bluuebunny/crossref_metadata_2025_split huggingface dataset:
Retinal microglial cells increase expression and release of IL-1β when exposed to ATP
Authors: Campagno Keith E. , Lu Wennan , Sripinun Puttipong , Albalawi Farraj , Cenaj Aurora , Mitchell Claire H. 
Published: June 2024

AbstractCytokine IL-1β is an early component of inflammatory cascades, with both priming and activation steps required before IL-1β release. Here, the P2X7 receptor (P2X7R) for ATP was shown to both prime and release IL-1β from retinal microglial cells. Isolated retinal microglial cells increased expression ofIl1bwhen stimulated with endogenous receptor agonist extracellular ATP; ATP also rapidly downregulated expression of microglial markersTmem119andCd206.Changes to all three genes were reduced by specific P2X7R antagonist A839977, implicating the P2X7R. Microglial cells expressed the P2X7R on ramifications and responded to receptor agonist BzATP with robust and rapid rises in intracellular Ca2+. BzATP increased expression of IL-1β protein colocalizing with CX3CR1-GFP in retinal wholemounts consistent with microglial cells. ATP also triggered release of IL-1β from isolated retinal microglia into the bath; release was inhibited by A839977 and induced by BzATP, supporting a role for the P2X7R in release as well as priming. The IL-1β release triggered by ATP was substantially greater from microglial cells compared to astrocytes from the optic nerve head region.Il1bexpression was increased by a transient rise in intraocular pressure andIl1blevels remained elevated 10 days after a single IOP elevation. In summary, this study suggests the P2X7 receptor can both prime IL-1β levels in microglial cells and trigger its release. The P2Y12R was previously identified as a chemoattractant for retinal microglia, suggesting the recruitment of the cells towards the source of released extracellular ATP could position microglia for P2X7R receptor, enabling both priming and release of IL-1β.
Modification of regulatory tyrosines biases human Hsp90α for interaction with cochaperones and clients
Authors: Huo Yuantao , Karnawat Rishabh , Liu Lixia , Knieß Robert A. , Gross Maike , Chen Xuemei , Mayer Matthias P. 
Published: June 2024

AbstractThe highly conserved Hsp90 chaperones control stability and activity of many essential signaling and regulatory proteins including many protein kinases, E3 ligases and transcription factors. Thereby, Hsp90s couple cellular homeostasis of the proteome to cell fate decisions. High-throughput mass spectrometry revealed 178 and 169 posttranslational modifications (PTMs) for human cytosolic Hsp90α and Hsp90β, but for only a few of the modifications the physiological consequences are investigated in some detail. In this study, we explored the suitability of the yeast model system for the identification of key regulatory residues in human Hsp90α. Replacement of three tyrosine residues known to be phosphorylated by phosphomimetic glutamate and by non-phosphorylatable phenylalanine individually and in combination influenced yeast growth and the maturation of 7 different Hsp90 clients in distinct ways. Furthermore, wild-type and mutant Hsp90 differed in their ability to stabilize known clients when expressed in HepG2HSP90AA1−/−cells. The purified mutant proteins differed in their interaction with the cochaperones Aha1, Cdc37, Hop and p23 and in their support of the maturation of glucocorticoid receptor ligand binding domainin vitro.In vivoandin vitrodata correspond well to each other confirming that the yeast system is suitable for the identification of key regulatory sites in human Hsp90s. Our findings indicate that even closely related clients are affected differently by the amino acid replacements in the investigated positions, suggesting that PTMs could bias Hsp90’s client specificity.
Cap-related modifications of RNA regulate binding to IFIT proteins
Authors: Geng Jingping , Chrabaszczewska Magdalena , Kurpiejewski Karol , Stankiewicz-Drogon Anna , Jankowska-Anyszka Marzena , Darzynkiewicz Edward , Grzela Renata 
Published: June 2024

