bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seroprevalence, waning, and correlates of anti-SARS-CoV-2 IgG antibodies in Tyrol, Austria: Large-scale study of 35,193 blood donors conducted between June 2020 and September 2021
Authors: Siller Anita , Seekircher Lisa , Wachter Gregor A. , Astl Manfred , Tschiderer Lena , Pfeifer Bernhard , Gaber Manfred , Schennach Harald , Willeit Peter 
Published: December 2021

AbstractBackgroundThere is uncertainty about the seroprevalence of anti-SARS-CoV-2 antibodies in the general population of Austria, and about the extent to which antibodies elicited by vaccination or infection wane over time.AimTo estimate seroprevalence, waning, and correlates of anti-SARS-CoV-2 IgG antibodies in the Federal State of Tyrol, Austria.MethodsWe conducted a seroepidemiological study between June 2020 and September 2021, enrolling blood donors aged 18-70 years across Tyrol, Austria (participation rate 84.0%). We analysed serum samples for antibodies against spike or nucleocapsid proteins of SARS-CoV-2 with Abbott SARS-CoV-2 IgG assays.ResultsWe performed 47,363 serological tests among 35,193 individuals (median age 43.1 years [IQR: 29.3-53.7], 45.3% women, 10.0% with prior SARS-CoV-2 infection). Seroprevalence increased from 3.4% (95% CI: 2.8-4.2%) in June 2020 to 82.7% (95% CI: 81.4-83.8%) in September 2021, largely due to vaccination. Anti-spike IgG seroprevalence was 99.6% (99.4-99.7%) among fully vaccinated individuals, 90.4% (88.8-91.7%) among unvaccinated with prior infection, and 11.5% (10.8-12.3%) among unvaccinated without known prior infection. Anti-spike IgG levels were reduced by 44.0% (34.9-51.7%) at 5-6 months compared to 0-3 months after infection. In fully vaccinated individuals, they decreased by 31.7% (29.4-33.9%) per month. In multivariable adjusted analyses, both seropositivity among unvaccinated and antibody levels among fully vaccinated individuals were higher at young age (<25 years), higher with a known prior infection, and lower in current smokers.ConclusionSeroprevalence in Tyrol increased to 82.7% in September 2021, with the bulk of seropositivity stemming from vaccination. Antibody levels substantially and gradually declined after vaccination or infection.
Aberrant paracrine signalling for bone remodelling underlies the mutant histone-driven giant cell tumour of bone
Authors: Cottone Lucia , Ligammari Lorena , Knowles Helen J. , Lee Hang-Mao , Henderson Stephen , Bianco Sara , Davies Christopher , Strauss Sandra , Amary Fernanda , Leite Ana Paula , Tirabosco Roberto , Haendler Kristian , Schultze Joachim L. , Herrero Javier , O’Donnell Paul , Grigoriadis Agamemnon E. , Salomoni Paolo , Flanagan Adrienne M. 
Published: December 2021

AbstractOncohistones represent compelling evidence for a causative role of epigenetic perturbations in cancer. Giant cell tumours of bone (GCTs) are characterised by a mutated histone H3.3 as the sole genetic driver present in bone-forming osteoprogenitor cells but absent from abnormally large bone-resorbing osteoclasts which represent the hallmark of these neoplasms. While these striking features imply a pathogenic interaction between mesenchymal and myelomonocytic lineages during GCT development, the underlying mechanisms remain unknown.We show that the changes in the transcriptome and epigenome in the mesenchymal cells caused by the H3.3-G34W mutation contribute to increase osteoclast recruitment in part via reduced expression of the TGFβ-like soluble factor, SCUBE3. In turn, osteoclasts secrete unregulated amounts of SEMA4D enhancing proliferation of mutated osteoprogenitors and arresting their maturation. These findings provide a mechanism by which GCTs undergo differentiation upon denosumab treatment, a drug that depletes osteoclasts. In contrast, gain of hTERT activity, commonly found in malignant GCT, makes neoplastic cells insensitive to osteoclasts, predicting the unresponsiveness to denosumab.We provide a mechanism for GCT initiation and its response to current treatment, the basis of which is dysfunctional cross-talk between bone-forming and bone-resorbing cells, emphasising the importance of tumor/microenvironment bidirectional interactions in tumorigenesis.
Functional heterogeneity of cell populations increases robustness of pacemaker function in a numerical model of the sinoatrial node tissue
Authors: Maltsev Alexander V. , Stern Michael D. , Lakatta Edward G , Maltsev Victor A. 
Published: December 2021

