bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure of human ferroportin bound to hepcidin reveals mechanisms of iron homeostasis
Authors: Billesbølle Christian B. , Azumaya Caleigh M. , Kretsch Rachael C. , Powers Alexander S. , Gonen Shane , Schneider Simon , Arvedson Tara , Dror Ron O. , Cheng Yifan , Manglik Aashish
Published: March 2020

The serum iron level in humans is tightly controlled by the action of the hormone hepcidin on the iron efflux transporter ferroportin. Hepcidin negatively regulates iron absorption and recycling by inducing ferroportin internalization and degradation. Aberrant ferroportin activity can lead to diseases of iron overload, like hemochromatosis, or iron limitation anemias. Here, we determined cryogenic electron microscopy (cryo-EM) structures of ferroportin in lipid nanodiscs, both in the apo state and in complex with cobalt, an iron mimetic, and hepcidin. These structures and accompanying molecular dynamics simulations identify two divalent metal binding sites within the N- and C-domains of ferroportin. Hepcidin binds ferroportin in an outward-open conformation and completely occludes the iron efflux pathway. The carboxy-terminus of hepcidin directly contacts the divalent metal in the FPN C-domain. We further show that hepcidin binding to ferroportin is coupled to iron binding, with an 80-fold increase in hepcidin affinity in the presence of iron. These results suggest a new model for hepcidin regulation of ferroportin, where only iron loaded ferroportin molecules are targeted for degradation. More broadly, our structural and functional insights are likely to enable more targeted manipulation of the hepcidin-ferroportin axis in disorders of iron homeostasis.
The polyol pathway is a crucial glucose sensor inDrosophila
Authors: Sano Hiroko , Nakamura Akira , Yamane Mariko , Niwa Hitoshi , Nishimura Takashi , Kojima Masayasu
Published: March 2020

A major nutrient source for animals is glucose, which induces transcriptional responses that shift metabolism. Such metabolic adaptation should be appropriately scaled to the ingested glucose levels, and decoupling causes human metabolic diseases. However, the identity of the crucial sensor metabolite(s) that transmit circulating glucose levels to the transcriptional machinery remains elusive. Here we show that the polyol pathway, which converts glucose to fructose via sorbitol, is required for activation of the master metabolic regulator Mondo, theDrosophilahomologue of MondoA/ChREBP. We demonstrate that under normal nutritional conditions polyol pathway metabolites promote Mondo’s nuclear localization and cause global changes in metabolic gene expression. Polyol pathway mutants block nuclear localization of Mondo and Mondo-mediated gene expression despite intact glycolytic and pentose phosphate pathways. Our results uncover the normal physiological function of this pathway and cast a new light on the adverse effects of high fructose diets in human health.
Structure of RNA-dependent RNA polymerase from 2019-nCoV, a major antiviral drug target
Authors: Gao Yan , Yan Liming , Huang Yucen , Liu Fengjiang , Zhao Yao , Cao Lin , Wang Tao , Sun Qianqian , Ming Zhenhua , Zhang Lianqi , Ge Ji , Zheng Litao , Zhang Ying , Wang Haofeng , Zhu Yan , Zhu Chen , Hu Tianyu , Hua Tian , Zhang Bing , Yang Xiuna , Li Jun , Yang Haitao , Liu Zhijie , Xu Wenqing , Guddat Luke W. , Wang Quan , Lou Zhiyong , Rao Zihe
Published: March 2020

A novel coronavirus (2019-nCoV) outbreak has caused a global pandemic resulting in tens of thousands of infections and thousands of deaths worldwide. The RNA-dependent RNA polymerase (RdRp, also named nsp12), which catalyzes the synthesis of viral RNA, is a key component of coronaviral replication/transcription machinery and appears to be a primary target for the antiviral drug, remdesivir. Here we report the cryo-EM structure of 2019-nCoV full-length nsp12 in complex with cofactors nsp7 and nsp8 at a resolution of 2.9-Å. Additional to the conserved architecture of the polymerase core of the viral polymerase family and a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain featured in coronaviral RdRp, nsp12 possesses a newly identified β-hairpin domain at its N-terminal. Key residues for viral replication and transcription are observed. A comparative analysis to show how remdesivir binds to this polymerase is also provided. This structure provides insight into the central component of coronaviral replication/transcription machinery and sheds light on the design of new antiviral therapeutics targeting viral RdRp.

One Sentence Summary

Structure of 2019-nCov RNA polymerase.
The ribosomal RNA m5C methyltransferase NSUN-1 modulates healthspan and oogenesis inCaenorhabditis elegans
Authors: Heissenberger Clemens , Krammer Teresa L. , Rollins Jarod A. , Nagelreiter Fabian , Stocker Isabella , Wacheul Ludivine , Shpylovyi Anton , Snow Santina , Grillari Johannes , Rogers Aric N. , Lafontaine Denis L.J. , Schosserer Markus
Published: March 2020

Our knowledge about the repertoire of ribosomal RNA modifications and the enzymes responsible for installing them is constantly expanding. Previously, we reported that NSUN-5 is responsible for depositing m5C at position C2381 on the 26S rRNA inCaenorhabditis elegans.

