bluuebunny/crossref_metadata_2025_split huggingface dataset:
The new kid on the block: A dominant-negative mutation of phototropin1 enhances carotenoid content in tomato fruits
Authors: Kilambi Himabindu Vasuki , Dindu Alekhya , Sharma Kapil , Nizampatnam Narasimha Rao , Gupta Neha , Thazath Nikhil Padmanabhan , Dhanya Ajayakumar Jaya , Tyagi Kamal , Sharma Sulabha , Kumar Sumit , Sharma Rameshwar , Sreelakshmi Yellamaraju 
Published: September 2020

AbstractPhototropins, the UVA-blue light photoreceptors, endow plants to detect the direction of light and optimize photosynthesis by regulating chloroplasts positioning and stomatal gas exchange. Little is known about their functions in other developmental responses. A tomatoNon-phototropic seedling1(Nps1) mutant, bearing an Arg495His substitution in the vicinity of LOV2 domain in phototropin1, dominant-negatively blocks phot1 and phot2 responses. The fruits ofNps1mutant were enriched in carotenoids, particularly lycopene, than its parent, Ailsa Craig. Contrarily, CRISPR/CAS9-edited loss of functionphototropin1mutants displayed subdued carotenoids than the parent. The enrichment of carotenoids inNps1fruits is genetically linked with the mutation and exerted in a dominant-negative fashion.Nps1also altered volatile profiles with high levels of lycopene-derived 6-methyl 5-hepten2-one. The transcript levels of several MEP and carotenogenesis pathways genes were upregulated inNps1.Nps1fruits showed altered hormonal profiles with subdued ethylene emission and reduced respiration. Proteome profiles showed a causal link between higher carotenogenesis and increased levels of protein protection machinery, which may stabilize proteins contributing to MEP and carotenogenesis pathways. Given the enhancement of carotenoid content byNps1in a dominant-negative fashion, it offers a potential tool for high lycopene-bearing hybrid tomatoes.One-sentence summaryA dominant-negative phototropin1 mutation enhances carotenoid levels, alters metabolite homeostasis, and protein quality control machinery in tomato fruits.
Accurate prediction of residue-residue contacts across homo-oligomeric protein interfaces through deep leaning
Authors: Yan Yumeng , Huang Sheng-You 
Published: September 2020

AbstractProtein-protein interactions play a fundamental role in all cellular processes. Therefore, determining the structure of protein-protein complexes is crucial to understand their molecular mechanisms and develop drugs targeting the protein-protein interactions. Recently, deep learning has led to a breakthrough in intraprotein contact prediction, achieving an unusual high accuracy in recent CASP structure prediction challenges. However, due to the limited number of known homologous protein-protein interactions and the challenge to generate joint multiple sequence alignments (MSA) of two interacting proteins, the advances in inter-protein contact prediction remain limited. Here, we have proposed a deep learning model to predict inter-protein residue-residue contacts across homo-oligomeric protein interfaces, named as DeepHomo, by integrating evolutionary coupling, sequence conservation, distance map, docking pattern, and physic-chemical information of monomers. DeepHomo was extensively tested on both experimentally determined structures and realistic CASP-CAPRI targets. It was shown that DeepHomo achieved a high accuracy of >60% for the top predicted contact and outperformed state-of-the-art direct-coupling analysis (DCA) and machine learning (ML)-based approaches. Integrating predicted contacts into protein docking with blindly predicted monomer structures also significantly improved the docking accuracy. The present study demonstrated the success of DeepHomo in inter-protein contact prediction. It is anticipated that DeepHomo will have a far-reaching implication in the inter-protein contact and structure prediction for protein-protein interactions.
Bacterial processing of glucose modulatesC. eleganslifespan and healthspan
Authors: Kingsley Samuel F. , Seo Yonghak , Allen Calista , Ghanta Krishna S. , Finkel Steven , Tissenbaum Heidi A. 
Published: September 2020

