bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contrasting patterns of foraging behavior in Neotropical stingless bees using pollen and honey metabarcoding
Authors: Martins Aline C. , Proença Carolyn E. B. , Vasconcelos Thais N. C. , Aguiar Antonio J. C. , Farinasso Hannah C. , de Lima Aluisio T. F. , Faria Jair E. Q. , Norrana Krissya , Costa Marcella B. R. , Carvalho Matheus M. , Dias Rodrigo L. , Bustamante Mercedes M. C. , Carvalho Fernanda A. , Keller Alexander 
Published: June 2023

AbstractStingless bees are major flower visitors in the tropics, but their foraging preferences and behavior are still poorly understood. Studying stingless bee interactions with angiosperms is methodologically challenging due to the high tropical plant diversity and inaccessibility of upper canopy flowers in forested habitats. Pollen DNA metabarcoding offers an opportunity of assessing floral visitation efficiently and was applied here to understand stingless bee floral resources spectra and foraging behavior. We analyzed pollen and honey of three distantly related species of stingless bees, with different body size and social behavior:Melipona rufiventris, Scaptotrigona posticaandTetragonisca angustula. Simultaneously, we evaluate the local floristic components through seventeen rapid botanical surveys conducted at different distances from the nests. We discovered a broad set of explored floral sources, with 46.3 plant species per bee species in honey samples and 53.67 in pollen samples. Plant families Myrtaceae, Asteraceae, Euphorbiaceae, Melastomataceae and Malpighiaceae dominated the records, indicating stingless bee preferences for abundant resources that flowers of these families provide in the region. Results also reinforce the preference of stingless bees for forest trees, even if only available at long distances. Our high-resolution results encourage future bee-plant studies using pollen and honey metabarcoding in hyper diverse tropical environments.
BOTTOM-UP EFFECTS AND DENSITY DEPENDENCE DRIVE THE DYNAMIC OF AN ANTARCTIC SEABIRD PREDATOR-PREY SYSTEM
Authors: Viollat Lise , Quéroué Maud , Delord Karine , Gimenez Olivier , Barbraud Christophe 
Published: June 2023

ABSTRACTUnderstanding how populations respond to variability in environmental conditions and interspecific interactions is one of the biggest challenges of population ecology, particularly in the context of global change. Although several studies have investigated population responses to climate change, very few have explicitly integrated interspecific relationships when studying these responses. Here, we aim to understand the combined effects of inter- and intraspecific interactions and environmental conditions on the demographic parameters of a prey-predator system of three sympatric seabird populations breeding in Antarctica: the south polar skua (Catharacta maccormicki), and its two main preys during the breeding season, the Adélie penguin (Pygoscelis adeliae) and the emperor penguin (Aptenodytes forsteri). We built a two-species integrated population model (IPM) with 31 years of capture-recapture and count data, and provided a framework that allows estimating demographic parameters and abundance of a predator-prey system in a context where capture-recapture data are not available for one species. Our results showed that predator–prey interactions and local environmental conditions affect differently south polar skuas depending on their breeding state of the previous year. Concerning prey-predator relationships, the number of Adélie penguin breeding pairs showed a positive effect on south polar skua survival and breeding probability, and the number of emperor penguin dead chicks showed a positive effect on the breeding success of south polar skuas. In contrast, there was no evidence for an effect of the number of south polar skuas on the demography of Adélie penguins. We also found an important impact of sea ice conditions on both the dynamics of south polar skuas and Adélie penguins. Our results suggest that this prey-predator system is mostly driven by bottom-up processes and local environmental conditions.
Localized measurements of water potential reveal large loss of conductance in living tissues of maize leaves
Authors: Jain Piyush , Huber Annika E. , Rockwell Fulton E. , Sen Sabyasachi , Holbrook N. Michele , Stroock Abraham D. 
Published: June 2023

