bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors
Authors: Heiser Cody N. , Simmons Alan J. , Revetta Frank , McKinley Eliot T. , Ramirez-Solano Marisol A. , Wang Jiawei , Shao Justin , Ayers Gregory D. , Wang Yu , Glass Sarah E. , Kaur Harsimran , Rolong Andrea , Chen Bob , Vega Paige N. , Drewes Julia L. , Saleh Nabil , Vandekar Simon , Jones Angela L. , Washington M. Kay , Roland Joseph T. , Sears Cynthia L. , Liu Qi , Shrubsole Martha J. , Coffey Robert J. , Lau Ken S.
Published: March 2023

Colorectal cancer exhibits dynamic cellular and genetic heterogeneity during progression from precursor lesions toward malignancy. Leveraging spatial molecular information to construct a phylogeographic map of tumor evolution can reveal individualized growth trajectories with diagnostic and therapeutic potential. Integrative analysis of spatial multi-omic data from 31 colorectal specimens revealed simultaneous microenvironmental and clonal alterations as a function of progression. Copy number variation served to re-stratify microsatellite stable and unstable tumors into chromosomally unstable (CIN+) and hypermutated (HM) classes. Phylogeographical maps classified tumors by their evolutionary dynamics, and clonal regions were placed along a global pseudotemporal progression trajectory. Cell-state discovery from a single-cell cohort revealed recurring epithelial gene signatures and infiltrating immune states in spatial transcriptomics. Charting these states along progression pseudotime, we observed a transition to immune exclusion in CIN+ tumors as characterized by a novel gene expression signature comprised ofDDR1, TGFBI, PAK4,andDPEP1. We demonstrated how these genes and their protein products are key regulators of extracellular matrix components, are associated with lower cytotoxic immune infiltration, and show prognostic value in external cohorts. Through high-dimensional data integration, this atlas provides insights into co-evolution of tumors and their microenvironments, serving as a resource for stratification and targeted treatment of CRC.
Impact and characterization of serial structural variations across humans and great apes
Authors: Höps Wolfram , Rausch Tobias , Ebert Peter ,   Human Genome Structural Variation Consortium (HGSVC), Korbel Jan O. , Sedlazeck Fritz J.
Published: March 2023

Modern sequencing technology enables the detection of complex structural variation (SV) across genomes. However, extensive DNA rearrangements arising through series of mutations, a phenomenon we term serial SV (sSV), remain understudied since their complexity poses a challenge for SV discovery. Here, we present NAHRwhals (https://github.com/WHops/NAHRwhals), a method to infer repeat-mediated series of SVs in long-read genomic assemblies. Applying NAHRwhals to 58 haplotype-resolved human genomes reveals 37 sSV loci of various length and complexity. These sSVs explain otherwise cryptic variation in medically relevant regions such as theTPSAB1gene, 8p23.1 and the DiGeorge and Sotos syndrome regions. Comparisons with great ape assemblies indicate that most human sSVs formed recently and involved non-repeat-mediated processes. NAHRwhals reliably discovers and characterizes sSVs at scale and independent of species, uncovering their genomic abundance and revealing broader implications for disease than prior studies suggested.
Senescence during early differentiation reduced chondrogenic differentiation capacity of mesenchymal progenitor cells
Authors: Voskamp Chantal , Koevoet Wendy J. L. M. , van Osch Gerjo J.V.M. , Narcisi Roberto
Published: March 2023

Mesenchymal stromal/progenitor cells (MSCs) are promising for cartilage cell-based therapies due to their differentiation capacity. However, MSCs can become senescent duringin vitroexpansion, a state characterized by stable cell cycle arrest, metabolic alterations, and substantial changes in the gene expression and secretory profile of the cell. In this study, we aimed to investigate how senescence and the senescence associated secretory phenotype (SASP) affect chondrogenic differentiation of MSCs. To study the effect of senescence, we exposed MSCs to gamma irradiation during expansion or during chondrogenic differentiation (pellet culture). When senescence was induced during expansion or at day-7 of chondrogenic differentiation, we observed a significant reduction in cartilage matrix. Interestingly, when senescence was induced at day-14 of differentiation, chondrogenesis was not significantly altered. Moreover, exposing chondrogenic pellets to medium conditioned by senescent pellets had no significant effect on the expression of anabolic or catabolic cartilage markers, suggesting a neglectable paracrine effect of senescence on cartilage generation in our model. Finally, we show that senescent MSCs had lower phosphorylated SMAD2 levels after TGFβ1stimulation compared to control MSCs. Overall, these results suggest that the occurrence of senescence in MSCs during expansion or early differentiation could be detrimental for cartilage tissue engineering.
Sodium channel subpopulations with distinct biophysical properties and subcellular localization enhance cardiac conduction
Authors: Weinberg Seth H.
Published: March 2023

