bluuebunny/crossref_metadata_2025 huggingface dataset:
A cellular and transcriptomic dissection of the human breast for studying mechanisms of cell and tissue function
Authors: Toro Katelyn Del , Sayaman Rosalyn W. , Thi Kate , Licon-Munoz Yamhilette , Hines William C.
Published: October 2022

A fundamental question in biology, central to our understanding of cancer and other pathologies, is determining how different cell types coordinate to form and maintain tissues. Recognizing the distinct features and capabilities of the cells that compose these tissues is critical. Unfortunately, the complexity of tissues often hinders our ability to distinguish between neighboring cell types and, in turn, scrutinize their transcriptomes and generate reliable and tractable cell models for studying their inherently different biologies. In a companion article, we introduced a novel method that permits the identification and purification of the twelve cell types that compo se the human breast—nearly all of which could be reliably propagated in the laboratory. Here, we explore the nature of these cell types. We sequence mRNAs from each purified population and investigate transcriptional patterns that reveal their distinguishing features. We describe the differentially expressed genes and enriched biological pathways that capture the essence of each cell type, and we highlight transcripts that display intriguing expression patterns. These data, analytic tools, and transcriptional analyses form a rich resource whose exploration provides remarkable insights into the inner workings of the cell types composing the breast, thus furthering our understanding of the rules governing normal cell and tissue function.
Proximity-dependent labeling identifies dendritic cells that drive the tumor-specific CD4+T cell response
Authors: Chudnovskiy Aleksey , Castro Tiago BR , Nakandakari-Higa Sandra , Cui Ang , Lin Chia-Hao , Sade-Feldman Moshe , Phillips Brooke K. , Pae Juhee , Mesin Luka , Bortolatto Juliana , Schweitzer Lawrence D. , Pasqual Giulia , Lu Li-Fan , Hacohen Nir , Victora Gabriel D.
Published: October 2022

Dendritic cells (DCs) are uniquely capable of transporting tumoral antigens to tumor-draining lymph nodes (tdLNs), and also interact with effector T cells within the tumor microenvironment (TME) itself, mediating both natural antitumor immunity and the response to checkpoint blockade immunotherapy. Using LIPSTIC (Labeling Immune Partnerships by SorTagging Intercellular Contacts)-based single-cell transcriptomics, we identify individual DCs capable of presenting antigen to CD4+T cells in the tdLN as well as inside the tumor microenvironment (TME). Our findings reveal that DCs with similar hyperactivated transcriptional phenotypes interact with helper T cells both within tumors and in the tdLN, and that checkpoint blockade drugs enhance these interactions. These findings show that a relatively small fraction of DCs is responsible for most of the antigen presentation within the tdLN and TME to both CD4+and CD8+tumor-specific T cells and that classical checkpoint blockade enhances CD40-driven DC activation at both sites.
The global anaerobic metabolism regulatorfnris necessary for the degradation of food dyes and drugs byEscherichia coli
Authors: Pieper Lindsey M. , Spanogiannopoulos Peter , Volk Regan F. , Miller Carson J. , Wright Aaron T. , Turnbaugh Peter J.
Published: October 2022

The microbiome is an underappreciated contributor to intestinal drug metabolism with broad implications for drug efficacy and toxicity. While considerable progress has been made towards identifying the gut bacterial genes and enzymes involved, the role of environmental factors in shaping their activity remains poorly understood. Here, we focus on the gut bacterial reduction of azo bonds (R-N=N-R’), found in diverse chemicals in both food and drugs. Surprisingly, the canonicalazoRgene inEscherichia coliwas dispensable for azo bond reduction. Instead, azo reductase activity was controlled by the fumarate and nitrate reduction (fnr) regulator, consistent with a requirement for the anoxic conditions found within the gastrointestinal tract. Paired transcriptomic and proteomic analysis of thefnrregulon revealed that in addition to altering the expression of multiple reductases, FNR is necessary for the metabolism of L-Cysteine to hydrogen sulfide, enabling the degradation of azo bonds. Taken together, these results show how gut bacteria sense and respond to their intestinal environment to enable the metabolism of chemical motifs found in both dietary and pharmaceutical compounds.