AbstractIntestinal microbiota play an essential role in the health of a host organism. Here, we define how commensalEscherichia coli (E. coli)alters its host after long term exposure to glucose using aC. elegans-E. colisystem. Our data reveal that bacterial processing of glucose, rather than direct ingestion by the animal, results in reduced lifespan and healthspan, including reduced locomotion, oxidative stress resistance, and heat stress resistance inC. elegans. Chronic exposure ofE. colito glucose produces growth defects and increased advanced glycation end products within theE. coli.These negative effects are abrogated when theE. coliis not able to process the additional glucose and by the addition of the anti-glycation compound carnosine. Physiological changes of the hostC. elegansare accompanied by dysregulation of detoxifying genes including glyoxalase, glutathione-S-transferase, and superoxide dismutase. Loss ofgst-4shortensC. eleganslifespan and blunts the animal’s response to a glucose-fed bacteria diet. Taken together, we reveal that added dietary sugar may alter intestinal microbialE. colito decrease lifespan and healthspan of the host and define the critical role of detoxification genes in maintaining health during a chronic high-sugar diet.
Genes with 5′ terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein
Authors: Rao Shilpa , Hoskins Ian , Tonn Tori , Garcia P. Daniela , Ozadam Hakan , Cenik Elif Sarinay , Cenik Can 
Published: September 2020

AbstractViruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms to co-opt host translation for their survival. SARS-CoV-2 relies on a non-structural protein, Nsp1, for shutting down host translation. However, it is currently unknown how viral proteins and host factors critical for viral replication can escape a global shutdown of host translation. Here, using a novel FACS-based assay called MeTAFlow, we report a dose-dependent reduction in both nascent protein synthesis and mRNA abundance in cells expressing Nsp1. We perform RNA-Seq and matched ribosome profiling experiments to identify gene-specific changes both at the mRNA expression and translation level. We discover a functionally-coherent subset of human genes are preferentially translated in the context of Nsp1 expression. These genes include the translation machinery components, RNA binding proteins, and others important for viral pathogenicity. Importantly, we uncovered a remarkable enrichment of 5′ terminal oligo-pyrimidine (TOP) tracts among preferentially translated genes. Using reporter assays, we validated that 5’ UTRs from TOP transcripts can drive preferential expression in the presence of NSP1. Finally, we found that LARP1, a key effector protein in the mTOR pathway may contribute to preferential translation of TOP transcripts in response to Nsp1 expression. Collectively, our study suggests fine tuning of host gene expression and translation by Nsp1 despite its global repressive effect on host protein synthesis.
The impact of vaccination on Neisseria gonorrhoeae antimicrobial resistance and prevalence in men who have sex with men: a mathematical modelling study
Authors: Heijne Janneke C.M. , Xiridou Maria , Turner Katy M.E. , Basten Maartje , Visser Maartje , van Benthem Birgit , Low Nicola 
Published: September 2020

SummaryBackgroundNeisseria gonorrhoeae (gonorrhoea) and antimicrobial-resistant (AMR) gonorrhoea infections disproportionately affect men who have sex with men (MSM). Vaccine development is challenging, but a N. meningitidis (group B) vaccine given to children and young adults was associated with a ca. ~30% reduction in gonorrhoea diagnoses. We investigated the impact of vaccination on N. gonorrhoeae AMR development and transmission in MSM.MethodsWe developed a compartmental model of N. gonorrhoeae transmission among MSM. AMR to ceftriaxone was incorporated as a stepwise increases in minimum inhibitory concentrations and eventual resistance (MIC drift). We estimated the impact of a partially protective vaccine (reducing susceptibility; 2-years protection) targeting high sexual activity MSM on AMR and prevalence until 2050. We performed sensitivity analyses assuming different levels of vaccine effectiveness (VE) and other modes of vaccine action.FindingsGonorrhoea model prevalence was 3·4% (95% credible interval 3·2% – 3·8%) in all MSM, 12·5% (95% credible interval 12·1% – 12·7%) in high sexual activity MSM. A vaccine with 30% VE cannot prevent AMR, even with high uptake or durable protection. However, it increases time to AMR development by several years. For a fixed uptake of 40% a vaccine needs a minimum VE of 90% to prevent AMR development completely. A vaccine providing complete protection to infection for those vaccinated was most effective in reducing population prevalence and preventing AMR.InterpretationA vaccine that has limited efficacy for the prevention of gonorrhoea could delay AMR development in MSM, providing time for developing new antimicrobials and more efficacious vaccines.FundingNone
Psychometric properties of the Depression Stigma Scale in the Portuguese population and its association with gender and depressive symptomatology
Authors: Conceição Virgínia da , Rothes Inês , Severo Milton , Griffiths Kathleen , Hegerl Ulrich , Gusmão Ricardo 
Published: September 2020

