bluuebunny/crossref_metadata_2025 huggingface dataset:
Differential metabolic adaptations define responses of winner and loser oncogenic mutant stem cells in skin epidermisin vivo
Authors: Hemalatha Anupama , Li Zongyu , Tai Karen , Gonzalez David G. , Lathrop Elizabeth , Gil Daniel , Matte-Martone Catherine , Ganesan Smirthy , Yun Sangwon , Gonzalez Lauren E. , Skala Melissa , Perry Rachel J. , Greco Valentina
Published: November 2022

Skin epithelial stem cells detect and correct aberrancies induced by oncogenic mutations. Different oncogenes invoke different mechanisms of epithelial tolerance: while wild-type cells outcompete β-catenin-Gain-of-Function (βcatGOF) mutant cells, HrasG12Vmutant cells outcompete wild-type cells1,2. Here we ask how metabolic states change as wild-type stem cells interface with mutant cells, and how this ultimately drives different cell competition outcomes. By adapting our live-imaging platform to track endogenous redox ratio (NAD(P)H/FAD) with single cell resolution in the same mice over time, we show that wild-type epidermal stem cells maintain robust redox ratio despite their heterogeneous cell cycle states. We discover that both βcatGOF and HrasG12Vmodels lead to a rapid drop in redox ratios. However, the “winner” cells in each model (wild-type in βcatGOF and mutant in HrasG12V), rapidly recover their redox ratios, irrespective of the mutation induced. Using mass spectrometry (13C-LC-MS/MS)3, we find that both mutants increase flux through the oxidative tricarboxylic acid cycle, but the “winner” HrasG12Vcells and the “loser” βcatGOF cells modulate glycolytic flux differently. Hence, we reveal the metabolic adaptations that define the hallmarks of winners and losers during cell competitionin vivoand uncover the nodes of regulation unique to each cell fate.
Relationship between Students’ Attitude towards, and Performance in Mathematics Word Problems
Authors: Wakhata Robert , Balimuttajjo Sudi , Mutarutinya Védaste
Published: November 2022

The study explored the direct and indirect relationship between students’ attitude towards, and performance in mathematics word problems (MWTs), mediated by the active learning heuristic problem solving (ALHPS) approach. Specifically, this study investigated the correlation between students’ performance and their attitude towards linear programming (LP) linear programming word tasks (ATLPWTs). Tools for data collection were: the adapted Attitude towards Mathematics Inventory-Short Form (ATMI-SF), (α=.75) as a multidimensional measurement tool, and linear programming achievement tests (pre-test and post-test). A quantitative approach with a quasi-experimental pre-test, post-test, and non-equivalent control group study design was adopted. A sample of 60811th-grade grade Ugandan students (291 male and 317 female) from eight secondary schools (both public and private) participated. Data were analyzed using PROCESS macro (v.4) for SPSS version 26. The results revealed a direct significant positive relationship between students’ performance and their ATLPWTs. Thus, it is likely that students’ attitude positively and directly impacted their performance. The present study contributes to the literature on performance and attitude towards learning mathematics. Overall, the findings carry useful practical implications that can support the theoretical framework for enhancing students’ performance and attitude towards mathematics word problems.
Ecological boundaries and constraints on viable eco-evolutionary pathways
Authors: Coblentz Kyle E. , DeLong John P.
Published: November 2022

Evolutionary dynamics are subject to constraints ranging from limitations on what is physically possible to limitations on the pathways that evolution can take. One set of evolutionary constraints, known as ‘demographic constraints’, constrain what can occur evolutionarily due to the population demographic or population dynamical consequences of evolution leading to conditions that make populations susceptible to extinction. These demographic constraints can limit the strength of selection or rates of environmental change populations can experience while remaining extant and the trait values a population can express. Here we further hypothesize that the population demographic and population dynamical consequences of evolution also can constrain the eco-evolutionary pathways that populations can traverse by defining ecological boundaries represented by areas of likely extinction. We illustrate this process using a model of predator evolution. Our results show that the populations that persist over time tend to be those whose eco-evolutionary dynamics have avoided ecological boundaries representing areas of likely extinction due to stochastic deviations from a deterministic eco-evolutionary expectation. We term this subset of persisting pathways viable eco-evolutionary pathways. The potential existence of ecological boundaries constraining evolutionary pathways has important implications for predicting evolutionary dynamics, interpreting past evolution, and understanding the role of stochasticity and ecological constraints on eco-evolutionary dynamics.
Assessment of Emerging Pretraining Strategies in Interpretable Multimodal Deep Learning for Cancer Prognostication
Authors: Azher Zarif L. , Suvarna Anish , Chen Ji-Qing , Zhang Ze , Christensen Brock C. , Salas Lucas A. , Vaickus Louis J. , Levy Joshua J.
Published: November 2022