Here, we show that NSUN-1 is writing the second known 26S rRNA m5C at position C2982. Depletion ofnsun-1ornsun-5improved locomotion at midlife and resistance against heat stress, however, only soma-specific knockdown ofnsun-1extended lifespan. Moreover, soma-specific knockdown ofnsun-1reduced body size and impaired fecundity, suggesting non-cell-autonomous effects. While ribosome biogenesis and global protein synthesis were unaffected bynsun-1depletion, translation of specific mRNAs was remodelled leading to reduced production of collagens, loss of structural integrity of the cuticle and impaired barrier function.

We conclude that loss of a single enzyme required for rRNA methylation has profound and highly specific effects on organismal physiology.
Multiple approaches for massively parallel sequencing of HCoV-19 (SARS-CoV-2) genomes directly from clinical samples
Authors: Xiao Minfeng , Liu Xiaoqing , Ji Jingkai , Li Min , Li Jiandong , Yang Lin , Sun Wanying , Ren Peidi , Yang Guifang , Zhao Jincun , Liang Tianzhu , Ren Huahui , Chen Tian , Zhong Huanzi , Song Wenchen , Wang Yanqun , Deng Ziqing , Zhao Yanping , Ou Zhihua , Wang Daxi , Cai Jielun , Cheng Xinyi , Feng Taiqing , Wu Honglong , Gong Yanping , Yang Huanming , Wang Jian , Xu Xun , Zhu Shida , Chen Fang , Zhang Yanyan , Chen Weijun , Li Yimin , Li Junhua
Published: March 2020

COVID-19 has caused a major epidemic worldwide, however, much is yet to be known about the epidemiology and evolution of the virus. One reason is that the challenges underneath sequencing HCoV-19 directly from clinical samples have not been completely tackled. Here we illustrate the application of amplicon and hybrid capture (capture)-based sequencing, as well as ultra-high-throughput metatranscriptomic (meta) sequencing in retrieving complete genomes, inter-individual and intra-individual variations of HCoV-19 from clinical samples covering a range of sample types and viral load. We also examine and compare the bias, sensitivity, accuracy, and other characteristics of these approaches in a comprehensive manner. This is, to date, the first work systematically implements amplicon and capture approaches in sequencing HCoV-19, as well as the first comparative study across methods. Our work offers practical solutions for genome sequencing and analyses of HCoV-19 and other emerging viruses.
Pitfalls in re-analysis of observational omics studies: a post-mortem of the human pathology atlas
Authors: Gilis Jeroen , Taelman Steff , Davey Lucas , Martens Lennart , Clement Lieven
Published: March 2020

Uhlenet al.(Reports, 18 august 2017) published an open-access resource with cancer-specific marker genes that are prognostic for patient survival in seventeen different types of cancer. However, their data analysis workflow is prone to the accumulation of false positives. A more reliable workflow with flexible Cox proportional hazards models employed on the same data highlights three distinct problems with such large-scale, publicly available omics datasets from observational studies today: (i) re-analysis results can not necessarily be taken forward by others, highlighting a need to cross-check important analyses with high impact outcomes; (ii) current methods are not necessarily optimal for the re-analysis of such data, indicating an urgent need to develop more suitable methods; and (iii) the limited availability of potential confounders in public metadata renders it very difficult (if not impossible) to adequately prioritize clinically relevant genes, which should prompt an in-depth discussion on how such information could be made more readily available while respecting privacy and ethics concerns.
Understanding the Lipidome at the Systems Level with lipidomeR
Authors: Suvitaival Tommi , Legido-Quigley Cristina
Published: March 2020

Lipidomics is one of the fastest-growing areas of molecular profiling in medicine. While increasing amounts of lipidomics data are generated, tools for analyzing and interpreting these data are not equally widely available. We present the lipidomeR -- a tool specifically designed for systematic interpretation of large lipidome-wide studies. The lipidomeR binds together statistical analysis and high-dimensional visualization, providing a reproducible pipeline for rapid interpretation of the lipidome via integrative publication-ready figures. The lipidomeR package is available through the Comprehensive R Archive (CRAN).

We demonstrate the lipidomeR with three studies from the Metabolomics Workbench repository, ranging from the human plasma reference material to breast tumor tissue and to the progression of non-alcoholic liver disease (NAFLD) in the liver. In these studies, lipidomeR reveals a diversity of lipidomic patterns, both, within and between the lipid classes as well as over the stages of progression of the diseases.
The sequence of human ACE2 is suboptimal for binding the S spike protein of SARS coronavirus 2
Authors: Procko Erik
Published: March 2020

The rapid and escalating spread of SARS coronavirus 2 (SARS-CoV-2) poses an immediate public health emergency. The viral spike protein S binds ACE2 on host cells to initiate molecular events that release the viral genome intracellularly. Soluble ACE2 inhibits entry of both SARS and SARS-2 coronaviruses by acting as a decoy for S binding sites, and is a candidate for therapeutic, prophylactic and diagnostic development. Using deep mutagenesis, variants of ACE2 are identified with increased binding to the receptor binding domain of S. Mutations are found across the interface, in the N90-glycosylation motif, and at buried sites where they are predicted to enhance local folding and presentation of the interaction epitope. When single substitutions are combined, large increases in binding can be achieved. The mutational landscape offers a blueprint for engineering high affinity proteins and peptides that block receptor binding sites on S to meet this unprecedented challenge.
DrosophilaHistone Locus Body assembly and function involves multiple interactions
Authors: Koreski Kaitlin P. , Rieder Leila E. , McLain Lyndsey M. , Marzluff William F. , Duronio Robert J.
Published: March 2020

