bluuebunny/crossref_metadata_2025_split huggingface dataset:
DistilProtBert: A distilled protein language model used to distinguish between real proteins and their randomly shuffled counterparts
Authors: Geffen Yaron , Ofran Yanay , Unger Ron 
Published: May 2022

AbstractSummaryRecently, Deep Learning models, initially developed in the field of Natural Language Processing (NLP), were applied successfully to analyze protein sequences. A major drawback of these models is their size in terms of the number of parameters needed to be fitted and the amount of computational resources they require. Recently, “distilled” models using the concept of student and teacher networks have been widely used in NLP. Here, we adapted this concept to the problem of protein sequence analysis, by developing DistilProtBert, a distilled version of the successful ProtBert model. Implementing this approach, we reduced the size of the network and the running time by 50%, and the computational resources needed for pretraining by 98% relative to ProtBert model. Using two published tasks, we showed that the performance of the distilled model approaches that of the full model. We next tested the ability of DistilProtBert to distinguish between real and random protein sequences. The task is highly challenging if the composition is maintained on the level of singlet, doublet and triplet amino acids. Indeed, traditional machine learning algorithms have difficulties with this task. Here, we show that DistilProtBert preforms very well on singlet, doublet, and even triplet-shuffled versions of the human proteome, with AUC of 0.92, 0.91, and 0.87 respectively. Finally, we suggest that by examining the small number of false-positive classifications (i.e., shuffled sequences classified as proteins by DistilProtBert) we may be able to identify de-novo potential natural-like proteins based on random shuffling of amino acid sequences.Availabilityhttps://github.com/yarongef/DistilProtBertContactyaron.geffen@biu.ac.il
Rapid covalent labeling of a GPCR on living cells using a nanobody-epitope tag pair to interrogate receptor pharmacology
Authors: Cabalteja Chino C. , Cheloha Ross W. 
Published: May 2022

AbstractSynthetic molecules that form a covalent bond upon binding to a targeted biomolecule (proximity-induced reactivity) are the subject of intense biomedical interest for the unique pharmacological properties imparted by irreversible binding. However, off-target covalent labeling and the lack of molecules with sufficient specificity limit more widespread applications. We describe the first example of a crosslinking platform that uses a synthetic peptide epitope and a single domain antibody (or nanobody) pair to form a covalent linkage rapidly and specifically. The rate of the crosslinking reaction between peptide and nanobody is faster than most other biocompatible crosslinking reactions, and it can be used to label live cells expressing receptor-nanobody fusions. The rapid kinetics of this system allowed us to probe the consequences on signaling for ligand crosslinking to the A2A-adenosine receptor. Our method may be generally useful to site-specifically link synthetic molecules to receptors on mammalian cell surfaces.
Fin ray branching is defined by TRAP+ osteolytic tubules
Authors: Cardeira-da-Silva João , Bensimon-Brito Anabela , Tarasco Marco , Brandão Ana S. , Rosa Joana , Almeida Paulo J. , Jacinto António , Cancela M. Leonor , Gavaia Paulo J. , Stainier Didier Y. R. , Laizé Vincent 
Published: May 2022

SUMMARYThe shaping of bone structures relies on various cell types and signalling pathways. Here, we use the zebrafish bifurcating fin rays during regeneration to investigate bone patterning. We found that the regenerating fin rays form via two mineralization fronts that undergo an osteoblast-dependent fusion/stitching until the branchpoint, and that bifurcation is not simply the splitting of one unit into two. We identified tartrate-resistant acid phosphatase-positive (TRAP+) osteolytic tubular structures at the branchpoints, here named osteolytic tubules (OLTs). Chemical inhibition of their bone-resorbing activity strongly impairs ray bifurcation, indicating that OLTs counteract the stitching process. Finally, by testing different osteoactive compounds, we show that the position of the branchpoint depends on the balance between bone mineralization and resorption activities. Overall, these findings provide a new perspective on fin ray formation and bifurcation, and reveal a key role for OLTs in defining the proximo-distal position of the branchpoint.Graphical summary
Single-molecule architecture and heterogeneity of human telomeric DNA and chromatin
Authors: Dubocanin Danilo , Sedeno Cortes Adriana E. , Ranchalis Jane , Real Taylor , Mallory Ben , Stergachis Andrew B. 
Published: May 2022