AbstractThe water status of the living tissue in leaves between the xylem and stomata (outside xylem zone - OXZ) play a critical role for plant function and global mass and energy balance but has remained largely inaccessible. We resolve the local water relations of OXZ tissue using a nanogel reporter of water potential (ψ), AquaDust, that enables an in-situ, non-destructive measurement of bothψof xylem and highly localizedψat the terminus of transpiration in the OXZ. Working in maize, these localized measurements reveal gradients in the OXZ that are several fold larger than those based on conventional methods, and values ofψin the mesophyll apoplast well below the macroscopic turgor loss potential. We find a strong loss of hydraulic conductance in both the bundle sheath and the mesophyll with decreasing xylem potential but not with evaporative demand. Our measurements suggest an active role played by the OXZ in regulating the transpiration path and our methods provide novel means to study this phenomenon.
Bringing up-to-date the toolkit for the catabolism of aromatic compounds in fungi: the unexpected 1,2,3,5–tetrahydroxybenzene central pathway
Authors: Martins Tiago M. , Bento Artur , Martins Celso , Tomé Ana S. , Moreira Carlos J.S. , Pereira Cristina Silva 
Published: June 2023

ABSTRACTSaprophytic fungi are able to catabolize many plant-derived aromatics, including, for example, gallate. The catabolism of gallate in fungi is assumed to depend on the five main central pathways,i.e., of the central intermediates’ catechol, protocatechuate, hydroxyquinol, homogentisate, and gentisate, but a definitive demonstration is lacking. To shed light on this process, we analyzed the transcriptional reprograming of the growth ofAspergillus terreuson gallate compared with acetate as the control condition. Surprisingly, the results revealed that the five main central pathways did not exhibit significant positive regulation. Instead, an in-depth analysis identified four highly expressed and upregulated genes that are part of a conserved gene cluster found in numerous species of fungi, though not inAspergilli. The cluster comprises a monooxygenase gene and a fumarylacetoacetate hydrolase-likegene, which are recognized as key components of catabolic pathways responsible for aromatic compound degradation. The other two genes encode proteins with no reported enzymatic activities. Through functional analyses of gene deletion mutants, the conserved short protein with no known domains could be linked to the conversion of the novel metabolite 5-hydroxydienelatone, whereas the DUF3500 gene likely encodes a ring-cleavage enzyme for 1,2,3,5–tetrahydroxybenzene. These significant findings establish the existence of a new 1,2,3,5-tetrahydroxybenzene central pathway for the catabolism of gallate and related compounds (e.g.,2,4,6-trihydroxybenzoate) in numerous fungi where this catabolic gene cluster was observed.IMPORTANCEThe lignin found in various economically significant plants, such as major grains like rice, wheat, and maize, comprises a substantial portion of syringyl units (up to 60%). As a result, the future utilization of residues from these plants in biorefineries will yield significant quantities of syringyl derivatives. However, our understanding of how fungi degrade these syringyl derivatives is to date scarce and mostly relies on unproven assumptions. Our study, demonstrates the existence of a new 1,2,3,5-tetrahydroxybenzene central intermediate for the catabolism of gallate in numerous fungi. This finding expands the toolkit of central pathways, proving that the generalized assumption that gallate catabolism depends on the previously known five main central pathways was incorrect. This research reveals a novel crucial central pathway of great ecological and biotechnological importance, not only for fungi but also potentially for bacteria.
Validation ofde novodesigned water-soluble and transmembrane proteins byin silicofolding and melting
Authors: Hermosilla Alvaro Martin , Berner Carolin , Ovchinnikov Sergey , Vorobieva Anastassia A. 
Published: June 2023

AbstractIn silicovalidation ofde novodesigned proteins with deep learning (DL)-based structure prediction algorithms has become mainstream. However, formal evidence of the relationship between a high-quality predicted model and the chance of experimental success is lacking. We used experimentally characterizedde novodesigns to show that AlphaFold2 and ESMFold excel at different tasks. ESMFold can efficiently identify designs generated based on high-quality (designable) backbones. However, only AlphaFold2 can predict which sequences have the best chance of experimentally folding among similar designs. We show that ESMFold can generate high-quality structures from just a few predicted contacts and introduce a new approach based on incremental perturbation of the prediction (“in silicomelting”), which can reveal differences in the presence of favorable contacts between designs. This study provides a new insight on DL-based structure prediction models explainability and on how they could be leveraged for the design of increasingly complex proteins; in particular membrane proteins which have historically lacked basicin silicovalidation tools.
MSModDetector: A Tool for Detecting Mass Shifts and Post-Translational Modifications in Individual Ion Mass Spectrometry Data
Authors: Faizi Marjan , Fellers Ryan T , Lu Dan , Drown Bryon S , Jambhekar Ashwini , Lahav Galit , Kelleher Neil L , Gunawardena Jeremy 
Published: June 2023

