bluuebunny/crossref_metadata_2025 huggingface dataset:
CRISPR-mediated germline mutagenesis for genetic sterilization ofAnopheles gambiaemales
Authors: Smidler Andrea L. , Paton Douglas G. , Church George M. , Esvelt Kevin M. , Shaw W. Robert , Catteruccia Flaminia
Published: June 2023

Rapid spread of insecticide resistance among anopheline mosquitoes threatens malaria elimination efforts, necessitating development of alternative vector control technologies. Sterile Insect Technique (SIT) has been successfully implemented in multiple insect pests to suppress field populations by the release of large numbers of sterile males, yet it has proven difficult to adapt toAnophelesvectors. Here we outline adaptation of a CRISPR-based genetic sterilization system to selectively ablate male sperm cells in the malaria mosquitoAnopheles gambiae. We achieve robust mosaic biallelic mutagenesis of zero population growth(zpg, a gene essential for differentiation of germ cells) in F1 individuals after intercrossing a germline-expressing Cas9 transgenic line to a line expressingzpg-targeting gRNAs. Approximately 95% of mutagenized males display complete genetic sterilization, and cause similarly high levels of infertility in their female mates. Using a fluorescence reporter that allows detection of the germline leads to a 100% accurate selection of spermless males, improving the system. These males cause a striking reduction in mosquito population size when released at field-like frequencies in competition cages against wild type males. These findings demonstrate that such a genetic system could be adopted for SIT against important malaria vectors.
Single-cell multiome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis
Authors: Mitra Sneha , Malik Rohan , Wong Wilfred , Rahman Afsana , Hartemink Alexander J. , Pritykin Yuri , Dey Kushal K. , Leslie Christina S.
Published: June 2023

We present a novel gene-level regulatory model called SCARlink that predicts single-cell gene expression from single-cell chromatin accessibility within and flanking (+/-250kb) the genic loci by training on multiome (scRNA-seq and scATAC-seq co-assay) sequencing data. The approach uses regularized Poisson regression on tile-level accessibility data to jointly model all regulatory effects at a gene locus, avoiding the limitations of pairwise gene-peak correlations and dependence on a peak atlas. SCARlink significantly outperformed existing gene scoring methods for imputing gene expression from chromatin accessibility across across high-coverage multiome data sets while giving comparable to improved performance on low-coverage data sets. Shapley value analysis on trained models identified cell-type-specific gene enhancers that are validated by promoter capture Hi-C and are 8x-35x enriched in fine-mapped eQTLs and 22x-35x enriched in fine-mapped GWAS variants across 83 UK Biobank traits. We further show that SCARlink-predicted and observed gene expression vectors provide a robust way to compute a chromatin potential vector field to enable developmental trajectory analysis.
Climate benefits of seaweed farming: estimating regional carbon emission and sequestration pathways
Authors: Bullen Cameron D. , Driscoll John , Burt Jenn , Stephens Tiffany , Hessing-Lewis Margot , Gregr Edward J.
Published: June 2023

Seaweed farming is widely promoted as an approach to mitigating climate change despite limited data on carbon removal pathways and uncertainty around benefits and risks at operational scales. We explored the feasibility of seaweed farms to contribute to atmospheric CO2reduction in coastal British Columbia, Canada, a region identified as highly suitable for seaweed farming. Using a place-based, quantitative model, we examined five scenarios spanning a range of industry development. Our intermediate growth scenario sequestered or avoided 0.20 Tg CO2e / year, while our most ambitious scenario (with more cultivation and higher production rates) yielded a reduction of 8.2 Tg CO2e /year, equivalent to 0.3% and 13% of annual greenhouse gas emissions in BC, respectively. Across all scenarios, climate benefits depended on seaweed-based products replacing more emissions-intensive products. Marine sequestration was relatively inefficient in comparison, although production rates and avoided emissions are key uncertainties prioritized for future research. Our results show how seaweed farming could contribute to Canada’s climate goals, and our model illustrates how farmers, regulators, and researchers could accurately quantify the climate benefits of seaweed farming in local contexts.
NOP16 is a histone mimetic that regulates Histone H3K27 methylation and gene repression
Authors: Takashima Ken , Lee Dian-Jang , Trovero María Fernanda , Rothi M. Hafiz , Mistry Meeta , Zhang Ying , Li Zhouyihan , Davis Christopher P. , Li Zilan , Natale Julia , Schmid Ernst , Al Haddad Joseph , Hoffmann Gabriela Brunsting , Dietmann Sabine , Sui Shannan Ho , Oshiumi Hiroyuki , Lieberman Judy , Greer Eric Lieberman
Published: June 2023

Post-translational modifications of histone tails alter chromatin accessibility to regulate gene expression. Some viruses exploit the importance of histone modifications by expressing histone mimetic proteins that contain histone-like sequences to sequester complexes that recognize modified histones. Here we identify an evolutionarily conserved and ubiquitously expressed, endogenous mammalian protein Nucleolar protein 16 (NOP16) that functions as a H3K27 mimic. NOP16 binds to EED in the H3K27 trimethylation PRC2 complex and to the H3K27 demethylase JMJD3. NOP16 knockout selectively globally increases H3K27me3, a heterochromatin mark, without altering methylation of H3K4, H3K9, or H3K36 or acetylation of H3K27. NOP16 is overexpressed and linked to poor prognosis in breast cancer. Depletion of NOP16 in breast cancer cell lines causes cell cycle arrest, decreases cell proliferation and selectively decreases expression of E2F target genes and of genes involved in cell cycle, growth and apoptosis. Conversely, ectopic NOP16 expression in triple negative breast cancer cell lines increases cell proliferation, cell migration and invasivityin vitroand tumor growthin vivo, while NOP16 knockout or knockdown has the opposite effect. Thus, NOP16 is a histone mimic that competes with Histone H3 for H3K27 methylation and demethylation. When it is overexpressed in cancer, it derepresses genes that promote cell cycle progression to augment breast cancer growth.
Processing and Storage Methods Affect Oral and Gut Microbiome Composition
Authors: Superdock Dorothy K. , Zhang Wei , Poole Angela C.
Published: June 2023

