bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling effects of inter-group contact on links between population size and cultural complexity
Authors: Ben-Oren Yotam , Strassberg Sarah Saxton , Hovers Erella , Kolodny Oren , Creanza Nicole 
Published: September 2022

AbstractHuman populations rely on cultural artifacts and complex cumulative culture for their survival. Populations vary dramatically in the size of their tool repertoires, and the determinants of these cultural repertoire sizes have been the focus of extensive study in recent years. A prominent hypothesis, supported by computational models of cultural evolution, asserts that tool repertoire size increases with population size. However, not all empirical studies seeking to test this hypothesis have found such a correlation; this has led to a contentious and ongoing debate. As a possible resolution to this longstanding controversy, we suggest that accounting for even rare cultural migration events that allow sharing of knowledge between different-sized populations may help explain why a population’s size might not always predict its cultural repertoire size. Using an agent-based model to explore different assumptions about the effects of population size and migration on tool repertoires, we find that connectivity of one population to others, particularly to large populations, may significantly boost its tool repertoire size when population interactions lead to cultural exchange. Thus, two populations of identical size may have drastically different tool repertoire sizes, hinging upon their access to other groups’ knowledge. Intermittent contact between populations boosts cultural repertoire size and still allows for the development of unique tool repertoires that have limited overlap between populations.
Percolate: an exponential family JIVE model to design DNA-based predictors of drug response
Authors: Mourragui Soufiane M.C. , Loog Marco , van Nee Mirrelijn , van de Wiel Mark A , Reinders Marcel J.T. , Wessels Lodewyk F.A. 
Published: September 2022

AbstractMotivationAnti-cancer drugs may elicit resistance or sensitivity through mechanisms which involve several genomic layers. Nevertheless, we have demonstrated that gene expression contains most of the predictive capacity compared to the remaining omic data types. Unfortunately, this comes at a price: gene expression biomarkers are often hard to interpret and show poor robustness.ResultsTo capture the best of both worlds, i.e. the accuracy of gene expression and the robustness of other genomic levels, such as mutations, copy-number or methylation, we developed Percolate, a computational approach which extracts the joint signal between gene expression and the other omic data types. We developed an out-of-sample extension of Percolate which allows predictions on unseen samples without the necessity to recompute the joint signal on all data. We employed Percolate to extract the joint signal between gene expression and either mutations, copy-number or methylation, and used the out-of sample extension to perform response prediction on unseen samples. We showed that the joint signal recapitulates, and sometimes exceeds, the predictive performance achieved with each data type individually. Importantly, molecular signatures created by Percolate do not require gene expression to be evaluated, rendering them suitable to clinical applications where only one data type is available.AvailabilityPercolate is available as a Python 3.7 package and the scripts to reproduce the results are available here.
A new route for integron cassette dissemination among bacterial genomes
Authors: Loot Céline , Millot Gael A. , Richard Egill , Littner Eloi , Vit Claire , Lemoine Frédéric , Cury Jean , Darracq Baptiste , Niault Théophile , Lapaillerie Delphine , Parissi Vincent , Rocha Eduardo PC , Mazel Didier 
Published: September 2022

AbstractIntegrons are genetic elements involved in bacterial adaptation. They can capture, shuffle and express adaptive functions embedded in cassettes. These events are governed by the integron integrase through site-specific recombination betweenattCandattIintegron sites. Here, we demonstrated that the integrase can efficiently catalyze insertion of cassettes in bacterial genomes, outside theattsites. We showed that, once inserted in genomes, cassettes can be expressed, if located near bacterial promoters, and can be excised at the insertion point and even outside, inducing chromosomal modifications in the latter case. Analysis of more than 5 × 105independent insertion events revealed a very large genomic insertion landscape with recombination sites greatly different, in terms of sequence and structure, from classicalattsites. We named these new sitesattG. These results unveil a new efficient route for dissemination of adaptive functions and expand the role of integrons in bacterial evolution.
Quantifying coexistence concentrations in multi-component phase-separating systems using analytical HPLC
Authors: Bremer Anne , Posey Ammon E. , Borgia Madeleine B. , Borcherds Wade M. , Farag Mina , Pappu Rohit V. , Mittag Tanja 
Published: September 2022