AbstractTelomeres are essential for linear genomes, yet their repetitive DNA content and somatic variability has hindered attempts to delineate their chromatin architectures. We performed single-molecule chromatin fiber sequencing (Fiber-seq) on human cells with a fully resolved genome, enabling nucleotide-precise maps of the genetic and chromatin structure of all telomeres. Telomere fibers are predominantly comprised of three distinct chromatin domains that co-occupy individual DNA molecules – multi- kilobase telomeric caps, highly accessible telomeric-subtelomeric boundary elements, and subtelomeric heterochromatin. Extended G-rich telomere variant repeats (TVRs) punctuate nearly all telomeres, and telomere caps imprecisely bridge these degenerate repeats. Telomeres demonstrate pervasive somatic alterations in length, sequence, and chromatin composition, with TVRs and adjacent CTCF-bound promoters impacting their stability and composition. Our results detail the structure and function of human telomeres.One sentence summaryWe use single-molecule chromatin fiber sequencing to detail the structure and function of human telomeric DNA and chromatin.
Persistent serum protein signatures define an inflammatory subset of long COVID
Authors: Talla Aarthi , Vasaikar Suhas V. , Szeto Gregory Lee , Lemos Maria P. , Czartoski Julie L. , MacMillan Hugh , Moodie Zoe , Cohen Kristen W. , Fleming Lamar B. , Thomson Zachary , Okada Lauren , Becker Lynne A. , Coffey Ernest M. , De Rosa Stephen C. , Newell Evan W. , Skene Peter J. , Li Xiaojun , Bumol Thomas F. , McElrath M. Juliana , Torgerson Troy R. 
Published: May 2022

ABSTRACTLong COVID or post-acute sequelae of SARS-CoV-2 (PASC) is a clinical syndrome featuring diverse symptoms that can persist for months after acute SARS-CoV-2 infection. The etiologies are unknown but may include persistent inflammation, unresolved tissue damage, or delayed clearance of viral protein or RNA. Attempts to classify subsets of PASC by symptoms alone have been unsuccessful. To molecularly define PASC, we evaluated the serum proteome in longitudinal samples from 55 PASC individuals with symptoms lasting ≥60 days after onset of acute infection and compared this to symptomatically recovered SARS-CoV-2 infected and uninfected individuals. We identified subsets of PASC with distinct signatures of persistent inflammation. Type II interferon signaling and canonical NF-κB signaling (particularly associated with TNF), were the most differentially enriched pathways. These findings help to resolve the heterogeneity of PASC, identify patients with molecular evidence of persistent inflammation, and highlight dominant pathways that may have diagnostic or therapeutic relevance.One Sentence SummarySerum proteome profiling identifies subsets of long COVID patients with evidence of persistent inflammation including key immune signaling pathways that may be amenable to therapeutic intervention.
A marine probiotic treatment against the bacterial pathogenVibrio coralliilyticusto improve the performance of Pacific (Crassostrea gigas) and Kumamoto (C. sikamea) oyster larvae
Authors: Madison David , Schubiger Carla , Lunda Spencer , Mueller Ryan S. , Langdon Chris 
Published: May 2022

AbstractOyster larvae reared in hatcheries on the U.S. West coast often experience severeVibrio coralliilyticus-related mortalities early in their development. Current treatment options for these molluscs are either not available or feasible; however, for decades, probiotics have been successfully used in finfish and crustacean shellfish culture. Consequently, the objectives of this work were to 1) isolate marine bacteria from oysters and evaluate their protective activity againstVibrio coralliilyticusinfection of Pacific oyster (Crassostrea gigas) larvae, and 2) to determine the long-term effects of probiotic additions on growth and metamorphosis of larval Pacific and Kumamoto oysters (C. sikamea). A combination of three probiotic strains applied once 24 hours post-fertilization was more effective in improving survival of larvalC. gigasexposed to lethal concentrations ofV. coralliilyticusstrain RE22, compared with separate additions of individual probiotics. In addition, a single application of the probiotic combination to one-day-old larvae increased the larval metamorphosis success ofC. sikameaand both the Midori and Myiagi stocks ofC. gigas. These results suggest that probiotics are effective at preventing bacterial infections and can significantly improve performance of oyster larvae, using a single application early in their development.Highlights• A combination of marine bacteria improved survival of Pacific oyster larvae exposed to virulentV. coralliilyticus.• Metamorphosis was increased after adding a single dose of probiotics to one-day-old larvae.• Repetitive dosing after each water change was not superior to a single dose one day post egg-fertilization.• A single dose of the probiotic combination resulted in larger size on day 12.
SIRT3 deficiency decreases oxidative-metabolism capacity but increases lifespan under caloric restriction
Authors: Dhillon Rashpal S , Qin Yiming (Amy) , van Ginkel Paul R , Fu Vivian X , Vann James M , Lawton Alexis J , Green Cara L , Manchado-Gobatto Fúlvia B , Gobatto Claudio A , Lamming Dudley W , Prolla Tomas A , Denu John M 
Published: May 2022