AbstractAll cells in our body are equipped with receptors to recognize pathogens and trigger a rapid defense response. As a result, foreign molecules are blocked and cells are alerted to the danger. Among the many molecules produced in response to viral infection are interferon-induced proteins with tetratricopeptide repeats (IFITs). Their role is to recognize foreign mRNA and eliminate it from the translational pool of transcripts. In the present study, we used biophysical methods to characterize the interactions between IFIT1 protein and its partners IFIT2 and IFIT3. IFIT1 interacts with IFIT3 with nanomolar binding affinity, which did not change significantly in the presence of the preformed IFIT2/3 complex. The interactions between IFIT2 and IFIT3 and IFIT1 and IFIT2 were one order of magnitude weaker. We also present kinetic data of the interactions between the IFIT protein complex and short RNA bearing various modifications at the 5’ end. We show kinetic parameters for interaction between IFIT complex and RNA with m6Ammodification. The results show that the cap adjacent m6Ammodification is a stronger signature than cap1 alone. It blocks the formation of a complex between IFIT proteins and m7Gpppm6Am-RNA much more effectively than other cap modifications. In contrast, m6A in the 5’UTR is not recognized by IFIT proteins and does not contribute to translation repression by IFIT proteins. The data obtained are important for understanding the regulation of expression of genetic information. They indicate that 2’-Oand m6Ammodifications modulate the availability of mRNA molecules for proteins of innate immune response.
Non-Human Recognition of Orthography: How is it implemented and how does it differ from Human orthographic processing
Authors: Gagl Benjamin , Weyers Ivonne , Eisenhauer Susanne , Fiebach Christian J. , Colombo Michael , Scarf Damian , Ziegler Johannes C. , Grainger Jonathan , Güntürkün Onur , Mueller Jutta L. 
Published: June 2024

The ability to robustly recognize strings of letters, a cornerstone of reading, was observed in Baboons and Pigeons despite their lack of phonological and semantic knowledge. Here, we apply a comparative modeling approach to investigate the neuro-cognitive basis of Human, Baboon, and Pigeon orthographic decision behavior, addressing whether phylogenetic relatedness entails similar underlying neuro-cognitive phenotypes. We use the highly transparent Speechless Reader Model (SLR), which assumes letter string recognition based on widely accepted computational principles of predictive coding so that orthographic decisions rely on a prediction error signal emerging from multiple, hierarchically ordered representational levels, i.e., low-level visual, letter, or letter sequence representations. We investigate which representations species use during successful orthographic decision-making. We introduce multiple SLR variants, each including one or multiple prediction error representations, and compare the simulations of each SLR variant to the orthographic decisions from individuals of three species after learning letter strings without meaning. Humans predominantly relied on letter-sequence-level representations, resulting in the highest task performance in behavior and model simulations. Baboons also relied on sequence-based representations but in combination with pixel- and letter-level representations. In contrast, all Pigeons relied on pixel-level representations, partly in combination with letter- and letter-sequence-level representations. These findings suggest that orthographic representations utilized in orthographic decisions reflect the phylogenetic distance between species: Humans and Baboons use more similar representations compared to Pigeons. Overall, the description of orthographic decisions based on a small set of representations and computations was highly successful in describing behavior, even for Humans who mastered reading in its entirety.Significance StatementImagine being able to read without ever learning the alphabet. Research has shown that baboons and pigeons can exhibit reading-like behavior, suggesting shared processes across the species involved. To increase our understanding of the similarities and differences between humans and animals in reading-like behavior, we use a computational model to uncover the underlying processes that enable humans, baboons, and pigeons to perform these tasks. We found that humans and baboons rely on similar processes, focusing on information related to letters and letter sequences. In contrast, pigeons rely more heavily on visual cues. This discovery sheds light on the evolution of processes underlying reading and reading-like behavior, indicating that the lower the evolutionary distance between species, the more similar processes are involved.
Adhesive interactions within microbial consortia can be differentiated at the single-cell level through expansion microscopy
Authors: Dong Pu-Ting , Shi Wenyuan , He Xuesong , Borisy Gary G. 
Published: June 2024