AbstractMotivationPost-translational modifications (PTMs) on proteins regulate protein structures and functions. A single protein molecule can possess multiple modification sites that can accommodate various PTM types, leading to a variety of different patterns, or combinations of PTMs, on that protein. Different PTM patterns can give rise to distinct biological functions. To facilitate the study of multiple PTMs, top-down mass spectrometry (MS) has proven to be a useful tool to measure the mass of intact proteins, thereby enabling even widely separated PTMs to be assigned to the same protein molecule and allowing determination of how many PTMs are attached to a single protein.ResultsWe developed a Python module called MSModDetector that studies PTM patterns from individual ion mass spectrometry (I MS) data. I MS is an intact protein mass spectrometry approach that generates true mass spectra without the need to infer charge states. The algorithm first detects and quantifies mass shifts for a protein of interest and subsequently infers potential PTM patterns using linear programming. The algorithm is evaluated on simulated I MS data and experimental I MS data for the tumor suppressor protein p53. We show that MSModDetector is a useful tool for comparing a protein’s PTM pattern landscape across different conditions. An improved analysis of PTM patterns will enable a deeper understanding of PTM-regulated cellular processes.AvailabilityThe source code is available athttps://github.com/marjanfaizi/MSModDetectortogether with the scripts used for analyses and to generate the figures presented in this study.
Structural variants and short tandem repeats impact gene expression and splicing in bovine testis tissue
Authors: Bhati Meenu , Mapel Xena Marie , Lloret-Villas Audald , Pausch Hubert 
Published: June 2023

AbstractStructural variants (SVs) and short tandem repeats (STRs) are significant sources of genetic variation. However, the impacts of these variants on gene regulation have not been investigated in cattle. Here, we genotyped and characterized 19,408 SVs and 374,821 STRs in 183 bovine genomes and investigated their impact on molecular phenotypes derived from testis transcriptomes. We found that 71% STRs were multiallelic. The vast majority (95%) of STRs and SVs were in intergenic and intronic regions. Only 37% SVs and 40% STRs were in high LD (R2>0.8) with surrounding SNPs/Indels, indicating that SNP-based association testing and genomic prediction are blind to a non-negligible portion of genetic variation. We showed that both SVs and STRs were more than two-fold enriched among expression and splicing QTL (e/sQTL) relative to SNPs/Indels and were often associated with differential expression and splicing of multiple genes. Deletions and duplications had larger impacts on splicing and expression than any other type of structural variant. Exonic duplications predominantly increased gene expression either through alternative splicing or other mechanisms, whereas expression- and splicing-associated STRs primarily resided in intronic regions and exhibited bimodal effects on the molecular phenotypes investigated. Most e/sQTL resided within 100 kb of the affected genes or splicing junctions. We pinpoint candidate causal STRs and SVs associated with the expression ofSLC13A4andTTC7B, and alternative splicing of a lncRNA andCAPP1. We provide a catalogue of STRs and SVs for taurine cattle and show that these variants contribute substantially to gene expression and splicing variation.
Disruption of Prostaglandin F2αReceptor Signaling Attenuates Fibrotic Remodeling and Alters Fibroblast Population Dynamics in A Preclinical Murine Model of Idiopathic Pulmonary Fibrosis
Authors: Rodriguez Luis R. , Tang Soon Yew , Barboza Willy Roque , Murthy Aditi , Tomer Yaniv , Cai Tian-Quan , Iyer Swati , Chavez Katrina , Das Ujjalkumar Subhash , Ghosh Soumita , Dimopoulos Thalia , Babu Apoorva , Connelly Caitlin , FitzGerald Garret A. , Beers Michael F. 
Published: June 2023