The histone locus body (HLB) assembles at replication-dependent (RD) histone loci and concentrates factors required for RD histone mRNA biosynthesis. TheD. melanogastergenome has a single locus comprised of ∼100 copies of a tandemly arrayed repeat unit containing one copy of each of the 5 RD histone genes. To determine sequence elements required forD. melanogasterHLB formation and histone gene expression, we used transgenic gene arrays containing 12 copies of the histone repeat unit that functionally complement loss of the ∼200 endogenous RD histone genes. A 12x histone gene array in which allH3-H4promoters were replaced withH2a-H2bpromoters does not form an HLB or express high levels of RD histone mRNA in the presence of the endogenous histone genes. In contrast, this same transgenic array is active in HLB assembly and RD histone gene expression in the absence of the endogenous RD histone genes and rescues the lethality caused by homozygous deletion of the RD histone locus. The HLB formed in the absence of endogenous RD histone genes on the mutant 12x array contains all known factors present in the wild type HLB including CLAMP, which normally binds to GAGA repeats in theH3-H4promoter. These data suggest that multiple protein-protein and/or protein-DNA interactions contribute to HLB formation, and that the large number of endogenous RD histone gene copies sequester available factor(s) from attenuated transgenic arrays, thereby preventing HLB formation and gene expression.
Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid-liquid phase separation
Authors: Ladouceur A-M , Parmar B , Biedzinski S , Wall J , Tope SG , Cohn D , Kim A , Soubry N , Reyes-Lamothe R , Weber SC
Published: March 2020

Once described as mere “bags of enzymes”, bacterial cells are in fact highly organized, with many macromolecules exhibiting non-uniform localization patterns. Yet the physical and biochemical mechanisms that govern this spatial heterogeneity remain largely unknown. Here, we identify liquid-liquid phase separation (LLPS) as a mechanism for organizing clusters of RNA polymerase (RNAP) inE. coli. Using fluorescence imaging, we show that RNAP quickly transitions from a dispersed to clustered localization pattern as cells enter log phase in nutrient-rich media. RNAP clusters are sensitive to hexanediol, a chemical that dissolves liquid-like compartments in eukaryotic cells. In addition, we find that the transcription antitermination factor NusA forms dropletsin vitroandin vivo, suggesting that it may nucleate RNAP clusters. Finally, we use single-molecule tracking to characterize the dynamics of cluster components. Our results indicate that RNAP and NusA molecules move inside clusters, with mobilities faster than a DNA locus but slower than bulk diffusion through the nucleoid. We conclude that RNAP clusters are biomolecular condensates that assemble through LLPS. This work provides direct evidence for LLPS in bacteria and suggests that this process serves as a universal mechanism for intracellular organization across the tree of life.

Significance

Bacterial cells are small and were long thought to have little to no internal structure. However, advances in microscopy have revealed that bacteria do indeed contain subcellular compartments. But how these compartments form has remained a mystery. Recent progress in larger, more complex eukaryotic cells has identified a novel mechanism for intracellular organization known as liquid-liquid phase separation. This process causes certain types of molecules to concentrate within distinct compartments inside the cell. Here, we demonstrate that the same process also occurs in bacteria. This work, together with a growing body of literature, suggests that liquid-liquid phase separation is a universal mechanism for intracellular organization that extends across the tree of life.
An easily adopted murine model of distal pancreatectomy for investigating immunotherapy efficacy in resectable pancreatic adenocarcinoma
Authors: Baxter Katherine E , de Souza Christiano Tanese , Tai Lee-Hwa , Yaghini Pasha , Daneshmand Manijeh , Bell John C , Lichty Brian D , Kennedy Michael A , Auer Rebecca C
Published: March 2020

Background

Although surgery provides the greatest therapeutic benefit to eligible pancreatic ductal adenocarcinoma (PDAC) patients it does not significantly improve survival for the majority of patients. Unfortunately our understanding of the therapeutic benefit of combining surgery with different treatment modalities including promising immunotherapeutics is limited by the current lack of easily adopted surgical models. The purpose of this study was to develop a surgically resectable model of PDAC in immunocompetent mice for use in preclinical investigations.

Materials and Methods

Surgically resectable orthotopic tumors were generated by injecting Pan02 cells into the tail of the pancreas. Fifteen days post implantation the primary tumors and tail of the pancreas were resected by laparotomy while preserving the spleen. Splenic function, tumor growth, immune phenotyping and survival were assessed following surgical resection of the primary tumor mass.

Results

As expected orthotopic tumor implants recapitulated many of the major histological hallmarks of PDAC including disrupted lobular structure and vascular invasion. Preservation of splenic immune cell viability and function was not associated with improved survival following surgery alone. However, pre-operative vaccination with GVAX was associated with improved survival which was not impacted by surgery.

