bluuebunny/crossref_metadata_2025 huggingface dataset:
Posterior parietal cortex is causally involved in reward valuation but not probability weighting during risky choice
Authors: Panidi Ksenia , Vorobiova Alicia Nunez , Feurra Matteo , Klucharev Vasily
Published: February 2023

This study provides evidence that the posterior parietal cortex (PPC) is causally involved in risky decision making via the processing of reward values but not reward probabilities. In the within-group experimental design, participants performed a binary lottery choice task following transcranial magnetic stimulation of the right PPC, left PPC and a right PPC sham (placebo) stimulation. Both, mean-variance and the prospect theory approach to risky choice showed that the PPC stimulation changed participants’ preferences towards greater risk aversion compared to sham. On the behavioral level, after the PPC stimulation the likelihood of choosing a safer option became more sensitive to the difference in standard deviations between lotteries, compared to sham, indicating greater risk avoidance within the meanvariance framework. We also estimated the shift in prospect theory parameters of risk preferences after PPC stimulation. The hierarchical Bayesian approach showed moderate evidence (BF = 7.44 and 5.41 for right and left PPC respectively) for a credible change in risk aversion parameter towards lower marginal reward value (and, hence, lower risk tolerance), while no credible change in probability weighting was observed. Additionally, we observed anecdotal evidence (BF = 2.9) for a credible increase in the consistency of responses after the left PPC stimulation compared to sham.
HMMSTRTM: A hidden Markov model for local structure prediction in globular and membrane associated proteins
Authors: Benavides Tiburon , Bystroff Christopher
Published: February 2023

Motivation

We present HMMSTRTM, a Hidden Markov Model (HMM) that is useful for predicting topology of trans-membrane (TM) proteins. HMMSTRTM provides additional prediction categories of TM regions provided by the PDBTM corpus such as transmembrane beta sheets, coils, and reentrant loops.

Results

HMMSTRTM is competitive with existing TM protein topology predictors like TMHMM, it correctly predicts at least half the residues in 96.18% of all transmembrane helices in a cross validation dataset.

Availability

Model architecture, source code, and supplementary figures are made available on github:github.com/TiburonB/HMMSTRTM.

Contact

bystrc@rpi.edu
Delineating regional vulnerability in the neurodegenerative disease SCA1 using a conditional mutant ATXN1 mouse
Authors: Duvick Lisa , Southern W. Michael , Benzow Kellie , Burch Zoe N. , Handler Hillary P. , Mitchell Jason S. , Kuivinen Hannah , Gadiparthi Udaya Keerthy , Yang Praseuth , Soles Alyssa , Scheeler Carrie , Rainwater Orion , Serres Shannah , Lind Erin , Nichols-Meade Tessa , O’Callaghan Brennon , Zoghbi Huda Y. , Cvetanovic Marija , Wheeler Vanessa C. , Ervasti James M. , Koob Michael D. , Orr Harry T.
Published: February 2023

Spinocerebellar ataxia type 1 (SCA1) is a fatal neurodegenerative disease caused by an expanded polyglutamine tract in the widely expressed ATXN1 protein. To elucidate anatomical regions and cell types that underlie mutant ATXN1-induced disease phenotypes, we developed a floxed conditional knockout mouse model (f-ATXN1146Q/2Q) having mouseAtxn1coding exons replaced by human exons encoding 146 glutamines.F-ATXN1146Q/2Qmice manifest SCA1-like phenotypes including motor and cognitive deficits, wasting, and decreased survival. CNS contributions to disease were revealed usingATXN1146Q/2Q;Nestin-Cremice, that showed improved rotarod, open field and Barnes maze performances. Striatal contributions to motor deficits were examined usingf-ATXN1146Q/2Q;Rgs9-Cremice. Mice lacking striatalATXN1146Q/2Qhad improved rotarod performance late in disease. Muscle contributions to disease were revealed inf-ATXN1146Q/2Q;ACTA1-Cremice which lacked muscle pathology and kyphosis seen inf-ATXN1146Q/2Qmice. Kyphosis was not improved inf-ATXN1146Q/2Q;Nestin-Cremice. Thus, optimal SCA1 therapeutics will require targeting mutant ATXN1 toxic actions in multiple brain regions and muscle.
Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR
Authors: Troussicot Laura , Vallet Alicia , Molin Mikael , Burmann Björn M. , Schanda Paul
Published: February 2023

Disulfide bond formation is fundamentally important for protein structure, and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide by using a catalytic cycle of Cys oxidation and reduction. High molecular-weight assemblies of PRDXs have recently been shown to additionally act as molecular chaperones. The consequences of disulfide bonds on the dynamics of these large assemblies are poorly understood. We show that formation of disulfide bonds along the catalytic cycle induces extensive μs time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfil other favorable contacts.
Size and locomotor ecology have differing effects on the external and internal morphologies of squirrel (Rodentia: Sciuridae) limb bones
Authors: Rickman Johannah , Burtner Abigail E , Linden Tate J , Santana Sharlene E , Law Chris J
Published: February 2023