AbstractOver the last decade, evidence has accumulated to suggest that numerous instances of cellular compartmentalization can be explained by the phenomenon of phase separation. This is a process by which a macromolecular solution separates spontaneously into dense and dilute coexisting phases. Semi-quantitative,in vitroapproaches for measuring phase boundaries have proven very useful in determining some key features of biomolecular condensates, but these methods often lack the precision necessary for generating quantitative models. Therefore, there is a clear need for techniques that allow quantitation of coexisting dilute and dense phase concentrations of phase-separating biomolecules, especially in systems with more than one type of macromolecule. Here we report the design and deployment of analytical High-Performance Liquid Chromatography (HPLC) forin vitroseparation and quantification of distinct biomolecules that allows us to measure dilute and dense phase concentrations needed to reconstruct coexistence curves in multicomponent mixtures. This approach is label-free, detects lower amounts of material than is accessible with classic UV-spectrophotometers, is applicable to a broad range of macromolecules of interest, is a semi-high-throughput technique, and if needed, the macromolecules can be recovered for further use. The approach promises to provide quantitative insights into the balance of homotypic and heterotypic interactions in multicomponent phase-separating systems.
Global phylogenomic assessment of Leptoseris and Agaricia reveals substantial undescribed diversity at mesophotic depths
Authors: Gijsbers JC , Englebert N , Prata KE , Pichon M , Dinesen Z , Brunner R , Eyal G , González-Zapata FL , Kahng SE , Latijnhouwers KRW , Muir P , Radice VZ , Sánchez JA , Vermeij MJA , Hoegh-Guldberg O , Jacobs SJ , Bongaerts P 
Published: September 2022

ABSTRACTMesophotic coral communities are increasingly gaining attention for the unique biological species they host, exemplified by the numerous mesophotic fish species that continue to be discovered. In contrast, many of the photosynthetic scleractinian corals observed at mesophotic depths are assumed to be depth-generalists, with very few species characterised as mesophotic-specialists. This presumed lack of a specialised community remains largely untested, as phylogenetic studies rarely include mesophotic samples and have long suffered from resolution issues associated with traditional sequence markers. Here, we used reduced-representation genome sequencing to provide a phylogenomic assessment of the two dominant mesophotic genera of plating corals in the Indo-Pacific and Western Atlantic, respectively, Leptoseris and Agaricia. While these genome-wide phylogenies broadly corroborated the morphological taxonomy, they also exposed substantial undescribed diversity (at least 24 molecular clades across the 8 species), including deep divergences within genera and current taxonomic species. Five of the eight focal species consisted of at least two sympatrically-occurring, genetically distinct clades, which were consistently detected across different methods. The repeated observation of genetically divergent clades associated with mesophotic depths highlights that there are many more mesophotic-specialist coral species than currently acknowledged, and that an urgent assessment of this largely unstudied biological diversity is warranted.
MAPK11 (p38β) is a major determinant of cellular radiosensitivity by enhancing IR-associated senescence
Authors: Fernández-Aroca DM , García-Flores N , Frost S , Jiménez-Suarez J , Rodríguez-González A , Fernández-Aroca P , Sabater S , Andrés I , Garnés-García C , Belandia B , Cimas FJ , Villar D , Ruiz-Hidalgo MJ , Sánchez-Prieto R 
Published: September 2022

