bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trait-based predictors of genomic diversity within freshwater fish communities of the Ozarks
Authors: Zbinden Zachery D. , Douglas Marlis R. , Chafin Tyler K. , Douglas Michael E. 
Published: October 2022

ABSTRACTPhenotypic traits modulate the fate of species interactions with one another and the environment; thus, traits directly shape the past, present, and future evolutionary trajectories of populations. As such, distinct species-specific responses to a shifting environment are widely documented in the form of distinct genetic signatures, i.e., genetic diversity, reflecting differential responses over time. While the link between genetic diversity and phenotypic traits is seemingly fundamental, it has been challenging to establish unequivocally. Across an exemplar freshwater fish metacommunity, we employ phenotypic traits to test if they are significantly related to observed genetic patterns among species. Associated traits were then used to construct trait-based predictive models of genetic diversity. We collected representative constituents of a freshwater fish community (N=31 species) sampled across 75 sites within the White River Basin (Ozark Plateau, USA). For each species, we derived three genetic diversity indices (=HS/HT/G”ST) from SNP data (N=2,000 loci) and assessed 28 phenotypic traits related to morphology, life history, and ecology. We identified a series of traits (N=2–5, depending upon the index) strongly associated with facets of genetic diversity. These were subsequently applied in predictive models that explained 31–68% of the genetic variability across species, suggesting a potential utility as an imputation tactic for data-deficient species. Our approach effectively linked species-specific traits with genetic diversity within and among populations, thereby further clarifying correlations between contemporary ecological processes, as modulated by species traits, and long-term evolutionary trajectories.
Genome-wide screening reveals metabolic regulation of translational fidelity
Authors: Lyu Zhihui , Villanueva Patricia , O’Malley Liam , Murphy Parker , Ling Jiqiang 
Published: October 2022

ABSTRACTTranslational quality control is critical for maintaining the accuracy of protein synthesis in all domains of life. Mutations in aminoacyl-tRNA synthetases and the ribosome are known to affect translational fidelity and alter fitness, viability, stress responses, neuron function, and life span. In this study, we used a high-throughput fluorescence-based assay to screen a knock-out library ofEscherichia coliand identified 30 nonessential genes that are critical for maintaining the fidelity of stop-codon readthrough. Most of these identified genes have not been shown to affect translational fidelity previously. Intriguingly, we show that several genes controlling metabolism, includingcyaAandguaA, unexpectedly enhance stop-codon readthrough. CyaA and GuaA catalyze the synthesis of cyclic adenosine monophosphate (cAMP) and guanosine monophosphate (GMP), respectively. Both CyaA and GuaA increase the expression of ribosomes and tRNAs, allowing aminoacyl-tRNAs to compete with release factors and suppress stop codons. In addition, the effect ofguaAdeletion on stop-codon readthrough is abolished by deletingprfC, which encodes release factor 3 (RF3). Our results suggest that nucleotide and carbon metabolism is tightly coupled with translational fidelity.
Semantic object processing is modulated by prior scene context
Authors: Krugliak Alexandra , Draschkow Dejan , Võ Melissa L.-H. , Clarke Alex 
Published: October 2022

AbstractObjects that are congruent with a scene are recognised more efficiently than objects that are incongruent. Further, semantic integration of incongruent objects elicits a stronger N300/N400 EEG component. Yet, the time course and mechanisms of how contextual information supports access to semantic object information is unclear. We used computational modelling and EEG to test how context influences semantic object processing. Using representational similarity analysis, we established that EEG patterns dissociated between objects in congruent or incongruent scenes from around 300 ms. By modelling semantic processing of objects using independently normed properties, we confirm that the onset of semantic processing of both congruent and incongruent objects is similar (∼150 ms). Critically, after ∼275 ms, we discover a difference in the duration of semantic integration, lasting longer for incongruent compared to congruent objects. These results constrain our understanding of how contextual information supports access to semantic object information.
High-Throughput Screening of theSaccharomyces cerevisiaeGenome for 2-Amino-3-Methylimidazo [4,5-f] Quinoline Resistance Identifies Colon Cancer-Associated Genes
Authors: Dolan Michael , St. John Nick , Zaidi Faizan , Doyle Francis , Fasullo Michael 
Published: October 2022

