2020

AbstractMitochondrial calcium (mt-Ca2+) uptake is central for the regulation of numerous cellular processes in eukaryotes1. This occurs through a highly selective Ca2+uniporter located at the inner mitochondrial membrane and driven by the membrane potential2–4. While the physiological role of the uniporter was extensively studied for decades, its genetic identity was only recently determined, with MCU5,6, MICU17and EMRE8constituting pore-forming and regulatory subunits. Preliminary evolutionary analyses suggested an ancient eukaryotic origin of mt-Ca2+uptake, but also pinpointed inconsistent phylogenetic distributions of MCU, MICU1, and EMRE within fungi, where homologs of MCU were present in the absence of the supposedly essential regulators, MICU1 and EMRE9,10. Here, we perform the most comprehensive phylogenomic analysis of the mt-Ca2+uptake system and trace its evolution across 1,156 fully-sequenced eukaryotes. In contrast to earlier assumptions9–11we find compelling evidence that previously identified animal and fungal MCUs, the targets of several structural and functional efforts11–16, represent two distinct paralogous subfamilies originating from an ancestral duplication. We further uncover a complete “animal-like” uniporter complex within chytrid fungi, including bona-fide orthologs of MCU, MICU1, and EMRE. This first identification of EMRE outside Holozoa (animals and their unicellular relatives) and its strong coevolution with “animal-like” MICU1 and MCU indicates that these three components formed the core of the ancestral opisthokont uniporter. We confirm this finding experimentally, by showing that chytrid EMRE orthologs in combination with either human or “animal-like” MCUs, but not with “fungal-specific” MCUs, can reconstitute mt-Ca2+uptakein vivoin the yeastSaccharomyces cerevisiae. Hence, we here solve a purported evolutionary paradox: the presence of MCU homologs in fungal species devoid of other uniporter components and with no detectable mt-Ca2+uptake. Altogether, our study clarifies the evolution of the mt-Ca2+uniporter and identifies new important targets for comparative structural and functional studies.
Landscape of oncoviral genotype and co-infection via Human papilloma and Hepatitis B viral tumor in-situ profiling
Authors: Bubie Adrian , Zoulim Fabien , Testoni Barbara , Miles Brett , Posner Marshall , Villanueva Augusto , Losic Bojan 
Published: March 2020

AbstractHepatitis B virus (HBV) and human papillomavirus (HPV) infection are known risk factors for developing several cancers. However, the effect of viral genotype and co-infection in actually driving oncogenesis remains unclear. We have developed and deployed a new scalable, high throughput tool (ViralMine) for sensitive and precise oncoviral genotype deconvolution using tumor RNA sequencing data from 537 virally infected liver, cervical, and head and neck tumors. We provide the first comprehensive integrative landscape of tumor-viral gene expression, viral antigen immunogenicity, patient survival, and mutational profiling organized by tumor onco-viral genotype. We find that HBV and HPV genotype, and surprisingly high rates of multi-genotype co-infection, serve as significant predictors of patient survival, tumor immune responsiveness, andAPOBECactivity modulation. Finally, we demonstrate that HPV genotype strongly associates with viral onco-gene expression over cancer type, implying expression may be similar across episomal and stochastic integration-based infections.Significance StatementWe demonstrate that scalable, high-accuracy oncoviral genotyping, gene expression, and co-infection estimation is feasible from legacy tumor RNA-seq data. While HBV and HPV genotype are known risk factors for oncogenesis, viral genotype and co-infection are shown to strongly associate with disease progression, patient survival, mutational signatures, and putative tumor neoantigen immunogenicity, facilitating novel clinical associations with infections.
Wavelet Screening: a novel approach to analysing GWAS data
Authors: Denault William , Gjessing Håkon K. , Juodakis Julius , Jacobsson Bo , Jugessur Astanand 
Published: March 2020