AbstractBackground and purposeMAPKs are among the most relevant signalling pathways involved in coordinating cell responses to different stimuli. This group includes p38MAPKs, constituted by 4 different proteins with a high sequence homology: MAPK14 (p38α), MAPK11 (p38β), MAPK12 (p38γ) and MAPK13 (p38δ). Despite their high similarity, each member shows unique expression patterns and even exclusive functions. Thus, analysing protein-specific functions of MAPK members is necessary to unequivocally uncover the roles of this signalling pathway. Here, we investigate the possible role of MAPK11 in the cell response to ionizing radiation (IR).Materials and methodsWe developed MAPK11/14 knockdown through shRNA and CRISPR interference gene perturbation approaches, and analysed the downstream effects on cell responses to ionizing radiation in A549, HCT-116 and MCF-7 cancer cell lines. Specifically, we assessed IR toxicity by clonogenic assays; DNA damage response activity by immunocytochemistry; apoptosis and cell cycle by flow cytometry (Annexin V and propidium iodide, respectively); DNA repair by comet assay; and senescence induction by both X-Gal staining and gene expression of senescence-associated genes by RT-qPCR.ResultsOur findings demonstrate a critical role of MAPK11 in the cellular response to IR by controlling the associated senescent phenotype, and without observable effects on DDR, apoptosis, cell cycle or DNA damage repair.ConclusionOur results highlight MAPK11 as a novel mediator of the cellular response to ionising radiation through the control exerted onto IR-associated senescence.HighlightsGenetic perturbation of MAPK11, but not MAPK14, promotes radiosensitivity in a panel of tumor cell lines.Abrogation of MAPK11 did not modify DNA damage response, proliferation, apoptosis or cell cycle in response to ionizing radiationMAPK11 controls ionizing radiation-induced senescenceMAPK11 expression could be a novel target and biomarker for radiosensitivity
Virucidal Activity of Potassium Hydroxide Modeling on Tospovirus
Authors: Zumrutdal Emin , Kamberoglu Muharrem Arap , Saglam Havva Nur 
Published: September 2022

ABSTRACTViral agents that cause disease in the respiratory system have led to widespread health problems in the world. The continuation of mutations in these viruses and the lack of an effective treatment agent bring possible public health risks. In this study, the virucidal activity of potassium hydroxide (KOH) was evaluated. The intermolecular interactions of KOH and envelope-structured molecules in enveloped viruses and the virucidal activity of these interactions on Tospovirus, which has the ability to infect, were evaluated.For this study model, the intermolecular interactions of KOH in the lipid bilayer of the virus envelope were evaluated in silico by Doking method. Then, the plant virulence ability of Tospovirus was observed by the direct interaction of KOH with Tospovirus.It was observed that KOH interacted exergonically with the glycerophosphate structure in the envelope structure. It was determined by clinical and laboratory observations that Tospovirus in plants lost its virucidal activity after interaction with KOH.In the light of this information, it was thought that KOH had a virucidal effect in enveloped viruses. It is thought that KOH creates this virucidal activity by KOH-glycerophosphate intermolecular interactions and viral envelope lipid layer hydrolysis.The mucolytic, alkalinizing and possible low-weight immunoglobulin-forming potential of KOH has been demonstrated in previous studies and no pathology was detected in toxicity studies in mice.In the light of this information, optimized KOH inhalation has a very serious potential as a virucidal agent in diseases caused by enveloped viruses in the respiratory system such as Coronavirus, H. influenza.
Modeling bee movement shows how a perceptual masking effect can influence flower discovery, foraging efficiency and pollination
Authors: Morán Ana , Lihoreau Mathieu , Pérez Escudero Alfonso , Gautrais Jacques 
Published: September 2022

AbstractUnderstanding how pollinators move across space is key to understanding plant mating patterns. Bees are typically assumed to search for flowers randomly or using simple movement rules, so that the probability of discovering a flower should primarily depend on its distance to the nest. However, experimental work shows this is not always the case. Here, we explored the influence of flower size and density on their probability of being discovered by bees by developing a movement model of central place foraging bees, based on experimental data collected on bumblebees. Our model produces realistic bee trajectories by taking into account the autocorrelation of the bee’s angular speed, the attraction to the nest, and a gaussian noise. Simulations revealed a « masking effect » that reduces the detection of flowers close to another, which may have critical consequences for pollination and foraging success. At the plant level, flowers distant to the nest were more often visited in low density environments, suggesting lower probabilities of pollination at high densities. At the bee colony level, foragers found more flowers when they were small and at medium densities, suggesting that there is an optimal flower size and density at which collective foraging efficiency is optimized. Our results indicate that the processes of search and discovery of resources are potentially more complex than usually assumed, and question the importance of resource distribution and abundance on plant-pollinator interactions.Author’s summaryUnderstanding how pollinators move in space is key to understanding plant reproduction, which in turn shapes entire ecosystems. Most current models assume simple movement rules that predict that flowers are more likely to be visited—and hence pollinated—the closer they are to the pollinators’ nest. Here we developed an explicit movement model that incorporates realistic features of bumblebees, including their flight characteristics and their tendency to return regularly to the nest, and calibrated it with experimental data collected in naturalistic conditions. This model revealed that the probability to visit a flower does not only depend on its position, but also on the position of other flowers that may mask it from the forager. This masking effect means that pollination efficiency depends on the density and spatial arrangement of flowers around the pollinator’s nest, often in counter-intuitive ways. Taking these effects into account will be key for improving precision pollination and pollinator conservation.
A high-throughput exonuclease assay based on the fluorescent base analog 2-aminopurine
Authors: Botto Margherita M. , Murthy Sudarshan , Lamers Meindert H. 
Published: September 2022