Sodium (Na+) current is responsible for the rapid depolarization of cardiac myocytes that triggers the cardiac action potential upstroke. Recent studies have illustrated the presence of multiple “pools” of Na+channels with distinct biophysical properties and subcellular localization, including clustering of channels at the intercalated disk and along the lateral membrane. Computational studies predict that Na+channel clusters at the intercalated disk can regulate cardiac conduction via modulation of the narrow intercellular cleft between electrically coupled myocytes. However, these studies have primarily focused on the redistribution of Na+channels between intercalated disk and lateral membranes and not considered the distinct biophysical properties of the Na+channel subpopulations. In this study, we simulate computational models of single cardiac cells and one-dimensional cardiac tissues to predict the functional consequence of distinct Na+channel subpopulations. Single cell simulations predict that a subpopulation of Na+channels with shifted steady-state activation and inactivation voltage-dependency promote an earlier action potential upstroke. In cardiac tissues that account for distinct subcellular spatial localization, simulations predict that “shifted” Na+channels contribute to faster and more robust conduction, with regards to sensitivity to tissue structural changes (i.e., cleft width), gap junctional coupling, and rapid pacing rates. Simulations predict that the intercalated disk-localized shifted Na+channels provide a disproportionally larger contribution to total Na+charge, relative to lateral membrane-localized Na+channels. Importantly, our work supports the hypothesis that Na+channel redistribution may be a critical mechanism by which cells can rapidly respond to perturbations to support fast and robust conduction.

Sodium channels are organized in multiple “pools” with distinct biophysical properties and subcellular localization, but the role of these subpopulations is not well-understood. Computational modeling predicts that intercalated disk-localized sodium channels with shifted steady-state activation and inactivation voltage-dependence promote faster cardiac conduction.
Anesthetic-Binding Induced Motion of GABAAReceptors Revealed by Coarse-Grained Molecular Dynamics Simulations
Authors: Nakata Shuya , Mori Yoshiharu , Tanaka Shigenori
Published: March 2023

General anesthetics are indispensable in modern medicine because they induce a reversible loss of consciousness and sensation in humans. On the other hand, their molecular mechanisms of action have not yet been elucidated. Several studies have identified the main targets of some general anesthetics. The structures of γ-aminobutyric acid A (GABAA) receptors with the intravenous anesthetics such as propofol and etomidate have recently been determined. Although these anesthetic-binding structures provide essential insights into the mechanism of action of anesthetics, the detailed molecular mechanism of how the anesthetic binding affects the Cl−permeability of GABAAreceptors remains to be elucidated. In this study, we performed coarse-grained molecular dynamics simulations for GABAAreceptors and analyzed the resulting simulation trajectories to investigate the effects of anesthetic binding on the motion of GABAAreceptors. The results showed large structural fluctuations in GABAAreceptors, correlations of motion between the amino-acid residues, large amplitude motion, and autocorrelated slow motion, which were obtained by advanced statistical analyses. In addition, comparison of the resulting trajectories in the presence or absence of the anesthetic molecules revealed a characteristic pore motion related to the gate-opening motion of GABAAreceptors.
Homoeologous non-reciprocal translocation explains a major QTL for seed lignin content in oilseed rape (Brassica napusL.)
Authors: Schilbert Hanna Marie , Holzenkamp Karin , Viehöver Prisca , Holtgräwe Daniela , Möllers Christian
Published: March 2023

Oilseed rape is a major oil crop and a valuable protein source for animal and human nutrition. Lignin is a non-digestible, major component of the seed coat with negative effect on sensory quality, bioavailability and usage of oilseed rape’s protein. Hence, seed lignin reduction is of economic and nutritional importance. In this study, the major QTL for reduced lignin content found on chromosome C05 in the DH population SGDH14 x Express 617 was further examined. SGDH14 had lower seed lignin content than Express 617. Harvested seeds from a F2 population of the same cross were additionally field tested and used for seed quality analysis. The F2 population showed a bimodal distribution for seed lignin content. F2 plants with low lignin content had thinner seed coats compared to high lignin lines. Both groups showed a dark seed colour with a slightly lighter colour in the low lignin group indicating that a low lignin content is not necessarily associated with yellow seed colour. Mapping of genomic long-reads from SGDH14 against the Express 617 genome assembly revealed a homoeologous non-reciprocal translocation (HNRT) in the confidence interval of the major QTL for lignin content. A homologous A05 region is duplicated and replaced the C05 region in SGDH14. As consequence several genes located in the C05 region were lost in SGDH14. Thus, a HNRT was identified in the major QTL region for reduced lignin content in the low lignin line SGDH14. The most promising candidate gene related to lignin biosynthesis on C05,PAL4, was deleted.

