bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Random Forest Classifier Uses Antibody Responses to Plasmodium Antigens to Reveal Candidate Biomarkers of the Intensity and Timing of Past Exposure to Plasmodium falciparum
Authors: Bérubé Sophie , Kobayashi Tamaki , Norris Douglas E. , Ruczinski Ingo , Moss William J. , Wesolowski Amy , Louis Thomas A. 
Published: February 2022

1AbstractImportant goals of malaria surveillance efforts include accurately quantifying the burden of malaria over time, which can be useful to target and evaluate interventions. The majority of malaria surveillance methods capture active or recent infections which poses several challenges to achieving malaria surveillance goals. In high transmission settings, asymptomatic infections are common and therefore accurate measurement of malaria burden often demands active surveillance; in low transmission regions where infections are rare accurate surveillance requires sampling a large subset of the population; and in any context monitoring malaria burden over time necessitates serial sampling. Antibody responses to Plasmodium falciparum parasites persist after infection and therefore measuring antibodies has the potential to overcome several of the current difficulties associated with malaria surveillance. However, identifying which antibody responses are markers of the timing and intensity of past exposure to P. falciparum is challenging, particularly among adults who tend to be re-exposed multiple times over the course of their lifetime and therefore have similarly high antibody responses to many P. falciparum antigens. A previous analysis of 479 serum samples from individuals in three regions in southern Africa with different historical levels of P. falciparum malaria transmission (high, intermediate, and low) revealed regional differences in antibody responses to P. falciparum antigens among children under 5 years of age. Using a novel bioinformatic pipeline optimized for protein microarrays that minimizes between-sample technical variation, we used antibody responses to P. falciparum and P. vivax antigens as predictors in random forest models to classify adult samples into these three regions of differing historical malaria transmission with high accuracy. Many of the antigens that were most important for classification in these models do not overlap with previously published results and are therefore novel candidate markers for the timing and intensity of past exposure to P. falciparum. Measuring antibody responses to these antigens could potentially lead to improved malaria serosurveillance that captures the timing and intensity of past exposure.
Lens aquaporin-5 inserts into bovine fiber cell plasma membranes through mitochondria-associated lysosome secretion
Authors: Gletten Romell B. , Cantrell Lee S. , Bhattacharya Sujoy , Schey Kevin L. 
Published: February 2022

AbstractPURPOSETo spatially map aquaporin-5 (AQP5) expression in bovine lens, molecularly characterize cytoplasmic AQP5-containing vesicles in the outer cortex, and elucidate AQP5 membrane trafficking mechanisms.METHODSImmunofluorescence was performed on bovine lens cryosections using AQP5, TOMM20, COX IV, calnexin, LC3B, LIMP-2, and connexin-50 antibodies and the fluorescent lipid membrane dye CM-DiI. AQP5 plasma membrane insertion was defined via line expression profile analysis. Transmission electron microscopy (TEM) was performed on bovine lens tissue sections to define cytoplasmic organelle identity, morphology, and subcellular localization in cortical fiber cells. Bovine lenses were treated with 10 nM bafilomycin A1 or 0.1% dimethyl sulfoxide vehicle control in ex vivo culture to determine changes in AQP5 plasma membrane expression.RESULTSImmunofluorescence analysis revealed cytoplasmic AQP5 expression in bovine lens epithelial cells and differentiating fiber cells. In the bovine lens cortex, complete AQP5 plasma membrane insertion occurs at r/a 0.951 + 0.005. AQP5-containing cytoplasmic vesicles are spheroidal, tubular in morphology, express TOMM20, and contain LC3B and LIMP-2 as fiber cells mature. TEM analysis revealed spheroidal, tubular autophagosomes, autolysosomes, and lysosomes with degrading mitochondria. AQP5-containing cytoplasmic vesicles and autolysosomes dock and fuse with the plasma membrane. Bafiloymcin A1 treatment reduced AQP5 plasma membrane expression by 27%.CONCLUSIONSAQP5 localizes to spheroidal, tubular cytoplasmic vesicles in the differentiating bovine lens fiber cells. During fiber cell differentiation, these vesicles incorporate LC3B and fuse with LIMP-2-positive lysosomes. AQP5 trafficking to the plasma membrane occurs through lysosome secretion as a novel mechanism of AQP5 trafficking.
Autoantibodies linked to autoimmune diseases associate with COVID-19 outcomes
Authors: Baiocchi Gabriela Crispim , Vojdani Aristo , Rosenberg Avi Z , Vojdani Elroy , Halpert Gilad , Ostrinski Yuri , Zyskind Israel , Filgueiras Igor Salerno , Schimke Lena F. , Marques Alexandre H. C. , Giil Lasse M. , Lavi Yael Bublil , Silverberg Jonathan I. , Zimmerman Jason , Hill Dana Ashley , Thornton Amanda , Kim Myungjin , De Vito Roberta , Fonseca Dennyson Leandro M. , Plaça Desireé Rodrigues , Freire Paula Paccielli , Camara Niels Olsen Saraiva , Calich Vera Lúcia Garcia , Heidecke Harald , Lattin Miriam T. , Ochs Hans D. , Riemekasten Gabriela , Amital Howard , Cabral-Marques Otavio , Shoenfeld Yehuda 
Published: February 2022