ABSTRACTExonucleases are essential enzymes that remove nucleotides from free DNA ends during DNA replication, DNA repair and telomere maintenance. Due to their essential role, they are potential targets for novel anticancer and antimicrobial drugs but have so far have been little exploited. Here we present a simple and versatile real-time exonuclease assay based on 2-aminopurine, an intrinsically fluorescent nucleotide that is quenched by neighboring bases when embedded in DNA. We show that our assay is applicable to different eukaryotic and bacterial exonucleases acting on both 3’ and 5’ DNA ends, over a wide range of protein activities and suitable for a high throughput inhibitor screening campaign. Using our assay, we discover a novel inhibitor of the Mycobacterium tuberculosis PHP-exonuclease that is part of the replicative DNA polymerase DnaE1. Hence, our novel assay will be a useful tool for high throughput screening for novel exonuclease inhibitors that may interfere with DNA replication or DNA maintenance.
Methamphetamine Self-Administration Differential Effects on Mesolimbic Glutathione Levels, Mitochondrial Respiration and Dopamine Neuron Firing Activity
Authors: Dominguez-Lopez Sergio , Ahn Bumsoo , Sataranatarajan Kavithalakshmi , Ranjit Rojina , Premkumar Pavithra , Van Remmen Holly , Beckstead Michael J. 
Published: September 2022

AbstractAcute and neurotoxic regimens of METH are known to increase reactive oxygen species (ROS), affect redox homeostasis, and lead to cellular damage in dopamine neurons. However, functional changes induced by long-term METH self-administration on mitochondrial respiratory metabolism and redox homeostasis are less known. To fill this gap in our knowledge, we implanted adult mice with a jugular catheter and trained them to nose poke for METH infusions in operant chambers. After completing several weeks of METH self-administration exposure, we collected samples of the ventral striatum (vSTR) and the ventral midbrain (vMB), containing the nucleus accumbens (NAc) and the ventral tegmental area (VTA), respectively. We used HPLC to determine the levels of the ROS scavenger glutathione in its reduced (GSH) and oxidized (GSSG) forms. Then, we used high-resolution respirometry to determine the oxygen consumption rate (OCR) of mitochondrial complexes under several substrates and inhibitors. Finally, we used in vivo single-unit extracellular recordings to assess changes in dopamine neuron firing activity in the VTA. METH self-administration produces a progressive decrease of the GSH pool in vST, which correlates with METH lifetime intake. We observed increased mitochondrial respiration across the two mesolimbic regions, but only vMB OCR correlates with METH lifetime intake. We recorded an increased number of spontaneously active dopamine neurons with decreased firing rate and burst activity in the VTA. METH lifetime intake inversely correlates with firing rate, the percentage of spikes in a burst, and directly correlates with the number of neurons per track. We conclude that METH self-administration progressively decreased the antioxidant pool in sites of higher dopamine release and produced an increased mitochondrial metabolism in the mesolimbic areas, probably derived from the increased number of dopamine neurons actively firing. However, dopamine neuron firing activity is decreased by METH self-administration, reflecting a new basal level of dopamine neurotransmission in response to the prolonged effects of METH on dopamine release and circuitry feedback.
Roles of the 5-HT2C receptor on zebrafish sociality
Authors: de Moura Layana Aquino , Pyterson Maryana Pereira , Pimentel Ana Flávia Nogueira , Araújo Fernanda , de Souza Loanne Valéria Xavier Bruce , Mendes Caio Henrique Moura , Costa Bruna Patrícia Dutra , de Siqueira-Silva Diógenes Henrique , Lima-Maximino Monica , Maximino Caio 
Published: September 2022