Mammals exhibit a diverse range of limb morphologies that are associated with different locomotor ecologies and structural mechanics. Much remains to be investigated, however, about the combined effects of locomotor modes and scaling on the external shape and structural properties of limb bones. Here, we used squirrels (Sciuridae) as a model clade to examine the effects of locomotor mode and scaling on the external shape and structure of the two major limb bones, the humerus and femur. We quantified humeral and femoral morphologies using 3D geometric morphometrics and bone structure analyses on a sample of 76 squirrel species across their four major ecotypes. We then used phylogenetic generalized linear models to test how locomotor ecology, size, and their interaction influenced morphological traits. We found that size and locomotor mode exhibit different relationships with the external shape and structure of the limb bones, and that these relationships differ between the humerus and femur. External shapes of the humerus and, to a lesser extent, the femur are best explained by locomotor ecology rather than by size, whereas structures of both bones are best explained by interactions between locomotor ecology and scaling. Interestingly, the statistical relationships between limb morphologies and ecotype were lost when accounting for phylogenetic relationships among species under Brownian motion. That assuming Brownian motion confounded these relationships is not surprising considering squirrel ecotypes are phylogenetically clustered; our results suggest that humeral and femoral variation partitioned early between clades and their ecomorphologies were maintained to the present. Overall, our results show how mechanical constraints, locomotor ecology, and evolutionary history may enact different pressures on the shape and structure of limb bones in mammals.
Ciliary ARL13B inhibits developmental kidney cystogenesis in mouse
Authors: Van Sciver Robert E. , Long Alyssa B. , Katz Harrison G. , Gigante Eduardo D. , Caspary Tamara
Published: February 2023

ARL13B is a small GTPase enriched in cilia. Deletion ofArl13bin mouse kidney results in renal cysts and an associated absence of primary cilia. Similarly, ablation of cilia leads to kidney cysts. To investigate whether ARL13B functions from within cilia to direct kidney development, we examined kidneys of mice expressing an engineered cilia-excluded ARL13B variant, ARL13BV358A. These mice retained renal cilia and developed cystic kidneys. Because ARL13B functions as a guanine nucleotide exchange factor (GEF) for ARL3, we examined kidneys of mice expressing an ARL13B variant that lacks ARL3 GEF activity, ARL13BR79Q. We found normal kidney development with no evidence of cysts in these mice. Taken together, our results show that ARL13B functions within cilia to inhibit renal cystogenesis during mouse development, and that this function does not depend on its role as a GEF for ARL3.
Modulation of Retinal Inflammation Delays Degeneration in a Mouse Model of Geographic Atrophy
Authors: Ridley Raela B , Bowman Brianna M , Lee Jieun , Walsh Erin , Massengill Michael T , Lewin Alfred S , Ildefonso Cristhian J
Published: February 2023

The advanced form of AMD, geographic atrophy, is associated with increased RPE oxidative stress and chronic inflammation. Here we evaluated the effects of delivering an anti-inflammatory viral gene by an AAV-vector in a mouse model of geographic atrophy. We measured changes in retinal function, structure, and morphology over nine months with electroretinography, optical coherence tomography, and fundoscopy, respectively. In addition, we used retinal tissue to quantify changes in markers of inflammation by multiplex ELISA, RT-qPCR, and immunofluorescence staining. Our AAV significantly delayed the loss of retinal function and structure and decreased retinal inflammation compared to the control AAV treatment. Our results suggest that modulating retinal inflammation could significantly slow the progression of geographic atrophy.
Impact of experimental bias on compositional analysis of microbiome data
Authors: Hu Yingtian , Satten Glen A. , Hu Yi-Juan
Published: February 2023

Microbiome data are subject to experimental bias that is caused by DNA extraction, PCR amplification among other sources, but this important feature is often ignored when developing statistical methods for analyzing microbiome data. McLaren, Willis and Callahan (2019) proposed a model for how such bias affects the observed taxonomic profiles, which assumes main effects of bias without taxon-taxon interactions. Our newly developed method, LOCOM (logistic regression for compositional analysis) for testing differential abundance of taxa, is the first method that accounted for experimental bias and is robust to the main effect biases. However, there is also evidence for taxon-taxon interactions. In this report, we formulated a model for interaction biases and used simulations based on this model to evaluate the impact of interaction biases on the performance of LOCOM as well as other available compositional analysis methods. Our simulation results indicated that LOCOM remained robust to a reasonable range of interaction biases. The other methods tended to have inflated FDR even when there were only main effect biases. LOCOM maintained the highest sensitivity even when the other methods cannot control the FDR. We thus conclude that LOCOM outperforms the other methods for compositional analysis of microbiome data considered here.
Massively parallel protein-protein interaction measurement by sequencing (MP3-seq) enables rapid screening of protein heterodimers
Authors: Baryshev Alexander , La Fleur Alyssa , Groves Benjamin , Michel Cirstyn , Baker David , Ljubetič Ajasja , Seelig Georg
Published: February 2023