ABSTRACTThe SARS-CoV-2 infection is associated with increased levels of autoantibodies targeting immunological proteins such as cytokines and chemokines. Reports further indicate that COVID-19 patients may develop a wide spectrum of autoimmune diseases due to reasons not fully understood. Even so, the landscape of autoantibodies induced by SARS-CoV-2 infection remains uncharted territory. To gain more insight, we carried out a comprehensive assessment of autoantibodies known to be linked to diverse autoimmune diseases observed in COVID-19 patients, in a cohort of 248 individuals, of which171 were COVID-19 patients (74 with mild, 65 moderate, and 32 with severe disease) and 77were healthy controls. Dysregulated autoantibody serum levels, characterized mainly by elevated concentrations, occurred mostly in patients with moderate or severe COVID-19 infection, and was accompanied by a progressive disruption of physiologic IgG and IgA autoantibody signatures. A similar perturbation was found in patients with anosmia. Notably, autoantibody levels often accompanied anti-SARS-CoV-2 antibody concentrations, being both indicated by random forest classification as strong predictors of COVID-19 outcome, together with age. Moreover, higher levels of autoantibodies (mainly IgGs) were seen in the elderly with severe disease compared with young COVID-19 patients with severe disease. These findings suggest that the SARS-CoV-2 infection induces a broader loss of self-tolerance than previously thought, providing new ideas for therapeutic interventions.
Immune system and blood-brain barrier-wide biomarker analyses provide causal evidence for autoimmunity in dementia
Authors: Lindbohm Joni V. , Mars Nina , Sipilä Pyry N. , Singh-Manoux Archana , Runz Heiko ,   FinnGen, Livingston Gill , Seshadri Sudha , Xavier Ramnik , Hingorani Aroon D. , Ripatti Samuli , Kivimäki Mika 
Published: February 2022

AbstractImmune system and blood brain barrier (BBB) dysfunction are implicated in the development of Alzheimer’s disease and other dementias, but their causal role remains unknown. We performed Mendelian randomization (MR) for over 43,643 immune system and BBB-related biomarkers and identified 126 potential causal risk factors for dementias. A phenome-wide analysis using MR-based polygenic risk score in FinnGen study (N=339,233) for these risk factors revealed a common genetic background for dementias and autoimmune diseases which was supported by further HLA analyses. Pathway analyses linked the 126 proteins to amyloid-β, tau and α-synuclein pathways, increased inflammatory responses, and altered self-tolerance mechanisms. In inverse-probability-weighted analyses simulating randomized controlled drug trials in observational data, anti-inflammatory and immunosuppressive medications were associated with reduced dementia risk (p<0.01 for methotrexate and TNF-α inhibitors). These converging results from different research lines suggest that autoimmunity is a modifiable component in diseases causing dementia.
Cross-kingdom metagenomic profiling of Lake Hillier reveals pigment-rich polyextremophiles and wide-ranging metabolic adaptations
Authors: Sierra Maria A. , Ryon Krista A. , Tierney Braden T. , Foox Jonathan , Bhattacharya Chandrima , Afshin Evan , Butler Daniel , Green Stefan J. , Thomas W. Kelley , Ramsdell Jordan , Bivens Nathan J. , McGrath Ken , Mason Christopher E. , Tighe Scott W. 
Published: February 2022