AbstractSerotonin (5-HT) receptors have been implicated in social behavior in vertebrates. Zebrafish (Danio rerio) have been increasingly being used behavioral neuroscience to study the neurobiological correlates of behavior, including sociality. Nonetheless, the role of 5-HT2C receptors in different social functions were not yet studied in this species. Zebrafish were treated with the agonist MK-212 (2 mg/kg) or the antagonist RS-102221 (2 mg/kg) and tested in the social interaction and social novelty tests, conditional approach test, or mirror-induced aggressive displays. MK-212 increased preference for an unknown conspecific in the social investigation test, but also increased preference for the known conspecific in the social novelty test; RS-102221, on the other hand, decreased preference in the social investigation test but increased preference for the novel conspecific in the social novelty test. MK-212 also decreased predator inspection in the conditional approach test. While RS-102221 decreased time in the display zone in the mirror-induced aggressive display test, it increased display duration. Overall, these results demonstrate the complex role of 5-HT2C receptors in different social contexts in zebrafish, revealing a participation in social plasticity in vertebrates.
Mining for ions: diagnostic feature detection in MS/MS spectra of post-translationally modified peptides
Authors: Geiszler Daniel J. , Polasky Daniel A. , Yu Fengchao , Nesvizhskii Alexey I. 
Published: September 2022

AbstractPost-translational modifications (PTMs) are an area of great interest in proteomics, with a surge in methods to detect them in recent years. However, PTMs can introduce complexity into proteomics searches by fragmenting in unexpected ways. Detecting post-translational modifications in mass spectrometry-based proteomics traditionally relies on identifying ions shifted by the masses of the modifications. This presents challenges for many PTMs. Labile PTMs lose part of their modification mass during fragmentation, rendering shifted fragment ions unidentifiable, and isobaric PTMs are indistinguishable by mass, requiring other diagnostic ions for disambiguation. Furthermore, even modifications that have undergone extensive characterization often produce different fragmentation patterns across instruments and conditions. To address these deficiencies and facilitate the next generation of PTM identification, we have developed a method to automatically find diagnostic spectral features for any PTM, allowing subsequent searches to take advantage of additional metrics and increase PTM identification and localization rates. The method has been incorporated into the open-search annotation tool PTM-Shepherd and the FragPipe computational platform.
Kinetic and Structural Analysis of Ribonucleotide Extension by DNA Polymerase η
Authors: Chang Caleb , Luo Christie Lee , Eleraky Sarah , Lin Aaron , Zhou Grace , Gao Yang 
Published: September 2022

AbstractDNA polymerases catalyze DNA synthesis with high fidelity, which is essential for all life. Extensive kinetic and structural efforts have been executed in exploring mechanisms of DNA polymerases, surrounding their kinetic pathway, catalytic mechanisms, and factors that dictate polymerase fidelity. Recent time-resolved crystallography studies on DNA polymerase η (Pol η) and β have revealed essential transient events during DNA synthesis reaction, such as mechanisms of primer deprotonation, separated roles of the three metal ions, and conformational changes that disfavor incorporation of the incorrect substrate. DNA-embedded ribonucleotides (rN) are the most common lesion on DNA and a major threat to genome integrity. While kinetics of rN incorporation has been explored and structural studies have revealed that DNA polymerases have a steric gate that destabilizes rNTP binding, mechanism of extension upon rN addition remains poorly characterized. Using steady-state kinetics, static and time-resolved X-ray crystallography with Pol η as a model system, we showed that the extra hydroxyl group on the primer terminus does not reduce the catalytic efficiency of Pol η. However, rN ended primers alter the dynamics of the polymerase active site as well as the catalysis and fidelity of DNA synthesis. During rN extension, Pol η fidelity drops significantly across different sequence context. Systematic structural studies suggest that the rN at the primer end improved primer alignment and reduced barriers in C2’-endo to C3’-endo sugar conformation change. Our work provides important insights for rN extension and implicates a possible mechanism for rN removal.