ABSTRACTHeterocyclic aromatic amines (HAAs) are potent carcinogenic agents found in charred meats and cigarette smoke. However, few eukaryotic resistance genes have been identified. We usedSaccharomyces cerevisiae(budding yeast) to identify genes that confer resistance to 2-amino-3-methylimidazo[4,5-f]quinoline (IQ). CYP1A2 and NAT2 activate IQ to become a mutagenic nitrenium compound. We introduced an expression vector that contains human CYP1A2 and NAT2 genes into selected mutant strains and the diploid yeast deletion collection. The deletion libraries expressing CYP1A2 and NAT2 or no human genes were exposed to either 400 or 800 μM IQ for five or ten generations. DNA barcodes were sequenced using the Illumina HiSeq 2500 platform and statistical significance was determined for exactly matched barcodes. Four screens for IQ resistance in the “humanized” collection identified 1160 unique ORFs, of which 337 were validated or duplicated in at least two screens. Two screens of the original yeast library identified 101 genes that overlap with the 337 previously identified. Selected genes were validated by growth curves, competitive growth assays, or trypan blue assays. Prominent among both sets are ribosomal protein genes, while nitrogen metabolism, cell wall synthesis, and phosphatase genes were identified among the “humanized” library. Protein complexes identified included the casein kinase 2 (CK2) and histone chaperone (HIR) complex. DNA repair genes includedNTG1, RAD18, RAD9, PSY2andUBC13. Polymorphisms in humanNTHL1, theNTG1ortholog, andRAD18are risk factors for colon cancer. These studies thus provoke questions of whether genetic risk factors for colon cancer confer more HAA-associated toxicity.
Structural role for DNA Ligase IV in promoting the fidelity of non-homologous end joining
Authors: Stinson Benjamin M. , Carney Sean M. , Walter Johannes C. , Loparo Joseph J. 
Published: October 2022

SUMMARYNonhomologous end joining (NHEJ) is the primary pathway of vertebrate DNA double-strand-break repair. NHEJ polymerases and nucleases can modify DNA ends to render them compatible for ligation, but these enzymes are usually deployed only when necessary for repair of damaged DNA ends, thereby minimizing mutagenesis. Using frog egg extracts, we reveal a structural role for the NHEJ-specific DNA Ligase IV (Lig4) in promoting NHEJ fidelity. Mutational analysis demonstrates that Lig4 must bind DNA ends to form the short-range synaptic complex, in which DNA ends are closely aligned prior to ligation. Furthermore, single-molecule experiments show that a single Lig4 binds both DNA ends at the instant of short-range synapsis. In this way, compatible ends can be rapidly ligated without polymerase or nuclease activity, which we previously showed is restricted to the short-range synaptic complex. Our results provide a molecular basis for the fidelity of NHEJ.
Approaching object acceleration differentially affects the predictions of neuronal collision-avoidance models
Authors: Gabbiani Fabrizio , Preuss Thomas , Dewell Richard B. 
Published: October 2022

AbstractThe processing of visual information for collision avoidance has been investigated at the biophysical level in several model systems. In grasshoppers, theηmodel captures reasonably well the visual processing performed by an identified neuron called the lobular giant movement detector (LGMD) as it tracks approaching objects. Similar phenomenological models have been used to describe either the firing rate or the membrane potential of neurons responsible for visually-guided collision avoidance in other animals. In goldfish, theκmodel has been proposed to describe the Mauthner cell, an identified neuron involved in startle escape responses. In the vinegar fly, a third model was developed for the giant fiber neuron, which trigger last resort escapes immediately before an impending collision. One key property of these models is their prediction that peak neuronal responses occur a fixed delay after the simulated approaching object reaches a threshold angular size on the retina. This prediction is valid for simulated objects approaching at a constant speed. We tested whether it remains valid when approaching objects accelerate. After characterizing and comparing the models’ responses to accelerating and constant speed stimuli, we find that the prediction holds true for theκand the giant fiber model, but not for theηmodel. These results suggest that acceleration in the approach trajectory of an object may help distinguish and further constrain the neuronal computations required for collision avoidance in grasshoppers, fish, and vinegar flies.
Statistical analysis supports pervasive RNA subcellular localization and alternative 3’ UTR regulation
Authors: Bierman Rob , Dave Jui M. , Greif Daniel M. , Salzman Julia 
Published: October 2022