Protein-protein interactions (PPIs) regulate many cellular processes, and engineered PPIs have cell and gene therapy applications. Here we introduce massively parallel protein-protein interaction measurement by sequencing (MP3-seq), an easy-to-use and highly scalable yeast-two-hybrid approach for measuring PPIs. In MP3-seq, DNA barcodes are associated with specific protein pairs, and barcode enrichment can be read by sequencing to provide a direct measure of interaction strength. We show that MP3-seq is highly quantitative and scales to over 100,000 interactions. We apply MP3-seq to characterize interactions between families of rationally designed heterodimers and to investigate elements conferring specificity to coiled-coil interactions. Finally, we predict coiled heterodimer structures using AlphaFold-Multimer (AF-M) and train linear models on physics simulation energy terms to predict MP3-seq values. We find that AF-M and AF-M complex prediction-based models could be valuable for pre-screening interactions, but that measuring interactions experimentally remains necessary to rank their strengths quantitatively.
Epidemiological analysis of the gender-age structure of hospitalized patients with COVID-19 and their mortality in 2020-2021
Authors: Voronin Evgeny M. , Khrapunova Izabella A. , Pechenik Andrey S. , Kravtsova Olga A. , Chen Zhang , Kostinov Mikhail P. , Loktionova Marina N. , Yakovleva Irina V. , Akimkin Vasily G. , Brazhnik Victoria A.
Published: February 2023

Background

The pandemic of the new coronavirus infection COVID-19 determines the relevance of conducting a study of the gender-age structure of hospitalized and deceased among the population of Moscow on the example of one of the city clinical hospitals in 2020 – 2021.

The aim of the work is to identify the patterns of the epidemic process of COVID-19 in connection with the gender and age characteristics of hospitalized adults and to establish the sex and age groups most susceptible to hospitalization and mortality from COVID-19.

Materials and methods

The analysis of the structure of hospitalized and deceased from COVID-19 in the context of their gender and age composition was carried out. The data of the statistical accounting form F-60u/lech “Journal of infectious diseases” of adults hospitalized in one of the city clinical hospitals of Moscow in 2020 – 2021 were used. Data processing was carried out by a set of standard statistical methods. To identify the true risk groups for hospitalization and mortality, a statistical correction of the sex and age composition of the population of Moscow was used.

Results and discussion

Using standard statistical methods in combination with the use of statistical correction of sex and age composition, data on the true risk groups for hospitalization and mortality among the population of Moscow in 2020 – 2021 were obtained.

Conclusion

The results obtained in our independent study on the true risk groups for hospitalization and mortality among the population of Moscow complement and introduce new knowledge about the true risk groups for hospitalization and mortality in COVID-19. The patterns identified in this epidemiological analysis are an important component of epidemiological surveillance for making managerial decisions to prevent the spread of SARS-CoV-2 and planning for the provision of inpatient medical care to established gender and age risk groups.
Explainable Machine Learning Predictions of Perceptual Sensitivity for Retinal Prostheses
Authors: Pogoncheff Galen , Hu Zuying , Rokem Ariel , Beyeler Michael
Published: February 2023

To provide appropriate levels of stimulation, retinal prostheses must be calibrated to an individual’s perceptual thresholds (‘system fitting’), despite thresholds varying drastically across subjects, across electrodes within a subject, and over time. Although previous work has identified electrode-retina distance and impedance as key factors affecting thresholds, an accurate predictive model is still lacking. To address these challenges, we 1) fitted machine learning (ML) models to a large longitudinal dataset with the goal of predicting individual electrode thresholds and deactivation as a function of stimulus, electrode, and clinical parameters (‘predictors’) and 2) leveraged explainable artificial intelligence (XAI) to reveal which of these predictors were most important. Our models accounted for up to 77% of the perceptual threshold response variance and enabled predictions of whether an electrode was deactivated in a given trial with F1 and AUC scores of up to 0.740 and 0.913, respectively. Deactivation and threshold models identified novel predictors of perceptual sensitivity, including subject age, time since blindness onset, and electrode-fovea distance. Our results demonstrate that routinely collected clinical measures and a single session of system fitting might be sufficient to inform an XAI-based threshold prediction strategy, which may transform clinical practice in predicting visual outcomes.
Association of Healthy Dietary Patterns and Cardiorespiratory Fitness in the Community
Authors: Mi Michael Y. , Gajjar Priya , Walker Maura E. , Miller Patricia , Xanthakis Vanessa , Murthy Venkatesh L. , Larson Martin G. , Vasan Ramachandran S. , Shah Ravi V. , Lewis Gregory D. , Nayor Matthew
Published: February 2023

Aims

To evaluate the associations of dietary indices and quantitative CRF measures in a large, community-based sample harnessing metabolomic profiling to interrogate shared biology.

Methods

Framingham Heart Study (FHS) participants underwent maximum effort cardiopulmonary exercise tests for CRF quantification (via peak VO2) and completed semi-quantitative FFQs. Dietary quality was assessed by the Alternative Healthy Eating Index (AHEI) and Mediterranean-style Diet Score (MDS), and fasting blood concentrations of 201 metabolites were quantified.