ABSTRACTEach heartbeat is initiated by specialized pacemaker cells operating within the sinoatrial node (SAN). While individual cells within SAN tissue exhibit substantial heterogeneity of their electrophysiological parameters and Ca cycling, the role of this heterogeneity for cardiac pacemaker function remains mainly unknown. Here we investigated the problem numerically in a 25×25 square grid of coupled-clock Maltsev-Lakatta cell models and tested the hypothesis that functional heterogeneity of cell populations increases robustness of SAN function. The tissue models were populated by cells with different degree of heterogeneity of the two key model parameters of the coupled-clock system, maximum L-type Ca current conductance (gCaL) and sarcoplasmic reticulum Ca pumping rate (Pup). Our simulations showed that in the areas of Pup-gCaL parametric space at the edge of the system stability where action potential (AP) firing was absent or dysrhythmic in tissues populated by identical cells, rhythmic AP generation was rescued in tissues populated by cells with uniformly random distributions of gCaL or Pup (but keeping the same average values). This effect to increase robust AP generation was synergistic with respect to heterogeneity in both gCaL and Pup and was further strengthened by clustering of cells with higher gCaL or Pup. The effect of functional heterogeneity was not due to a simple summation of activity of intrinsically firing cells naturally present in SAN; rather AP firing cells locally and critically interacted with non-firing/dormant cells. When firing cells prevailed, they recruited many dormant cells to fire, strongly enhancing overall SAN function. And vice versa, prevailing dormant cells suppressed AP firing in cells with intrinsic automaticity and halted SAN automaticity.
A miRNAs Based Exploration of promising Biomarkers in Cervical Cancer using Bioinformatic Methods
Authors: Elumalai Elakkiya , Malarvizhi A. , Sri Shyla T. , Aruna devi OM. , Gupta Krishna Kant 
Published: December 2021

AbstractCervical Cancer (CC) is a gynecologic cancer. In this cancer early detection is incredibly tough because most of the patients are not have any specific symptoms that results in suspending the proper identification. In this work, we selected TCGA CESC datasets and miRNA Seq analysis was done. The expression profiles of miRNAs in cervical cancer datasets were investigated using bioinformatics tools. The expression profiles of miRNA in Normal tissue, primary tumor and metastatic samples were analyzed. Based on p-value, principal component analysis and comparative literature survey, we reported 6 over-expressed (5X) miRNA at metastatic stage namely, hsa-mir-363, hsa-mir-429, hsa-mir-141, hsa-mir-93, hsa-mir-203b and hsa-mir-18a. Expression profiles were compared in heatmap. The target genes for the selected miRNAs were investigated for interaction and pathway details. The identification of two hub proteins (PTEN and MYC) in Protein-Protein Interaction Network was followed by pathway analysis. Our results indicate thathsa-mir-363,hsa-mir-429, hsa-mir-141, hsa-mir-93, hsa-mir-203b and hsa-mir-18acould be a potential diagnostic biomarkers for early-stage CESC and serve as prognostic predictors for patients with CESC.
Evolution of synchronous bilateral breast cancers provide insights into interactions between host, tumor and immunity
Authors: Hamy Anne-Sophie , Abecassis Judith , Darrigues Lauren , Laurent Cecile , Zaccarini François , Sadacca Benjamin , Delomenie Myriam , Laas Enora , Mariani Odette , Lam Thanh , Grandal Beatriz , Lae Marick , Bieche Ivan , Vacher Sophie , Pierga Jean-Yves , Brain Etienne , Vallot Celine , Hotton Judicael , Richer Wilfrid , Waterfall Joshua , Reyal Fabien 
Published: December 2021