AbstractTargeted low-throughput studies have previously identified subcellular RNA localization as necessary for cellular functions including polarization, and translocation. Further, these studies link localization to RNA isoform expression, especially 3’ Untranslated Region (UTR) regulation. The recent introduction of genome-wide spatial transcriptomics techniques enable the potential to test if subcellular localization is regulated in situ pervasively. In order to do this, robust statistical measures of subcellular localization and alternative poly-adenylation (APA) at single cell resolution are needed. Developing a new statistical framework called SPRAWL, we detect extensive cell-type specific subcellular RNA localization regulation in the mouse brain and to a lesser extent mouse liver. We integrated SPRAWL with a new approach to measure cell-type specific regulation of alternative 3’ UTR processing and detected examples of significant correlations between 3’ UTR length and subcellular localization. Included examples, Timp3, Slc32a1, Cxcl14, and Nxph1 have subcellular localization in the brain highly correlated with regulated 3’ UTR processing that includes use of unannotated, but highly conserved, 3’ ends. Together, SPRAWL provides a statistical framework to integrate multi-omic single-cell resolved measurements of gene-isoform pairs to prioritize an otherwise impossibly large list of candidate functional 3’ UTRs for functional prediction and study. SPRAWL predicts 3’ UTR regulation of subcellular localization may be more pervasive than currently known.
Convergent escape behavior from distinct visual processing of impending collision in fish and grasshoppers
Authors: Dewell Richard B. , Carroll-Mikhail Terri , Eisenbrandt Margaret R. , Preuss Thomas , Gabbiani Fabrizio 
Published: October 2022

AbstractIn animal species ranging from invertebrate to mammals, visually guided escape behaviors have been studied using looming stimuli, the two-dimensional expanding projection on a screen of an object approaching on a collision course at constant speed. The peak firing rate or membrane potential of neurons responding to looming stimuli often tracks a fixed threshold angular size of the approaching stimulus that contributes to the triggering of escape behaviors. To study whether this result holds more generally, we designed stimuli that simulate acceleration or deceleration over the course of object approach on a collision course. Under these conditions, we found that collision detecting neurons in grasshoppers were sensitive to acceleration whereas the triggering of escape behaviors was less so. In contrast, neurons in goldfish identified indirectly through the characteristic features of the escape behaviors they trigger, showed little sensitivity to acceleration. This closely mirrored a broader lack of sensitivity to acceleration of the goldfish escape behavior. Thus, although the sensory coding of simulated colliding stimuli with non-zero acceleration likely differs in grasshoppers and goldfish, the triggering of escape behaviors converges towards similar characteristics. Approaching stimuli with non-zero acceleration may help refine our understanding of neural computations underlying escape behaviors in a broad range of animal species.Key pointsA companion manuscript showed that two mathematical models of collision-detecting neurons in grasshoppers and goldfish make distinct predictions for their responses to simulated objects approaching on a collision course with non-zero acceleration.Testing these experimental predictions showed that grasshopper neurons are sensitive to acceleration while goldfish neurons are not, in agreement with the distinct models proposed previously in these species using constant velocity approaches.Both the escape behaviors of grasshopper and goldfish were insensitive to acceleration suggesting a further transformation downstream in grasshopper motor circuits that matches the computation observed in the goldfish Mauthner cell.Thus, in spite of different sensory processing in the two species, escape behaviors converge towards similar solutions.The use of object acceleration during approach on a collision course may help better understand the neural computations implemented for collision avoidance in a broad range of species.
Human T follicular helper clones seed the germinal center-resident regulatory pool
Authors: Le Coz Carole , Oldridge Derek A. , Herati Ramin S. , De Luna Nina , Garifallou James , Cabrera Emylette Cruz , Belman Jonathan P , Pueschl Dana , Silva Luisa V. , Knox Ainsley V. C. , Yoon Samuel , Zur Karen B. , Handler Steven D. , Hakonarson Hakon , Wherry E. John , Gonzalez Michael , Romberg Neil 
Published: October 2022