SummaryWe present here an alternative method for genome-wide association study (GWAS) that is more powerful than traditional GWAS methods for locus detection. Single-variant GWAS methods incur a substantial multiple-testing burden because of the vast number of single nucleotide polymorphisms (SNPs) being tested simultaneously. Furthermore, these methods do not consider the functional genetic effect on the outcome because they ignore more complex joint effects of nearby SNPs within a region. By contrast, our method reduces the number of tests to be performed by screening the entire genome for associations using a sliding-window approach based on wavelets. In this context, a sequence of SNPs represents a genetic signal, and for each screened region, we transform the genetic signal into the wavelet space. The null and alternative hypotheses are modelled using the posterior distribution of the wavelet coefficients. We enhance our decision procedure by using additional information from the regression coefficients and by taking advantage of the pyramidal structure of wavelets. When faced with more complex signals than single-SNP associations, we show through simulations that Wavelet Screening provides a substantial gain in power compared to both the traditional GWAS modelling as well as another popular regional-based association test called ‘SNP-set (Sequence) Kernel Association Test’ (SKAT). To demonstrate feasibility, we re-analysed data from the large Norwegian HARVEST cohort.
High-Throughput 5’ UTR Engineering for Enhanced Protein Production in Non-Viral Gene Therapies
Authors: Cao Jicong , Novoa Eva Maria , Zhang Zhizhuo , Chen William C.W. , Liu Dianbo , Choi Gigi C G , Wong Alan S L , Wehrspaun Claudia , Kellis Manolis , Lu Timothy K 
Published: March 2020

ABSTRACTDespite significant clinical progress in cell and gene therapies, maximizing protein expression in order to enhance potency remains a major challenge. One approach to increase protein expression is by optimizing translation through the engineering of 5’ untranslated regions (5’ UTRs). Here, we developed a high-throughput strategy to design, screen, and optimize novel 5’UTRs that enhance protein expression from a strong human cytomegalovirus (CMV) promoter. We first identified naturally occurring 5’ UTRs with high translation efficiencies and used this information within silicogenetic algorithms to generate synthetic 5’ UTRs. A total of ∼12,000 5’ UTRs were then screened using a recombinase-mediated integration strategy that greatly enhances the sensitivity of high-throughput screens by eliminating copy number and position effects that limit lentiviral approaches. Using this approach, we identified three synthetic 5’ UTRs that outperformed commonly used non-viral gene therapy plasmids in expressing protein payloads. Furthermore, combinatorial assembly of these 5’ UTRs enabled even higher protein expression than obtained with each individual 5’ UTR. In summary, we demonstrate that high-throughput screening of 5’ UTR libraries with recombinase-mediated integration can identify genetic elements that enhance protein expression, which should have numerous applications for engineered cell and gene therapies.
Sub-3 Å resolution structure of apoferritin using a multi-purpose TEM with a side-entry cryo-holder
Authors: Kayama Yoko , Burton-Smith Raymond N. , Song Chihong , Terahara Naoya , Kato Takayuki , Murata Kazuyoshi 
Published: March 2020

SummaryThe structural analysis of protein complexes by cryo-electron microscopy (cryo-EM) single particle analysis (SPA) has had great impact as a biophysical method in recent years. Many results of cryo-EM SPA are based on state-of-the-art cryo-electron microscopes customized for SPA. These are currently only available in limited locations around the world, where securing machine time is highly competitive. One potential solution for this time-competitive situation is to reuse existing multi-purpose equipment. Here, we used a multi-purpose TEM with a side entry cryo-holder at our facility to evaluate the potential of high-resolution SPA. We report a 3 Å resolution map of apoferritin with local resolution extending to 2.6 Å. The map clearly showed two positions of an aromatic side chain. We also verified the optimal imaging conditions depending on different electron microscope and camera combinations. This study demonstrates the possibilities of more widely available and established electron microscopes, and their applications for cryo-EM SPA.
Human microglia upregulate cytokine signatures and accelerate maturation of neural networks
Authors: Schmunk Galina , Kim Chang N. , Soliman Sarah S. , Keefe Matthew G. , Bogdanoff Derek , Tejera Dario , Ziffra Ryan S. , Shin David , Allen Denise E. , Chhun Bryant B. , McGinnis Christopher S. , Winkler Ethan A. , Abla Adib A. , Chang Edward F. , Gartner Zev J. , Mehta Shalin B. , Piao Xianhua , Hengen Keith B. , Nowakowski Tomasz J. 
Published: March 2020