AbstractBackground Lake Hillier is a hypersaline lake known for its distinctive bright pink color. The cause of this phenomenon in other hypersaline sites has been attributed to halophiles, Dunaliella, and Salinibacter, however, a systematic analysis of the microbial communities, their functional features, and the prevalence of pigment-producing-metabolisms has not been previously studied.Our results are evidence that Lake Hillier is composed of a diverse set of microorganisms including archaea, bacteria, algae, and viruses. Our data indicate a core microbiome in Lake Hillier composed of multiple pigment-producer microbes, many of which are cataloged as polyextremophiles. Additionally, we estimated the diversity of metabolic pathways in the lake and determined that many of these are related to pigment production. We reconstructed complete or partial genomes for 21 discrete bacteria (N = 14) and archaea (N = 7), only 2 of which could be taxonomically annotated to previously observed species.Our findings provide the first metagenomic study to decipher the source of the pink color of Australia’s Lake Hillier. The study of this pink hypersaline environment is evidence of a microbial consortium of pigment producers, a repertoire of polyextremophiles, a core microbiome and potentially novel species.
The Mycobacterium tuberculosis protein O-phosphorylation landscape
Authors: Frando Andrew , Boradia Vishant , Gritsenko Marina , Beltejar Michael-Claude , Day Le , Sherman David R. , Ma Shuyi , Jacobs Jon M. , Grundner Christoph 
Published: February 2022

SUMMARYBacterial phosphosignaling has long been synonymous with the histidine kinases of the two component systems, but many bacteria, including Mycobacterium tuberculosis (Mtb), also code for Ser/Thr protein kinases (STPKs). STPKs are the main phosphosignaling enzymes in eukaryotes, but the full extent of phosphorylation on protein Ser/Thr and Tyr (O-phosphorylation) in bacteria remains unclear. Here, we explored the global signaling capacity of the STPKs in Mtb. We generated STPK loss-and gain-of-function strains and measured the resulting O-phosphorylation and transcriptional changes. This deep phosphoproteome shows that O-phosphorylation in Mtb is an underexplored protein modification that affects >70% of the proteome. The substrate-STPK interactions show an extensive interface with the transcriptional machinery, resulting in regulation of gene expression of ∼30% of Mtb genes. Mtb O-phosphorylation gives rise to an expansive, distributed, and cooperative network of a complexity that has previously only been associated with eukaryotic phosphosignaling networks.
Molecular architecture of the human caveolin-1 complex
Authors: Porta Jason C. , Han Bing , Gulsevin Alican , Chung Jeongmin , Peskova Yelena , Connolly Sarah , Mchaourab Hassane S. , Meiler Jens , Karakas Erkan , Kenworthy Anne K. , Ohi Melanie D. 
Published: February 2022

AbstractMembrane sculpting proteins shape the morphology of cell membranes and facilitate remodeling in response to physiological and environmental cues. Complexes of the monotopic membrane protein caveolin function as essential curvature-generating components of caveolae, flask-shaped invaginations that sense and respond to plasma membrane tension. However, the structural basis for caveolin’s membrane remodeling activity is currently unknown. Here, we show, using cryo-electron microscopy, that the human caveolin-1 complex is composed of 11 protomers organized into a tightly packed disc with a flat membrane-embedded surface. The structural insights suggest a new mechanism for how membrane sculpting proteins interact with membranes and reveal how key regions of caveolin-1, including its scaffolding, oligomerization, and intramembrane domains, contribute to its function.One-Sentence SummaryCryo-electron microscopy reveals that Caveolin-1 oligomerizes into a tightly packed disc with a flat membrane-binding surface.
Minus one frameshifted puromycin N-acetyltransferase is targeted to the nucleolus: sporadic but reproducible chimera formation by a transfected Lc3b construct
Authors: Thekkinghat Arvind A. , Rangarajan Pundi N. 
Published: February 2022