AbstractBackgroundStigma is one of the most significant constraints on people living with depression. There is a lack of validated scales in Portugal to measure depression stigma; therefore, validation of the Depression Stigma Scale (DSS) is an essential step to the depression stigma research in Portugal.MethodsWe developed the adaptation process with the ITC Guidelines for Translation and Adapting Tests taken into consideration. We collected the sample as part of the OSPI program – Optimizing suicide prevention programs and their implementation in Europe, specifically within the application in Portugal, and included 1693 participants. Floor-ceiling effects and response ranges were analyzed, and we calculated Cronbach alphas, conducted a Principal Component Analysis and Confirmatory Analysis. Validity evidence was tested with two well-documented hypotheses, using data on gender and depression symptoms.ResultsThe sample was well comparable with the general Portuguese population, indicating its representativeness. We identified a three-factor structure in each subscale (personal and perceived stigma): weak-not-sick, discrimination, and dangerous/unpredictable. The Cronbach’s alphas were satisfactory, and validity was confirmed.ConclusionsThis study established the validity and demonstrated good psychometric properties of the DSS in the Portuguese population. The validation of the DSS can be beneficial in exploring stigma predictors and evaluating the effectiveness of stigma reduction interventions.
Ablation of STAT3 in Purkinje Cells Reorganizes Cerebellar Synaptic Plasticity in Long-Term Fear Memory Network
Authors: Han Jeong-Kyu , Kwon Sun-Ho , Kim Yong Gyu , Choi Jaeyong , Kim Jong-Il , Lee Yong-Seok , Ye Sang-Kyu , Kim Sang Jeong 
Published: September 2020

ABSTRACTEmotional memory processing, such as fear memory, engages a large neuronal network of brain regions including the cerebellum. However, the molecular and cellular mechanisms of the cerebellar cortex modulating the fear memory network is largely unknown. Here, we illustrate a novel mechanism by which synaptic signaling in cerebellar Purkinje cells (PCs)viaSTAT3 regulates long-term fear memory. Firstly, we generated PC-specific STAT3 knockout (STAT3PKO) mice. Transcriptome analyses revealed that STAT3 deletion results in transcriptional changes that lead to an increase in the expression of glutamate receptors. The amplitude of AMPA receptor-mediated excitatory postsynaptic currents at parallel fiber to PC synapses was larger in STAT3PKOmice than in wild-type littermates. Conditioning at the parallel fiber induced long-term depression of parallel fiber-PC synapses in STAT3PKOmice while the same manipulation induced long-term potentiation in wild-type littermates. Interestingly, STAT3PKOmice showed an aberrantly enhanced long-term fear memory. Neuronal activity in fear-related regions increased in fear-conditioned STAT3PKOmice. Our data suggest that STAT3-dependent molecular regulation in PCs is indispensable for proper expression of fear memory processing.
How to build a water-splitting machine: structural insights into photosystem II assembly
Authors: Zabret Jure , Bohn Stefan , Schuller Sandra K. , Arnolds Oliver , Möller Madeline , Meier-Credo Jakob , Liauw Pasqual , Chan Aaron , Tajkhorshid Emad , Langer Julian D. , Stoll Raphael , Krieger-Liszkay Anja , Engel Benjamin D. , Rudack Till , Schuller Jan M. , Nowaczyk Marc M. 
Published: September 2020