Across microbiome studies, fecal and oral samples are stored and processed in different ways, which could affect the observed microbiome composition. Here, we compared treatment methods, which included both storage conditions and processing methods, applied to samples prior to DNA extraction to determine how each affects microbial community diversity as assessed by 16S rRNA gene sequencing. We collected dental swab, saliva, and fecal samples from 10 individuals, with three technical replicates per treatment method. We assessed four methods of processing fecal samples prior to DNA extraction. We also compared different fractions of frozen saliva and dental samples to fresh samples. We found that lyophilized fecal samples, fresh whole saliva samples, and the supernatant fraction of thawed dental samples retained the highest levels of alpha diversity in samples. The supernatant fraction of thawed saliva samples had the second highest alpha diversity compared to fresh. Then we investigated the differences in microbes between different treatments at the domain and phylum levels as well as identified the amplicon sequence variants (ASVs) that were significantly different between the methods producing the highest alpha diversity and the other treatment methods. Lyophilized fecal samples had a greater prevalence of Archaea as well as a greater ratio of Firmicutes to Bacteroidetes compared to the other treatment methods. Our results provide practical considerations, not only for selection of processing method, but also for comparing results across studies that use these methods. Our findings also indicate differences in treatment method could be a confounding factor influencing the presence, absence, or differential abundance of microbes reported in conflicting studies.
Agent Orange exposure and prostate cancer risk in the Million Veteran Program
Authors: Lui Asona J. , Pagadala Meghana S. , Zhong Allison Y. , Lynch Julie , Karunamuni Roshan , Lee Kyung Min , Plym Anna , Rose Brent S. , Carter Hannah , Kibel Adam S. , DuVall Scott L. , Gaziano J. Michael , Panizzon Matthew S. , Hauger Richard L. , Seibert Tyler M.
Published: June 2023

Purpose

Exposure to Agent Orange, a known carcinogen, might increase risk of prostate cancer (PCa). We sought to investigate the association of Agent Orange exposure and PCa risk when accounting for race/ethnicity, family history, and genetic risk in a diverse population of US Vietnam War veterans.

Methods & Materials

This study utilized the Million Veteran Program (MVP), a national, population-based cohort study of United States military veterans conducted 2011-2021 with 590,750 male participants available for analysis. Agent Orange exposure was obtained using records from the Department of Veterans Affairs (VA) using the US government definition of Agent Orange exposure: active service in Vietnam while Agent Orange was in use. Only veterans who were on active duty (anywhere in the world) during the Vietnam War were included in this analysis (211,180 participants). Genetic risk was assessed via a previously validated polygenic hazard score calculated from genotype data. Age at diagnosis of any PCa, diagnosis of metastatic PCa, and death from PCa were assessed via Cox proportional hazards models.

Results

Exposure to Agent Orange was associated with increased PCa diagnosis (HR 1.04, 95% CI 1.01–1.06, p=0.003), primarily among Non-Hispanic White men (HR 1.09, 95% CI 1.06– 1.12, p<0.001). When accounting for race/ethnicity and family history, Agent Orange exposure remained an independent risk factor for PCa diagnosis (HR 1.06, 95% CI 1.04–1.09, p<0.05). Univariable associations of Agent Orange exposure with PCa metastasis (HR 1.08, 95% CI 0.99–1.17) and PCa death (HR 1.02, 95% CI 0.84–1.22) did not reach significance on multivariable analysis. Similar results were found when accounting for polygenic hazard score.

Conclusions

Among US Vietnam War veterans, Agent Orange exposure is an independent risk factor for PCa diagnosis, though associations with PCa metastasis or death are unclear when accounting for race/ethnicity, family history, and/or polygenic risk.
Reliable, standardized measurements for cell mechanical properties
Authors: Pérez-Domínguez Sandra , Kulkarni Shruti G. , Pabijan Joanna , Gnanachandran Kajangi , Holuigue Hatice , Eroles Mar , Lorenc Ewelina , Berardi Massimiliano , Antonovaite Nelda , Marini Maria Luisa , Alonso Javier Lopez , Redonto-Morata Lorena , Dupres Vincent , Janel Sebastien , Acharya Sovon , Otero Jorge , Navajas Daniel , Bielawski Kevin , Schillers Hermann , Lafont Frank , Rico Felix , Podestà Alessandro , Radmacher Manfred , Lekka Małgorzata
Published: June 2023