Conclusion

This represents the first murine model of surgically resectable murine model of PDAC which recapitulates known pathological hallmarks of human disease in an immune competent model while allowing spleen preservation. This relatively simple and easily adopted approach provides an ideal platform to examine the efficacy of potential immunotherapy combinations for PDAC surgery patients.
RAD50 promotes DNA repair by homologous recombination and restrains antigenic variation in African trypanosomes
Authors: Mehnert Ann-Kathrin , Prorocic Marco , Dujeancourt-Henry Annick , Hutchinson Sebastian , McCulloch Richard , Glover Lucy
Published: March 2020

Homologous recombination dominates as the major form of DNA repair inTrypanosoma brucei, and is especially important for recombination of the subtelomeric variant surface glycoprotein during antigenic variation. RAD50, a component of the MRN complex (MRE11, RAD50, NBS1), is central to homologous recombination through facilitating resection and governing the DNA damage response. The function of RAD50 in trypanosomes is untested. Here we report that RAD50 is required for RAD51-dependent homologous recombination, phosphorylation of histone H2A and controlled resection following a DNA double strand break (DSB). Perhaps surprisingly, DSB resection in therad50nulls was not impaired and appeared to peak earlier than in the parental strains. Finally, we show that RAD50 suppresses DNA repair using donors with short stretches of homology at a subtelomeric locus, with null strains producing a greater diversity of expressed VSG variants following DSB repair. We conclude that RAD50 promotes stringent homologous recombination at subtelomeric loci and restrains antigenic variation.
Stability and detection of nucleic acid from viruses and hosts in mosquito blood meals
Authors: Drummond Coyne , Gebhardt Mary E. , Sáenz Robles Maria Teresa , Carpi Giovanna , Hoyer Isaiah , Pastusiak Andrzej , Reddy Michael R. , Norris Douglas E. , Pipas James M. , Jackson Ethan K.
Published: March 2020

Monitoring the presence and spread of pathogens in the environment is of critical importance. Rapid detection of infectious disease outbreaks and prediction of their spread can facilitate early responses of health agencies and reduce the severity of outbreaks. Current sampling methods are sorely limited by available personnel and throughput. For instance, xenosurveillance utilizes captured arthropod vectors, such as mosquitoes, as sampling tools to access blood from a wide variety of vertebrate hosts. Next generation sequencing (NGS) of nucleic acid from individual blooded mosquitoes can be used to identify mosquito and host species, and microorganisms including pathogens circulating within either host. However, there are practical challenges to collecting and processing mosquitoes for xenosurveillance, such as the rapid metabolization or decay of microorganisms within the mosquito midgut. This particularly affects pathogens that do not replicate in mosquitoes, preventing their detection by NGS or other methods. Accordingly, we performed a series of experiments to establish the windows of detection for DNA or RNA from human blood and/or viruses present in mosquito blood meals. Our results will contribute to trap design for mosquito-based xenosurveillance, including sample stabilization and ideal time spent from collection to NGS processing.
Mitochondrial dysfunction underlying sporadic inclusion body myositis is ameliorated by the mitochondrial homing drug MA-5
Authors: Oikawa Yoshitsugu , Izumi Rumiko , Koide Masashi , Hagiwara Yoshihiro , Kanzaki Makoto , Suzuki Naoki , Kikuchi Koichi , Matsuhashi Tetsuro , Akiyama Yukako , Ichijo Mariko , Toyohara Takafumi , Suzuki Takehiro , Mishima Eikan , Akiyama Yasutoshi , Ogata Yoshiaki , Suzuki Chitose , Aoki Masashi , Itoi Eiji , Kure Shigeo , Hayashi Ken-ichiro , Abe Takaaki
Published: March 2020

Sporadic inclusion body myositis (sIBM) is the most common idiopathic inflammatory myopathy, and several reports have suggested that mitochondrial abnormalities are involved in its etiology.

We recruited 9 sIBM patients and found significant histological changes and an elevation of growth differential factor 15 (GDF15), a marker of mitochondrial disease, strongly suggesting the involvement of mitochondrial dysfunction. Bioenergetic analysis of sIBM patient myoblasts revealed impaired mitochondrial function.

Decreased ATP production, reduced mitochondrial size and reduced mitochondrial dynamics were also observed in sIBM myoblasts. Cell vulnerability to oxidative stress also suggested the existence of mitochondrial dysfunction.

Mitochonic acid-5 (MA-5) increased the cellular ATP level, reduced mitochondrial ROS, and provided protection against sIBM myoblast death.

MA-5 also improved the survival of sIBM skin fibroblasts as well as mitochondrial morphology and dynamics in these cells. The reduction in the gene expression levels of Opa1 and Drp1 was also reversed by MA-5, suggesting the modification of the fusion/fission process. These data suggest that MA-5 may provide an alternative therapeutic strategy for treating not only mitochondrial diseases but also sIBM.
Pan-genome analysis ofMycobacterium africanum: insights to dynamics and evolution
Authors: Olawoye Idowu B. , Frost Simon D.W. , Happi Christian T.
Published: March 2020

Mycobacterium tuberculosiscomplex (MTBC) consists of seven major lineages with three of them reported to circulate within West Africa: lineage 5 (West African 1) and lineage 6 (West African 2) which are geographically restricted to West Africa and lineage 4 (Euro-American lineage) which is found globally. It is unclear why the West African lineages are not found elsewhere; some hypotheses suggest that it could either be harboured by an animal reservoir which is restricted to West Africa, or strain preference for hosts of West African ethnicity, or inability to compete with other lineages in other locations.

We tested the hypothesis thatM. africanum(MAF) might have emigrated out of West Africa but was outcompeted by more virulent strains ofM. tuberculosis(MTB).