Results

In 2380 FHS participants (54±9 years, 54% female, BMI 28±5 kg/m2), 1-SD higher AHEI and MDS were associated with 5.1% (1.2 ml/kg/min, p<0.0001) and 4.4% (1.0 ml/kg/min, p<0.0001) greater peak VO2in linear models adjusted for age, sex, total energy intake, cardiovascular risk factors, and physical activity. In participants with metabolite profiling (N=1154), 24 metabolites were concordantly associated with both dietary indices and peak VO2in multivariable-adjusted linear models (FDR<5%). These metabolites included C6 and C7 carnitines, C16:0 ceramide, and dimethylguanidino valeric acid, which were higher with lower CRF and poorer dietary quality and are known markers of insulin resistance and cardiovascular risk. Conversely, C38:7 phosphatidylcholine plasmalogen and C38:7 and C40:7 phosphatidylethanolamine plasmalogens were associated with higher CRF and favorable dietary quality and may link to lower cardiometabolic risk.

Conclusion

Higher diet quality is associated with greater CRF cross-sectionally in a middle-aged community-dwelling sample, and metabolites highlight potential shared favorable effects on health.
Social deprivation and SARS-CoV-2 testing: a population-based analysis in a highly contrasted Southern France region
Authors: Landier Jordi , Bassez Léa , Bendiane Marc-Karim , Chaud Pascal , Franke Florian , Nauleau Steve , Danjou Fabrice , Malfait Philippe , Rebaudet Stanislas , Gaudart Jean
Published: February 2023

Background

Testing was the cornerstone of the COVID-19 epidemic response in most countries until vaccination became available for the general population. Social inequalities generally affect access to healthcare and health behaviours, and COVID-19 was rapidly shown to impact deprived population more drastically. In support of the regional health agency in Provence-Alpes-Côte d’Azur (PACA) in South-Eastern France, we analysed the relationship between testing rate and socio-demographic characteristics of the population, to identify gaps in testing coverage and improve targeting of response strategies.

Methods

We conducted an ecological analysis of SARS-CoV-2/COVID-19 testing rate in the PACA region, based on data aggregated at the finest spatial resolution available in France (IRIS) and by periods defined by public health implemented measures and major epidemiological changes. Using general census data, population density, and specific deprivation indices, we used principal component analysis followed by hierarchical clustering to define profiles describing local socio-demographic characteristics. We analysed the association between these profiles and testing rates in a generalized additive multilevel model, adjusting for access to healthcare, presence of a retirement home, and the age profile of the population.

Results

We identified 6 socio-demographic profiles across the 2,306 analysed IRIS spatial units: privileged, remote, intermediate, downtown, deprived and very deprived (ordered by increasing social deprivation index). Profiles also ranged from rural (remote) to high density urban areas (downtown, very deprived). From July 2020 to December 2021, we analysed SARS-CoV-2/COVID-19 testing rate over 10 periods. Testing rates fluctuated strongly but were highest in privileged and downtown areas, and lowest in very deprived ones. The lowest adjusted testing rate ratios (aTRR) between privileged (reference) and other profiles occurred after implementation of a mandatory healthpass for many leisure activities in July 2021. Periods of contextual testing near Christmas displayed the largest aTRR, especially during the last periods of 2021 after the end of free convenience testing for unvaccinated individuals.

Conclusions

We characterized in-depth local heterogeneity and temporal trends in testing rates and identified areas and circumstances associated with low testing rates, which the regional health agency targeted specifically for the deployment of health mediation activities.
GENIUS: GEnome traNsformatIon and spatial representation of mUltiomicS data
Authors: Sokač Mateo , Kjær Asbjørn , Dyrskjøt Lars , Haibe-Kains Benjamin , Aerts Hugo J.W.L. , Birkbak Nicolai J
Published: February 2023

The application of next-generation sequencing (NGS) has transformed cancer research. As costs have decreased, NGS has increasingly been applied to generate multiple layers of molecular data from the same samples, covering genomics, transcriptomics, and methylomics. Integrating these types of multi-omics data in a combined analysis is now becoming a common issue with no obvious solution, often handled on an ad-hoc basis, with multi-omics data arriving in a tabular format and analyzed using computationally intensive statistical methods. These methods particularly ignore the spatial orientation of the genome and often apply stringent p-value corrections that likely result in the loss of true positive associations. Here, we present GENIUS (GEnome traNsformatIon and spatial representation of mUltiomicS data), a framework for integrating multi-omics data using deep learning models developed for advanced image analysis. The GENIUS framework is able to transform multi-omics data into images with genes displayed as spatially connected pixels and successfully extract relevant information with respect to the desired output. Here, we demonstrate the utility of GENIUS by applying the framework to multi-omics datasets from the Cancer Genome Atlas. Our results are focused on predicting the development of metastatic cancer from primary tumors, and demonstrate how through model inference, we are able to extract the genes which are driving the model prediction and likely associated with metastatic disease progression. We anticipate our framework to be a starting point and strong proof of concept for multi-omics data transformation and analysis without the need for statistical correction.
Prioritizing Complex Disease Genes from Heterogeneous Public Databases
Authors: Gong Eric , Chen Jake Y.
Published: February 2023

Background

Complex human diseases are defined not only by sophisticated patterns of genetic variants/mutations upstream but also by many interplaying genes, RNAs, and proteins downstream. Analyzing multiple genomic and functional genomic data types to determine a short list of genes or molecules of interest is a common task called “gene prioritization” in biology. There are many statistical, biological, and bioinformatic methods developed to perform gene prioritization tasks. However, little research has been conducted to examine the relationships among the technique used, merged/separate use of each data modality, the gene list’s network/pathway context, and various gene ranking/expansions.