SignificanceA single-cell understanding of microbe-microbe interactions is critical for unraveling the organization and dynamics of microbial communities. Through an unconventional application of expansion microscopy, we oppose the adhesive force holding microbes together by an expansion force pulling them apart, resulting in microbial separation dependent on the strength of microbial adhesion. Our new approach establishes a proof-of-principle for differentiating adhesive interactions within microbial consortia at the single-cell level.AbstractInvestigating microbe-microbe interactions at the single-cell level is critical to unraveling the ecology and dynamics of microbial communities. In many situations, microbes assemble themselves into densely packed multi-species biofilms. The density and complexity pose acute difficulties for visualizing individual cells and analyzing their interactions. Here, we address this problem through an unconventional application of expansion microscopy, which allows for the ‘decrowding’ of individual bacterial cells within a multispecies community. Expansion microscopy generally has been carried out under isotropic expansion conditions and used as a resolution-enhancing method. In our variation of expansion microscopy, we carry out expansion under heterotropic conditions; that is, we expand the space between bacterial cells but not the space within individual cells. The separation of individual bacterial cells from each other reflects the competition between the expansion force pulling them apart and the adhesion force holding them together. We employed heterotropic expansion microscopy to study the relative strength of adhesion in model biofilm communities. These included mono and dual-speciesStreptococcusbiofilms, and a three-species synthetic community (Fusobacterium nucleatum,Streptococcus mutans, andStreptococcus sanguinis) under conditions that facilitated interspecies coaggregation. Using adhesion mutants, we investigated the interplay betweenF. nucleatumouter membrane protein RadD and differentStreptococcusspecies. We also examined theSchaalia-TM7epibiont association. Quantitative proximity analysis was used to evaluate the separation of individual microbial members. Our study demonstrates that heterotropic expansion microscopy can ‘decrowd’ dense biofilm communities, improve visualization of individual bacterial members, and enable analysis of microbe-microbe adhesive interactions at the single-cell level.
Genomic evidence ofEscherichia coligut population diversity translocation in leukemia patients
Authors: Marin Julie , Walewski Violaine , Braun Thorsten , Dziri Samira , Magnan Mélanie , Denamur Erick , Carbonnelle Etienne , Bridier-Nahmias Antoine 
Published: June 2024

AbstractEscherichia coli, a commensal species of the human gut, is an opportunistic pathogen which can reach extra-intestinal compartments, including the bloodstream and the bladder, among others. In non-immunosuppressed patients, purifying or neutral evolution ofE. colipopulations has been reported in the gut. Conversely, it has been suggested that when migrating to extra-intestinal compartments,E. coligenomes undergo diversifying selection as supported by strong evidence for adaptation. The level of genomic polymorphism and the size of the populations translocating from gut to extra-intestinal compartments is largely unknown.To gain insights in the pathophysiology of these translocations, we investigated the level of polymorphism and the evolutionary forces acting on the genomes of 77E. coliisolated from various compartments in three immunosuppressed patients. Each patient had a unique strain which was a mutator in one case. In all instances, we observed that translocation encompasses the majority of the genomic diversity present in the gut. The same signature of selection, whether purifying or diversifying, and as anticipated, neutral for mutator isolates, was observed in both the gut and bloodstream. Additionally, we found a limited number of non-specific mutations among compartments for non-mutator isolates. In all cases, urine isolates were dominated by neutral selection. These findings indicate that substantial proportions of populations are undergoing translocation and that they present a complex compartment-specific pattern of selection at the patient level.ImportanceIt has been suggested that intra and extra-intestinal compartments differentially constrain the evolution ofE. colistrains. Whether host particular conditions, such as immunosuppression, could affect the strain evolutionary trajectories remain understudied. We found that, in immunosuppressed patients, large fractions ofE. coligut populations are translocating with variable modifications of the signature of selection for commensal and pathogenic isolates according to the compartment and/or the patient. Such multiple site sampling should be performed in large cohorts of patients to get a better understanding ofE. coliextra-intestinal diseases.
The Conserved Transcription Factor Krüppel Regulates the Survival and Neurogenesis of Mushroom Body Neuroblasts inDrosophilaAdult Brains
Authors: Man Jin , Shu Xian , Shi Haoer , Xia Xue , Abula Yusanjiang , Kimata Yuu 
Published: June 2024