Whole genome sequences of MTB from Nigeria (n=21), China (n=21) and MAF from Mali (n=24) were retrieved, and a pan-genome analysis was performed after fully annotating these genomes. The outcome of this analysis shows that Lineages 4, 5 and 6 have relatively close pan-genomes whilst lineage 2 has an open pan-genome. We also see a correlation in numbers of some multiple copy core genes and amino acid substitution with lineage specificity that may have contributed to geographical distribution of these lineages.

The findings in this study provides a perspective to one of the hypotheses thatM. africanummight find it difficult to compete against the more modern lineages outside West Africa hence its localization to the geographical region.
Catch composition and life history characteristics of sharks and rays (Elasmobranchii) landed in the Andaman and Nicobar Islands, India
Authors: Tyabji Zoya , Wagh Tanmay , Patankar Vardhan , Jabado Rima W. , Sutaria Dipani
Published: March 2020

The scientific literature on the diversity and biological characteristics of sharks and rays from the Andaman and Nicobar Archipelago fishing grounds is scarce and compromised by species misidentifications. We carried out systematic fish landing surveys in South Andamans from January 2017 to May 2018, a comprehensive and cost-effective way to fill this data gap. We sampled 5,742 individuals representing 57 shark and ray species. Of the 36 species of sharks and 21 species of rays landed, six species of sharks -Loxodon macrorhinus, Carcharhinus amblyrhynchos, Sphyrna lewini, Carcharhinus albimarginatus,Carcharhinus brevipinna,andParagaelus randallidominated landings and comprised 83.35 % of shark landings, while three species of rays were most abundant –Pateobatis jenkinsii,Himantura leopardaandH. tutul, and comprised 48.82 % of ray landings. We report size extensions for seven shark species as well as three previously unreported ray species, increasing the known diversity for the islands and for India. For sharks, mature individuals of small-bodied species (63.48 % males of total landings of species less than 1.5 m total length) and immature individuals of larger species (84.79 % males of total landings of species larger than 1.5 m total length) were mostly landed; whereas for rays, mature individuals were predominantly landed (80.71 % males of total landings) likely reflecting differences in fishing patterns as well as habitat preferences and life history stages across species. Further, juvenile sharks and gravid females were landed in large quantities which might be unsustainable in the long-term. Landings were female-biased inC. amblyrhynchos, S. lewiniandP. jenkinsii,and male-biased inL. macrorhinusandH. leoparda, indicating either spatio-temporal or gear specific sexual segregation in these species. Understanding these nuances - the composition and biology of sharks and rays landed in different fisheries seasonally will inform future conservation and fishery management measures for these species in the Andaman and Nicobar Islands.
Inhibitory effect of the TSG-6 on the BMP-4/Smad signaling pathway and odonto/osteogenic differentiation of dental pulp stem cells
Authors: Wang Ying , Yuan Shuai , Sun Jingjing , Gong Yuping , Liu Sirui , Guo Runying , He Wei , Liu Yiming , Kang Peng , Li Rui
Published: March 2020

This study aimed to observe the molecular mechanism underlying the effect of tumor necrosis factor–inducible protein 6 (TSG-6) on the bone morphogenetic protein-4 (BMP-4)/drosophila mothers against decapentaplegic protein(Smad) signaling pathway and mineralization of dental pulp stem cells (DPSCs) in inflammatory environment. Normal and TSG-6 gene–modified DPSCs were cultured in a mineralization-inducing fluid containing 0 and 50 ng/mL TNF-α separately. The real-time polymerase chain reaction was used to measure the expression of TSG-6 and odonto/osteogenic differentiation makers at the mRNA level. Western blot analysis and cellular immunofluorescence were used to observe the odonto/osteogenic differentiation of DPSCs and the variation of BMP-4/Smad signaling pathway at the protein level. Moreover, normal and modified DPSCs combined with hydrogel were used for subcutaneous implantation in nude mice. The expression of odonto/osteogenic markers and BMP-4/Smad-related proteins was lower in Ad-TSG-6 DPSCs than in normal DPSCs after mineralization induction, and was higher in TSG-6-RNAi DPSCs than in normal DPSCs after culturing with mineralization-inducing fluid containing 50 ng/mL TNF-α. The subcutaneous transplantation of normal and modified DPSCs combined with hydrogel in nude mice demonstrated that normal DPSCs were formed in the tissue containing collagen. The tissue formed by Ad-TSG-6 DPSCs was highly variable, and the cells were very dense. The expression of odonto/osteogenic markers of Ad-TSG-6 DPSCs were lower in Ad-TSG-6 DPSCs than in normal DPSCs. We can know that TNF-α regulates the expression of TSG-6, thereby inhibiting the BMP-4/Smad signaling pathway and the odonto/osteogenic differentiation ability of DPSCs.
CHOmics: a web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines
Authors: Lin Dongdong , Yalamanchili Hima , Zhang Xinmin , Lewis Nathan E. , Alves Christina S. , Groot Joost , Arnsdorf Johnny , Bjørn Sara Peterson , Wulff Tune , Voldborg Bjørn Gunnar Rude , Zhou Yizhou , Zhang Baohong
Published: March 2020