Key message

A homoeologous non-reciprocal translocation was identified in the major QTL for seed lignin content in the low lignin line SGDH14. The lignin biosynthetic genePAL4was deleted.
Disequilibrium betweenBRCA1andBRCA2circular and messenger RNAs plays a role in breast cancer
Authors: Levacher C. , Viennot M. , Drouet A. , Beaussire L. , Coutant S. , Théry JC , Baert-Desurmont S. , Laé M. , Ruminy P. , Houdayer C.
Published: March 2023

Abstract

Breast cancer is a frequent disease for which the discovery of markers for early detection or prognostic assessment remains challenging. Circular RNAs (circRNAs) are single-stranded structures in closed loops, produced by backsplicing. CircRNA and messenger RNA (mRNA) are generated cotranscriptionally and backsplicing and linear splicing compete against each other. As mRNAs are key players in tumorigenesis, we hypothesize that a balance disruption between circRNAs and mRNAs could promote breast cancer. Hence, we developed an assay for a simultaneous study of circRNAs and mRNAs, called Splice and Expression Analyses by exon Ligation and High Throughput Sequencing (SEALigTHS). Following SEALigHTS validation forBRCA1andBRCA2, our hypothesis was tested using an independent research set of 95 pairs of tumour and adjacent normal breast tissues. On this research set, ratios ofBRCA1andBRCA2circRNAs/mRNAs were significantly lower in tumour breast tissue compared to normal tissue (p=1.6e-09 and p=4.4e-05 forBRCA1andBRCA2, respectively). Overall, we developed an innovative method to study linear and backsplicing, described the repertoire ofBRCA1andBRCA2circRNAs, including 10 novel ones, and showed for the first time that a disequilibrium betweenBRCA1andBRCA2circRNAs and mRNAs plays a role in breast cancer.
The effects of artificial light at night (ALAN) on the gaping activity and feeding of mussels
Authors: Christoforou Eleni , Dominoni Davide , Lindström Jan , Diamantopoulou Christina , Czyzewski Jakub , Mirzai Nosrat , Spatharis Sofie
Published: March 2023

Artificial light at night (ALAN) is one of the most widespread forms of environmental pollution. Studies on terrestrial organisms have shown that the effects of ALAN can be pervasive, and importantly, can depend on the colour (i.e., wavelength) of light. ALAN also affects marine environments as it is present in more than 22% of the world’s coastlines and can reach depths of up to 100m. However, the impact of different colour ALAN on coastal marine organisms is under-investigated. In this study, we tested the effects of different ALAN colours onMytilus edulis, a widespread coastal bivalve known for its high phytoplankton clearance capacity amongst other valuable ecosystem services. Using a lab-based valvometry system, we recorded the impact of red, green, and white ALAN on gaping activity patterns and phytoplankton clearance capacity of individual mussels and compared these to dark night control. Mussels exhibited a semi-diel activity pattern in both proportion of time open and gaping frequency. Although ALAN did not have significant effects on the proportion of time open it did significantly affect the gaping frequency. This effect was colour-specific with red and white ALAN resulting in lower activity compared to the dark night control but there were no effects on the phytoplankton consumption. Under green light, however, mussels showed a higher gaping frequency and reduced phytoplankton consumption with increasing time spent open compared to the other ALAN treatments and the dark control. Our findings suggest that ALAN does have colour-specific effects on mussels and indicate the importance of further investigating the physiological mechanisms behind these patterns, and their potential ecological consequences.
OptEnvelope: a target point guided method for growth-coupled production using knockouts
Authors: Motamedian Ehsan , Berzins Kristaps , Muiznieks Reinis , Stalidzans Egils
Published: March 2023

Finding the best knockout strategy for coupling biomass growth and production of a target metabolite using a metabolic model is a challenge in biotechnology. In this research, a three-step method named OptEnvelope is developed based on finding minimal active reactions for a target point in the feasible solution space using a mixed-integer linear programming formula. The method initially finds the reduced desirable solution space (envelope) in the product versus biomass plot by removing all inactive reactions. Then, with reinsertion of the deleted reactions, OptEnvelope attempts to reduce the number of knockouts so that the desirable envelope is preserved. Additionally, OptEnvelope searches for envelopes with higher minimum production rates or fewer knockouts by evaluating different target points within the desired solution space. It is possible to limit the maximal number of knockouts. The method was implemented on metabolic models ofE. coliandS. cerevisiaeto test the method benchmarking the capability of these industrial microbes for overproduction of acetate and glycerol under aerobic conditions and succinate and ethanol under anaerobic conditions. The results indicate thatE. coliis more appropriate to produce acetate and succinate whileS. cerevisiaeis a better host for glycerol production. Gene deletions for some of the proposed reaction knockouts have been previously reported to increase the production of these metabolites in experiments. Both organisms are suitable for ethanol production, however, more knockouts for the adaptation ofE. coliare required. OptEnvelope is available athttps://github.com/lv-csbg/optEnvelope.
Ship-to-Shore Training for Active Deep-Sea Capacity Development
Authors: Barnhill Kelsey Archer , Vinha Beatriz , Smith Alycia J. , de Jonge Daniëlle S.W. , Gaurisas Daniela Y. , Segura Roger Mocholí , Madureira Pedro , Albuquerque Mónica , Huvenne Veerle A.I. , Orejas Covadonga , Gunn Vikki
Published: March 2023