Atomic force microscopy (AFM) has become indispensable for studying biological and medical samples. More than two decades of experiments have revealed that cancer cells are softer than healthy cells (for measured cells cultured on stiff substrates). The softness or, more precisely, the larger deformability of cancer cells, primarily independent of cancer types, could be used as a sensitive marker of pathological changes. The wide application of biomechanics in clinics would require designing instruments with specific calibration, data collection, and analysis procedures. For these reasons, such development is, at present, still very limited, hampering the clinical exploitation of mechanical measurements. Here, we propose a standardized operational protocol (SOP), developed within the EU ITN network Phys2BioMed, which allows the detection of the biomechanical properties of living cancer cells regardless of the nanoindentation instruments used (AFMs and other indenters) and the laboratory involved in the research. We standardized the cell cultures, AFM calibration, measurements, and data analysis. This effort resulted in a step-by-step SOP for cell cultures, instrument calibration, measurements, and data analysis, leading to the concordance of the results (Young’s modulus) measured among the six EU laboratories involved. Our results highlight the importance of the SOP in obtaining a reproducible mechanical characterization of cancer cells and paving the way toward exploiting biomechanics for diagnostic purposes in clinics.
Immunogenicity of COVID-19 vaccines and their effect on the HIV reservoir in older people with HIV
Authors: Matveev Vitaliy A. , Mihelic Erik Z. , Benko Erika , Budylowski Patrick , Grocott Sebastian , Lee Terry , Korosec Chapin S. , Colwill Karen , Stephenson Henry , Law Ryan , Ward Lesley A. , Sheikh-Mohamed Salma , Mailhot Geneviève , Delgado-Brand Melanie , Pasculescu Adrian , Wang Jenny H. , Qi Freda , Tursun Tulunay , Kardava Lela , Chau Serena , Samaan Philip , Imran Annam , Copertino Dennis C. , Chao Gary , Choi Yoojin , Reinhard Robert J. , Kaul Rupert , Heffernan Jane M. , Jones R. Brad , Chun Tae-Wook , Moir Susan , Singer Joel , Gommerman Jennifer , Gingras Anne-Claude , Kovacs Colin , Ostrowski Mario
Published: June 2023

Older individuals and people with HIV (PWH) were prioritized for COVID-19 vaccination, yet comprehensive studies of the immunogenicity of these vaccines and their effects on HIV reservoirs are not available. We followed 68 PWH aged 55 and older and 23 age-matched HIV-negative individuals for 48 weeks from the first vaccine dose, after the total of three doses. All PWH were on antiretroviral therapy (cART) and had different immune status, including immune responders (IR), immune non-responders (INR), and PWH with low-level viremia (LLV). We measured total and neutralizing Ab responses to SARS-CoV-2 spike and RBD in sera, total anti-spike Abs in saliva, frequency of anti-RBD/NTD B cells, changes in frequency of anti-spike, HIV gag/nef-specific T cells, and HIV reservoirs in peripheral CD4+T cells. The resulting datasets were used to create a mathematical model for within-host immunization. Various regimens of BNT162b2, mRNA-1273, and ChAdOx1 vaccines elicited equally strong anti-spike IgG responses in PWH and HIV-participants in serum and saliva at all timepoints. These responses had similar kinetics in both cohorts and peaked at 4 weeks post-booster (third dose), while half-lives of plasma IgG also dramatically increased post-booster in both groups. Salivary spike IgA responses were low, especially in INRs. PWH had diminished live virus neutralizing titers after two vaccine doses which were ‘rescued’ after a booster. Anti-spike T cell immunity was enhanced in IRs even in comparison to HIV-participants, suggesting Th1 imprinting from HIV, while in INRs it was the lowest. Increased frequency of viral ‘blips’ in PWH were seen post-vaccination, but vaccines did not affect the size of the intact HIV reservoir in CD4+T cells in most PWH, except in LLVs. Thus, older PWH require three doses of COVID-19 vaccine to maximize neutralizing responses against SARS-CoV-2, although vaccines may increase HIV reservoirs in PWH with persistent viremia.
Acute stress reshapes third-party punishment and help decisions: Behavioral evidence and neurocomputational mechanisms
Authors: Wang Huagen , Wu Xiaoyan , Xu Jiahua , Zhu Ruida , Zhang Sihui , Xu Zhenhua , Mai Xiaoqin , Liu Chao , Qin Shaozheng
Published: June 2023

People tend to intervene in others’ injustices by either punishing the transgressor or helping the victim. Injustice events often occur under stressful circumstances. However, how acute stress affects a third party’s intervention in injustice events remains open. Here, we show a stress-induced shift in third parties’ willingness to engage in help instead of punishment by acting on emotional salience and central-executive and theory-of-mind networks. Acute stress decreased the third party’s willingness to punish the violator and the severity of the punishment and increased their willingness to help the victim. Computational modeling revealed a shift in intervention severity bias from punishment toward help under stress. This finding is consistent with the increased dorsolateral prefrontal engagement observed with higher amygdala activity and greater connectivity with the ventromedial prefrontal cortex. A brain connectivity theory-of-mind network predicted stress-induced severity bias in punishment. Our findings suggest a neurocomputational mechanism of how acute stress reshapes third parties’ decisions by reallocating neural resources in emotional, executive and mentalizing networks to inhibit punishment bias and decrease punishment severity.
A transcriptomics-based drug repositioning approach to identify drugs with similar activities for the treatment of muscle pathologies in spinal muscular atrophy (SMA) models
Authors: Hoolachan Joseph M , McCallion Eve , Sutton Emma R , Çetin Özge , Pacheco-Torres Paloma , Dimitriadi Maria , Okoh Magnus , Walter Lisa M , Claus Peter , Wood Matthew JA , Tonge Daniel P , Bowerman Melissa
Published: June 2023