SummaryMitochondrial NAD+-dependent protein deacetylase Sirtuin3 (SIRT3) has been proposed to mediate calorie restriction (CR)-dependent metabolic regulation and lifespan extension. Here, we investigated the role of SIRT3 in CR-mediated longevity, mitochondrial function, and aerobic fitness. We report that SIRT3 is required for whole-body aerobic capacity but is dispensable for CR-dependent lifespan extension. Under CR, loss of SIRT3 (Sirt3-/-) yielded a longer overall and maximum lifespan as compared to Sirt3+/+ mice. This unexpected lifespan extension was associated with altered mitochondrial protein acetylation in oxidative metabolic pathways, reduced mitochondrial respiration, and reduced aerobic exercise capacity. Also, Sirt3-/- CR mice exhibit lower physical activity and favor fatty acid oxidation during the postprandial period, leading to a pseudo-fasting condition that extends the fasting period. This study shows uncoupling of lifespan and healthspan parameters (aerobic fitness and spontaneous activity), and provides new insights into SIRT3 function in CR adaptation, fuel utilization, and aging.
Cellular And Molecular Effects Of Understudied Kinase Pregnancy-Upregulated Non-Ubiquitous Calcium-Calmodulin Dependent Kinase (PNCK) In Renal Cell Carcinoma
Authors: Essegian Derek J. , Chavez Valery , Bustamante Floritza , Schürer Stephan C. , Merchan Jaime R. 
Published: May 2022

ABSTRACTRenal Cell Carcinoma (RCC) is a uniformly fatal disease when advanced. While immunotherapy and tyrosine kinase inhibitor-based combinations are associated with improved progression-free and overall survival, the majority of patients eventually develop treatment resistance and succumb to progressive, refractory disease. This underscores the urgent need to identify novel, non-canonical RCC targets for drug development. Through a comprehensive pan-cancer, pan-kinome analysis of the Cancer Genome Atlas (TCGA), the understudied kinase, pregnancy upregulated non-ubiquitous calcium-calmodulin dependent kinase (PNCK) was identified as the most differentially overexpressed kinase in RCC. PNCK mRNA was significantly overexpressed in RCC tissues compared to adjacent normal tissue, and its overexpression correlated with tumor T-stage grade and poor disease specific survival in both clear cell and papillary RCCs. PNCK overexpression in VHL mutant and VHL wild type RCC cell lines was associated with increased CREB phosphorylation, as well as increased cell proliferation and cell cycle progression. PNCK down-regulation, conversely, was associated with inhibition of CREB phosphorylation, decreased cell proliferation, cell cycle arrest and increased apoptosis, with differential effects observed between VHL mutant and VHL wild type cell lines. Pathway analyses in PNCK knockdown cells showed significant down regulation of hypoxia and angiogenesis pathways, as well as modulation of pathways promoting cell cycle arrest and apoptosis. The above results demonstrate for the first time the biological role of PNCK, an understudied kinase, in renal cell carcinoma and validate PNCK as a potential novel target for drug development in this fatal disease.
A requirement for Krüppel-Like Factor-4 in the maintenance of endothelial cell quiescence
Authors: Mastej Victoria , Axen Cassondra , Wary Anita , Minshall Richard D. , Wary Kishore K. 
Published: May 2022