Sailing on scientific expeditions as an early career researcher (ECR) offers the beneficial opportunity to gain field experience and training. However, the number of available berths to achieve the scientific goals of an expedition limits the number of onboard participants. Telepresence and remote learning can be utilised to increase the number of active participants, broadening the reach of capacity development. The 2021 iMirabilis2 expedition on board the Spanish Research VesselSarmiento de Gamboaused telepresence to virtually involve ECRs from several countries in deep-sea science. One year post-expedition, a survey of onshore participants was conducted to assess and quantify the effectiveness of the peer-to-peer ECR ship-to-shore scheme. During the expedition, live, interactive training via WhatsApp and Zoom was utilised by onshore ECRs more than traditional static, uni-directional methods of blog posts and pre-recorded videos. All respondents either agreed or strongly agreed that the scheme provided an inclusive and accessible platform to share deep-sea science. These results suggest similar schemes could be used to supplement shorter duration at-sea-training, used prior to a seagoing experience to better prepare ECRs, or to allow members of the science community unable to join an expedition in person to actively participate remotely, increasing inclusivity.
Neural manifolds and learning regimes in neural-interface tasks
Authors: Payeur Alexandre , Orsborn Amy L. , Lajoie Guillaume
Published: March 2023

Abstract

Neural activity tends to reside on manifolds whose dimension is lower than the dimension of the whole neural state space. Experiments using brain-computer interfaces (BCIs) with microelectrode arrays implanted in the motor cortex of nonhuman primates have provided ways to test whether neural manifolds influence learning-related neural computations. Starting from a learned BCI-controlled motor task, these experiments explored the effect of changing the BCI decoder to implement perturbations that were either “aligned” or not with the pre-existing neural manifold. In a series of studies, researchers found that within-manifold perturbations (WMPs) evoked fast reassociations of existing neural patterns for rapid adaptation, while outside-manifold perturbations (OMPs) triggered a slower adaptation process that led to the emergence of new neural patterns. Together, these findings have been interpreted as suggesting that these different rates of adaptation might be associated with distinct learning mechanisms. Here, we investigated whether gradient-descent learning could alone explain these differences. Using an idealized model that captures the fixed-point dynamics of recurrent neural networks, we uncovered gradient-based learning dynamics consistent with experimental findings. Crucially, this experimental match arose only when the network was initialized in a lazier learning regime, a concept inherited from deep learning theory. A lazy learning regime—in contrast with a rich regime—implies small changes on synaptic strengths throughout learning. For OMPs, these small changes were less effective at increasing performance and could lead to unstable adaptation with a heightened sensitivity to learning rates. For WMPs, they helped reproduce the reassociation mechanism on short adaptation time scales, especially with large input variances. Since gradient descent has many biologically plausible variants, our findings establish lazy gradient-based learning as a plausible mechanism for adaptation under network-level constraints and unify several experimental results from the literature.
Data-Driven Mathematical Approach for Removing Rare Features in Zero-Inflated Datasets
Authors: Ortiz-Velez Adrian N , Kelley Scott T
Published: March 2023

Sparse feature tables, in which many features are present in very few samples, are common in big biological data (e.g., metagenomics, transcriptomics). Ignoring the problem of zero-inflation can result in biased statistical estimates and decrease power in downstream analyses. Zeros are also a particular issue for compositional data analysis using log-ratios since the log of zero is undefined. Researchers typically deal with zero-inflated data by removing low frequency features, but the thresholds for removal differ markedly between studies with little or no justification. Here, we present CurvCut, a data-driven mathematical approach to zero-inflated feature removal based on curvature analysis of a “ball rolling down a hill”, where the hill is a histogram of feature distribution. These histograms typically contain a point of regime change, a discontinuity with a sharp change in the characteristics of the distribution, that can be used as a cutoff point for low frequency feature removal that considers the data-specific nature of the feature distribution. Our results show that CurvCut works well across a variety of biological data types, including ones with both right- and left-skewed feature distributions, and rapidly generates clear visual results allowing researchers to select data-appropriate cutoffs for feature removal.
IL-15 promotes inflammatory Th17 cells in the intestine
Authors: Golob Jonathan G. , Hou Guoqing , Lee Allen , Grassberger Helmut , Berinstein Elliott M , Zataari Mohamed El , Khaykin Valerie , Fry Christopher , Berinstein Jeff B. , Nemzek Jean , Kamada Nobuhiko , Kao John Y , Bishu Shrinivas
Published: March 2023

Ulcerative Colitis (UC) is a chronic gastrointestinal condition with high morbidity. While modern medical therapies have revolutionized the care of UC, 10-25% of patients fail medications and still progress to surgery. Thus, developing new treatments is a core problem in UC. T-cells, especially Th17 cells, are strongly linked with UC and are major targets of medications in UC. Tissue-resident memory T-cells (TRM) are a distinct class of T-cells that are highly enriched in the intestine, closely aligned with the microbiota, and are implicated in the pathogenesis of UC. Unlike circulating T-cells, TRMare difficult to target because they do not recirculate. Thus, we focused on cytokines like IL-15 which act as a tissue danger signal and regulate T-cellsin situ. We found that theIL15axis is upregulated in UC and predicts treatment response. IL-15 was redundant for Th17 differentiation but could activate terminally differentiated Th17 cells to promote intestinal inflammation. Finally, in CD4+TRMfrom patients with UC, IL-15 upregulatedRORC, the master transcription factor for Th17 cells, via a Janus Kinase (JAK)1 pathway. Thus, IL-15 promotes terminally differentiated inflammatory Th17 cells in the intestine raising the possibility that IL-15 may be a target for UC treatments.
Maximum Mutational Robustness in Genotype-Phenotype Maps Follows a Self-similar Blancmange-like Curve
Authors: Mohanty Vaibhav , Greenbury Sam F. , Sarkany Tasmin , Narayanan Shyam , Dingle Kamaludin , Ahnert Sebastian E. , Louis Ard A.
Published: March 2023