Methods

We introduce a new analytical framework called “Gene Ranking and Iterative Prioritization based on Pathways” (GRIPP) to prioritize genes derived from different modalities. Multiple data sources, such as CBioPortal, PAGER, and COSMIC were used to compile the initial gene list. We used the PAGER software to expand the gene list based on biological pathways and the BEERE software to construct protein-protein interaction networks that include the gene list to rank order genes. We produced a final gene list for each data modality iteratively from an initial draft gene list, using glioblastoma multiform (GBM) as a case study.

Conclusion

We demonstrated that GBM gene lists obtained from three modalities (differential gene expressions, gene mutations, and copy number alterations) and several data sources could be iteratively expanded and ranked using GRIPP. While integrating various modalities of data can be useful to generate an integrated ranked gene list related to any specific disease, the integration may also decrease the overall significance of ranked genes derived from specific data modalities. Therefore, we recommend carefully sorting and integrating gene lists according to each modality, such as gene mutations, epigenetic controls, or differential expressions, to procure modality-specific biological insights into the prioritized genes.
Single cell transcriptomics identifies adipose tissue CD271+ progenitors for enhanced angiogenesis in limb ischemia
Authors: Inoue Oto , Goten Chiaki , Hashimuko Daiki , Yamaguchi Kosei , Takeda Yusuke , Nomura Ayano , Ootsuji Hiroshi , Takashima Shinichiro , Iino Kenji , Takemura Hirofumi , Halurkar Manasi , Lim Hee-Woong , Hwa Vivian , Sanchez-Gurmaches Joan , Usui Soichiro , Takamura Masayuki
Published: February 2023

Therapeutic angiogenesis using mesenchymal stem/stromal cell grafts have shown modest and controversial effects in preventing amputation for patients with critical limb ischemia. Through single-cell transcriptomic analysis of human tissues, we identified CD271+progenitors specifically from subcutaneous adipose tissue (AT) as having the most prominent pro-angiogenic gene profile distinct from other stem cell populations. AT-CD271+progenitors demonstrated robustin vivoangiogenic capacity, over conventional adipose stromal cell grafts, characterized by long-term engraftment, augmented tissue regeneration, and significant recovery of blood flow in a xenograft model of limb ischemia. Mechanistically, the angiogenic capacity of CD271+progenitors is dependent on functional CD271 and mTOR signaling. Notably, the number and angiogenic capacity of CD271+progenitors was strikingly reduced in insulin resistant donors. Our study highlights the identification of AT-CD271+progenitors within vivosuperior efficacy for limb ischemia. Furthermore, we showcase comprehensive single-cell transcriptomics strategies for identification of suitable grafts for cell therapy.

HIGHLIGHTS

Adipose tissue stromal cells have a distinct angiogenic gene profile among human cell sources.

CD271+progenitors in adipose tissue have a prominent angiogenic gene profile.

CD271+progenitors show superior therapeutic capacities for limb ischemia.

CD271+progenitors are reduced and functionally impaired in insulin resistant donors.

GRAPHICAL ABSTRACT
Nicotinic acetylcholine receptor signaling maintains epithelial barrier integrity
Authors: Katheder Nadja S. , Browder Kristen C. , Chang Diana , De Mazière Ann , Kujala Pekka , van Dijk Suzanne , Klumperman Judith , Lai Zijuan , Sangaraju Dewakar , Jasper Heinrich
Published: February 2023

Disruption of epithelial barriers is a common disease manifestation in chronic degenerative diseases of the airways, lung and intestine. Extensive human genetic studies have identified risk loci in such diseases, including in chronic obstructive pulmonary disease (COPD) and inflammatory bowel diseases (IBD). The genes associated with these loci have not fully been determined, and functional characterization of such genes requires extensive studies in model organisms. Here, we report the results of a screen inDrosophila melanogasterthat allowed for rapid identification, validation and prioritization of COPD risk genes that were selected based on risk loci identified in human genome-wide association studies (GWAS) studies. Using intestinal barrier dysfunction in flies as a readout, our results validate the impact of candidate gene perturbations on epithelial barrier function in 56% of the cases, resulting in a prioritized target gene list. We further report the functional characterization in flies of one family of these genes, encoding for nicotinic acetylcholine receptor subunits (nAchR). We find that nAchR signaling in enterocytes of the fly gut promotes epithelial barrier function and epithelial homeostasis by regulating the production of the peritrophic matrix. Our findings identify COPD associated genes critical for epithelial barrier maintenance, and provide insight into the role of epithelial nAchR signaling for homeostasis.
Severe neurometabolic phenotype innpc1-/-zebrafish with a C-terminal mutation
Authors: Quelle-Regaldie Ana , Gandoy-Fieiras Nerea , Rodríguez-Villamayor Paula , Maceiras Sandra , Losada Ana Paula , Folgueira Mónica , Cabezas-Sáinz Pablo , Barreiro-Iglesias Antón , Villar-López María , Quiroga Berdeal María Isabel , Sánchez Laura , Sobrido María-Jesús
Published: February 2023