Spinal muscular atrophy (SMA) is a genetic neuromuscular disorder caused by the reduction of survival of motor neuron (SMN) protein levels. Although three SMN-augmentation therapies are clinically approved that significantly slow down disease progression, they are unfortunately not cures. Thus, complementary SMN-independent therapies that can target key SMA pathologies and that can support the clinically approved SMN-dependent drugs are the forefront of therapeutic development. We have previously demonstrated that prednisolone, a synthetic glucocorticoid (GC) improved muscle health and survival in severeSmn-/-;SMN2and intermediateSmn2B/-SMA mice. However, long-term administration of prednisolone can promote myopathy. We thus wanted to identify genes and pathways targeted by prednisolone in skeletal muscle to discover clinically approved drugs that are predicted to emulate prednisolone’s activities. Using an RNA-sequencing, bioinformatics and drug repositioning pipeline on skeletal muscle from symptomatic prednisolone- treated and untreatedSmn-/-;SMN2SMA andSmn+/-;SMN2healthy mice, we identified molecular targets linked to prednisolone’s ameliorative effects and a list of 580 drug candidates with similar predicted activities. Two of these candidates, metformin and oxandrolone, were further investigated in SMA cellular and animal models, which highlighted that these compounds do not have the same ameliorative effects on SMA phenotypes as prednisolone; however, a number of other important drug targets remain. Overall, our work further supports the usefulness of prednisolone’s potential as a second-generation therapy for SMA, identifies a list of potential SMA drug treatments and highlights improvements for future transcriptomic-based drug repositioning studies in SMA.
Visual mental imagery in typical imagers and in aphantasia: A millimeter-scale 7-T fMRI study
Authors: Liu Jianghao , Zhan Minye , Hajhajate Dounia , Spagna Alfredo , Dehaene Stanislas , Cohen Laurent , Bartolomeo Paolo
Published: June 2023

Most of us effortlessly describe visual objects, whether seen or remembered. Yet, around 4% of people report congenital aphantasia: they struggle to visualize objects despite being able to describe their visual appearance. What neural mechanisms create this disparity between subjective experience and objective performance? Aphantasia can provide novel insights into conscious processing and awareness. We used ultra-high field 7T fMRI to establish the neural circuits involved in visual mental imagery and perception, and to elucidate the neural mechanisms associated with the processing of internally generated visual information in the absence of imagery experience in congenital aphantasia. Ten typical imagers and 10 aphantasic individuals performed imagery and perceptual tasks in five domains: object shape, object color, written words, faces, and spatial relationships. In typical imagers, imagery tasks activated left-hemisphere frontoparietal areas, the relevant domain-preferring areas in the ventral temporal cortex partly overlapping with the perceptual domain-preferring areas, and a domain-general area in the left fusiform gyrus (the Fusiform Imagery Node). The results were valid for each individual participant. In aphantasic individuals, imagery activated similar visual areas, but there was reduced functional connectivity between the Fusiform Imagery Node and frontoparietal areas. Our results unveil the domain-general and domain-specific circuits of visual mental imagery, their functional disorganization in aphantasia, and support the general hypothesis that conscious visual experience - whether perceived or imagined - depends on the integrated activity of high-level visual cortex and frontoparietal networks.
Inclusion of glycopeptides in hydrogen/deuterium exchange mass spectrometry analysis of SARS-CoV-2 spike ectodomain provides in-creased sequence coverage
Authors: Haynes Christopher A. , Keppel Theodore R. , Mekonnen Betlehem , Osman Sarah H. , Zhou Yu , Woolfitt Adrian R. , Baudys Jakub , Barr John R. , Wang Dongxia
Published: June 2023

Hydrogen/deuterium exchange mass spectrometry (HDX-MS) can provide precise analysis of a protein’s conformational dynamics across varied states, such as heat-denatured vs. native protein structures, localizing regions that are specifically affected by such conditional changes. Maximizing protein sequence coverage provides high confidence that regions of interest were located by HDX-MS, but one challenge for complete sequence coverage is N-glycosylation sites. The deuteration of glycopeptides has not always been identified in previous reports of HDX-MS analyses, causing significant sequence coverage gaps in heavily glycosylated proteins and uncertainty in structural dynamics in many regions throughout a glycoprotein. We report HDX-MS analysis of the SARS-CoV-2 spike protein ectodomain in its trimeric pre-fusion form, which has 22 predicted N-glycosylation sites per monomer, with and without heat treatment. We identified glycopeptides and calculated their isotopic mass shifts from deuteration. Inclusion of the deu-terated glycopeptides increased sequence coverage of spike ectodomain from 76% to 84%, demonstrated that glycopeptides had been deuterated, and improved confidence in results localizing structural re-arrangements. Inclusion of deuterated glycopeptides improves the analysis of the conformational dynamics of glycoproteins such as viral surface antigens and cellular receptors.

Abstract Figure
Mapping neurodevelopmental diversity in executive function
Authors: Mareva Silvana ,   The CALM Team, Holmes Joni
Published: June 2023