Deep learning models have demonstrated the remarkable ability to infer cancer patient prognosis from molecular and anatomic pathology information. Studies in recent years have demonstrated that leveraging information from complementary multimodal data can improve prognostication, further illustrating the potential utility of such methods. Model interpretation is crucial for facilitating the clinical adoption of deep learning methods by fostering practitioner understanding and trust in the technology. However, while prior works have presented novel multimodal neural network architectures as means to improve prognostication performance, these approaches: 1) do not comprehensively leverage biological and histomorphological relationships and 2) make use of emerging strategies to “pretrain” models (i.e., train models on a slightly orthogonal dataset/modeling objective) which may aid prognostication by reducing the amount of information required for achieving optimal performance. Here, we develop an interpretable multimodal modeling framework that combines DNA methylation, gene expression, and histopathology (i.e., tissue slides) data, and we compare the performances of crossmodal pretraining, contrastive learning, and transfer learning versus the standard procedure in this context. Our models outperform the existing state-of-the-art method (average 11.54% C-index increase), and baseline clinically driven models. Our results demonstrate that the selection of pretraining strategies is crucial for obtaining highly accurate prognostication models, even more so than devising an innovative model architecture, and further emphasize the all-important role of the tumor microenvironment on disease progression.
RE2DC: a robust and efficient 2D classifier with visualization for processing massive and heterogeneous cryo-EM data
Authors: Chung Szu-Chi , Lin Hsin-Hung , Wu Kuen-Phon , Chen Ting-Li , Chang Wei-Hau , Tu I-Ping
Published: November 2022

Despite the fact that single particle cryo-EM has become a powerful method of structural biology, processing cryo-EM images are challenging due to the low SNR, high-dimension and un-label nature of the data. Selecting the best subset of particle images relies on 2D classification—a process that involves iterative image alignment and clustering. This process, however, represents a major time sink, particularly when the data is massive or overly heterogeneous. Popular approaches to this process often trade its robustness for efficiency. Here, we introduced a new unsupervised 2D classification method termed RE2DC. It is built upon a highly efficient variant ofγ-SUP, a robust statistical cryo-EM clustering algorithm resistant to the attractor effect. To develop this efficient variant, we employed a tree-based approximation to reduce the computation complexity fromO(N2) toO(N), withNas the number of images. In addition, we exploited t-SNE visualization to unveil the process of 2D classification. Our tests of RE2DC using various datasets demonstrate it is both robust and efficient, with the potential to reveal subtle structural intermediates. Using RE2DC to curate a dataset of sub-millions of COVID-19 spike particles picked from 3,511 movies only takes 8 hours, suggesting its capability of accelerating cryo-EM structural determination. Currently, RE2DC is available with both CPU and GPU versions, where the implementation only requires modest hardware resources.
Terraces in Species Tree Inference from Gene Trees
Authors: Habib Mursalin , Roy Kowshic , Hasan Saem , Rahman Atif Hasan , Bayzid Md. Shamsuzzoha
Published: November 2022