AbstractMap1Lc3b is a protein that has pivotal functions in cellular autophagy. At least three groups in the past decade have reported its presence in the nucleoli of cells, but its functions in that organelle remain unknown. We isolated a few clonal populations of cells stably expressing V5-tagged mouse Lc3b highly enriched in the nucleoli, but the frequency of occurrence of such clones was strikingly low. The phenomenon was readily reproducible, though the protein in the nucleolus puzzlingly had varying molecular masses in different clones but consistently displayed a very strong interaction with the mitochondrial protein C1qbp, which has well-documented functions in the nucleolus. We investigated further and discovered that, in at least one of the clones, Lc3b had formed a chimera with the puromycin resistance gene in the plasmid, plausibly by illegitimate recombination during or after integration of the construct into the cellular genomic DNA. The -1 shifted reading frame of puromycin N-acetyltransferase (pac) can encode a protein that is equally long as the one encoded by the complete pac ORF, but is targeted to the nucleoli due to a drastic shift in the isoelectric point (pI). Notably, this set of events again brings into focus the low threshold often reported for recombination events to occur in eukaryotic cells, the multiple factors influencing them, and calls for increased vigilance in experiments involving DNA transfection and gene targeting.
mRNA 5′ terminal sequences drive 200-fold differences in expression through effects on synthesis, translation and decay
Authors: van den Elzen Antonia M.G. , Watson Maegan J. , Thoreen Carson C. 
Published: February 2022

AbstractmRNA regulatory sequences control gene expression at multiple levels including translation initiation and mRNA decay. The 5′ terminal sequences of mRNAs have unique regulatory potential because of their proximity to key post-transcriptional regulators. Here we have systematically probed the function of 5′ terminal sequences in gene expression in human cells. Using a library of reporter mRNAs initiating with all possible 7-mer sequences at their 5′ ends, we find an unexpected impact on transcription that underlies 200-fold differences in mRNA expression. Library sequences that promote high levels of transcription mirrored those found in native mRNAs and define two basic classes with similarities to classic Initiator (Inr) and TCT core promoter motifs. By comparing transcription, translation and decay rates, we identify sequences that are optimized for both efficient transcription and growth-regulated translation and stability, including variants of terminal oligopyrimidine (TOP) motifs. We further show that 5′ sequences of endogenous mRNAs are enriched for multi-functional TCT/TOP hybrid sequences. Together, our results reveal how 5′ sequences define two general classes of mRNAs with distinct growth-responsive profiles of expression across synthesis, translation and decay.
Refolding of lid subdomain of SARS-CoV-2 nsp14 upon nsp10 interaction releases exonuclease activity
Authors: Czarna Anna , Plewka Jacek , Kresik Leanid , Matsuda Alex , Karim Abdulkarim , Robinson Colin , O’Byrne Sean , Cunningham Fraser , Georgiou Irene , Pachota Magdalena , Popowicz Grzegorz , Wyatt Paul Graham , Dubin Grzegorz , Pyrć Krzysztof 
Published: February 2022

AbstractDuring the RNA replication, coronaviruses require proofreading to maintain the integrity of their large genomes. Nsp14 associates with viral polymerase complex to excise the mismatched nucleotides. Aside from the exonuclease activity, nsp14 methyltransferase domain mediates cap methylation, facilitating translation initiation and protecting viral RNA from recognition by the innate immune sensors. The nsp14 exonuclease activity is modulated by a protein co-factor nsp10. While the nsp10/nsp14 complex structure is available, the mechanistic basis for nsp10 mediated modulation remains unclear in the absence of nsp14 structure. Here we provide a crystal structure of nsp14 in an apo-form. Comparative analysis of the apo- and nsp10 bound structures explain the modulatory role of the co-factor protein. Further, the structure presented in this study rationalizes the recently proposed idea of nsp14/nsp10/nsp16 ternary complex.
CRISPR-mediated correction of skeletal muscle Ca2+handling in a novel DMD patient-derived pluripotent stem cell model
Authors: Morera Cristina , Kim Jihee , Paredes-Redondo Amaia , Nobles Muriel , Rybin Denis , Moccia Robert , Kowala Anna , Meng Jinhong , Garren Seth , Liu Pentao , Morgan Jennifer E , Muntoni Francesco , Christoforou Nicolas , Owens Jane , Tinker Andrew , Lin Yung-Yao 
Published: February 2022