AbstractBiogenesis of photosystem II (PSII), nature’s water splitting catalyst, is assisted by auxiliary proteins that form transient complexes with PSII components to facilitate stepwise assembly events. Using cryo-electron microscopy, we solved the structure of such a PSII assembly intermediate with 2.94 Å resolution. It contains three assembly factors (Psb27, Psb28, Psb34) and provides detailed insights into their molecular function. Binding of Psb28 induces large conformational changes at the PSII acceptor side, which distort the binding pocket of the mobile quinone (QB) and replace bicarbonate with glutamate as a ligand of the non-heme iron, a structural motif found in reaction centers of non-oxygenic photosynthetic bacteria. These results reveal novel mechanisms that protect PSII from damage during biogenesis until water splitting is activated. Our structure further demonstrates how the PSII active site is prepared for the incorporation of the Mn4CaO5cluster, which performs the unique water splitting reaction.One Sentence HighlightThe high-resolution Cryo-EM structure of the photosystem II assembly intermediate PSII-I reveals how nature’s water splitting catalyst is assembled, protected and prepared for photoactivation by help of the three assembly factors Psb27, Psb28 and Psb34.
Human INCL fibroblasts display abnormal mitochondrial and lysosomal networks and heightened susceptibility to ROS-induced cell death
Authors: Balouch Bailey , Nagorsky Halle , Pham Truc , LaGraff Thai , Chu-LaGraff Quynh 
Published: September 2020

AbstractInfantile Neuronal Ceroid Lipofuscinosis (INCL) is a pediatric neurodegenerative disorder characterized by progressive retinal and central nervous system deterioration during infancy. This lysosomal storage disorder results from a deficiency in the Palmitoyl Protein Thioesterase 1 (PPT1) enzyme - a lysosomal hydrolase which cleaves fatty acid chains such as palmitate from lipid-modified proteins. In the absence of PPT1 activity, these proteins fail to be degraded, leading to the accumulation of autofluorescence storage material in the lysosome. The underlying molecular mechanisms leading to INCL pathology remain poorly understood. A role for oxidative stress has been postulated, yet little evidence has been reported to support this possibility. Here we present a comprehensive cellular characterization of human PPT1-deficient fibroblast cells harboring Met1Ile and Tyr247His compound heterozygous mutations. We detected autofluorescence storage material and observed distinct organellar abnormalities of the lysosomal and mitochondrial structures, which supported previous postulations about the role of ER, mitochondria and oxidative stress in INCL. An increase in the number of lysosomal structures was found in INCL patient fibroblasts, which suggested an upregulation of lysosomal biogenesis, and an association with endoplasmic reticulum stress response. The mitochondrial network also displayed abnormal spherical punctate morphology instead of normal elongated tubules with extensive branching, supporting the involvement of mitochondrial and oxidative stress in INCL cell death. Autofluorescence accumulation and lysosomal pathologies can be mitigated in the presence of conditioned wild type media suggesting that a partial restoration via passive introduction of the enzyme into the cellular environment may be possible. We also demonstrated, for the first time, that human INCL fibroblasts have a heightened susceptibility to exogenous reactive oxygen species (ROS)-induced cell death, which suggested an elevated basal level of endogenous ROS in the mutant cell. Collectively, these findings support the role of intracellular organellar networks in INCL pathology, possibly due to oxidative stress.
AFLAP: Assembly-Free Linkage Analysis Pipeline usingk-mers from whole genome sequencing data
Authors: Fletcher Kyle , Zhang Lin , Gil Juliana , Han Rongkui , Cavanaugh Keri , Michelmore Richard 
Published: September 2020

AbstractBackgroundGenetic maps are an important resource for validation of genome assemblies, trait discovery, and breeding. Next generation sequencing has enabled production of high-density genetic maps constructed with 10,000s of markers. Most current approaches require a genome assembly to identify markers. Our Assembly Free Linkage Analysis Pipeline (AFLAP) removes this requirement by using uniquely segregatingk-mers as markers to rapidly construct a genotype table and perform subsequent linkage analysis. This avoids potential biases including preferential read alignment and variant calling.ResultsThe performance of AFLAP was determined in simulations and contrasted to a conventional workflow. We tested AFLAP using 100 F2individuals ofArabidopsis thaliana, sequenced to low coverage. Genetic maps generated usingk-mers contained over 130,000 markers that were concordant with the genomic assembly. The utility of AFLAP was then demonstrated by generating an accurate genetic map using genotyping-by-sequencing data of 235 recombinant inbred lines ofLactucaspp. AFLAP was then applied to 83 F1individuals of the oomyceteBremia lactucae, sequenced to >5x coverage. The genetic map contained over 90,000 markers ordered in 19 large linkage groups. This genetic map was used to fragment, order, orient, and scaffold the genome, resulting in a much-improved reference assembly.ConclusionsAFLAP can be used to generate high density linkage maps and improve genome assemblies of any organism when a mapping population is available using whole genome sequencing or genotyping-by-sequencing data. Genetic maps produced forB. lactucaewere accurately aligned to the genome and guided significant improvements of the reference assembly.
ZnJ6 is a DnaJ-like Chaperone with Oxidizing Activity in the Thylakoid Membrane inChlamydomonas reinhardtii
Authors: Amiya Richa , Shapira Michal 
Published: September 2020