AbstractSynchronous bilateral breast cancer (sBBC) occurs after both breasts have been affected by the same germline genetics, reproductive life factors and environmental exposures for decades. It represents an opportunity to decipher the complex interplay between host, tumor, immune system and response to neoadjuvant chemotherapy (NAC). On a cohort of 17575 BCs treated between 2005 and 2012, sBBCs (n=404) were associated with less aggressive proliferative patterns and higher rates of luminal breast cancers (BCs) when compared with unilateral BCs (n=17171). The left and right tumors were concordant for the majority of clinical and pathological features. Tumor pairs of concordant BC subtype were more frequent than pairs of discordant BC subtype, with notably a particularly high frequency of pairs of luminal BCs. Intriguingly, both the levels of tumor infiltrating lymphocytes (TILs) and the response to NAC were modified by the subtype of the contralateral tumors. Whole exome sequencing and RNAseq analyses revealed that left and right tumors were independent from a somatic mutation and transcriptomic point of view, while primary tumors (PT) before NAC and specimens with residual disease (RD) after NAC were more closely related. The analysis of the TCR repertoire identified very little overlap between patients, while common clones were shared in bilateral tumors within each patient. After NAC, the TCR repertoire of RD was enriched and expanded with clones edited by the contralateral PT.
Increased persuadability and credulity in people with corpus callosum dysgenesis
Authors: Barnby JM , Dean R. , Burgess H , Kim J , Teunisse A.K. , Mackenzie L , Robinson G , Dayan P , Richards LJ. 
Published: December 2021

AbstractCorpus callosum dysgenesis is one of the most common congenital neurological malformations. Despite being a clear and identifiable structural alteration of the brain’s white matter connectivity, the impact of corpus callosum dysgenesis on cognition and behaviour has remained unclear. Here we build upon past clinical observations in the literature to define the clinical phenotype of corpus callosum dysgenesis better using unadjusted and adjusted group differences compared with a neurotypical sample on a range of social and cognitive measures that have been previously reported to be impacted by a corpus callosum dysgenesis diagnosis. Those with a diagnosis of corpus callosum dysgenesis (n = 22) demonstrated significantly higher persuadability, credulity, and insensitivity to social trickery than neurotypical (n = 86) participants, after controlling for age, sex, education, autistic-like traits, social intelligence, and general cognition. To explore this further, machine learning, utilising a set neurotypical sample for training the normative covariance structure of our psychometric variables, was used to test whether these dimensions possessed the capability to discriminate between a test-set of neurotypical and corpus callosum dysgenesis participants. We found that participants with a diagnosis of corpus callosum dysgenesis were best classed within dimension space along the same axis as persuadability, credulity, and insensitivity to social trickery after controlling for age and sex, with Leave-One-Out-Cross-Validation across 250 training-set permutations providing a mean accuracy of 71.7%. These results have wide- reaching implications for a) the characterisation of corpus callosum dysgenesis, and b) the role of the corpus callosum in social inference.
Clathrin-mediated Endocytosis Facilitates Internalization ofMagnaporthe oryzaeEffectors into Rice Cells
Authors: Oliveira-Garcia Ely , Tamang Tej Man , Park Jungeun , Dalby Melinda , Martin-Urdiroz Magdalena , Herrero Clara Rodriguez , Vu An Hong , Park Sunghun , Talbot Nicholas J. , Valent Barbara 
Published: December 2021

ABSTRACTFungi and oomycetes deliver effectors into living plant cells to suppress defenses and control plant processes needed for infection. Little is known about the mechanism by which these pathogens translocate effector proteins across the plasma membrane into the plant cytoplasm. The blast fungusMagnaporthe oryzaesecretes cytoplasmic effectors into a specialized biotrophic interfacial complex (BIC) before translocation. Here we show that cytoplasmic effectors within BICs are packaged into vesicles that are occasionally observed in the host cytoplasm. Live cell imaging with fluorescently-labeled rice showed that effector vesicles colocalize with plant plasma membrane and with clathrin light chain-1, a marker for clathrin-mediated endocytosis (CME). Inhibition of CME using Virus-Induced Gene Silencing (VIGS) and chemical treatments results in cytoplasmic effectors in swollen BICs lacking vesicles. In contrast, fluorescent marker co-localization, VIGS and chemical inhibitor studies failed to support a major role for clathrin-independent endocytosis in effector vesicle formation. Localization studies of two novel effectors, and of known effectors after CME inhibition, indicate that cytoplasmic effector translocation occurs underneath appressoria before invasive hyphal growth. Taken together, this study provides evidence that cytoplasmic effector translocation is mediated by clathrin-mediated endocytosis in BICs and suggests a role forM. oryzaeeffectors in co-opting plant endocytosis.
Assessment of chimeric antigen receptor T (CAR-T) cytotoxicity by droplet microfluidics in vitro
Authors: Wong Kuan Un , Shi Jingxuan , Li Peng , Wang Haitao , Jia Yanwei , Deng Chuxia , Jang Lianmei , Wong Ada Hang-Heng 
Published: December 2021