IMPORTANCE

This work has broad relevance due to the ubiquity of dyes containing azo bonds in food and drugs. We report that azo dyes can be degraded by human gut bacteria through both enzymatic and non-enzymatic mechanisms, even from a single gut bacterial species. Furthermore, we revealed that environmental factors, oxygen and cysteine, control the ability ofE. colito degrade azo dyes due to their impacts on bacterial transcription and metabolism. These results open up new opportunities to manipulate the azoreductase activity of the gut microbiome through the manipulation of host diet, suggest that azoreductase potential may be altered in patients suffering from gastrointestinal disease, and highlight the importance of studying bacterial enzymes for drug metabolism in their natural cellular and ecological context.
The impact of inhibitor size and flexibility on the binding pathways to c-Src kinase
Authors: Shinobu Ai , Re Suyong , Sugita Yuji
Published: October 2022

Considering dynamical aspects of protein-drug binding processes is inevitable in current drug compound design. Conformational plasticity of protein kinases poses a challenge for the design of their inhibitors, and therefore, atomistic molecular dynamics (MD) simulations have often been utilized. While protein conformational changes have been increasingly discussed, a fundamental yet non-trivial question remains for the effect of drug compound flexibility, which is hardly detectable from experiments. In this study, we apply two-dimensional replica-exchange MD simulations as enhanced sampling to investigate how c-Src kinase can bind PP1, a small inhibitor, and dasatinib, a larger inhibitor with greater flexibility. 600 microseconds simulations in total sample binding and unbinding events of these inhibitors much more frequently than conventional MD simulation, resulting in statistically converged binding pathways. While the two inhibitors adopt a similar mechanism of multiple binding pathways, the non-canonical binding poses become less feasible for dasatinib. A notable difference is apparent in their energetics where dasatinib stabilizes at intermediate states more than PP1 to raise the barrier toward the canonical pose. Conformational analysis shows that dasatinib adopts linear and bent forms for which relative populations are altered upon binding. We further find hidden conformations of dasatinib at intermediate regions, and unexpectedly one of them could efficiently bypasses the intermediate-to-bound state transition. The results demonstrate that inhibitor size and flexibility impact the binding mechanism, which could potentially modulate inhibitor residence time.
Smoother: A Unified and Modular Framework for Incorporating Structural Dependency in Spatial Omics Data
Authors: Su Jiayu , Reynier Jean-Baptiste , Fu Xi , Zhong Guojie , Jiang Jiahao , Escalante Rydberg Supo , Wang Yiping , Aparicio Luis , Izar Benjamin , Knowles David A , Rabadan Raul
Published: October 2022

Spatial omics technologies can help identify spatially organized biological processes, but existing computational approaches often overlook structural dependencies in the data. Here, we introduce Smoother, a unified framework that integrates positional information into non-spatial models via modular priors and losses. In simulated and real datasets, Smoother enables accurate data imputation, cell-type deconvolution, and dimensionality reduction with remarkable efficiency. In colorectal cancer, Smoother-guided deconvolution revealed plasma cell and fibroblast subtype localizations linked to tumor microenvironment restructuring. Additionally, joint modeling of spatial and single-cell human prostate data with Smoother allowed for spatial mapping of reference populations with significantly reduced ambiguity.
Nonlinear microscale mechanics of actin networks governed by coupling of filament crosslinking and stabilization
Authors: Dwyer Mike , Robertson-Anderson Rae M. , Gurmessa Bekele J.
Published: October 2022