Chinese hamster ovary (CHO) cell lines are widely used in industry for biological drug production. During cell culture development, considerable effort is invested to understand the factors that greatly impact cell growth, specific productivity and product qualities of the biotherapeutics. High-throughput omics approaches have been increasingly utilized to reveal cellular mechanisms associated with cell line phenotypes and guide process optimization, comprehensive omics data analysis and management have been a challenge. Here we developed CHOmics, a web-based tool for integrative analysis of CHO cell line omics data that provides an interactive visualization of omics analysis outputs and efficient data management. CHOmics has a built-in comprehensive pipeline for RNA sequencing data processing and multilayer statistical modules to explore relevant genes or pathways. Moreover, advanced functionalities were provided to enable users to customize their analysis and visualize the output systematically and interactively. The tool was also designed with the flexibility to allow other omics data input and thereby enabling multi-omics comparison and visualization at both gene and pathway levels. Collectively, CHOmics is an integrative platform for data analysis, visualization and management with expectations to promote the broader use of omics in CHO cell research. The open-source tool is freely available athttp://www.chomics.org.
Comparative Pathogenesis Of COVID-19, MERS And SARS In A Non-Human Primate Model
Authors: Rockx Barry , Kuiken Thijs , Herfst Sander , Bestebroer Theo , Lamers Mart M. , de Meulder Dennis , van Amerongen Geert , van den Brand Judith , Okba Nisreen M.A. , Schipper Debby , van Run Peter , Leijten Lonneke , Verschoor Ernst , Verstrepen Babs , Langermans Jan , Drosten Christian , van Vlissingen Martje Fentener , Fouchier Ron , de Swart Rik , Koopmans Marion , Haagmans Bart L.
Published: March 2020

A novel coronavirus, SARS-CoV-2, was recently identified in patients with an acute respiratory syndrome, COVID-19. To compare its pathogenesis with that of previously emerging coronaviruses, we inoculated cynomolgus macaques with SARS-CoV-2 or MERS-CoV and compared with historical SARS-CoV infections. In SARS-CoV-2-infected macaques, virus was excreted from nose and throat in absence of clinical signs, and detected in type I and II pneumocytes in foci of diffuse alveolar damage and mucous glands of the nasal cavity. In SARS-CoV-infection, lung lesions were typically more severe, while they were milder in MERS-CoV infection, where virus was detected mainly in type II pneumocytes. These data show that SARS-CoV-2 can cause a COVID-19-like disease, and suggest that the severity of SARS-CoV-2 infection is intermediate between that of SARS-CoV and MERS-CoV.

One Sentence Summary

SARS-CoV-2 infection in macaques results in COVID-19-like disease with prolonged virus excretion from nose and throat in absence of clinical signs.
TRTools: a toolkit for genome-wide analysis of tandem repeats
Authors: Mousavi Nima , Margoliash Jonathan , Pusarla Neha , Saini Shubham , Yanicky Richard , Gymrek Melissa
Published: March 2020

A rich set of tools have recently been developed for performing genome-wide genotyping of tandem repeats (TRs). However, standardized tools for downstream analysis of these results are lacking. To facilitate TR analysis applications, we present TRTools, a Python library and a suite of command-line tools for filtering, merging, and quality control of TR genotype files. TRTools utilizes an internal harmonization module making it compatible with outputs from a wide range of TR genotypers.

Availability

TRTools is freely available athttps://github.com/gymreklab/TRTools.

Contact

mgymrek@eng.ucsd.edu

Supplementary information

Supplementary data are available atbioRxiv.
Expanding the chemical space of synthetic cyclic peptides using a promiscuous macrocyclase from prenylagaramide biosynthesis
Authors: Sarkar Snigdha , Gu Wenjia , Schmidt Eric W.
Published: March 2020

Cyclic peptides are excellent drug candidates, placing macrocyclization reactions at the apex of drug development. PatG and related dual-action proteases from cyanobactin biosynthesis are responsible for cleaving off the C-terminal recognition sequence and macrocyclizing the substrate to provide cyclic peptides. This reaction has found use in the enzymatic synthesis of diverse macrocycles. However, these enzymes function best on substrates that terminate with the non-proteinogenic thiazole/thiazoline residue, complicating synthetic strategies. Here, we biochemically characterize a new class of PatG-like macrocyclases that natively use proline, obviating the necessity of additional chemical or biochemical steps. We experimentally define the biochemical steps involved in synthesizing the widespread prenylagaramide-like natural products, including macrocyclization and prenylation. Using saturation mutagenesis, we show that macrocyclase PagG and prenyltransferase PagF are highly promiscuous, producing a library of more than 100 cyclic peptides and their prenylated derivativesin vitro. By comparing our results to known cyanobactin macrocyclase enzymes, we catalog a series of enzymes that collectively should synthesize most small macrocycles. Collectively, these data reveal that, by selecting the right cyanobactin macrocyclase, a large array of enzymatically synthesized macrocycles are accessible.
An 1,4-α-glucosyltransferase defines a new maltodextrin catabolism scheme inLactobacillus acidophilus
Authors: Andersen Susan , Møller Marie S. , Poulsen Jens-Christian N. , Pichler Michael J. , Svensson Birte , Goh Yong Jun , Leggio Leila Lo , Hachem Maher Abou
Published: March 2020