AbstractMicroglia are the resident macrophages of the brain that emerge in early development and play vital role disease states, as well as in normal development. Many fundamental questions about microglia diversity and function during human brain development remain unanswered, as we currently lack cellular-resolution datasets focusing on microglia in developing primary tissue, or experimental strategies for interrogating their function. Here, we report an integrative analysis of microglia throughout human brain development, which reveals molecular signatures of stepwise maturation, as well as human-specific cytokine-associated subtype that emerges around the onset of neurogenesis. To demonstrate the utility of this atlas, we have compared microglia across several culture models, including cultured primary microglia, pluripotent stem cell-derived microglia. We identify gene expression signatures differentially recruited and attenuated across experimental models, which will accelerate functional characterization of microglia across perturbations, species, and disease conditions. Finally, we identify a role for human microglia in development of synchronized network activity using a xenotransplantation model of human microglia into cerebral organoids.
Genetically Encoded, Multivalent Liquid Glycan Array (LiGA)
Authors: Sojitra Mirat , Sarkar Susmita , Maghera Jasmine , Rodrigues Emily , Carpenter Eric , Seth Shaurya , Vinals Daniel Ferrer , Bennett Nicholas , Reddy Revathi , Khalil Amira , Xue Xiaochao , Bell Michael , Zheng Ruixiang Blake , Zhang Ping , Nycholat Corwin , Ling Chang-Chun , Lowary Todd L. , Paulson James C. , Macauley Matthew S. , Derda Ratmir 
Published: March 2020

AbstractThe Central Dogma of Biology does not allow for the study of glycans using DNA sequencing. We report a “Liquid Glycan Array” (LiGA) platform comprising a library of DNA ‘barcoded’ M13 virions that display 30-1500 copies of glycans per phage. A LiGA is synthesized by acylation of phage pVIII protein with a dibenzocyclooctyne, followed by ligation of azido-modified glycans. Pulldown of the LiGA with lectins followed by deep sequencing of the barcodes in the bound phage decodes the optimal structure and density of the recognized glycans. The LiGA is target agnostic and can measure the glycan-binding profile of lectins such as CD22 on cellsin vitroand immune cells in a live mouse. From a mixture of multivalent glycan probes, LiGAs identifies the glycoconjugates with optimal avidity necessary for binding to lectins on living cellsin vitroandin vivo; measurements that cannot be performed with canonical glass slide-based glycan arrays.DedicationThe paper is dedicated to Laura L. Kiessling on the occasion of her 60thbirthday.
The functional landscape of patient derived RNF43 mutations predicts Wnt inhibitor sensitivity
Authors: Yu Jia , Yuso Permeen Akhtar Bt Mohamed , Goh Pamela , Harmston Nathan , Epstein David M. , Virshup David M. , Madan Babita 
Published: March 2020