Actin plays a vital role in maintaining the stability and rigidity of biological cells while allowing for cell motility and shape change. The semiflexible nature of actin filaments – along with the myriad actin-binding proteins (ABPs) that serve to crosslink, bundle, and stabilize filaments – are central to this multifunctionality. The effect of ABPs on the structural and mechanical properties of actin network mechanics has been the topic of fervent investigation over the past few decades, revealing diverse structures from isotropic percolated networks to heterogeneous bundles that depend on the crosslinker type and concentration. Yet, the impact of filament stabilization and stiffening via ABPs on the nonlinear response of crosslinked networks has yet to be explored. Here, we perform optical tweezers microheology measurements to characterize the nonlinear force response and relaxation dynamics of actin networks in the presence of varying concentrations ofα-actinin, which transiently crosslinks actin filaments, and phalloidin, which stabilizes filamentous actin and increases its persistence length. We show that crosslinking and stabilization can act both synergistically and antagonistically to tune the network resistance to nonlinear straining. For example, phalloidin-stabilization leads to enhanced elastic response and reduced dissipation at large strains and timescales, while the initial microscale force response is reduced compared to networks without phalloidin. Moreover, we find that stabilization switches this initial response from that of stress-stiffening to softening despite the increased filament stiffness that phalloidin confers. Finally, we show that both crosslinking and stabilization are necessary to elicit these emergent features, while the effect of stabilization on networks without crosslinkers is much more subdued. We suggest that these intriguing mechanical properties arise from the competition and cooperation between filament connectivity, bundling, and rigidification, shedding light on how ABPs with distinct roles can act in concert to mediate diverse mechanical properties of the cytoskeleton and bio-inspired polymeric materials.
Homotopic local-global parcellation of the human cerebral cortex from resting-state functional connectivity
Authors: Yan Xiaoxuan , Kong Ru , Xue Aihuiping , Yang Qing , Orban Csaba , An Lijun , Holmes Avram J. , Qian Xing , Chen Jianzhong , Zuo Xi-Nian , Zhou Juan Helen , Fortier Marielle V , Tan Ai Peng , Gluckman Peter , Chong Yap Seng , Meaney Michael J , Bzdok Danilo , Eickhoff Simon B. , Yeo B.T. Thomas
Published: October 2022

Resting-state fMRI is commonly used to derive brain parcellations, which are widely used for dimensionality reduction and interpreting human neuroscience studies. We previously developed a model that integrates local and global approaches for estimating areal-level cortical parcellations. The resulting local-global parcellations are often referred to as the Schaefer parcellations. However, the lack of homotopic correspondence between left and right Schaefer parcels has limited their use for brain lateralization studies. Here, we extend our previous model to derive homotopic areal-level parcellations. Using resting-fMRI and task-fMRI across diverse scanners, acquisition protocols, preprocessing and demographics, we show that the resulting homotopic parcellations are as homogeneous as the Schaefer parcellations, while being more homogeneous than five publicly available parcellations. Furthermore, weaker correlations between homotopic parcels are associated with greater lateralization in resting network organization, as well as lateralization in language and motor task activation. Finally, the homotopic parcellations agree with the boundaries of a number of cortical areas estimated from histology and visuotopic fMRI, while capturing sub-areal (e.g., somatotopic and visuotopic) features. Overall, these results suggest that the homotopic local- global parcellations represent neurobiologically meaningful subdivisions of the human cerebral cortex and will be a useful resource for future studies. Multi-resolution parcellations estimated from 1479 participants are publicly available (GITHUB_LINK).
Visual awareness during the attentional blink is determined by representational similarity
Authors: Tang Matthew F. , Shapiro Kimron L. , Enns James T. , Visser Troy A.W. , Mattingley Jason B. , Arabzadeh Ehsan
Published: October 2022

Our visual perception seems effortless, but the brain has a limited processing capacity which curtails the amount of sensory information that can be brought into conscious awareness at any moment in time. A widely studied exemplar of this limitation is the ‘attentional blink’ (AB), in which observers are unable to report the second of two rapidly sequential targets if it appears within 200-500 ms of the first. Despite the apparent ubiquity of the AB effect, its computational and neurophysiological underpinnings have remained elusive. Here we propose a simple computational model of temporal attention that unifies the AB with spatial and feature-based attention. We took a novel, integrative approach involving human psychophysics and functional brain imaging, along with neuronal recordings in mice to test this model. Specifically, we demonstrate that the AB only arises when visual targets have dissimilar representations in the brain but is absent when both targets have the same representation. Similarity in this context can be determined either by elementary features such as edge orientation, or by acquired, high-level factors such as numerical or alphabetical order. In this parsimonious model of the AB, attention to an initial target establishes a perceptual filter that is tuned to its unique representation in the brain. Subsequent items that match the filter remain available for conscious report, whereas those that do not match elude awareness altogether.
A novel non-invasive biomarker based on oral microbiome dysbiosis for detection of Community-Acquired Pneumonia
Authors: Sun Ni , Zhang Xuhan , Hou Yating , Zhong Ting
Published: October 2022

Background

Early diagnosis of pathogenic bacteria is crucial for the treatment of community-acquired pneumonia (CAP), but conventional diagnostics are limited by sampling difficulties. Oral microbiota has also been explored as a noninvasive biomarker of lung diseases, but it’s role in CAP has been neglected. We aimed to investigate whether the oral bacteria can be novel non-invasive biomarkers for CAP.