Phenotype robustness, defined as the average mutational robustness of all the genotypes that map to a given phenotype, plays a key role in facilitating neutral exploration of novel phenotypic variation by an evolving population. By applying results from coding theory, we prove that the maximum phenotype robustness occurs when genotypes are organised as bricklayer’s graphs, so called because they resemble the way in which a bricklayer would fill in a Hamming graph. The value of the maximal robustness is given by a fractal continuous everywhere but differentiable nowhere sums-of-digits function from number theory. Interestingly, genotype-phenotype (GP) maps for RNA secondary structure and the HP model for protein folding can exhibit phenotype robustness that exactly attains this upper bound. By exploiting properties of the sums-of-digits function, we prove a lower bound on the deviation of the maximum robustness of phenotypes with multiple neutral components from the bricklayer’s graph bound, and show that RNA secondary structure phenotypes obey this bound. Finally, we show how robustness changes when phenotypes are coarse-grained and derive a formula and associated bounds for the transition probabilities between such phenotypes.
Antibody targeting of aging damaged isoDGR-proteins doubles lifespan in a mouse model of chronic inflammation
Authors: Kalailingam Pazhanichamy , Mohd-Kahliab Khalilatul-Hanisah , Ngan SoFong Cam , Iyappan Ranjith , Melekh Evelin , Lu Tian , Zien Gan Wei , Sharma Bhargy , Guo Tiannan , MacNeil Adam J. , Macpherson Rebecca E. K. , Tsiani Evangelia Litsa , O’Leary Deborah D. , Lim Kah Leong , Su I Hsin , Gao Yong-Gui , Richard A Mark , Kalaria Raj N. , Chen Christopher P. , McCarthy Neil E. , Sze Siu Kwan
Published: March 2023

Aging is the result of the accumulation of molecular damages that impair normal biochemical activities. We previously reported that aging-damaged amino acid sequence NGR (Asn-Gly-Arg) results in a ‘gain-of-function’ conformational switching to isoDGR (isoAsp-Gly-Arg) motif. This integrin-binding motif activates leukocytes to induce chronic inflammation, which are characteristic features of age-linked cardiovascular disorders. We now report that anti-isoDGR immunotherapy doubles lifespan in mouse model of chronic inflammation. We observed extensive accumulation of isoDGR and inflammatory cytokine expression in multiple tissues from Pcmt1-KO and old WT animals, which could also be induced via injection of isoDGR-modified plasma proteins or synthetic peptides into young WT animals. However, weekly injection of anti-isoDGR mAb (1mg/kg) was sufficient to significantly reduce isoDGR-modified proteins and pro-inflammatory cytokine expression, improve behaviour and coordination, and double the average lifespan of Pcmt1-KO mice. Mechanistically, isoDGR-mAb mediated the immune clearance of damaged isoDGR-proteins by antibody-dependent cellular phagocytosis. These results indicate that immunotherapy targeting aging-damaged proteins may represent effective interventions for a range of age-linked degenerative disorders.

Graphical Abstract

Anti-isoDGR immunotherapy induces immune clearance of aging damaged isoDGR-proteins to reduce chronic inflammation, improve behaviour and coordination, and double lifespan in PCMT-/-mice.
Benchmarking large language models for genomic knowledge with GeneTuring
Authors: Hou Wenpin , Shang Xinyi , Ji Zhicheng
Published: March 2023

Large language models have demonstrated great potential in biomedical research. However, their ability to serve as a knowledge base for genomic research remains unknown. We developed GeneTuring, a comprehensive Q&A database containing 1,200 questions in genomics, and manually scored 25,200 answers provided by six GPT models, including GPT-4o, Claude 3.5, and Gemini Advanced. GPT-4o with web access showed the best overall performance and excelled in most tasks. However, it still failed to correctly answer all questions and may not be fully reliable for providing answers to genomic inquiries.
eOmics: an R package for improved omics data analysis
Authors: Liu Yu
Published: March 2023

Many computational tools have been developed for high-throughput omics data, and some are very popular, such as limma, WGCNA, and EnrichR. However, they also exhibit disadvantages in some special cases, such as imbalanced data analysis, causal inference, gene network functional enrichment, etc. Hence, we developed the R package eOmics to provide a comprehensive pipeline with these problems addressed. It combines an ensemble framework with limma, improving its performance on imbalanced data. Moreover, it couples a mediation model with WGCNA, so the causal relationship among WGCNA modules, module features, and phenotypes can be found, and this model is also used to explore the relationship between different omics. In addition, our package has some novel functional enrichment methods, capturing the influence of topological structure on gene set functions. Finally, it contains multi-omics clustering and classification functions to facilitate machine-learning tasks. Some basic functions, such as ANOVA analysis, are also available in it. The effectiveness of our package is proved by its performance on the three single or multi-omics datasets here. eOmics is available at: https://github.com/yuabrahamliu/eOmics.
Characterization of extracellular matrix deposited by segmental trabecular meshwork cells
Authors: Raghunathan VijayKrishna , Nartey Andrews , Dhamodaran Kamesh , Baidouri Hasna , Staverosky Julia A. , Keller Kate E , Zientek Keith , Reddy Ashok , Acott Ted , Vranka Janice A
Published: March 2023