AbstractA subset of Wnt-addicted cancers are sensitive to targeted therapies that block Wnt secretion or receptor engagement. RNF43 loss-of-function mutations that increase cell surface Wnt receptor abundance cause sensitivity to Wnt inhibitors. However, it is not clear which of the clinically identified RNF43 mutations affect its functionin vivo. We assayed 90 missense and 45 truncating RNF43 mutations found in human cancers, using a combination of cell-based reporter assays, genome editing, flow cytometry and immunofluorescence microscopy. Patent-derived xenograft (PDX) models with C-terminal truncating RNF43 mutations were tested for Wnt inhibitor sensitivity. We find that five common germline variants of RNF43 have wild-type activity. The majority of cancer-associated missense mutations in the RING and PA domains are either loss of function or hyperactivating. Hyperactivating mutants appear to function through formation of inactive dimers with endogenous RNF43 and/or ZNRF3. C-terminal truncation mutants including the common G659fs mutant, have discordant behavior inin vitroversusin vivoassays. PDXs and cell lines with C-terminal truncations show increased cell surface FZD, Wnt/β-catenin signaling and are responsive to PORCN inhibitionin vivo, providing clear evidence of RNF43 loss of function. In conclusion, RNF43 nonsense and frameshift mutations, including those in the C-terminal domain, and specific missense mutations in RING and PA are loss of function and predict response to upstream Wnt inhibitors in microsatellite stable cancers. This study expands the landscape of actionable RNF43 mutations, potentially extending the benefit of these therapies to additional patients.Statement of SignificanceLoss of function RNF43 mutations, first described in pancreatic cancers, drive progression of multiple cancers by increasing cellular sensitivity to Wnt ligands. These cancers are therefore uniquely sensitive to agents such as PORCN inhibitors that block Wnt production. As the PORCN inhibitors and other upstream inhibitors advance into clinical trials it is important to identify the right patients to treat with these upstream Wnt inhibitors. Hence a detailed map of mutations that are actionable is required.Here we systematically examined a spectrum of 135 patient-derived RNF43 mutations from multiple cancers. Using cell-based reporter assays, genome editing and patient-derived xenografts, we identify rules to guide patient selection. MSS cancers with either truncating mutations anywhere in the gene, including C-terminal truncations around the G659 position, or point mutations in well-defined functional domains, are likely to have RNF43 loss of function and hence a response to therapy.
Temporal transcription factors determine circuit membership by permanently altering motor neuron-to-muscle synaptic partnerships
Authors: Meng Julia L. , Wang Yupu , Carrillo Robert A. , Heckscher Ellie S. 
Published: March 2020

AbstractPreviously, using the Drosophila motor system as a model, we found the classic temporal transcription factor, Hunchback acts in NB7-1 neuronal stem cells as a molecular switch to control which circuits are populated by NB7-1 neuronal progeny (Meng et al., 2019). Here, we manipulate cardinal transcription factors, Nkx6 and Hb9, which are candidate effectors of Hunchback and which alter axon pathfinding in embryos. Yet manipulation of these cardinal transcription factors does not permanently alter neuromuscular synaptic partnerships. This demonstrates that compensation can correct early defects. We perform additional temporal transcription factor manipulations, precociously expressing Pdm and Castor in NB7-1 and prolonging expression of Hunchback in NB3-1. In every case, we find permanent alterations in neuromuscular synaptic partnerships. These data support the idea that temporal transcription factors are uniquely potent determinants of circuit membership, which do not trigger compensatory programs because they act to establish the expected pattern of wiring for the motor system.
The type 2 diabetes gene product STARD10 is a phosphoinositide binding protein that controls insulin secretory granule biogenesis
Authors: Carrat Gaelle R. , Haythorne Elizabeth , Tomas Alejandra , Haataja Leena , Müller Andreas , Arvan Peter , Piunti Alexandra , Cheng Kaiying , Huang Mutian , Pullen Timothy J. , Georgiadou Eleni , Stylianides Theodoros , Amirruddin Nur Shabrina , Salem Victoria , Distaso Walter , Cakebread Andrew , Heesom Kate J. , Lewis Philip A. , Hodson David J. , Briant Linford J. , Fung Annie C.H. , Sessions Richard B. , Alpy Fabien , Kong Alice P.S. , Benke Peter I. , Torta Federico , Teo Adrian Kee Keong , Leclerc Isabelle , Solimena Michele , Wigley Dale B. , Rutter Guy A. 
Published: March 2020