Executive functions can be conceptualised as either a set of higher-order cognitive skills that enable us to engage in flexible thinking and regulate our thoughts and behaviours, or as the ability to integrate knowledge, beliefs, and values when applying cognitive control in everyday situations. These two perspectives map onto the ways in which executive function is measured in childhood – using either structured laboratory tasks or ratings of everyday behaviours. Differences in executive functioning are associated with neurodevelopmental differences, but evidence for associations between specific profiles of executive function and specific neurodevelopmental conditions is mixed. In this study, we adopt a data-driven approach to identify common profiles of executive function in a transdiagnostic sample of 566 neurodivergent children, using both performance and rating-based measures of executive function. Three profiles of executive function were identified: one had consistent difficulties across both types of assessments, while the other two had inconsistent profiles of predominantly rating- or predominantly task-based difficulties. Children with these different profiles had differences in academic achievement and mental health outcomes and could further be differentiated from a comparison group of neurotypical children on both shared and profile-unique patterns of neural white matter organisation. Importantly, children’s executive function profiles were not directly related to diagnostic categories or to dimensions of neurodiversity associated with specific diagnoses (e.g., hyperactivity, inattention, social communication). These findings support the idea that there are separate domains of executive function and that the two types of assessment tapping these functions are dissociable and provide non-redundant information related to neurodevelopmental differences. These findings advance our understanding of executive function profiles in neurodivergent populations and their relationship to behavioural outcomes and neural variation.
Deep Learning in Automating Breast Cancer Diagnosis from Microscopy Images
Authors: Gu Qiangqiang , Prodduturi Naresh , Hart Steven N.
Published: June 2023

Context

Breast cancer is one of the most common cancers in women. With early diagnosis, some breast cancers are highly curable. However, the concordance rate of breast cancer diagnosis from histology slides by pathologists is unacceptably low. Classifying normal versus tumor breast tissues from microscopy images of breast histology is an ideal case to use for deep learning and could help to more reproducibly diagnose breast cancer. Since data preprocessing and hyperparameter configurations have impacts on breast cancer classification accuracies of deep learning models, training a deep learning classifier with appropriate data preprocessing approaches and optimized hyperparameter configurations could improve breast cancer classification accuracy.

Methods and Material

Using 12 combinations of deep learning model architectures (i.e., including 5 non-specialized and 7 digital pathology-specialized model architectures), image data preprocessing, and hyperparameter configurations, the validation accuracy of tumor versus normal classification were calculated using theBreAstCancerHistology (BACH) dataset.

Results

The DenseNet201, a non-specialized model architecture, with transfer learning approach achieved 98.61% validation accuracy compared to only 64.00% for the digital pathology-specialized model architecture.

Conclusions

The combination of image data preprocessing approaches and hyperparameter configurations have a profound impact on the performance of deep neural networks for image classification. To identify a well-performing deep neural network to classify tumor versus normal breast histology, researchers should not only focus on developing new models specifically for digital pathology, since hyperparameter tuning for existing deep neural networks in the computer vision field could also achieve a high (often better) prediction accuracy.
Transgene directed induction of a stem cell-derived human embryo model
Authors: Weatherbee Bailey AT , Gantner Carlos W , Daza Riza M , Hamazaki Nobuhiko , Iwamoto-Stohl Lisa K. , Shendure Jay , Zernicka-Goetz Magdalena
Published: June 2023

The human embryo undergoes morphogenetic transformations following implantation into the uterus, yet our knowledge of this crucial stage is limited by the inability to observe the embryoin vivo. Stem cell-derived models of the embryo are important tools to interrogate developmental events and tissue-tissue crosstalk during these stages1. Here, we establish a human post-implantation embryo model comprised of embryonic and extraembryonic tissues. We combine two types of extraembryonic-like cells generated by transcription factor overexpression with wildtype embryonic stem cells and promote their self-organization into structures that mimic aspects of the post-implantation human embryo. These self-organized aggregates contain a pluripotent epiblast-like domain surrounded by hypoblast-and trophoblast-like tissues. We demonstrate that these inducible human embryoids robustly generate several cell types, including amnion, extraembryonic mesenchyme, and primordial germ cell-like cells in response to BMP signaling. This model also allowed us to identify an inhibitory role for SOX17 in the specification of anterior hypoblast-like cells2. Modulation of the subpopulations in the hypoblast-like compartment demonstrated that extraembryonic-like cells impact epiblast-like domain differentiation, highlighting functional tissue-tissue crosstalk. In conclusion, we present a modular, tractable, integrated3model of the human embryo that will allow us to probe key questions of human post-implantation development, a critical window when significant numbers of pregnancies fail.
Calculating and applying pathogen mutational spectra using MutTui
Authors: Ruis Christopher , Tonkin-Hill Gerry , Floto R. Andres , Parkhill Julian
Published: June 2023

Mutational spectra describe the pattern of mutations acquired during evolution and are driven by factors including mutagens, repair processes and selection. Calculating mutational spectra of pathogen genomic datasets may enable analysis of factors that influence these mutational processes, including replication niches, transmission routes and pathogen biology. Here, we introduce MutTui, which can leverage multiple types of sequence data to calculate and compare mutational spectra of DNA and RNA pathogens. MutTui is available athttps://github.com/chrisruis/MutTui.
AddBiomechanics: Automating model scaling, inverse kinematics, and inverse dynamics from human motion data through sequential optimization
Authors: Werling Keenon , Bianco Nicholas A. , Raitor Michael , Stingel Jon , Hicks Jennifer L. , Collins Steven H. , Delp Scott L. , Liu C. Karen
Published: June 2023