AbstractHow FOXP3+T follicular regulatory (Tfr) cells simultaneously steer antibody formation toward microbe/vaccine recognition and away from self-reactivity remains unsettled. To explore human Tfr cell provenance, function and location heterogeneity, we used pairedTCRVA/TCRVBsequencing to distinguish tonsillar Tfr cells clonally related to natural Tregs (nTfr) from those likely induced from Tfh cells (iTfr). The proteins iTfr and nTfr cells differentially expressed were utilized to pinpoint theirin situlocations via multi-plex microscopy and establish divergent functional roles.In-silicoand tonsil organoid tracking models corroborated the existence of separate Treg-to-nTfr and Tfh-to-iTfr developmental trajectories. In total, we have identified human iTfr cells as a distinct CD38-expressing, GC-resident, Tfh-descended subset that gains suppressive function while retaining capacities for B-cell help whereas CD38-nTfr cells are elite suppressors primarily localized to follicular mantles. Interventions differentially targeting Tfr subsets may provide therapeutic opportunities to boost immunity or more precisely treat autoimmune diseases.One sentence summaryHuman tonsillar Tfr clones descend from either Treg or Tfh lineages and provenance predicts their TCR repertoires, locations and functional characteristics.
Tropomyosin 1-I/C co-ordinates kinesin-1 and dynein motors duringoskarmRNA transport
Authors: Heber Simone , McClintock Mark A. , Simon Bernd , Hennig Janosch , Bullock Simon L. , Ephrussi Anne 
Published: October 2022

AbstractDynein and kinesin motors mediate long-range intracellular transport, translocating towards microtubule minus and plus ends, respectively. Cargoes often undergo bidirectional transport by binding to both motors simultaneously. However, it is not known how motor activities are coordinated in such circumstances. InDrosophila, sequential activities of the dynein-dynactin-BicD-Egalitarian (DDBE) complex and of kinesin-1 deliveroskarmRNA from nurse cells to the oocyte, and within the oocyte to the posterior pole. Here, throughin vitroreconstitution, we show that Tm1-I/C, a Tropomyosin-1 isoform, links kinesin-1 in an inactive state to DDBE-associatedoskarmRNA. NMR spectroscopy, small-angle X-ray scattering and structural modeling indicate that Tm1-I/C suppresses kinesin-1 activity by stabilizing its autoinhibited conformation, thus preventing a tug-of-war between the opposite polarity motors until kinesin-1 is activated in the oocyte. Our work reveals a novel strategy ensuring sequential activity of microtubule motors.
Closed genomes uncover a saltwater species ofCandidatusElectronema and shed new light on the boundary between marine and freshwater cable bacteria
Authors: Sereika Mantas , Petriglieri Francesca , Jensen Thomas Bygh Nymann , Sannikov Artur , Hoppe Morten , Nielsen Per Halkjær , Marshall Ian P.G. , Schramm Andreas , Albertsen Mads 
Published: October 2022

AbstractCable bacteria of theDesulfobulbaceaefamily are centimeter-long filamentous bacteria, which are capable of conducting long-distance electron transfer. Currently, all cable bacteria are classified into two candidate genera:CandidatusElectronema, typically found in freshwater environments, andCandidatusElectrothrix, typically found in saltwater environments. This taxonomic framework is based on both 16S rRNA gene sequences and metagenome-assembled genome (MAG) phylogenies. However, most of the currently available MAGs are highly fragmented, incomplete, and thus likely miss key genes essential for deciphering the physiology of cable bacteria. To address this, we performed Nanopore long read (total 162.4 Gbp) and Illumina short read (total 148.3 Gbp) shotgun sequencing of selected environmental samples and a single-strain enrichment ofCa. Electronema aureum. We recovered multiple cable bacteria MAGs, including two circular and one single-contig. Phylogenomic analysis, also confirmed by 16S rRNA gene-based phylogeny, classified one circular MAG and the single-contig MAG as novel species of cable bacteria, which we propose to nameCa. Electronema halotolerans andCa. Electrothrix laxa, respectively. TheCa. Electronema halotolerans, despite belonging to the previously recognized freshwater genus of cable bacteria, was retrieved from brackish-water sediment. Metabolic predictions showed several adaptations to a high salinity environment, similar to the “saltwater”Ca. Electrothrix species, indicating howCa. Electronema halotolerans may be the evolutionary link between marine and freshwater cable bacteria lineages.
Resting-state EEG dynamics help explain differences in response control in ADHD: Insight into electrophysiological mechanisms and sex differences
Authors: Kember J. , Stepien L. , Panda E. , Tekok-Kilic A 
Published: October 2022