AbstractIdiopathic Pulmonary Fibrosis (IPF) is a chronic parenchymal lung disease characterized by repetitive alveolar cell injury, myofibroblast proliferation, and excessive extracellular matrix deposition for which unmet need persists for effective therapeutics. The bioactive eicosanoid, prostaglandin F2α, and its cognate receptor FPr (Ptfgr) are implicated as a TGFβ1 independent signaling hub for IPF. To assess this, we leveraged our published murine PF model (IER−SftpcI73T) expressing a disease-associated missense mutation in the surfactant protein C (Sftpc) gene. Tamoxifen treated IER-SftpcI73Tmice develop an early multiphasic alveolitis and transition to spontaneous fibrotic remodeling by 28 days. IER-SftpcI73Tmice crossed to a Ptgfr null (FPr−/−) line showed attenuated weight loss and gene dosage dependent rescue of mortality compared to FPr+/+cohorts. IER-SftpcI73T/FPr−/−mice also showed reductions in multiple fibrotic endpoints for which administration of nintedanib was not additive. Single cell RNA sequencing, pseudotime analysis, and in vitro assays demonstratedPtgfrexpression predominantly within adventitial fibroblasts which were reprogrammed to an “inflammatory/transitional” cell state in a PGF2α/ FPr dependent manner. Collectively, the findings provide evidence for a role for PGF2αsignaling in IPF, mechanistically identify a susceptible fibroblast subpopulation, and establish a benchmark effect size for disruption of this pathway in mitigating fibrotic lung remodeling.
Genetic architecture of individual meiotic crossover rate and distribution in a large Atlantic Salmon (Salmo salar)breeding population
Authors: Brekke Cathrine , Johnston Susan E. , Knutsen Tim M. , Berg Peer 
Published: June 2023

AbstractMeiotic recombination through chromosomal crossovers ensures proper segregation of homologous chromosomes in meiosis, while also breaking down linkage disequilibrium and shuffling alleles at loci located on the same chromosome. Rates of recombination can vary between species, but also between and within individuals, sex and chromosomes within species. Indeed, the Atlantic salmon genome is known to have clear sex differences in recombination with female biased heterochiasmy and markedly different landscapes of crossovers between males and females. In male meiosis, crossovers occur strictly in the telomeric regions, whereas in female meiosis crossovers tend to occur closer to the centromeres. However, little is known about the genetic control of these patterns and how this differs at the individual level. Here, we investigate genetic variation in individual measures of recombination in >5000 large full-sib families of a Norwegian Atlantic salmon breeding population with high-density SNP genotypes. We show that females had 1.6× higher crossover counts (CC) than males, with autosomal linkage maps spanning a total of 2174 cM in females and 1483 cM in males. However, because of the extreme telomeric bias of male crossovers, female recombination is much more important for generation of new haplotypes with 8x higher intra-chromosomal genetic shuffling than males. CC was heritable in females (h2= 0.11) and males (h2= 0.10), and shuffling was also heritable in both sex but with a lower heritability in females (h2= 0.06) than in males (h2= 0.11). Inter-sex genetic correlations for both traits were close to zero, suggesting that rates and distribution of crossovers are genetically distinct traits in males and females, and that there is a potential for independent genetic change in both sexes in the Atlantic Salmon. Together, these findings give novel insights into the genetic architecture of recombination in salmonids and contribute to a better understanding of how rates and distribution of recombination may evolve in eukaryotes more broadly.
Imagination as predictive perception: mental imagery predictively biases perceptual judgments of observed action kinematics
Authors: Parrotta Eleonora , McDonough Katrina L. , Bach Patric 
Published: June 2023