Creating large-scale public datasets of human motion biomechanics could unlock data-driven breakthroughs in our understanding of human motion, neuromuscular diseases, and assistive devices. However, the manual effort currently required to process motion capture data and quantify the kinematics and dynamics of movement is costly and limits the collection and sharing of large-scale biomechanical datasets. We present a method, called AddBiomechanics, to automate and standardize the quantification of human movement dynamics from motion capture data. We use linear methods followed by a non-convex bilevel optimization to scale the body segments of a musculoskeletal model, register the locations of optical markers placed on an experimental subject to the markers on a musculoskeletal model, and compute body segment kinematics given trajectories of experimental markers during a motion. We then apply a linear method followed by another non-convex optimization to find body segment masses and fine tune kinematics to minimize residual forces given corresponding trajectories of ground reaction forces. The optimization approach requires approximately 3-5 minutes to determine a subject’s skeleton dimensions and motion kinematics, and less than 30 minutes of computation to also determine dynamically consistent skeleton inertia properties and fine-tuned kinematics and kinetics, compared with about one day of manual work for a human expert. We used AddBiomechanics to automatically reconstruct joint angle and torque trajectories from previously published multi-activity datasets, achieving close correspondence to expert-calculated values, marker root-mean-square errors less than 2 cm, and residual force magnitudes smaller than 2% of peak external force. Finally, we confirmed that AddBiomechanics accurately reproduced joint kinematics and kinetics from synthetic walking data with low marker error and residual loads. We have published the algorithm as an open source cloud service atAddBiomechanics.org, which is available at no cost and asks that users agree to share processed and de-identified data with the community. As of this writing, hundreds of researchers have used the prototype tool to process and share about ten thousand motion files from about one thousand experimental subjects. Reducing the barriers to processing and sharing high-quality human motion biomechanics data will enable more people to use state-of-the-art biomechanical analysis, do so at lower cost, and share larger and more accurate datasets.
Centrifugal Gel Crushing for Gel-based Proteome Analysis
Authors: Nishida Hiroshi , Kanao Eisuke , Ishihama Yasushi
Published: June 2023

We have developed a centrifugal gel crushing method using a pipette tip. Polyacrylamide gel slices are extruded from the narrowing cavity of a pipette tip by centrifugation in a few minutes to crush them into pieces of appropriate size. The size of the crushed gel could be controlled by several parameters, including centrifugal force and pipette tip cavity. In shotgun proteomics, gel-based LC/MS/MS, so-called GeLC/MS/MS, involves the essential but tedious processes of pre-fractionation by SDS-PAGE, followed by dicing the entire gel lane into several parts, fine dicing, and in-gel digestion after the diced gel is manually transferred to a microtube. In this study, we developed an alternative way to crush the pre-fractionated gel slice into small and irregular-shaped gels by centrifugal extrusion of the sliced gel from the narrow cavity of a pipette tip. As a result, we observed an improved recovery and reproducibility of digested proteins compared to the conventional method of manual dicing. We believe that this simple and rapid method of crushing polyacrylamide gels, which allows for parallel operations and automation, is useful for GeLC/MS/MS analysis and applicable to other approaches including top-down proteomics.

Abstract Figure
Mechanism of negativeμ-opioid receptor modulation by sodium ions
Authors: Thomson Neil J. , Zachariae Ulrich
Published: June 2023

The negative allosteric modulation of G-protein coupled receptors (GPCRs) by Na+ions, known as the sodium effect, was first described in the 1970s for opioid receptors (ORs). Since then, it has been detected almost universally amongst class A GPCRs. High-resolution structures of class A GPCRs in the inactive state exhibit a Na+ion bound to a conserved pocket near residue D2.50, whereas the active state structures of GPCRs are incompatible with Na+binding. Correspondingly, Na+ions diminish the affinity of receptor agonists, stabilize the receptors in the inactive state, and reduce basal signalling levels. Despite these observations, a detailed mechanistic explanation of how Na+ions negatively modulate the receptor and inhibit activation has remained elusive. Here, we apply a mutual-information based analysis method to μs-timescale all-atom molecular dynamics simulations of the μ-OR to decipher conformational changes within the protein matrix and protein-internal water molecules that are directly coupled to the binding of Na+. Our results reveal that Na+binding is tightly coupled to a water wire that links the Na+binding site with the agonist binding pocket. Furthermore, Na+binding leads to rearrangements in polar protein networks that propagate conformational changes both to the agonist and the intracellular G-protein binding sites via conserved micro-switch motifs. Our findings provide a mechanistic link between the presence of the ion and altered agonist binding affinity, receptor deactivation and the depression of basal signalling.
M3NetFlow: A novel multi-scale multi-hop graph AI model for integrative multi-omic data analysis
Authors: Zhang Heming , Goedegebuure S. Peter , Ding Li , DeNardo David , Fields Ryan C. , Chen Yixin , Payne Philip , Li Fuhai
Published: June 2023

Multi-omic data-driven studies, characterizing complex disease signaling system from multiple levels, are at the forefront of precision medicine and healthcare. The integration and interpretation of multi-omic data are essential for identifying molecular targets and deciphering core signaling pathways of complex diseases. However, it remains an open problem due the large number of biomarkers and complex interactions among them. In this study, we propose a novel Multi-scale Multi-hop Multi-omic graph model,M3NetFlow, to facilitate generic multi-omic data analysis to rank targets and infer core signaling flows/pathways. To evaluate M3NetFlow, we applied it in two independent multi-omic case studies: 1) uncovering mechanisms of synergistic drug combination response (defined as anchor-target guided learning), and 2) identifying biomarkers and pathways of Alzheimer ‘s disease (AD). The evaluation and comparison results showedM3NetFlowachieves the best prediction accuracy (accurate), and identifies a set of essential targets and core signaling pathways (interpretable). The model can be directly applied to other multi-omic data-driven studies. The code is publicly accessible at:https://github.com/FuhaiLiAiLab/M3NetFlow
Task-driven neural network models predict neural dynamics of proprioception
Authors: Vargas Alessandro Marin , Bisi Axel , Chiappa Alberto , Versteeg Chris , Miller Lee , Mathis Alexander
Published: June 2023