AbstractObjectiveRisk alleles for type 2 diabetes at theSTARD10locus are associated with loweredSTARD10expression in the β-cell, impaired glucose-induced insulin secretion and decreased circulating proinsulin:insulin ratios. Although likely to serve as a mediator of intracellular lipid transfer, the identity of the transported lipids, and thus the pathways through which STARD10 regulates β-cell function, are not understood. The aim of this study was to identify the lipids transported and affected by STARD10 in the β-cell and its effect on proinsulin processing and insulin granule biogenesis and maturation.MethodsWe used isolated islets from mice deleted selectively in the β-cell forStard10(βStarD10KO) and performed electron microscopy, pulse-chase, RNA sequencing and lipidomic analyses. Proteomic analysis of STARD10 binding partners was executed in INS1 (832/13) cell line. X-ray crystallography followed by molecular docking and lipid overlay assay were performed on purified STARD10 protein.ResultsβStarD10KO islets had a sharply altered dense core granule appearance, with a dramatic increase in the number of “rod-like” dense cores. Correspondingly, basal secretion of proinsulin was increased. Amongst the differentially expressed genes in βStarD10KO islets, expression of the phosphoinositide binding proteinsPirtandSynaptotagmin 1were decreased while lipidomic analysis demonstrated changes in phosphatidyl inositol levels. The inositol lipid kinase PIP4K2C was also identified as a STARD10 binding partner. STARD10 bound to inositides phosphorylated at the 3’ position and solution of the crystal structure of STARD10 to 2.3 Å resolution revealed a binding pocket capable of accommodating polyphosphoinositides.ConclusionOur data indicate that STARD10 binds to, and may transport, phosphatidylinositides, influencing membrane lipid composition, insulin granule biosynthesis and insulin processing.
Unpacking the relationship between external IT capability and open innovation performance: evidence from China
Authors: Wu Su-Ming , Ding Xiu-Hao 
Published: March 2020

PurposeInformation technology plays a critical role in the open innovation process. The purpose of this study is to explore the inner mechanism of external information technology (IT) capability that affects open innovation performance.Design/methodology/approachIn this paper, responses to 232 questionnaires from different firms were collected in China. Then, the proposed hypotheses were tested using regression analysis by statistical product and service solutions (SPSS).FindingsThe results indicate that external knowledge integration plays a mediating role in the relationship between external IT capability and open innovation performance, openness breadth positively moderates the influence of external IT capability on external knowledge integration and openness depth negatively moderates the relationship between external IT capability and external knowledge integration.Practical implicationsThe results, which are based on Chinese responses, provide useful suggestions for firms in China. To use external IT capability to improve open innovation performance, firms should not only stress the role of external knowledge integration but also consider their search strategy.Originality/valueBoth researchers and practitioners are interested in the relationship between information technology and open innovation. However, the way in which the inner mechanism of external IT capability affects open innovation performance has not been thoroughly researched. Based on knowledge integration theory, the authors construct a model that includes external IT capability, external knowledge integration, search strategy and open innovation performance. The results of this paper confirm the mediating and moderating roles of external knowledge integration and search strategy, respectively.
Corporate-startup collaboration: effects on large firms' business transformation
Authors: Steiber Annika , Alänge Sverker 
Published: March 2020

PurposeCorporations' emphasis on startup collaboration for corporate innovation has reached a new level in the context of digital transformation. The purpose of this paper is to examine three different models of corporate-startup collaboration and the models' effects on the case companies' capabilities for, and actual outcome in regards to their business transformations.Design/methodology/approachThe theory and case studies on corporate-startup collaboration models are based on several years' empirical study on 30+ multi-national corporations in the Western world. Further, iterative literature reviews on digital and business transformation have been conducted, leading to the identification of two different, but complementing frameworks used to analyze each case's capabilities and outcome in regards to business transformation.FindingsCollaboration with startups was found to positively affect the firms' business transformation. Further, the three-step analytical process is a valuable path to better understand, and improve, the cases' capability for, and outcome in regards to their business transformations.Research limitations/implicationsThe paper includes three case studies and a new process for analyzing their effects on capabilities for, and actual outcome in regards to business transformation. More research is needed, both on cases and on how to refine the analytical process.Practical implicationsThe practical contributions from this paper are the in-depth description of the three operational cases, as well as insights on how each model's set up (approach) can affect both capabilities for, but also level of business transformation. As a result, a company might need a portfolio of different startup collaboration initiatives in order to manage a more holistic transformation of their business.Originality/valueThe paper's main theoretical and practical contributions are further knowledge on organizations and organizational practices for corporate-startup collaboration, as well as a three-step process for analyzing each case's effect on the respective firm's capabilities for, and actual outcome in regards to business transformation.