AbstractRationale and GoalEndothelial cells (ECs) are quiescent and critical for maintaining homeostatic functions of the mature vascular system, while disruption of quiescence is at the heart of endothelial to mesenchymal transition (EndMT) and tumor angiogenesis. Here, we addressed the hypothesis that KLF4 maintains the EC quiescence.Methods and ResultsIn ECs, KLF4 bound to KLF2, and the KLF4-transctivation domain (TAD) interacted directly with KLF2. KLF4-depletion increased KLF2 expression, accompanied by phosphorylation of SMAD3, increased expression of alpha-smooth muscle actin (αSMA), VCAM-1, TGF-β1 and ACE2, but decreased VE-cadherin expression. In the absence of Klf4, Klf2 bound to the Klf2-promoter/enhancer region and autoregulated its own expression. Loss of EC-Klf4 in RosamT/mG::Klf4fl/fl::Cdh5CreERT2 engineered mice, increased Klf2 levels and these cells underwent EndMT.ConclusionIn quiescent ECs, KLF2 and KLF4 partnered to regulate a combinatorial mechanism. The loss of KLF4 disrupted this combinatorial mechanism, thereby upregulating KLF2 as an adaptive response. However, increased KLF2 expression overdrives for the loss of KLF4, giving rise to an EndMT phenotype.Key PointsAdult endothelial cells (ECs) are quiescent in that these cells are arrested at G0-phase of the cell cycle, but mechanisms of EC quiescence are not well understood.The Krüppel-like factors (KLFs) -2 and -4 are transcriptional regulators, highly expressed in quiescent ECs, however, their roles in this process have not been addressed.Elucidation of the mechanisms of KLF function in quiescent ECs should provide clues to the translational discoveries intended for the treatment of EC-dysfunction, such as endothelial to mesenchymal transition (EndMT) associated with several vascular diseases including tumor angiogenesis.Graphical Abstract
Differentiation of semi-transparent tissue phantom inclusions using optical coherence tomography towards label-free neurography and lymphography
Authors: Qureshi Muhammad Mohsin , Peters Taylor , Allam Nader , Demidov Valentin , Vitkin Alex 
Published: May 2022

AbstractSignificanceLymphatic and peripheral nervous system imaging is of prime importance for monitoring various important pathologic processes including cancer development, metastasis, and response to therapy.AimOptical coherence tomography (OCT) is a promising approach for this imaging task but is challenged by the near-transparent nature of these structures. Our aim is to detect and differentiate semi-transparent materials using OCT texture analysis, towards label-free neurography and lymphography.ApproachWe have recently demonstrated a novel OCT texture analysis-based approach that used speckle statistics to image lymphatics and nerves in-vivo that does not rely on negative contrast. However, these two near-transparent structures could not be differentiated from each other easily in the texture analysis parameter space. Here we perform a rigorous follow-up study to improve upon this differentiation in controlled phantoms mimicking the optical properties of these tissues.ResultsThe results of the three-parameter Rayleigh distribution fit to the OCT images of six types of tissue-mimicking materials varying in transparency and biophysical properties demonstrate clear differences between them, suggesting routes for improved lymphatics-nerves differentiation.ConclusionsWe demonstrate a novel OCT texture analysis based lymphatics-nerves differentiation methodology in tissue-simulating phantoms. Future work will focus on in-vivo lymphangiography and neurography studies of longitudinal treatment monitoring for therapy feedback and optimization.
A single helix repression domain is functional across eukaryotes
Authors: Leydon Alexander R. , Baez Román Ramos , Nemhauser Jennifer L. 
Published: May 2022

AbstractThe corepressor TOPLESS (TPL) and its paralogs coordinately regulate a large number of genes critical to plant development and immunity. As in many members of the larger pan-eukaryotic Tup1/TLE/Groucho corepressor family, TPL contains a Lis1 Homology domain (LisH), whose function is not well understood. We have previously found that the LisH in TPL—and specifically the N-terminal 18 amino acid alpha-helical region (TPL-H1) —can act as an autonomous repression domain. We hypothesized that homologous domains across diverse LisH-containing proteins could share the same function. To test that hypothesis, we built a library of H1s that broadly sampled the sequence and evolutionary space of LisH domains, and tested their activity in a synthetic transcriptional repression assay in Saccharomyces cerevisiae. Using this approach, we found that repression activity was highly conserved and likely the ancestral function of this motif. We also identified key residues that contribute to repressive function. We leveraged this new knowledge for two applications. First, we tested the role of mutations found in somatic cancers on repression function in two human LisH-containing proteins. Second, we validated function of many of our repression domains in plants, confirming that these sequences should be of use to synthetic biology applications across eukaryotes.
Orphan C/D box snoRNAs modulate fear-related memory processes in mice
Authors: Leighton Laura J. , Zhao Qiongyi , Marshall Paul R. , Madugalle Sachithrani U. , Chan Angelo H. C. , Musgrove Mason R. B. , Ren Haobin , Periyakaruppiah Ambika , Edson Janette , Wei Wei , Li Xiang , Spitale Robert C. , Bredy Timothy W. 
Published: May 2022