AbstractRecent approaches conceptualize mental imagery as a simulatory mode of perceptual experience, which relies on the voluntary engagement of the same top-down prediction processes that shape our perception of the external world. If so, then imagery should induce similar predictive biases as those that are known to govern the perceptual representation of others’ behaviour. In four experiments, participants saw object-directed approach and avoidance actions and reported the hands’ last seen location after their sudden disappearance. All revealed robust predictive biases, showing that perceptual judgments are illusorily distorted towards the implied goals of the actions and away from obstacles. Importantly, the experiments also showed that prior action imagery suffices to induce similar biases, so that perceptual judgments become distorted not only towards the action’s expected next steps but also the imagined ones. These imagery-induced biases were robust across stimulus sets and measurement methods. They reflect prior knowledge of how people move and can be induced not only through imagery of the actions itself, but also through imagery of situations in which the actions are merely expected. These data show that imagery induces similar perceptual expectations as other prediction processes, in line with the proposal that imagery reflects the voluntary control of predictive pathways that govern an event’s perceptual representation. Moreover, imagery candriveprediction processes, inducing expectations about events likely to occur in the imagined (not observed) realities, suggesting shared pathways through which imagery and prediction may support mental simulation and counterfactual reasoning.Public Significance StatementThis study uses the perception of other people’s behaviour as a testing bed to advance the hypothesis that imagery can be understood aspredictedperception: that, when people imagine, they make voluntary use of the same prediction mechanisms that otherwise allow them to anticipate – and visualise – how a situation will develop further. In four experiments, the study shows (1) that imagining another’s behaviour induces the expectation that their actions will develop in the imagined manner, (2) that imagining situations elicits expectations about how people will behave within them, (3) that these imagery-induced expectations are integrated with other expectations people have about others’ behaviour and (4) subtly distort how these behaviours are visuospatially represented. The findings demonstrate a link between imagery and predictive perceptual abilities and reveal how imagery can act as a key tool in people’s ability to anticipate relevant futures and explore counterfactual realities.
Comprehensive Characterization of tRNA by Ultra High-Performance Liquid Chromatography High-Resolution Accurate Mass Spectrometry
Authors: Ross Robert L , Cowley Ryan , Murphy Keeley , Gamez Roberto , Gazis Paul R , Sutton Jennifer , Du Min 
Published: June 2023

AbstractTransfer ribonucleic acid (tRNA) are the smallest RNA in the translational triune and contain the greatest density of post-transcriptional modifications than any other RNA types in the cell. Due to the size of tRNA studying these modifications usually entails enzymatic digestion followed by liquid chromatography tandem mass spectrometry (LC-MS/MS). Here we report an advancement in Intact Mass Analysis for identification of tRNA through deconvolution of high resolution accurate mass spectrometry facilitated using a secondary alkylamine as an ion pairing reagent during reverse phase chromatography. We identify in isolated and totalS. cerevisiaetRNA 3’ CCA variations and show that most tRNA lack a 3’ adenosine with the lesser abundant species having the expected CCA termini. We identify a previously unknown stable demethylated Wybutosine intermediate for tRNAPHEand identify low abundant contaminating tRNAs in an isolated tRNAPHEsample. Confirmation of identities was verified through traditional mass spectrometric nucleoside and mass mapping experiments.
Sequence and epigenetic landscapes of active and silenced nucleolus organizers in Arabidopsis
Authors: Fultz Dalen , McKinlay Anastasia , Enganti Ramya , Pikaard Craig S. 
Published: June 2023

AbstractArabidopsis thalianahas two ribosomal RNA gene loci, nucleolus organizer regionsNOR2andNOR4, whose complete sequences remain undefined. Ultra-long DNA sequences assembled using an unconventional approach yielded 5.5 and 3.9 Mbp sequences forNOR2andNOR4(in the reference strain, Col-0), revealing their distinct gene subtype compositions. RNA sequencing and identification of genes associated with flow-sorted nucleoli of wild-type or silencing-defective mutant plants shows that most ofNOR4is comprised of active genes whereas most, but not all,NOR2genes are epigenetically silenced. Long intervals of low CG and CHG methylation overlap regions of gene activity and gene subtype homogenization. Collectively, the data reveal the genetic and epigenetic landscapes of the NORs and implicate transcription in rRNA gene concerted evolution.One Sentence SummaryNOR2andNOR4sequences fill genome gaps and enable megabase-scale analyses of rRNA gene regulation and concerted evolution.