A terrace in a phylogenetic tree space is a region where all trees contain the same set of subtrees, due to certain patterns of missing data among the taxa sampled, resulting in an identical optimality score for a given data set. This was first investigated in the context of phylogenetic tree estimation from sequence alignments using maximum likelihood (ML) and maximum parsimony (MP). The concept of terraces was later extended to the species tree inference problem from a collection of gene trees, where a set of equally optimal species trees was referred to as a “pseudo” species tree terrace. Pseudo terraces do not consider the topological proximity of the trees in terms of the induced subtrees resulting from certain patterns of missing data. In this study, we mathematically characterize species tree terraces and investigate the mathematical properties and conditions that lead multiple species trees to induce/display an identical set of locus-specific subtrees owing to missing data. We report that species tree terraces are agnostic to gene tree topologies and the discordance therein. Therefore, we introduce and characterize a special type of gene tree topology-aware terrace which we call “peak terrace”, and investigate conditions on the patterns of missing data that give rise to peak terraces. In addition to the theoretical and analytical results, we empirically investigated different challenges as well as various opportunities pertaining to the multiplicity of equally good species trees in terraced landscapes. Based on an extensive experimental study involving both simulated and real biological datasets, we present the prevalence of species tree terraces and the resulting ambiguity created for tree search algorithms. Remarkably, our findings indicate that the identification of terraces and the trees within them can substantially enhance the accuracy of summary methods. Furthermore, we demonstrate that reasonably accurate branch support can be computed by leveraging trees sourced from these terraces.
Stretch-activated ion channel TMEM63B associates with developmental and epileptic encephalopathies and progressive neurodegeneration
Authors: Vetro Annalisa , Balestrini Simona , Pelorosso Cristiana , Masi Alessio , Hambleton Sophie , Argilli Emanuela , Conti Valerio , Giubbolini Simone , Barrick Rebekah , Bergant Gaber , Writzl Karin , Bijlsma Emilia K. , Brunet Theresa , Cacheiro Pilar , Mei Davide , Devlin Anita , Hoffer Mariëtte J.V. , Machol Keren , Mannaioni Guido , Sakamoto Masamune , Menezes Manoj P. , Courtin Thomas , Sherr Elliott , Parra Riccardo , Richardson Ruth , Roscioli Tony , Scala Marcello , Stülpnagel Celina von , Smedley Damian ,   TMEM63B collaborators,   The Genomics England Research Consortium, Torella Annalaura , Tohyama Jun , Koichihara Reiko , Hamada Keisuke , Ogata Kazuhiro , Suzuki Takashi , Sugie Atsushi , van der Smagt Jasper J. , van Gassen Koen , Valence Stephanie , Vittery Emma , Kato Mitsuhiro , Matsumoto Naomichi , Ratto Gian Michele , Guerrini Renzo
Published: November 2022

By converting physical forces into electrical signals or triggering intracellular cascades, stretch-activated ion channels (SACs) allow the cell to respond to osmotic and mechanical stress. Knowledge of the pathophysiological mechanisms underlying associations of SACs with human disease is limited. Here we describe 16 unrelated patients, with severe early onset developmental and epileptic encephalopathy (DEE), intellectual disability, and severe motor and cortical visual impairment, associated with progressive neurodegenerative brain changes, carrying ten distinctde novovariants ofTMEM63B, encoding for a highly conserved SAC. Variants were missense, including the recurrent V44M in 7/16 patients, or in-frame, and affected conserved residues located in transmembrane regions of the protein. In 12 patients, haematological abnormalities co-occurred, such as macrocytosis and haemolysis, requiring blood transfusions in some. We modelled V44M, R443H, and T481N in transfected Neuro2a cells and demonstrated leak inward cation currents across the mutated channel even in isotonic conditions, while the response to hypo-osmotic challenge was impaired, as were the Ca2+transients generated under hypo-osmotic stimulation. Ectopic expression of the V44M and G580C variants inDrosophilaresulted in early death.TMEM63B-associated DEE represents a novel clinicopathological entity in which altered cation conductivity results in a severe neurological phenotype with progressive brain damage and early onset epilepsy, associated with haematological abnormalities in most patients.
Systematic violations of patients’ rights and safety: Forced medication of a cohort of 30 patients in Alaska
Authors: Tasch Gail , Gøtzsche Peter C
Published: November 2022