AbstractChimeric antigen receptor T (CAR-T) cells are cytotoxic T cells engineered to specifically kill cancer cells expressing specific target receptor(s). Prior CAR-T efficacy tests include CAR expression analysis by qPCR or ELISA, in vitro measurement of interferon-γ (IFNγ) or interleukin-2 (IL-2), and xenograft models. However, the in vitro measurements did not reflect CAR-T cytotoxicity, whereas xenograft models are low throughput and costly. Here we presented a robust in vitro droplet microfluidic assay for CAR-T cytotoxicity assessment. This method not only enabled assessment of CAR-T cytotoxic activity under different fluid viscosity conditions, but also facilitated measurement of CAR-T expansion and dissection of mechanism of action via phenotype analysis in vitro. Furthermore, our data suggested that label-free cytotoxicity analysis is feasible by acquiring data before and after treatment. Hence, this study presented a novel in vitro method for assessment of cellular cytotoxicity that could potentially be applied to any cell-kill-cell experiment with varying solvent composition.
Identifying challenges and opportunities for histone peptides in protein engineering platforms
Authors: Meanor Jenna N , Keung Albert J , Rao Balaji M 
Published: December 2021

AbstractHistone post-translational modifications are small chemical changes to histone protein structure that have cascading effects on diverse cellular functions. Detecting histone modifications and characterizing their binding partners are critical steps in understanding chromatin biochemistry and have been accessed using common reagents such as antibodies, recombinant assays, and FRET based systems. High throughput platforms could accelerate work in this field, and also could be used to engineer de novo histone affinity reagents; yet published studies on their use with histones have been noticeably sparse. Here we describe specific experimental conditions that affect binding specificities of post-translationally modified histones in classic protein engineering platforms and likely explain the relative difficulty with histone targets in these platforms. We also show that manipulating avidity of binding interactions may improve specificity of binding.
Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Enzyme Redesign
Authors: Aggarwal Tushar , Hansen William A. , Hong Jonathan , Ganguly Abir , York Darrin M. , Khare Sagar D. , Izgu Enver Cagri 
Published: December 2021

ABSTRACTDNA polymerases have evolved to feature a highly conserved activity across the tree of life: formation of, without exception, phosphodiester linkages that create the repeating sugarphosphate backbone of DNA. Can this linkage selectivity observed in nature be overcome by design to produce non-natural nucleic acids? Here, we report that structure-guided redesign of an archaeal DNA polymerase (9°N) enables a new polymerase activity that is undetectable in the wild type enzyme: catalyzing the formation of N3’→P5’ phosphoramidate linkages in the presence of 3’-amino-2’,3’-dideoxynucleoside 5’-triphosphate (3’-NH2-ddNTP) building blocks. Replacing a highly conserved metal-binding aspartate in the 9°N active site (Asp-404) with asparagine was key to the emergence of this unnatural enzyme activity. Molecular dynamics simulations provided insights into how a single substitution could enhance the productive positioning of the 3’-amino nucleophile in the active site. Further remodeling of the protein-nucleic acid interface with substitutions in the finger subdomain led to a quadruple-mutant variant (9°N-NRQS) that incorporated 3’-NH2-ddNTPs into a 3’-amino-primer on various DNA templates. This work presents the first example of an active-site substitution of a metal-binding residue that leads to a novel activity in a DNA polymerase, and sheds light on the molecular basis of substrate fidelity and latent promiscuity in enzymes.
VRK1 is required in VRK2-methylated cancers of the nervous system
Authors: So Jonathan , Mabe Nathaniel W. , Englinger Bernhard , Moyer Sydney M. , Trissal Maria C. , Marques Joana G. , Kwon Jason , Shim Brian , Panditharatna Eshini , Jeong Daeun , Mayhew David , Hwang Justin , Stegmaier Kimberly , Filbin Mariella G. , Hahn William C. 
Published: December 2021