Biophysical and biochemical attributes of the extracellular matrix are major determinants of cell fate in homeostasis and disease. Ocular hypertension and glaucoma are diseases where the trabecular meshwork tissue responsible for aqueous humor egress becomes stiffer accompanied by changes in its matrisome in a segmental manner with regions of high or low flow. Prior studies demonstrate these alterations in the matrix are dynamic in response to age and pressure changes. The underlying reason for segmentation or differential response to pressure and stiffening are unknown. This is largely due to a lack of appropriate models (in vitroorex vivo) to study this phenomena. In this study, we characterize the biomechanical attributes, matrisome, and incidence of crosslinks in the matrix deposited by primary cells isolated from segmental flow regions and when treated with glucocorticosteroid. Data demonstrate that matrix deposited by cells from low flow regions are stiffer and exhibit a greater number of immature and mature crosslinks, and that these are exacerbated in the presence of steroid. We also show a differential response of high or low flow cells to steroid via changes observed in the matrix composition. We conclude that although a mechanistic basis for matrix stiffness was undetermined in this study, it is a viable tool to study cell-matrix interactions and further our understanding of trabecular meshwork pathobiology.
Metabolic profiling stratifies colorectal cancer and reveals adenosylhomocysteinase as a therapeutic target
Authors: Voorde Johan Vande , Najumudeen Arafath K. , Steven Rory T. , Nikula Chelsea J. , Dexter Alex , Zeiger Lucas B. , Elia Efstathios A. , Nasif Ammar , Gonzalez-Fernandez Ariadna , Murta Teresa , Gillespie Michael , Ford Catriona A. , Lannagan Tamsin R.M. , Vlahov Nikola , Ridgway Rachel A. , Nixon Colin , Gilroy Kathryn , Gay David M. , Burton Amy , Yan Bin , Sellers Katherine , Wu Vincen , Xiang Yuchen , Shokry Engy , Clark William , Li Vivian S.W. , Barry Simon T. , Goodwin Richard J.A. , Takats Zoltan , Maddocks Oliver D.K. , Sumpton David , Yuneva Mariia O. , Campbell Andrew D. , Bunch Josephine , Sansom Owen J.
Published: March 2023

With colorectal cancer (CRC) being the second most common cause of cancer-related deaths worldwide1, there is an urgent need for better diagnostic tools and new, more targeted therapies. Here we used genetically engineered mouse models (GEMMs), and multimodal mass spectrometry-based metabolomics to study the impact of common genetic drivers of CRC on the metabolic landscape of the intestine. We show that unsupervised metabolic profiling can stratify intestinal tissues according to underlying genetic alterations, and use mass spectrometry imaging (MSI) to identify tumour, stromal and normal adjacent tissues. By identifying ions that drive variation between normal and transformed tissues, we found dysregulation of the methionine cycle to be a hallmark of APC-mutant CRC, and propose one of its enzymes, i.e. adenosylhomocysteinase (AHCY), as a new therapeutic target. Collectively, we show that the profound genotype-dependent alterations in both lipid and small molecule metabolism in CRC may be exploited for tissue classification with no need for ion identification, and we applied further data analysis to expose a novel metabolic vulnerability of CRC.
The analytical Flory random coil is a simple-to-use reference model for unfolded and disordered proteins
Authors: Alston Jhullian J. , Ginell Garrett M. , Soranno Andrea , Holehouse Alex S.
Published: March 2023

Denatured, unfolded, and intrinsically disordered proteins (collectively referred to here as unfolded proteins) can be described using analytical polymer models. These models capture various polymeric properties and can be fit to simulation results or experimental data. However, the model parameters commonly require users’ decisions, making them useful for data interpretation but less clearly applicable as stand-alone reference models. Here we use all-atom simulations of polypeptides in conjunction with polymer scaling theory to parameterize an analytical model of unfolded polypeptides that behave as ideal chains (ν = 0.50). The model, which we call the analytical Flory Random Coil (AFRC), requires only the amino acid sequence as input and provides direct access to probability distributions of global and local conformational order parameters. The model defines a specific reference state to which experimental and computational results can be compared and normalized. As a proof-of-concept, we use the AFRC to identify sequence-specific intramolecular interactions in simulations of disordered proteins. We also use the AFRC to contextualize a curated set of 145 different radii of gyration obtained from previously published small-angle X-ray scattering experiments of disordered proteins. The AFRC is implemented as a stand-alone software package and is also available via a Google colab notebook. In summary, the AFRC provides a simple-to-use reference polymer model that can guide intuition and aid in interpreting experimental or simulation results.
Evolutionary changes in the number of dissociable amino acids on spike proteins and nucleoproteins of SARS-CoV-2 variants
Authors: Božič Anže , Podgornik Rudolf
Published: March 2023