Methods

Oral swab samples were collected from 29 patients with CAP and 26 healthy volunteers and characterized based on clinical parameters and 16S rRNA profiling of oral bacteria. A predict functional profiling was performed for the functional and metabolic changes in oral microbial communities.

Results

Oral microbial of patients with CAP had a lower diversity than healthy group. And the dominant bacteria wereStreptococcus, PrevotellaandNeisseriain CAP. Higher abundance ofPrevotella(particularlyPrevotella_melaninogenica),VeillonellaandCampylobacter, and lower abundance ofNeisseriaandFusobacteriumwere detected in CAP group. Analysis of the functional potential of oral microbiota demonstrated that the pathway involving infectious disease was overrepresented in the CAP groups relative to that in the healthy controls.

Conclusions

Oral microbial dysbiosis was found in patients with CAP, supporting the use of this non-invasive specimen for biomarkers of CAP.

Highlights

Oral microbial diversity was significantly lower in community-acquired pneumonia (CAP) patients than healthy controls.

GeneraNeisseriaandFusobacteriumwere decreased, while generaPrevotella, VeillonellaandCampylobacterwere increased in CAP versus healthy controls.

Oral microbiota-based biomarkers can serve as a promising non-invasive tool for the detection of CAP.
Detecting Heart Failure using novel bio-signals and a Knowledge Enhanced Neural Network
Authors: Nogueira Marta Afonso , Calcagno Simone , Campbell Niall , Zaman Azfar , Koulaouzidis Georgios , Jalil Anwar , Alam Firdous , Stankovic Tatjana , Szabo Erzsebet , Szabo Aniko B. , Kecskes Istvan
Published: October 2022

1

Background

Clinical decisions about Heart Failure (HF) are frequently based on measurements of left ventricular ejection fraction (LVEF), relying mainly on echocardiography measurements for evaluating structural and functional abnormalities of heart disease. As echocardiography is not available in primary care, this means that HF cannot be detected on initial patient presentation. Instead, physicians in primary care must rely on a clinical diagnosis that can take weeks, even months of costly testing and clinical visits. As a result, the opportunity for early detection of HF is lost.

Methods and results

The standard 12-Lead ECG provides only limited diagnostic evidence for many common heart problems. ECG findings typically show low sensitivity for structural heart abnormalities and low specificity for function abnormalities, e.g., systolic dysfunction. As a result, structural and functional heart abnormalities are typically diagnosed by echocardiography in secondary care, effectively creating a diagnostic gap between primary and secondary care. This diagnostic gap was successfully reduced by an AI solution, the Cardio-HART™ (CHART), which uses Knowledge-enhanced Neural Networks to process novel bio-signals. Cardio-HART reached higher performance in prediction of HF when compared to the best ECG-based criteria: sensitivity increased from 53.5% to 82.8%, specificity from 85.1% to 86.9%, positive predictive value from 57.1% to 70.0%, the F-score from 56.4% to 72.2%, and area under curve from 0.79 to 0.91. The sensitivity of the HF-indicated findings is doubled by the AI compared to the best rule-based ECG-findings with a similar specificity level: from 38.6% to 71%.

Conclusion

Using an AI solution to process ECG and novel bio-signals, the CHART algorithms are able to predict structural, functional, and valve abnormalities, effectively reducing this diagnostic gap, thereby allowing for the early detection of most common heart diseases and HF in primary care.
Augmenting CAR NK cell Anti-tumor Activity by Synapse Tuning
Authors: Chockley Peter J , Ibanez-Vega Jorge , Krenciute Giedre , Talbot Lindsay J , Gottschalk Stephen
Published: October 2022

Introductory Paragraph

Chimeric antigen receptor (CAR) technologies have been clinically implemented for the treatment of hematological malignancies; however, solid tumors remain resilient to CAR therapeutics1-3. Natural Killer (NK) cells may provide an optimal class of immune cells for CAR-based approaches due to their inherent anti-tumor functionality. We sought to tune CAR synapses in NK cells by adding an intracellular scaffolding protein binding site to the CAR. We employed a PDZ binding motif (PDZbm) that specifically binds Scribble4resulting in additional scaffolding crosslinking to enhance synapse formation and cell polarization5,6. Combined effects of this novel CAR design resulted in increased effector cell functionalityin vitroandin vivo. Synapse-tuned CAR-NK cells exhibited amplified synaptic strength, number and abundance of secreted cytokines, enhanced killing of tumor cells, and prolonged survival with tumor clearance in two solid tumor models. Thus, synapse tuning has the potential to improve the efficacy of CAR-based cell therapeutics.
Limited Defense of Liver Energy Status in Rats Susceptible to Diet-induced Obesity
Authors: Friedman Mark I , Ji Hong
Published: October 2022