The maltooligosaccharide (MOS) utilization locus inLactobacillus acidophilusNCFM, a model for human small-intestine lactobacilli, encodes a family 13 subfamily 31 glycoside hydrolase (GH13_31), annotated as an 1,6-α-glucosidase. Here, we reveal that this enzyme (LaGH13_31B) is an 1,4-α-glucosyltransferase that disproportionates MOS with preference for maltotriose.LaGH13_31B acts in concert with a maltogenic α-amylase that efficiently releases maltose from MOS larger than maltotriose. Collectively, these two enzymes promote efficient conversion of preferentially odd-numbered MOS to maltose that is phosphorolysed by a maltose phosphorylase, encoded by the same locus. Structural analyses revealed the presence of a flexible elongated loop, which is unique forLaGH13_31B and its close homologues. The identified loop insertion harbours a conserved aromatic residue that modulates the activity and substrate affinity of the enzyme, thereby offering a functional signature of this previously undescribed clade, which segregates from described activities such as 1,6-α-glucosidases and sucrose isomerases within GH13_31. Sequence analyses revealed that theLaGH13_31B gene is conserved in the MOS utilization loci of lactobacilli, including acidophilus cluster members that dominate the human small intestine.

IMPORTANCE

The degradation of starch in the small intestine generates short linear and branched α-glucans. The latter are poorly digestible by humans, rendering them available to the gut microbiotae.g. lactobacilli adapted to the human small intestine and considered as beneficial to health. This study unveils a previously unknown scheme of maltooligosaccharide (MOS) catabolism, via the concerted action of activity together with a classical hydrolase and a phosphorylase. The intriguing involvement of a glucosyltransferase is likely to allow fine-tuning the regulation of MOS catabolism for optimal harnessing of this key metabolic resource in the human small intestine. The study extends the suite of specificities that have been identified in GH13_31 and highlights amino acid signatures underpinning the evolution of 1,4-α-glucosyl transferases that have been recruited in the MOS catabolism pathway in lactobacilli.
Hybrid quantum dot - collagen extracellular matrices for in situ optical monitoring of cardiomyocyte activity by two-photon fluorescence
Authors: Jooken Stijn , de Coene Yovan , Deschaume Olivier , Krylychkina Olga , Verbiest Thierry , Clays Koen , Callewaert Geert , Bartic Carmen
Published: March 2020

The incorporation of functional nanoparticles in scaffolds for tissue constructs has led to the creation of artificial extracellular matrices that more accurately mimic the cues present in the native microenvironment of developing tissue. Additionally, light-sensitive inorganic nanoparticles can act as cell biosensors and report on the physiological parameters during tissue growth and organization. In this work, we functionalized collagen nanofibers with semiconductor quantum dots (QDs) and thereby created artificial extracellular matrices that can optically report on cardiomyocyte activity based on QD two-photon fluorescence. We have applied these optically-addressable nanofiber matrices to monitor activities of primary cardiomyocytes and compared the optical responses with patch-clamp data. Combining the long-term stability of QD fluorescence with the deeper light penetration depths achievable through multiphoton imaging, this approach can be used for continuous monitoring of cellular functions in cardiac tissue engineering.

Abstract Figure

Concept illustration: optical readout of cardiomyocyte activity with QD-functionalized collagen networks. Whole-cell current-clamp mode is used here to simultaneously monitor changes in the transmembrane voltage while the QD two-photon fluorescence is recorded.
Development of a scanning soft X-ray spectromicroscope to investigate local electronic structures on surfaces and interfaces of advanced materials under conditions ranging from low vacuum to helium atmosphere
Authors: Oura Masaki , Ishihara Tomoko , Osawa Hitoshi , Yamane Hiroyuki , Hatsui Takaki , Ishikawa Tetsuya
Published: March 2020

A scanning soft X-ray spectromicroscope was recently developed based mainly on the photon-in/photon-out measurement scheme for the investigation of local electronic structures on the surfaces and interfaces of advanced materials under conditions ranging from low vacuum to helium atmosphere. The apparatus was installed at the soft X-ray beamline (BL17SU) at SPring-8. The characteristic features of the apparatus are described in detail. The feasibility of this spectromicroscope was demonstrated using soft X-ray undulator radiation. Here, based on these results, element-specific two-dimensional mapping and micro-XAFS (X-ray absorption fine structure) measurements are reported, as well as the observation of magnetic domain structures from using a reference sample of permalloy micro-dot patterns fabricated on a silicon substrate, with modest spatial resolution (e.g. ∼500 nm). Then, the X-ray radiation dose for Nafion® near the fluorine K-edge is discussed as a typical example of material that is not radiation hardened against a focused X-ray beam, for near future experiments.
Revisiting dynamic capability for organizations' innovation types
Authors: Ilmudeen Aboobucker , Bao Yukun , Alharbi Ibraheem Mubarak , Zubair Nawaz
Published: March 2020

Purpose

Despite the existing literature on the impact of IT capability and innovation capabilities, this study examines how IT-enabled dynamic capability dimensions impact on firm innovative capability to achieve organizational performance.

Design/methodology/approach

Drawing on the dynamic capability theory, this study empirically investigates the entire chain of relationships among dynamic capability, innovative capability, organizational performance and turbulent environment.

Findings

Using the data from 254 Chinese firms, this study reveals IT-enabled dynamic capability dimensions have positive and significant relationship with firm innovative capability types, which in turn have significant relationship with organizational performance except the process innovation.

Research limitations/implications

This study contributes to the growing information systems literature and also suggests theoretical and practical implications.