Niemann Pick disease type C (NPC) is an autosomal recessive neurodegenerative lysosomal disorder characterized by an accumulation of lipids in different organs. Clinical manifestations can start at any age and include hepatosplenomegaly, intellectual impairment, and cerebellar ataxia.NPC1is the most common causal gene, with over 460 different mutations with heterogeneous pathological consequences. We generated a zebrafish NPC1 model by CRISPR/Cas9 carrying a homozygous mutation in exon 22, which encodes the end of the cysteine-rich luminal loop of the protein. This is the first zebrafish model with a mutation in this gene region, which is frequently involved in the human disease. We observed a high lethality innpc1mutants, with all larvae dying before reaching the adult stage.Npc1mutant larvae were smaller than wild type (wt) and their motor function was impaired. We observed vacuolar aggregations positive to cholesterol and sphingomyelin staining in the liver, intestine, renal tubules and cerebral gray matter of mutant larvae. RNAseq comparison betweennpc1mutants and controls showed 249 differentially expressed genes, including genes with functions in neurodevelopment, lipid exchange and metabolism, muscle contraction, cytoskeleton, angiogenesis, and hematopoiesis. Lipidomic analysis revealed significant reduction of cholesteryl esters and increase of sphingomyelin in the mutants. Compared to previously available zebrafish models, our model seems to recapitulate better the early onset forms of the NPC disease. Thus, this new model of NPC will allow future research in the cellular and molecular causes/consequences of the disease and on the search for new treatments.
DRomics, a workflow to exploit dose-response omics data in ecotoxicology
Authors: Delignette-Muller Marie Laure , Siberchicot Aurélie , Larras Floriane , Billoir Elise
Published: February 2023

Omics technologies has opened new possibilities to assess environmental risks and to understand the mode(s) of action of pollutants. Coupled to dose-response experimental designs, they allow a non-targeted assessment of organism responses at the molecular level along an exposure gradient. However, describing the dose-response relationships on such high-throughput data is no easy task. In a first part, we review the software available for this purpose, and their main features. We set out arguments on some statistical and modeling choices we have made while developing the R package DRomics and its positioning compared to others tools. The DRomics main analysis workflow is made available through a web interface, namely a shiny app named DRomics-shiny. Next, we present the new functionalities recently implemented. DRomics has been augmented especially to be able to handle varied omics data considering the nature of the measured signal (e.g. counts of reads in RNAseq) and the way data were collected (e.g. batch effect, situation with no experimental replicates). Another important upgrade is the development of tools to ease the biological interpretation of results. Various functions are proposed to visualize, summarize and compare the responses, for different biological groups (defined from biological annotation), optionally at different experimental levels (e.g. measurements at several omics level or in different experimental conditions). A new shiny app named DRomicsInterpreter-shiny is dedicated to the biological interpretation of results. The institutional web pagehttps://lbbe.univ-lyon1.fr/fr/dromicsgathers links to all resources related to DRomics, including the two shiny applications.
Plastid fatty acid export (FAX) proteins inArabidopsis thaliana- the role of FAX1 and FAX3 in growth and development
Authors: Bugaeva Wassilina , Könnel Anne , Peter Janick , Mees Julia , Hankofer Valentin , Schick Cordula , Schmidt Alexander , Banguela-Castillo Alexander , Philippar Katrin
Published: February 2023

In plant cells, fatty acid (FA) synthesis occurs in the plastid stroma and thus requires subsequent FA export for lipid assembly in the endoplasmic reticulum. In this context, the membrane-intrinsic protein FAX1 has been described to mediate FA-export across the plastid inner envelope (IE). InArabidopsis,FAX1 function is crucial for pollen cell wall formation, male fertility, cellular lipid homeostasis and plant biomass. Based on conserved structural features and sequence motifs, we here define the plant FAX-protein family localized in plastids. Besides their membrane-intrinsic domain, the plastid-targeted FAX1-FAX3 contain distinct N-terminal stretches. Among them, the apolipoprotein-like α-helical bundle of FAX2 is the most prominent. Further, we could unequivocally localize FAX2 and FAX3 proteins together with FAX1 to the IE membrane of chloroplasts and develop a topology model for FAX1, FAX2, and FAX3. In yeast, all plastid FAX proteins – i.e. FAX1, FAX2, FAX3, FAX4 – can complement for FA-transport function. For FAX1 we show a new function in pollen tube growth as well as together with FAX3 in seed/embryo development and in rosette leaf growth. Since in comparison tofax1single knockout mutants,fax1/fax3double knockouts are seedling lethal and not able to develop mature rosette leaves, we conclude that FAX1 and FAX3 function together in vegetative leaf growth.