The spike protein of SARS-CoV-2 is responsible for target recognition, cellular entry, and endosomal escape of the virus. At the same time, it is the part of the virus which exhibits the greatest sequence variation across the many variants which have emerged during its evolution. Recent studies have indicated that with progressive lineage emergence, the positive charge on the spike protein has been increasing, with certain positively charged amino acids improving the binding of the spike protein to cell receptors. We have performed a detailed analysis of dissociable amino acids of more than 1400 different SARS-CoV-2 lineages which confirms these observations while suggesting that this progression has reached a plateau with omicron and its subvariants and that the positive charge is not increasing further. Analysis of the nucleocapsid protein shows no similar increase of positive charge with novel variants, which further indicates that positive charge of the spike protein is being evolutionarily selected for. Furthermore, comparison with the spike proteins of known coronaviruses shows that already the wild-type SARS-CoV-2 spike protein carries an unusually large amount of positively charged amino acids when compared to most other betacoronaviruses. Our study sheds a light on the evolutionary changes in the number of dissociable amino acids on the spike protein of SARS-CoV-2, complementing existing studies and providing a stepping stone towards a better understanding of the relationship between the spike protein charge and viral infectivity and transmissibility.
Cortical changes during the learning of sequences of simultaneous finger presses
Authors: Garzón Benjamín , Helms Gunther , Olsson Hampus , Brozzoli Claudio , Ullén Fredrik , Diedrichsen Jörn , Lövdén Martin
Published: March 2023

The cortical alterations underpinning the acquisition of motor skills remain debated. In this longitudinal study in younger adults, we acquired performance and neuroimaging (7T MRI) measures weekly over the course of 6 weeks to investigate neural changes associated with learning sequences of simultaneous finger presses executed with the non-dominant hand. Both the intervention group (n= 33) and the control group (n= 30) showed general performance improvements, but performance improved more and became more consistent for sequences that were intensively trained by the intervention group, relative to those that were not. Brain activity for trained sequences decreased compared with untrained sequences in the bilateral parietal and premotor cortices. No training-related changes in the primary sensorimotor areas were detected. The similarity of activation patterns between trained and untrained sequences decreased in secondary, but not primary, sensorimotor areas, while the similarity of the activation patterns between different trained sequences did not show reliable changes. Neither the variability of activation patterns across trials, nor the estimates of brain structure displayed practice-related changes that reached statistical significance. Overall, the main correlate of learning configural sequences was a reduction in brain activity in secondary motor areas.
Monoclonal antibodies against human coronavirus NL63 spike
Authors: Conlan Meghan , Tan Hyon-Xhi , Esterbauer Robyn , Kelly Andrew , Kent Stephen J , Wheatley Adam K , Lee Wen Shi
Published: March 2023

The COVID-19 pandemic has illustrated the potential for monoclonal antibody therapeutics as prophylactic and therapeutic agents against pandemic viruses. No such therapeutics currently exist for other human coronaviruses. NL63 is a human alphacoronavirus that typically causes the common cold and uses the same receptor, ACE2, as the highly pathogenic SARS-CoV and SARS-CoV-2 pandemic viruses. In a cohort of healthy adults, we characterised humoral responses against the NL63 spike protein. While NL63 spike and receptor binding domain-specific binding antibodies and neutralisation activity could be detected in plasma of all subjects, memory B cells against NL63 spike were variable and relatively low in frequency compared to that against SARS-CoV-2 spike. From these donors, we isolated a panel of antibodies against NL63 spike and characterised their neutralising potential. We identified potent neutralising antibodies that recognised the receptor binding domain (RBD) and other non-RBD epitopes within spike.
PandoraRLO: DQN and Graph convolution based method for optimized ligand pose
Authors: Jose Justin , Alam Ujjaini , Singh Divye , Jatana Nidhi , Arora Pooja
Published: March 2023

Predicting how proteins interact with small molecules is a complex and challenging task in the field of drug discovery. Two important aspects in this are shape complementarity and inter molecular interactions which are highly driven by the binding site and the ultimate pose of the ligand in which it interacts with the protein. Various state of the art methods exist which provide a range of ligand poses that are potentially a good fit for a given specific receptor, these are usually compute intensive and expensive. In this study, we have designed a method that provides a single optimized ligand pose for a specific receptor. The method is based on reinforcement learning where when exposed to a diverse protein ligand data set the agent is able to learn the underlying complex biochemistry of the protein ligand pair and provide an optimized pair. As a first study on usage of reinforcement learning for optimized ligand pose, the PandoraRLO model is able to predict pose within a range of 0.5Å to 4Å for a large number of test complexes. This indicates the potential of reinforcement learning in uncovering the inherent patterns of protein-ligand pair in 3D space.
The Clash of Academic Hierarchy and Inclusive Leadership: Evolution of Leadership in a Nationwide Diversity, Equity, and Inclusion Initiative
Authors: Codding Diane , Goldberg Bennett B.
Published: March 2023