AbstractCollateral lethality occurs when loss of one paralog renders cancer cells dependent on the remaining paralog. Combining genome scale CRISPR/Cas9 screens coupled with RNA-sequencing in over 900 cancer cell lines, we found that cancers of nervous system lineage, including adult and pediatric gliomas and neuroblastomas, required the nuclear kinase Vaccinia-Related Kinase 1 (VRK1) for their survival. VRK1 dependency was inversely correlated with expression of its paralog VRK2. VRK2 knockout (KO) sensitized cells to VRK1 suppression, and conversely, VRK2 overexpression increased cell fitness in the setting of VRK1 suppression. DNA methylation of the VRK2 promoter was associated with low VRK2 expression in human neuroblastomas, and adult and pediatric gliomas. Mechanistically, depletion of VRK1 reduced Barrier-to-Autointegration Factor (BAF) phosphorylation during mitosis, resulting in DNA damage and apoptosis. Together, these studies identify VRK1 as a synthetic lethal target in VRK2 promoter-methylated adult and pediatric gliomas and neuroblastomas.Statement of SignificanceWe credential VRK1 as a target in adult and pediatric gliomas, and neuroblastomas with VRK2 promoter methylation. This demonstrates the utility of paralog-driven synthetic lethal interactions for biomarker-linked, targeted therapeutics.
The P2Y2 Nucleotide Receptor Mediates Monocyte Tissue Factor Expression and Endotoxemia Death in Mice
Authors: Peng Qianman , Qian Shenqi , Alqahtani Saud , Panizzi Peter , Shen Jianzhong 
Published: December 2021

AbstractRecently we reported that in human coronary artery endothelial cells, activation of the P2Y2 receptor (P2Y2R) induces up-regulation of tissue factor (TF), a vital initiator of the coagulation cascade. However, others have shown that monocyte TF is more critical than endothelial TF in provoking a pro-thrombotic state. Thus, we aimed to study whether monocytes express the P2Y2R, its role in controlling TF expression, and its relevance in vivo. RT-PCR and receptor activity assays revealed that among the eight P2Y nucleotide receptors, the P2Y2 subtype was selectively and functionally expressed in human monocytic THP-1 cells and primary monocytes. Stimulation of the cells by ATP or UTP dramatically increased TF protein expression, which was abolished by AR-C118925, a selective P2Y2R antagonist, or by siRNA silencing the P2Y2R. In addition, UTP or ATP treatment induced a rapid accumulation of TF mRNA preceded with an increased TF pre-mRNA, indicating enhanced TF gene transcription. In addition, stimulation of the monocyte P2Y2R significantly activated ERK1/2, JNK, p38, and Akt, along with their downstream transcription factors including c-Jun, c-Fos, and ATF-2, whereas blocking these pathways respectively, all significantly suppressed P2Y2R-mediated TF expression. Furthermore, we found that LPS triggered ATP release and TF expression, the latter of which was suppressed by apyrase or P2Y2R blockage. Importantly, P2Y2R-null mice were more resistant than wild-type mice in response to a lethal dose of LPS, accompanied by much less TF expression in bone marrow cells. These findings demonstrate for the first time that the P2Y2R mediates TF expression in human monocytes through mechanisms involving ERK1/2, JNK, p38, and AKT, and that P2Y2R deletion protects the mice from endotoxemia-induced TF expression and death, highlighting monocyte P2Y2R may be a new drug target for the prevention and/or treatment of relevant thrombotic disease.
Comparative analysis of Lysine and Arginine biosynthesis pathway in Deinococcus genomes
Authors: Mahesh Sankar , Sethi Deepa , Priyadarshini Richa , Yennamalli Ragothaman M. 
Published: December 2021

AbstractThe members of the Deinococcaceae family have the ability to survive extreme environmental conditions. Deinococcus species have a complex cell envelope composed of L-ornithine containing peptidoglycan. Anabolism of L-ornithine is intrinsically linked to L-lysine and L-arginine biosynthetic pathways. To understand these two pathways, we analyzed the L-lysine and L-arginine pathways using 23 Deinococcus genomes, including D. indicus. We used BLAST-P based ortholog identification using D. radiodurans’ genes as the query. We identified some BLAST-P hits that shared the same functional annotation. We analyzed three (class I aminotransferase, acetyl-lysine deacetylase, and acetyl glutamate/acetyl aminoadipate kinase) from L-lysine biosynthesis pathway and three (bifunctional ornithine acetyltransferase or N-acetyl glutamate synthase protein, nitric oxide synthase-like protein, and Acetyl-lysine deacetylase) from L-arginine biosynthesis pathway. Two proteins showed certain structural variations. Specifically, [LysW]-lysine hydrolase protein’s sequence and structure level changes indicated changes in oligomeric conformation, which could likely be a result of divergent evolution. And, bifunctional ornithine acetyltransferase or N-acetyl glutamate synthase had its active site pocket positions shifted at the structural level and we hypothesize that it may not perform at the optimal level. Thus, we were able to compare and contrast different Deinococcus species indicating some genes occurring because of divergent evolution.