Highlight

We define distinct structural features of plant FAX proteins in plastids and demonstrate that FAX1 and FAX3 have complementary functions in vegetative leaf growth.
The critical role ofDmnt1during spermatogenesis is not predictable, but knockdown does cause pervasive differential transcription
Authors: Cunningham Christopher B. , Shelby Emily A. , McKinney Elizabeth C. , Schmitz Robert J. , Moore Allen J. , Moore Patricia J.
Published: February 2023

Cytosine methylation and its machinery influence the gene expression of many eukaryotes; however, insects are an exception to this general tenet despite many lineages retaining methyltransferases and methylated genomes. Here, we tested thea priorihypothesis that perturbed genetic pathways will be associated with meiosis using transcriptomics because previous our work usingOncopeltus fasciatusshows that gametogenesis is interrupted at meiosis following knockdown ofDNA methyltransferase 1(Dnmt1). Testes, which are almost exclusively contain gametes at varying stages of development, were sampled at 7-days and 14-days following knockdown ofDmnt1using RNAi. Using microscopy, we found actively dividing spermatocysts were reduced at both sampling points. However, we found limited support of perturbation for our predicted cell cycle and meiotic pathways and only at 14-days. We found that Gene Ontology terms had no preferential enrichment for meiosis-associated genes. Following oura prioritests, we used the full dataset to uncover further candidate pathways influenced byDnmt1knockdown. Very few genes were differentially expressed at 7-days, but nearly half were at 14-days. We did not find strong candidate pathways for howDnmt1knockdown was achieving its effect through Gene Ontology term overrepresentation analysis. Given the evidence from microscopy, we proposeDnmt1knockdown results in condensed nuclei after mitosis-meiosis transition and then cellular arrest. This explanation posits that differential gene expression is a product of comparing healthy to arrested cells and is not a targeted response.
Dissecting 16p11.2 hemi-deletion to study sex-specific striatal phenotypes of neurodevelopmental disorders
Authors: Kim Jaekyoon , Vanrobaeys Yann , Peterson Zeru , Kelvington Benjamin , Gaine Marie E. , Nickl-Jockschat Thomas , Abel Ted
Published: February 2023

Neurodevelopmental disorders (NDDs) are polygenic in nature and copy number variants (CNVs) are ideal candidates to study the nature of this polygenic risk. The disruption of striatal circuits is considered a central mechanism in NDDs. The 16p11.2 hemi-deletion (16p11.2 del) is one of the most common CNVs associated with NDD, and 16p11.2 del/+ mice show sex-specific striatum-related behavioral phenotypes. However, the critical genes among the 27 genes in the 16p11.2 region that underlie these phenotypes remain unknown. Previously, we applied a novel strategy to identify candidate genes associated with the sex-specific phenotypes of 16p11.2 del/+ mice and identified 3 genes of particular importance within the deleted region: thousand and one amino acid protein kinase 2 (Taok2), seizure-related 6 homolog-like 2 (Sez6l2), and major vault protein (Mvp). Using the CRISPR/Cas9 technique, we generated 3 gene hemi-deletion (3g del/+) mice carrying null mutations inTaok2, Sez6l2, andMvp. We assessed striatum-dependent phenotypes of these 3g del/+ mice in behavioral, molecular, and imaging studies. Hemi-deletion ofTaok2, Sez6l2, andMvpinduces sex-specific behavioral alterations in striatum-dependent behavioral tasks, specifically male-specific hyperactivity and impaired motivation for reward seeking, resembling behavioral phenotypes of 16p11.2 del/+ mice. Moreover, RNAseq analysis revealed that 3g del/+ mice exhibit gene expression changes in the striatum similar to 16p11.2 del/+ mice, but only in males. Pathway analysis identified ribosomal dysfunction and translation dysregulation as molecular mechanisms underlying male-specific, striatum-dependent behavioral alterations. Together, the mutation of 3 genes within the 16p11.2 region phenocopies striatal sex-specific phenotypes of 16p11.2 del/+ mice, unlike single gene mutation studies. These results support the importance of a polygenic approach to study NDDs and our novel strategy to identify genes of interest using gene expression patterns in brain regions, such as the striatum, which are impacted in these disorders.
The role of the epipeptide EpeX in defining competitive fitness in intra-species mixed isolate colony biofilms ofBacillus subtilis
Authors: Kalamara Margarita , Abbott James , Sukhodub Tetyana , MacPhee Cait , Stanley-Wall Nicola R.
Published: February 2023