ABSTRACTAssembly of photosynthetic complexes is sensitive to changes in light intensities, drought, and pathogens that induce a redox imbalance, and require a variety of substrate-specific chaperones to overcome the stress. Proteins with cysteine (C) residues and disulfide bridges are more responsive to the redox changes. This study reports on a thylakoid membrane-associated DnaJ-like protein, ZnJ6 (ZnJ6.g251716.t1.2) inChlamydomonas reinhardtii. The protein has four CXXCX(G)X(G) motifs that form a functional zinc-binding domain. Site-directed mutagenesis (Cys to Ser) in all the CXXCX(G)X(G) motifs eliminates its zinc-binding ability. In vitro chaperone assays using recombinant ZnJ6 confirm that it is a chaperone that possesses both holding and oxidative refolding activities. Although mutations (Cys to Ser) do not affect the holding activity of ZnJ6, they impair its ability to promote redox-controlled reactivation of reduced and denatured RNaseA, a common substrate protein. The presence of an intact zinc-binding domain is also required for protein stability at elevated temperatures, as suggested by a single spectrum melting curve. Pull-down assays with recombinant ZnJ6 revealed that it interacts with oxidoreductases, photosynthetic proteins (mainly PSI), and proteases. Ourin vivoexperiments withChlamydomonas reinhardtiiinsertional mutants (ΔZnJ6) expressing a low level of ZnJ6, suggested that the mutant is more tolerant to oxidative stress. In contrast, the wild type has better protection at elevated temperature and DTT induced stress. We propose that DnaJ-like chaperone ZnJ6 assists in the prevention of protein aggregation, stress endurance, and maintenance of redox balance.One-sentence summaryZnJ6 is a redox-regulated DnaJ-like chaperone associated with the thylakoid membrane and involved in the prevention of protein aggregation and stress endurance.
Resiniferatoxin (RTX) ameliorates acute respiratory distress syndrome (ARDS) in a rodent model of lung injury
Authors: Hahka Taija M. , Xia Zhiqiu , Hong Juan , Kitzerow Oliver , Nahama Alexis , Zucker Irving H. , Wang Hanjun 
Published: September 2020

AbstractAcute lung injury (ALI) is associated with cytokine release, pulmonary edema and in the longer term, fibrosis. A severe cytokine storm and pulmonary pathology can cause respiratory failure due to acute respiratory distress syndrome (ARDS), which is one of the major causes of mortality associated with ALI. In this study, we aimed to determine a novel neural component through cardiopulmonary spinal afferents that mediates lung pathology during ALI/ARDS. We ablated cardiopulmonary spinal afferents through either epidural T1-T4 dorsal root ganglia (DRG) application or intra-stellate ganglia delivery of a selective afferent neurotoxin, resiniferatoxin (RTX) in rats 3 days post bleomycin-induced lung injury. Our data showed that both epidural and intra-stellate ganglia injection of RTX significantly reduced plasma extravasation and reduced the level of lung pro-inflammatory cytokines providing proof of principle that cardiopulmonary spinal afferents are involved in lung pathology post ALI. Considering the translational potential of stellate ganglia delivery of RTX, we further examined the effects of stellate RTX on blood gas exchange and lung edema in the ALI rat model. Our data suggest that intra-stellate ganglia injection of RTX improved pO2and blood acidosis 7 days post ALI. It also reduced wet lung weight in bleomycin treated rats, indicating a reduction in lung edema. Taken together, this study suggests that cardiopulmonary spinal afferents play a critical role in lung inflammation and edema post ALI. This study shows the translational potential for ganglionic administration of RTX in ARDS.