SummaryIn various metazoans, includingDrosophilaand humans, neural progenitors exit the cell cycle and are eliminated by the end of development, limiting adult neurogenesis. We demonstrate that inDrosophila,the conserved transcription factorKrüppel(Kr) controls neurogenic capacity of a specific subset of neuroblasts that forms the mushroom body (MBNBs), analogous to the mammalian hippocampus. TheIrregular facetmutation, which altersKrexpression, and neuroblast-specific Kr depletion allow MBNBs, but not other neuroblasts, to persist beyond development and generate neurons in adult brains. Persisting MBNBs express Imp, an RNA-binding protein that promotes neuroblast proliferation and survival. Our results underscore a critical role for Kr in the developmental control of a specific progenitor population, uncovering a novel mechanism controlling adult neurogenesis.
Bridging the Sequencing Gap: N501Y SNP RT-qPCR Assay Detects First SARS-CoV-2 Beta Variant in the Philippines
Authors: Bado Samantha Louise P. , Galap Niquitta B. , Manalo Joanna Ina G. , Onza Othoniel Jan T. , Pelingon Mary Rose B. , Parayray Joy Mariette L. , Palciso Justine Mae , Tomas Karen Iana C. , Abulencia Miguel Francisco B. , Polotan Francisco Gerardo M. , Dancel Lei Lanna M. , Nicolasora Amalea Dulcene 
Published: June 2024

ABSTRACTWhole genome sequencing (WGS) is used extensively in identifying SARS-CoV-2 variants. However, this method requires stringent sample acceptance criteria, long turn-around time (TAT), expensive processing and maintenance costs, and highly skilled staff. Although sequencing offers comprehensive pathogen insights, a cost-effective tool with faster TAT is beneficial in detecting SARS-CoV-2 variants of concern (VOCs). Here, we used a single nucleotide polymorphism (SNP) RT-qPCR assay to detect the N501Y mutation in banked SARS-CoV-2 RNA extracts (N=452) collected from December 2020 to April 2021. Of the SARS-CoV-2 positives (n=367), 22% carried the N501Y mutation and were classified as probable VOCs. This includes a sample that was confirmed to belong to the Beta lineage and was collected earlier than the first reported Beta variant in the country suggesting an earlier emergence of the variant. Validation experiments for the SNP RT-qPCR assay showed a limit of detection (LOD) of 3.01 copies/μL for both N501 and 501Y targets. A 99.35% concordance with partial S gene Sanger sequencing was observed confirming the presence of the N501Y SNP in 83 samples. In conclusion, the optimized SNP RT-qPCR assay serves as an important complementary or alternative tool for detecting probable SARS-CoV-2 variants, ensuring that samples ineligible for WGS are not overlooked. This effectively resolves sequencing gaps, including stringent sample acceptance criteria, extended TAT, and rigorous data analysis. Therefore, embracing this technology provides a rapid, economical, and dependable solution for managing pathogens of public health concern.
Evaluation of population immunity against SARS-CoV-2 variants, EG.5.1, FY.4, BA.2.86, JN.1, and JN.1.4, using samples from two health demographic surveillance systems in Kenya
Authors: Lugano Doreen , Kutima Bernadette , Kimani Makobu , Sigilai Antipa , Gitonga John , Karani Angela , Akech Donald , Karia Boniface , Ziraba Abdhalah K. , Maina Angela , Lambisia Arnold , Omuoyo Donwilliams , Mugo Daisy , Lucinde Ruth , Newman Joseph , Bailey Dalan , Nduati Eunice , Githinji George , Agoti Charles N. , Bejon Philip , Scott J Anthony G , Agweyu Ambrose , Kagucia Wangeci , Warimwe George M , Sande Charles , Ochola-Oyier Lynette I , Nyagwange James 
Published: June 2024