Bacteria engage in competitive interactions with neighbours that can either be of the same or different species. Multiple mechanisms are deployed to ensure the desired outcome and one tactic commonly implemented is the production of specialised metabolites. The Gram-positive bacteriumBacillus subtilisuses specialised metabolites as part of its intraspecies competition determinants to differentiate between kin and non-kin isolates. It is, however, unknown if the collection of specialised metabolites defines competitive fitness when the two isolates start as a close, interwoven community that grows into a densely packed colony biofilm. Moreover, the identity of the most effective specialised metabolites has not been revealed. Here, we determine the competition outcomes that manifest when 21 environmental isolates ofB. subtilisare individually co-incubated with the model isolate NCIB 3610 in a colony biofilm. We correlated these data with the suite of specialised metabolite biosynthesis clusters encoded by each isolate. We found that theepeXEPABgene cluster correlated with a strong competitive phenotype. This cluster is responsible for producing the epipeptide EpeX. We demonstrated that EpeX is a competition determinant ofB. subtilisin an otherwise isogenic context. When we competed the NCIB 3610 EpeX deficient strain against our suite of environmental isolates we found that the impact of EpeX in competition is isolate-specific, as only one of the 21 isolates showed increased survival when EpeX was lacking. Taken together, we have shown that EpeX is a competition determinant used byB. subtilisthat impacts intra-species interactions in an isolate-specific manner.
A Single-Cell RNA-Seq Analysis Unravels the Heterogeniety of Primary Cultured Human Corneal Endothelial Cells
Authors: Català Pere , Groen Nathalie , LaPointe Vanessa L.S. , Dickman Mor M.
Published: February 2023

The primary culture of donor-derived human corneal endothelial cells (CECs) is a promising cell therapy. It confers the potential to treat multiple patients from a single donor, alleviating the global donor shortage. Nevertheless, this approach has limitations preventing its adoption, particularly culture protocols allow limited expansion of CECs and there is a lack of clear parameters to identify therapy-grade CECs. To address this limitation, a better understanding of the molecular changes arising from the primary culture of CECs is required. Using single- cell RNA sequencing on primary cultured CECs, we identify their variable transcriptomic fingerprint at the single cell level, provide a pseudo temporal reconstruction of the changes arising from primary culture, and suggest markers to assess the quality of primary CEC cultures. This research depicts a deep transcriptomic understanding of the cellular heterogeneity arising from the primary expansion of CECs and sets the basis for further improvement of culture protocols and therapies.
The Burden of Reliability: How Measurement Noise Limits Brain-Behaviour Predictions
Authors: Gell Martin , Eickhoff Simon B. , Omidvarnia Amir , Küppers Vincent , Patil Kaustubh R. , Satterthwaite Theodore D. , Müller Veronika I. , Langner Robert
Published: February 2023

Major efforts in human neuroimaging strive to understand individual differences and find biomarkers for clinical applications by predicting behavioural phenotypes from brain imaging data. An essential prerequisite for identifying generalizable and replicable brain-behaviour prediction models is sufficient measurement reliability. However, the selection of prediction targets is predominantly guided by scientific interest or data availability rather than reliability considerations. Here we demonstrate the impact of low phenotypic reliability on out-of-sample prediction performance. Using simulated and empirical data from the Human Connectome Projects, we found that reliability levels common across many phenotypes can markedly limit the ability to link brain and behaviour. Next, using 5000 subjects from the UK Biobank, we show that only highly reliable data can fully benefit from increasing sample sizes from hundreds to thousands of participants. Overall, our findings highlight the importance of measurement reliability for identifying brain–behaviour associations from individual differences.
Smooth pursuit eye movements contribute to anticipatory force control during mechanical stopping of moving objects
Authors: Sinha Oindrila , Madarshahian Shirin , Gomez-Granados Ana , Paine Morgan L , Kurtzer Isaac , Singh Tarkeshwar
Published: February 2023

When stopping a closing door or catching an object, humans process the motion of inertial objects and apply reactive limb force over short period to interact with them. One way in which the visual system processes motion is through extraretinal signals associated with smooth pursuit eye movements (SPEM). We conducted three experiments to investigate how SPEM contribute to anticipatory and reactive hand force modulation when interacting with a virtual object moving in the horizontal plane. We hypothesized that SPEM signals are critical for timing motor responses, anticipatory control of hand force, and task performance. Participants held a robotic manipulandum and attempted to stop an approaching simulated object by applying a force impulse (area under force-time curve) that matched the object’s virtual momentum upon contact. We manipulated the object’s momentum by varying either its virtual mass or its speed under free gaze or constrained gaze conditions. We examined gaze variables, timing of hand motor responses, anticipatory force control, and overall task performance. Our results show that when SPEM were constrained, anticipatory modulation of hand force prior to contact decreased. However, constraining SPEM did not seem to affect the timing of the motor response or the task performance. Together, these results suggest that SPEM may be important for anticipatory control of hand force prior to contact and may also play a critical role in anticipatory stabilization of limb posture when humans interact with moving objects.

New and Noteworthy

We show for the first time that smooth pursuit eye movements (SPEM) play a role in modulation of anticipatory control of hand force to stabilize posture against contact forces. SPEM are critical for tracking moving objects, facilitate processing motion of moving objects, and are impacted during aging and in many neurological disorders, such as Alzheimer’s disease and Multiple Sclerosis. These results provide a novel basis to probe how changes in SPEM could contribute to deficient limb motor control in older adults and patients with neurological disorders.