Proprioception tells the brain the state of the body based on distributed sensors in the body. However, the principles that govern proprioceptive processing from those distributed sensors are poorly understood. Here, we employ a task-driven neural network modeling approach to investigate the neural code of proprioceptive neurons in both cuneate nucleus (CN) and somatosensory cortex area 2 (S1). We simulated muscle spindle signals through musculoskeletal modeling and generated a large-scale, naturalistic movement repertoire to train thousands of neural network models on 16 behavioral tasks, each reflecting a hypothesis about the neural computations of the ascending proprioceptive pathway. We found that the network’s internal representations developed through task-optimization generalize from synthetic data to predict single-trial neural activity in CN and S1 of primates performing center-out reaching. Task-driven models outperform linear encoding models and data-driven models. Behavioral tasks, which aim to predict the limb position and velocity were the best to predict the neural activity in both areas. Architectures that are better at solving the tasks are also better at predicting the neural data. Last, since task-optimization develops representations that better predict neural activity during active but not passively generated movements, we hypothesize that neural activity in CN and S1 is top-down modulated during goal-directed movements.
ASCL1-ERK1/2 Axis: ASCL1 restrains ERK1/2 via the dual specificity phosphatase DUSP6 to promote survival of a subset of neuroendocrine lung cancers
Authors: Martin-Vega Ana , Earnest Svetlana , Augustyn Alexander , Wichaidit Chonlarat , Gazdar Adi , Girard Luc , Peyton Michael , Kollipara Rahul K. , Minna John D. , Johnson Jane E. , Cobb Melanie H.
Published: June 2023

The transcription factor achaete-scute complex homolog 1 (ASCL1) is a lineage oncogene that is central for the growth and survival of small cell lung cancers (SCLC) and neuroendocrine non-small cell lung cancers (NSCLC-NE) that express it. Targeting ASCL1, or its downstream pathways, remains a challenge. However, a potential clue to overcoming this challenage has been information that SCLC and NSCLC-NE that express ASCL1 exhibit extremely low ERK1/2 activity, and efforts to increase ERK1/2 activity lead to inhibition of SCLC growth and surival. Of course, this is in dramatic contrast to the majority of NSCLCs where high activity of the ERK pathway plays a major role in cancer pathogenesis. A major knowledge gap is defining the mechanism(s) underlying the low ERK1/2 activity in SCLC, determining if ERK1/2 activity and ASCL1 function are inter-related, and if manipulating ERK1/2 activity provides a new therapeutic strategy for SCLC. We first found that expression of ERK signaling and ASCL1 have an inverse relationship in NE lung cancers: knocking down ASCL1 in SCLCs and NE-NSCLCs increased active ERK1/2, while inhibition of residual SCLC/NSCLC-NE ERK1/2 activity with a MEK inhibitor increased ASCL1 expression. To determine the effects of ERK activity on expression of other genes, we obtained RNA-seq from ASCL1-expressing lung tumor cells treated with an ERK pathway MEK inhibitor and identified down-regulated genes (such as SPRY4, ETV5, DUSP6, SPRED1) that potentially could influence SCLC/NSCLC-NE tumor cell survival. This led us to discover that genes regulated by MEK inhibition suppress ERK activation and CHIP-seq demonstrated these are bound by ASCL1. In addition, SPRY4, DUSP6, SPRED1 are known suppressors of the ERK1/2 pathway, while ETV5 regulates DUSP6. Survival of NE lung tumors was inhibited by activation of ERK1/2 and a subset of ASCL1-high NE lung tumors expressed DUSP6. Because the dual specificity phosphatase 6 (DUSP6) is an ERK1/2-selective phosphatase that inactivates these kinases and has a pharmacologic inhibitor, we focused mechanistic studies on DUSP6. These studies showed: Inhibition of DUSP6 increased active ERK1/2, which accumulated in the nucleus; pharmacologic and genetic inhibition of DUSP6 affected proliferation and survival of ASCL1-high NE lung cancers; and that knockout of DUSP6 “cured” some SCLCs while in others resistance rapidly developed indicating a bypass mechanism was activated. Thus, our findings fill this knowledge gap and indicate that combined expression of ASCL1, DUSP6 and low phospho-ERK1/2 identify some neuroendocrine lung cancers for which DUSP6 may be a therapeutic target.
FLOWERING LOCUS Cdrives delayed flowering inArabidopsisgrown and selected at elevated CO2
Authors: Henderson-Carter Aleah , Kinmonth-Schultz Hannah , Hileman Lena , Ward Joy K.
Published: June 2023

Altered flowering time at elevated [CO2] is well documented, although mechanisms are not well understood. AnArabidopsisgenotype previously selected for high fitness at elevated [CO2] (SG) showed delayed flowering and larger size at flowering when grown at elevated (700 ppm) versus current (380 ppm) [CO2]. This response was correlated with prolonged expression ofFLOWERING LOCUS C(FLC), a vernalization-responsive floral repressor gene.

To determine ifFLCdirectly delays flowering at elevated [CO2] in SG, we used vernalization (extended cold) to downregulateFLCexpression. We hypothesized that vernalization would eliminate delayed flowering at elevated [CO2] through the direct reduction ofFLCexpression, eliminating differences in flowering time between current and elevated [CO2].

We found that with downregulation ofFLCexpression via vernalization, SG plants grown at elevated [CO2] no longer delayed flowering compared to current [CO2]. Thus, vernalization returned the earlier flowering phenotype, counteracting effects of elevated [CO2] on flowering.