AbstractIncreased immune evasion by emerging and highly mutated SARS-CoV-2 variants is a key challenge to the control of COVID-19. The majority of these mutations mainly target the spike protein, allowing the new variants to escape the immunity previously raised by vaccination and/or infection by earlier variants of SARS-CoV-2. In this study, we investigated the neutralizing capacity of antibodies against emerging variants of interest circulating between May 2023 and March 2024 using sera from representative samples of the Kenyan population. From our genomics data, we identified the most prevalent Kenyan and global variants and performed pseudoviruses neutralization assays with the most recent SARS-CoV-2 variants. Our data show that antibodies from individuals in the general population in Kenya were less effective against the recent prevalent SARS-CoV-2 omicron variants (i.e. EG.5.1, FY.4, BA.2.86, JN.1, and JN.1.4) compared to the ancestral wildtype strain. Although there was increased neutralization following multiple doses of vaccine, antibodies from >40% of the vaccinated individuals did not neutralize the omicron variants, suggesting that individuals were susceptible to infection by these variants.
A proteomic signature of healthspan
Authors: Kuo Chia-Ling , Liu Peiran , Drouard Gabin , Vuoksimaa Eero , Kaprio Jaakko , Ollikainen Miina , Chen Zhiduo , Pilling Luke C. , Atkins Janice L. , Fortinsky Richard H. , Kuchel George A. , Diniz Breno S. 
Published: June 2024

AbstractThe focus of aging research has shifted from increasing lifespan to enhancing healthspan to reduce the time spent living with disability. Despite significant efforts to develop biomarkers of aging, few studies have focused on biomarkers of healthspan. We developed a proteomics-based signature of healthspan (healthspan proteomic score (HPS)) using proteomic data from the Olink Explorer 3072 assay in the UK Biobank Pharma Proteomics Project (53,018 individuals and 2920 proteins). A lower HPS was associated with higher mortality risk and several age-related conditions, such as COPD, diabetes, heart failure, cancer, myocardial infarction, dementia, and stroke. HPS showed superior predictive accuracy for these outcomes compared to other biological age measures. Proteins associated with HPS were enriched in hallmark pathways such as immune response, inflammation, cellular signaling, and metabolic regulation. The external validity was established using the Essential Hypertension Epigenetics study with proteomic data also from the Olink Explorer 3072 and complementary epigenetic data, making it a valuable tool for assessing healthspan and as a potential surrogate marker to complement existing proteomic and epigenetic biological age measures in geroscience-guided studies.SignificanceDespite substantial efforts to develop biomarkers of aging, few studies have focused on biomarkers of healthspan. The challenge lies in the need for long follow-up periods and large sample sizes of healthy individuals to observe aging outcomes. Therefore, developing surrogate biomarkers that can predict healthspan is crucial. We addressed this by developing a proteomics-based signature of healthspan, termed the Healthspan Proteomic Score (HPS), in a healthy cohort. We demonstrated its clinical, predictive, and biological validity in the UK Biobank and Essential Hypertension Epigenetics study, which represents a focused subset of the Finland Twin Cohort. The HPS, serving as a surrogate marker of healthspan, is useful for gauging an individual’s biological health and monitoring the impact of geroscience-guided interventions.
A biosensor-based phage display selection method for automated, high-throughput Nanobody discovery
Authors: De Keyser Phebe , Kalichuk Valentina , Zögg Thomas , Wohlkönig Alexandre , Schenck Stephan , Brunner Janine , Pardon Els , Steyaert Jan 
Published: June 2024

AbstractBiopanning methods to select target-specific Nanobodies®(Nbs) involve presenting the antigen, immobilized on plastic plates or magnetic beads, to Nb libraries displayed on phage. Most routines are operator-dependent, labor-intensive and often material- and time-consuming. Here we validate an improved panning strategy that uses biosensors to present the antigen to phage-displayed Nbs in a well. The use of automated Octet biolayer interferometry sensors (Sartorius) enables high throughput and precise control over each step. By playing with association and dissociation times and buffer composition, one can efficiently decrease the background of aspecific and low-affinity Nbs, reducing the rounds of panning needed for the enrichment of high-affinity binders. Octet panning also enables the use of unpurified target proteins and unpurified phage from a bacterial culture supernatant. Additionally, downscaling to a 384-well format significantly reduces the amount of protein required. Moreover, enrichment of binders can be quantified by monitoring phage binding to the target by interferometry, omitting additional phage titration steps. Routinely, up to three rounds of Octet panning can be performed in only five days to deliver target-specific binders, ready for screening and characterization using the same Octet instrument.Graphical abstract