Rats that are susceptible to diet-induced obesity have a preexisting reduced capacity for hepatic fatty acid oxidation compared with those resistant to diet-induced obesity. The eating response to administration of a fatty acid oxidation inhibitor is more closely associated with low liver energy status than it is with reduced hepatic fatty acid oxidation, a finding consistent with studies showing that lowered liver energy status stimulates food intake. To evaluate whether susceptibility to diet-induced obesity is associated with a preexisting impairment in liver energy status, we conducted two experiments in obesity-prone (OP) and -resistant (OR) outbred rats. In one experiment, OP rats increased food intake more than did OR rats during refeeding after a 24 h fast. When fasted and refed again, liver energy status (i.e., liver ATP content, ATP:ADP ratio and phosphorylation index) was lower in OP rats after a fast. When OP animals were refed fixed rations of food, liver energy status increased more slowly during refeeding than it did in OR rats. The delay in restoration of liver energy status during refeeding corresponded to the interval during which OP rats ate significantly more food in the intake test. In a second experiment, liver energy status was lower in OP than it was in OR rats after injection of the fructose analogue, 2,5-anhydro-D-mannitol, which depletes liver ATP. These results suggest that liver energy status is more vulnerable in rats susceptible to diet-induced obesity.
Development and Validation of theVanderbilt PRS-KS, an Instrument to Quantify Polygenic Risk Score Knowledge
Authors: Stubbs Doug , Hooker Gillian , Le Yajing , Richter Lucas , Bick Alexander
Published: October 2022

Purpose

As polygenic risk scores (PRS) enter clinical practice, healthcare providers’ and the publics’ comprehension of PRS results are of great importance, yet poorly understood. We present the Vanderbilt Polygenic Risk Scores Knowledge Score (Vanderbilt PRS-KS), a tool to quantify PRS knowledge.

Methods

The Vanderbilt PRS-KS was developed by a team of genetic counselors and physicians to cover key conceptual facts pertaining to PRSs. We recruited (n=500) individuals with demographics representative of a U.S. sample and graduate-level healthcare students (n=74) at a large academic medical center to participate in this validation study. We evaluated the Vanderbilt PRS-KS’s psychometric properties using confirmatory factor analysis (CFA) and item response theory (IRT).

Results

The 7-item Vanderbilt PRS-KS correlated to a single latent construct on CFA (Λ=0.31-0.61). The scale showed promising reliability (Cronbach’s α=0.66) with IRT summed scores of ≥2 to ≤5, demonstrating reliability > 0.70. The Vanderbilt PRS-KS significantly correlated with genetic knowledge and applied PRS knowledge (r=0.55, r=0.29), and graduate-level healthcare students had significantly higher scores compared to the representative sample (p<0.01).

Conclusions

The Vanderbilt PRS-KS is a rigorously validated measure to quantify PRS knowledge.
Exploring the potential of using simulation games for engaging with sheep farmers about lameness recognition
Authors: Jones Matt L. , Barnish Maxwell S. , Hughes Robert R. , Murray Aimee , Mansour Omid , Loni Tiziana , Vickery Holly , Evans Myfanwy Lloyd , Green Laura , Verdezoto Nervo
Published: October 2022

Introduction

Computer simulation games are increasingly being used in agriculture as a promising tool to study, support and influence real-life farming practices. We explored the potential of using simulation games to engage with sheep farmers on the ongoing challenge of reducing lameness. Working with UK stakeholders, we developed a game in which players are challenged with identifying all the lame sheep in a simulated flock. Here, we evaluate the game’s potential to act as a tool for to help assess, train and understand farmers’ ability to recognise the early signs of lameness.