This study indicates that elevated [CO2] can delay flowering directly throughFLC, and downregulation ofFLCunder elevated [CO2] reverses this effect. Moreover, this study demonstrates that increasing [CO2] may potentially drive major changes in development throughFLC.
Pneumatically Controlled Non-Equibiaxial Cell Stretching Device with Live-cell Imaging
Authors: Wang Jue , Chatterjee Aritra , Zigan Clarisse , Alborn Maya , Chan Deva D. , Chortos Alex
Published: June 2023

Objective

Adherent cell behavior is influenced by a complex interplay of factors, including chemical and mechanical signals.In vitroexperiments that mimic the mechanical environment experienced by cellsin vivoare crucial for understanding cellular behavior and the progression of disease. In this study, we developed and validated a low-cost pneumatically-controlled cell stretcher with independent control of strain in two directions of a membrane, enabling unequal biaxial stretching and realtime microscopy during actuation.

Methods

The stretching was achieved by two independent pneumatic channels controlled by electrical signals. We used finite element simulations to compute the membrane’s strain field and particle tracking algorithms based on image processing techniques to validate the strain fields and measure the cell orientation and morphology.

Results

The device can supply uniaxial, equibiaxial, and unequal biaxial stretching up to 15% strain in each direction at a frequency of 1Hz, with a strain measurement error of less than 1%. Through live cell imaging, we determined that distinct stretching patterns elicited differing responses and alterations in cell orientation and morphology, particularly in terms of cell length and area.

Conclusion

The device successfully provides a large, uniform, and variable strain field for cell experiments, while also enabling real-time, live cell imaging.

Significance

This scalable, low-cost platform provides mechanical stimulation to cell cultures by independently controlling strains in two directions. This could contribute to a deeper understanding of cellular response to biorealistic strains and could be useful for futurein vitrodrug testing platforms.
Structure of a superoxide dismutase from a tardigrade: Ramazzottius varieornatus strain YOKOZUNA-1
Authors: Sim Kee-Shin , Inoue Tsuyoshi
Published: June 2023

Superoxide dismutase (SOD) is an essential and ubiquitous antioxidant protein that is widely present in biological systems. The anhydrobiotic tardigrades are some of the toughest micro-animals. They have an expanded set of genes for antioxidant proteins such as SODs. These proteins are thought to play an essential role in oxidative stress resistance in critical situations such as desiccation, although their functions at the molecular level have yet to be explored. Here, crystal structures of a copper/zinc-containing SOD (RvSOD15) from an anhydrobiotic tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1, are reported. In RvSOD15, one of the histidine ligands of the catalytic copper center is replaced by a valine (Val87). The crystal structures of the wild type and the V87H mutant show that even though a histidine is placed at position 87, a nearby flexible loop can destabilize the coordination of His87 to the Cu atom. Model structures of other RvSODs were investigated and it was found that some of them are also unusual SODs, with features such as deletion of the electrostatic loop or β3 sheet and unusual metal-binding residues. These studies show that RvSOD15 and some other RvSODs may have evolved to lose the SOD function, suggesting that gene duplications of antioxidant proteins do not solely explain the high stress tolerance of anhydrobiotic tardigrades.
Crystal structure of 5-(β-D-glucopyranosylthio)-N-(4-methylphenyl)-1,3,4-thiadiazol-2-amine
Authors: Abu-Zaied Mamdouh A. , Hebishy Ali M. S. , Elgemeie Galal H. , Salama Hagar T. , Jones Peter G.
Published: June 2023

In the structure of the title compound, C15H19N3O5S2, the bond lengths at the linking sulfur atom are significantly different [1.7473 (17) and 1.811 (2) Å], and the angle at the exocyclic nitrogen atom is wide at 128.45 (18)°. The interplanar angle between the tolyl and thiadiazole rings is 9.2 (1)°. The complex hydrogen-bonding pattern, involving five donors and five acceptors, can be broken down into a one-dimensional ribbon parallel to the b axis, involving hydrogen bonds of the sugar residues only, and a two-dimensional layer structure parallel to the ab plane, based on the N—H...O and O—H...N hydrogen bonds.
3,5-Lutidine pentaaqua sulfate complexes of first-row transition metals: [M(3,5-lutidine)(H2O)5]SO4, with M = Mn, Co, Ni, and Zn
Authors: Golen James A. , Manke David R.
Published: June 2023

The reactions of MnSO4·H2O, CoSO4·7H2O, NiSO4·6H2O and ZnSO4·7H2O with 3,5-lutidine (3,5-dimethylpyridine) yield crystals of pentaaqua(3,5-dimethylpyridine-κN)manganese(II) sulfate, [Mn(C7H9N)(H2O)5]SO4, (1), pentaaqua(3,5-dimethylpyridine-κN)cobalt(II) sulfate, [Co(C7H9N)(H2O)5]SO4, (2), pentaaqua(3,5-dimethylpyridine-κN)nickel(II) sulfate, [Ni(C7H9N)(H2O)5]SO4, (3), and pentaaqua(3,5-dimethylpyridine-κN)zinc(II) sulfate, [Zn(C7H9N)(H2O)5]SO4, (4), which were characterized by single-crystal X-ray diffraction. The four crystals are isostructural, demonstrating near identical unit-cell parameters and atomic positions. The metal atoms are all octahedrally coordinated, with one lutidine ligand and five water ligands. The sulfate dianion hydrogen bonds with the coordinated water molecules of the dicationic metal complex salts, generating infinite three-dimensional networks.