AbstractReductions in response control (greater reaction time variability and commission error rate) are consistently observed in those diagnosed with attention-deficit/hyperactivity disorder (ADHD). Previous research suggests these reductions arise from a dysregulation of large-scale cortical networks. Here, we extended our understanding of this cortical-network/response-control pathway important to the neurobiology of ADHD. First, we assessed how dynamic changes in three resting-state EEG network properties thought to be relevant to ADHD (phase-synchronization, modularity, oscillatory power) covaried with response control during a simple perceptual decision-making task in 112 children/adolescents (aged 8-16) with and without formal ADHD diagnoses. Second, we tested whether these associations differed in males and females who were matched in age, ADHD-status and ADHD-subtype. We found that changes in oscillatory power (as opposed to phase-synchrony and modularity) are most related with response control, and that this relationship is stronger in ADHD compared to controls. Specifically, a tendency to dwell in an electrophysiological state characterized by high alpha/beta power (8-12/13-30Hz) and low delta/theta power (1-3/4-7Hz) supported response control, particularly in those with ADHD. Time in this state might reflect an increased initiation of alpha-suppression mechanisms, recruited by those with ADHD to suppress processing unfavourable to response control. We also found marginally significant evidence that this relationship is stronger in males compared to females, suggesting a distinct etiology for response control in the female presentation of ADHD.Highlights-Hidden Markov modeling of EEG functional network properties in ADHD and controls.-EEG power dynamics, not phase-synchrony or modularity, covary with response control.-Association between EEG dynamics and response control is more pronounced in ADHD.-ADHD cortical-network/response-control pathway is more prominent in males vs. females.
Being natural is aesthetic: the effects of “natural” labeling on lay beliefs and the purchase intention of unattractive produce
Authors: Wang Haiyan , Li Huijuan , Zhao Yinfei , Xi Nannan 
Published: October 2022

PurposeIndividuals, organizations, firms, and governments have been making strenuous effort to promote sustainable and green consumption. However, it is noticeable that a large amount of unattractive produce is ruthlessly discarded and wasted around the globe, resulting in unsustainable consumption behavior, harming long-term business development, and breaking the harmonious relationship between humans and nature. Therefore, to increase consumer literacy toward unaesthetic produce, this research investigates the pivotal role of “natural” labeling in increasing purchase intention toward visually unattractive fruits and vegetables.Design/methodology/approachBy recruiting participants from one of the largest online crowdsourcing platforms (the Credamo), this research conducts three online experimental studies (with two pilot studies) to test three hypotheses based on the cue utilization theory and the lay belief theory.FindingsThe results show that unattractive produce with the “natural” label could significantly increase consumers' purchase intention compared with those without specific labels. The results also reveal that consumers' lay beliefs that natural foods are perceived to be tastier and healthier mediate the positive effects of “natural” labeling (vs no specific labeling) on willingness to purchase.Originality/valueThis research explores competing lay beliefs about unattractive produce. It identifies the positive effects of lay beliefs “natural = tasty and healthy” through “natural” labeling appeal, thus attenuating the misapplication of lay beliefs “unattractive = tasteless and unhealthy” and broadening the application scope of consumer lay belief theory. The findings also contribute to the cue literature by manifesting the positive consequences of the “natural” label playing as a cognitive cue in priming lay beliefs about naturalness. In addition, it also paves a positive way for business practitioners and marketers to develop the produce industry sustainably.