AbstractC/D box small nucleolar RNAs (snoRNAs) comprise a class of small noncoding RNAs with important regulatory effects on cellular RNA function. Although it is well established that snoRNAs coordinate the post-transcriptional modification of pre-ribosomal and small nuclear RNAs by 2’-O-methylation, which leads to enhanced RNA stability, whether they are necessary for memory-related processes remains relatively unexplored. Using targeted sequencing, we have identified more than 150 C/D box snoRNAs in the prefrontal cortex of male C57BL/6J mice, 31 of which are differentially expressed in response to fear extinction learning. We have also discovered a subset of snoRNAs, including many orphans, that are enriched in the synaptic compartment, including the orphan snoRNA snord64. An extinction learning-induced increase in synapse-enriched snord64 led to increased 2’-O-methylation within the 3-UTR of the mRNA encoding the ubiquitin ligase RNF146. This effect was blocked by snord64 knockdown and was accompanied by attenuated forgetting of conditioned fear and the enhanced retrieval of fear extinction memory. Localized activity of orphan snoRNAs therefore represents a novel mechanism associated with fear-related learning and memory.Significance statementWe have discovered a population of experience-dependent small nucleolar RNAs (snoRNAs), and found that several of these are recruited to the synaptic compartment in response to fear extinction learning. In particular, the orphan snoRNA, snord64, drives the methylation of the mRNA encoding the ubiquitin ligase, RNF146, with a reduction in snord64 attenuating forgetting of conditioned fear and enhancing the retrieval of fear extinction memory. This study reveals a new mechanism of gene regulation associated with fear-related memory that involves the activity of synapse-enriched snoRNAs.
Delayed antigen-specific CD4+ T-cell induction correlates with impaired immune responses to SARS-COV-2 mRNA vaccination in the elderly
Authors: Jo Norihide , Hidaka Yu , Kikuchi Osamu , Fukahori Masaru , Sawada Takeshi , Aoki Masahiko , Yamamoto Masaki , Nagao Miki , Morita Satoshi , Nakajima Takako E , Muto Manabu , Hamazaki Yoko 
Published: May 2022

AbstractDespite the clinical efficacy of coronavirus disease 2019 mRNA vaccines, the elderly demonstrate lower IgG levels and neutralizing titers and a higher risk of severe diseases. CD4+ T cells play a central role in regulating antigen-specific antibody and CD8+ T-cell responses; however, because their composition and functionality change significantly with age, relationships between age-associated defects in T cells and the immunogenicity of or reactogenicity to mRNA vaccines are unclear. Using a vaccine cohort (n = 216), we found that the elderly (aged ≥65 years) showed delayed induction and early contraction of vaccine-specific CD4+ T cells, and that the compromised C–X–C motif chemokine receptor 3+ circulating T follicular helper cell response after the first dose was associated with the lower IgG levels. Additionally, the elderly experienced significantly fewer systemic adverse effects (AEs) after the second dose, with those exhibiting few AEs showing lower cytokine+ CD4+ T cells after the first dose and lower antibody levels after the second dose. Furthermore, T helper 1 cells in the elderly expressed higher levels of programmed cell death protein-1, a negative regulator of the T-cell response, which was associated with less production of vaccine-specific CD4+ T cells and impaired CD8+ T-cell expansion. Thus, efficient induction of vaccine-specific effector/memory CD4+ T cells after the first dose may trigger robust cytokine production after the second dose, leading to effective vaccine responses and higher systemic reactogenicity. These results suggested that an enhanced CD4+ T-cell response after the first dose is key to improved vaccination efficacy in the elderly.One Sentence SummaryWe compared immunogenicity and reactogenicity to COVID-19 mRNA vaccine in 107 adults (aged <65 years) and 109 elderly (aged ≥65) individuals.