Originality/value

This study examines IT-enabled dynamic capability with firm innovative capability types, which has received limited attention in the past.
Assessment of information literacy skills
Authors: Okeji Chukwuma Clement , Ilika Obiageli Martina , Baro Emmanuel Ebikabowei
Published: March 2020

Purpose

The purpose of this study is to assess information literacy skills of undergraduates in Nigerian universities.

Design/methodology/approach

A self-assessed questionnaire was developed to collect data from the final year undergraduates in 15 universities. A total of 1,350 final year Library and Information Science (LIS) students responded to the questionnaire which was used for analysis.

Findings

The study revealed that the majority of the LIS final year undergraduates mostly consult journal articles, followed by internet information and online databases during their research process. The undergraduates rated well-known author(s), current information, credible information, accurate and relevant information as very important when evaluating online information resources. It was found that the students rated their ability to organize information and integrate ideas from consulted information as high. While they were deficient in ability to correctly paraphrase ideas to avoid plagiarism and use citation and referencing styles correctly. On the whole, almost half of the final year undergraduates of LIS rated their level of information literacy skills to be moderate.

Practical implications

The findings of the study will inform librarians and faculty in universities in developing countries like Nigeria to develop an information literacy instruction policy.

Originality/value

Assessing information literacy skills will provide the foundation and knowledge to improve the development of information literacy training programmes.
How mindset and store familiarity impact online stockout responses
Authors: Gunness Aneeshta , Oppewal Harmen
Published: March 2020

Purpose

Effects of stockouts on purchase decisions have been examined from a variety of perspectives; little is yet known about how consumers react to stockouts in online shopping contexts. The present study investigates how stockout reactions depend on a consumer's mindset and familiarity with a website and investigates the role of negative affect in determining a consumer's stockout reaction.

Design/methodology/approach

Shopping mindsets (deliberative vs. implemental) and website familiarity (high vs. low) were manipulated in an online experiment consisting of a simulated shopping task at an existing website which next was presented as having a stockout. The study observed the participants' switching responses and measured their negative affect.

Findings

Findings indicate that when encountering an online stockout, consumers in an implemental mindset are more likely to switch away from the website than those in a deliberative mindset and are more likely to search for additional items at a competing site. Consumers who are more familiar with the website where they encounter the stockout display a higher likelihood of defecting to a competing site; however, when they are in an implemental mindset, their inclination to defect decreases. The study also shows that the strength of negative emotions affects OOS responses in that buyers that experience more negative emotions are more likely to defect from the site.

Practical implications

The study's findings provide suggestions as to how retailers can manage and minimize defection behaviours associated with online stockouts. In designing operational and marketing strategies retailers need to pay close attention to how consumers' individual mindsets may vary by trait or circumstance and how they hence may respond differently to stockouts.

Originality/value

The authors introduce a novel perspective to the literature on stockout induced reactions and contribute by furthering investigation into previously unexplored specific consumer characteristics and intricacies of stockouts that drive particular stockout reactions.
Governance and customer value creation in business solutions
Authors: Mooi Erik , Kashyap Vishal , van Aken Marc
Published: March 2020

Purpose

This paper aims to consider the impact of contractual and normative governance mechanisms on recommendation intent in a context of healthcare and professional lighting where repeat business from a customer is absent. The authors suggest both contractual and normative governance can create recommendation intent, but only when sufficient customer value is created.

Design/methodology/approach

The authors draw on a combination of survey and archival data from the supplier and customer in the medical equipment and advanced (business) lighting systems industries. The authors analyze the data using seemingly unrelated regression and mediation tests.

Findings

Contracts and relational norms can increase customer recommendation intent, but only when the supplier creates customer value.

Practical implications

The paper’s findings suggest that customers of business solutions are more likely to recommend their supplier when contracts are relatively detailed and when buyers and suppliers attempt to craft strong relational norms, despite service solutions being delivered during a relatively short time span.

Originality/value

The extant research on business solutions has focused on extended relationships between exchange partners with a high likelihood of repeated transactions. The authors demonstrate how to govern relationships in a solutions context where the likelihood of repeat business from the same customer is low using contractual and normative governance.
Quantifying the sustainability of Bitcoin and Blockchain
Authors: Fry John , Serbera Jean-Philippe
Published: March 2020

Purpose

The authors develop new quantitative methods to estimate the level of speculation and long-term sustainability of Bitcoin and Blockchain.

Design/methodology/approach

The authors explore the practical application of speculative bubble models to cryptocurrencies. They then show how the approach can be extended to provide estimated brand values using data from Google Trends.

Findings

The authors confirm previous findings of speculative bubbles in cryptocurrency markets. Relatedly, Google searches for cryptocurrencies seem to be primarily driven by recent price rises. Overall results are sufficient to question the long-term sustainability of Bitcoin with the suggestion that Ethereum, Bitcoin Cash and Ripple may all enjoy technical advantages relative to Bitcoin. Our results also demonstrate that Blockchain has a distinct value and identity beyond cryptocurrencies – providing foundational support for the second generation of academic work on Blockchain. However, a relatively low estimated long-term growth rate suggests that the benefits of Blockchain may take a long time to be fully realised.

Originality/value

The authors contribute to an emerging academic literature on Blockchain and to a more established literature exploring the use of Google data within business analytics. Their original contribution is to quantify the business value of Blockchain and related technologies using Google Trends