AbstractMutations in thedystrophingene cause the most common and currently incurable Duchenne muscular dystrophy (DMD) characterized by progressive muscle wasting. Although abnormal Ca2+handling is a pathological feature of DMD, mechanisms underlying defective Ca2+homeostasis remain unclear. Here we generate a novel DMD patient-derived pluripotent stem cell (PSC) model of skeletal muscle with an isogenic control using clustered regularly interspaced short palindromic repeat (CRISPR)- mediated precise gene correction. Transcriptome analysis identifies dysregulated gene sets in the absence of dystrophin, including genes involved in Ca2+handling, excitation-contraction coupling and muscle contraction. Specifically, analysis of intracellular Ca2+transients and mathematical modeling of Ca2+dynamics reveal significantly reduced cytosolic Ca2+clearance rates in DMD-PSC derived myotubes. Pharmacological assays demonstrate Ca2+flux in myotubes is determined by both intracellular and extracellular sources. DMD-PSC derived myotubes display significantly reduced velocity of contractility. Compared with a non-isogenic wild type PSC line, these pathophysiological defects could be rescued by CRISPR-mediated precise gene correction. Our study provides new insights into abnormal Ca2+homeostasis in DMD and suggests that Ca2+signaling pathways amenable to pharmacological modulation are potential therapeutic targets. Importantly, we have established a human physiology-relevantin vitromodel enabling rapid pre-clinical testing of potential therapies for DMD.
Intramuscular mRNA BNT162b2 vaccine against SARS-CoV-2 induces robust neutralizing salivary IgA
Authors: Stolovich-Rain Miri , Kumari Sujata , Friedman Ahuva , Kirillov Saveliy , Socol Yakov , Billan Maria , Pal Ritesh Ranjan , Golding Peretz , Oiknine-Djian Esther , Sirhan Salim , Sagie Michal Bejerano , Cohen-Kfir Einav , Elgrably-Weiss Maya , Zhou Bing , Ravins Miriam , Gatt Yair E , Das Kathakali , Zelig Orly , Wiener Reuven , Wolf Dana G , Elinav Hila , Strahilevitz Jacob , Padawer Dan , Baraz Leah , Rouvinski Alexander 
Published: February 2022

AbstractIntramuscularly administered vaccines stimulate robust serum neutralizing antibodies, yet they are often less competent in eliciting sustainable ‘sterilizing immunity’ at the mucosal level. Our study uncovers, strong neutralizing mucosal component (NT50 ≤ 50pM), emanating from intramuscular administration of an mRNA vaccine. We show that saliva of BNT162b2 vaccinees contains temporary IgA targeting the Receptor-Binding-Domain (RBD) of SARS-CoV-2 spike protein and demonstrate that these IgAs are key mediators of potent neutralization. RBD-targeting IgAs were found to associate with the Secretory Component, indicating their bona-fide transcytotic origin and their dimeric tetravalent nature. The mechanistic understanding of the exceptionally high neutralizing activity provided by mucosal IgA, acting at the first line of defence, will advance vaccination design and surveillance principles, pointing to novel treatment approaches, and to new routes of vaccine administration and boosting.Significance statementWe unveiled powerful mucosal neutralization upon BNT162b2 vaccination, mediated by temporary polymeric IgA and explored its longitudinal properties. We present a model, whereby the molecular architecture of polymeric mucosal IgA and its spatial properties are responsible for the outstanding SARS-CoV-2 neutralization potential. We established a methodology for quantitative comparison of immunoreactivity and neutralization for IgG and IgAs in serum and saliva in molar equivalents for standardization in diagnostics, surveillance of protection and for vaccine evaluations.
LncRNA RUS shapes the gene expression program towards neurogenesis
Authors: Schneider Marius F. , Müller Veronika , Müller Stephan A. , Lichtenthaler Stefan F. , Becker Peter B. , Scheuermann Johanna C. 
Published: February 2022

AbstractThe evolution of brain complexity correlates with an increased expression of long, non- coding (lnc) RNAs in neural tissues. Although prominent examples illustrate the potential of lncRNAs to scaffold and target epigenetic regulators to chromatin loci, only few cases have been described to function during brain development. We present a first functional characterization of the lncRNA LINC01322, which we term RUS for ‘RNA upstream of Slitrk3’. The RUS gene is well conserved in mammals by sequence and synteny next to the neurodevelopmental gene Slitrk3. RUS is exclusively expressed in neural cells and its expression increases along with neuronal markers during neuronal differentiation of mouse embryonic cortical neural stem cells. Depletion of RUS locks neuronal precursors in an intermediate state towards neuronal differentiation resulting in arrested cell cycle and increased apoptosis. RUS associates with chromatin in the vicinity of genes involved in neurogenesis, most of which change their expression upon RUS depletion. The identification of a range of epigenetic regulators as specific RUS interactors suggests that the lncRNA may mediate gene activation and repression in a highly context-dependent manner.