Methods

Participants in the UK were invited to play the game in an online study, sharing with us their in-game scores alongside information relating to their real-life farming experience, how they played the game, and feedback on the game. Mixed methods were used to analyse this information in order to evaluate the game. Quantitative analyses consisted of linear modelling to test for statistical relationships between participants’ in-game recall (% of the total number of lame sheep that were marked as lame), and the additional information they provided. Qualitative analyses of participants’ feedback on the game consisted of thematic analysis and a Likert Scale questionnaire to contextualise the quantitative results and identify additional insights from the study.

Results

Quantitative analyses identified no relationships between participants’ (n = 63) recall scores and their real life farming experience, or the lameness signs they looked for when playing the game. The only relationship identified was a relationship between participants’ recall score and time spent playing the game. Qualitative analyses identified that participants did not find the game sufficiently realistic or engaging, though several enjoyed playing it and saw potential for future development. Qualitative analyses also identified several interesting and less-expected insights about real-life lameness recognition practices that participants shared after playing the game.

Discussion

Simulation games have potential as a tool in livestock husbandry education and research, but achieving the desired levels of realism and/or engagingness may be an obstacle to realising this. Future research should explore this potential further, aided by larger budgets and closer collaboration with farmers, stockpeople and veterinarians.
Optimizing and benchmarking polygenic risk scores with GWAS summary statistics
Authors: Zhao Zijie , Gruenloh Tim , Yan Meiyi , Wu Yixuan , Sun Zhongxuan , Miao Jiacheng , Wu Yuchang , Song Jie , Lu Qiongshi
Published: October 2022

Background Polygenic risk score (PRS) is a major research topic in human genetics. However, a significant gap exists between PRS methodology and applications in practice due to often unavailable individual-level data for various PRS tasks including model fine-tuning, benchmarking, and ensemble learning. Results We introduce an innovative statistical framework to optimize and benchmark PRS models using summary statistics of genome-wide association studies. This framework builds upon our previous work and can fine-tune virtually all existing PRS models while accounting for linkage disequilibrium. In addition, we provide an ensemble learning strategy named PUMAS-ensemble to combine multiple PRS models into an ensemble score without requiring external data for model fitting. Through extensive simulations and analysis of many complex traits in the UK Biobank, we demonstrate that this approach closely approximates gold-standard analytical strategies based on external validation, and substantially outperforms state-of-the-art PRS methods. Conclusions Our method is a powerful and general modeling technique that can continue to combine the best-performing PRS methods out there through ensemble learning and could become an integral component for all future PRS applications.
Amount of antigen, T follicular helper cells and quality of seeder cells shape the diversity of germinal center B cells
Authors: Garg Amar K. , Mitra Tanmay , Schips Marta , Bandyopadhyay Arnab , Meyer-Hermann Michael
Published: October 2022

A variety of B cell clones seed the germinal centers, where a selection stringency expands the fitter clones to generate higher affinity antibodies. However, recent experiments suggest that germinal centers often retain a diverse set of B cell clones with a range of affinities and concurrently carry out affinity maturation. Amid a tendency to flourish germinal centers with fitter clones, how several B cell clones with differing affinities can be concurrently selected remains poorly understood. Such a permissive selection may allow non-immunodominant clones, which are often rare and of low-affinity, to somatically hypermutate and result in a broad and diverse B cell response. How the constituent elements of germinal centers, their quantity and kinetics may modulate diversity of B cells, has not been addressed well. By implementing a state-of-the-art agent-based model of germinal center, here, we study how these factors impact temporal evolution of B cell clonal diversity and its underlying balance with affinity maturation. While we find that the extent of selection stringency dictates clonal dominance, limited antigen availability on follicular dendritic cells is shown to expedite the loss of diversity of B cells as germinal centers mature. Intriguingly, the emergence of a diverse set of germinal center B cells depends on high affinity founder cells. Our analysis also reveals a substantial number of T follicular helper cells to be essential in balancing affinity maturation with clonal diversity, as a low number of T follicular helper cells impedes affinity maturation and also contracts the scope for a diverse B cell response. Our results have implications for eliciting antibody responses to non-immunodominant specificities of the pathogens by controlling the regulators of the germinal center reaction, thereby pivoting a way for vaccine development to generate broadly protective antibodies.
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

Phenotypic 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

Translational 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

Objects 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

Heterocyclic 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

Nonhomologous 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

The 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

Targeted 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

In 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 points

A 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

How 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 summary

Human 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

Dynein 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

Cable 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.