Leadership has been traditionally envisioned and enacted as a top-down structure that reinforces positionality and power dynamics that are antithetical to the fundamental values and desired outcomes of equity-focused change work. This paper critically examines the evolution of leadership structures, agenda setting, and decision-making within a large, multi-institution, federally funded, and equity-focused alliance. Findings from this case study suggest that developing and sustaining inclusive leadership structures requires significant resources and an enduring commitment to engaging in a critically reflexive process to redress inequities within equity-focused initiatives.
Nanopore sequencing for the 17 modification types in 36 locations inE. coliribosomal RNA enables monitoring of stress-dependent changes
Authors: Fleming Aaron M. , Xiao Songjun , Burrows Cynthia J.
Published: March 2023

Escherichia colipossess the 16S and 23S rRNA strands that have 36 chemical modification sites with 17 different structures. Direct RNA nanopore sequencing using a protein nanopore sensor and helicase brake, which is also a sensor, was applied to the rRNAs. Nanopore current levels, base calling profile, and helicase dwell times for the modifications relative to non-modified synthetic rRNA controls found signatures for nearly all modifications. Signatures for clustered modifications were determined by selective sequencing of writer knock-outE. coliand sequencing of synthetic RNAs utilizing some custom-synthesized nucleotide triphosphates for their preparation. The knowledge of each modification’s signature, apart from 5-methylcytidine, was used to determine how metabolic and cold-shock stress impact rRNA modifications. Metabolic stress resulted in either no change or a decrease, and one site increased in modification occupancy, while cold-shock stress led to either no change or a decrease. In the 16S rRNA, there resides an m4Cmmodification at site 1402 that decreased with both stressors. Using helicase dwell time, it was determined that theN4methyl group is lost during both stressors, and the 2’-OMe group remained. In the ribosome, this modification stabilizes binding to the mRNA codon at the P-site resulting in increased translational fidelity that is lost during stress. TheE. coligenome has seven rRNA operons (rrn), and earlier studies aligned the nanopore reads to a single operon (rrnA). Here, the reads were aligned to the seven operons to identify operon-specific changes in the 11 pseudouridines. This study demonstrates that direct sequencing for >16 different RNA modifications in a strand is achievable.
A Stealthy Player in Lipid Experiments? EDTA Binding to Phosphatidylcholine Membranes Probed by Simulations and Monolayer Experiments
Authors: Vazdar Katarina , Tempra Carmelo , Olzynska Agnieszka , Biriukov Denys , Cwiklik Lukasz , Vazdar Mario
Published: March 2023

Ethylenediaminetetraacetic acid (EDTA) is frequently used in lipid experiments to remove redundant ions, such as Ca2+, from the sample solution. In this work, combining molecular dynamics (MD) simulations and Langmuir monolayer experiments, we show that on top of the expected Ca2+ depletion, EDTA anions themselves bind to phosphatidylcholine (PC) monolayers. This binding, originating from EDTA interaction with choline groups of PC lipids, leads to the adsorption of EDTA anions at the monolayer surface and concentration-dependent changes in surface pressure as measured by monolayer experiments and explained by MD simulations. This surprising observation emphasizes that lipid experiments carried out using EDTA-containing solutions, especially of high concentrations, must be interpreted very carefully due to potential interfering interactions of EDTA with lipids and other biomolecules involved in the experiment, e.g., cationic peptides, that may alter membrane-binding affinities of studied compounds.
Improvements in the detection power of algorithms for analyzing next-generation sequencing based bulked segregant analysis data via estimating thresholds at the genomic region level
Authors: Zhang Jianbo , Panthee Dilip R
Published: March 2023

Next-generation sequencing based bulked segregant analysis (BSA-Seq) has been widely used in identifying genomic regions associated with a trait of interest. However, the most popular algorithms for BSA-Seq data analysis have relatively low detection power, and high sequencing depths are required for the detection of genomic regions linked to the trait. Here we estimated the confidence intervals/thresholds of the popular algorithms at the genomic region level and increased the detection power of these algorithms by at least 5 folds, which should drastically reduce the sequencing cost of BSA-Seq studies.
Linking B-factor and temperature-induced conformational transition
Authors: de Sá Ribeiro Fernando , T. R. Lima Luís Maurício
Published: March 2023

The crystallographic B-factor, also called temperature factor or Debye-Waller factor, has long been used as a surrogate for local protein flexibility. However, the use of the absolute B-factor as a probe for protein motion requires reproducibility and intervalidation against chemical and physical variables. Here we report the investigation of the thermal dependence of the crystallographic B-factor and its correlation with protein conformational changes. We solved the B-factor reproducibility issue at high resolution (1.5 Å) over a broad temperature range (100 K to 325 K) by protecting crystals with hydrocarbon grease during data collection. We found that the crystallographic protein conformation varies as a function of temperature. Further, the demonstrated that the thermal dependence of B-factor as a function of temperature were similar for all atoms (Cα, N-amide and side chains), without local variations, indicating lack of correlation between temperature-dependent conformational change and the B-factor. These data indicate a linear correlation of B-factor with temperature due to global rigid body motion.