We assessed the records for 30 consecutive petitions for mental health commitment in which an involuntary medication order was requested from Anchorage, Alaska. In 29 cases, the commitment petition was granted. One patient requested a jury trial and the jury found in her favor. The forced medication order was granted in 27 of the 30 cases. In 26 cases, in violation of previous Supreme Court rulings, the patients’ desires, fears, wishes and experiences were totally ignored even when the patients were afraid that the drugs used for psychosis might kill them or when they had experienced serious harms such as tardive dyskinesia. The ethical and legal imperative of offering a less intrusive treatment was ignored. Benzodiazepines were not offered. Psychotherapy was not offered or mentioned in fifteen of the 30 cases. The providers claimed it does not work, even though that statement is blatantly false. The legal procedures can best be characterized as a sham where the patients are defenseless. The power imbalance and abuse were extreme and several of the psychiatrists who argued for forced treatment obtained court orders for administering drugs and dosages that were dangerous. Forced medication should be abandoned.
Plant-TFClass: a structural classification for plant transcription factors
Authors: Blanc-Mathieu Romain , Dumas Renaud , Turchi Laura , Lucas Jérémy , Parcy François
Published: November 2022

Transcription factors (TFs) bind DNA at specific sequences to regulate gene expression. This universal process is achieved thanks to the DNA-binding domain (DBD) present in each TF. DBDs show a vast diversity of protein folds within and across organisms, ranging from simple long basic alpha helices to complex structural combinations of alpha, beta and loop folds. In mammals, the structural conformation of the DBDs and the way it establishes contact with DNA has been used to organize TFs in a hierarchical classification named TFClass. However, such classification is missing from plants that possess many DBD types absent from mammals. Here, we reviewed the numerous TF DBD 3D-structures and models available for plants to organize all plant TFs types following the TFClass hierarchy (Superclass/Class/Family/Subfamily). We classified most of the 55 recognized plant TF types within the existing TFClass framework. This extended classification led us to add six new classes and 34 new families corresponding to TF DBD structures absent in mammals. Plant-TFClass provides a unique resource for TF and TF binding sites comparison across TF families and across organisms.
Plasmodium exoerythrocytic parasites redirect trafficking of human proteins to the parasitophorous vacuole
Authors: Calla Jaeson , Mittal Nimisha , LaMonte Greg , Liffner Benjamin , Godinez-Macias Karla P. , Carolino Krypton , Walker Gregory T. , Zou Bing Yu , Paytas Emma , Guerra Layné , Tong-Rios Carlos , Campo Brice , Vinetz Joseph M. , Gamboa Dionicia , Raffatellu Manuela , Absalon Sabrina , Winzeler Elizabeth A.
Published: November 2022

Abstract

Changes in host cell morphology and transcription after apicomplexan parasite infection have long been noted, but there have been few studies of the functional consequences of host cell remodeling. Here we show, using time-dependent immunofluorescence microscopy of multiple human cell lines (HepG2, HC-04, Huh7.5.1 and primary human hepatocytes), infected with multiplePlasmodiumspecies (Plasmodium berghei, P. falciparumandP. vivax(hypnozoites and schizonts)), and antibodies to multiple human proteins (HsNR4A3, HsMUC13, HsGOLGA8A, HsCGA, HsBiP, HsCXCL2), that human protein trafficking is extensively modified inPlasmodiuminfected cells. Using conventional as well as ultrastructure expansion microscopy we show that newly-synthesized human proteins are trafficked to the parasitophorous vacuole instead of the infected-cell plasma membrane, nucleus or extracellular space. Universal redirection of human signaling proteins cells the parasitophorous vacuole may provide a mechanistic explanation for how apicomplexan parasites can block host cells response to infection.
Recording animal-view videos of the natural world
Authors: Vasas Vera , Lowell Mark C. , Villa Juliana , Jamison Quentin D. , Siegle Anna G. , Katta Pavan Kumar Reddy , Bhagavathula Pushyami , Kevan Peter G. , Fulton Drew , Losin Neil , Kepplinger David , Salehian Shakiba , Forkner Rebecca E. , Hanley Daniel
Published: November 2022

Plants, animals, and fungi display a rich tapestry of colors. Animals, in particular, use colors in dynamic displays performed in spatially complex environments. In such natural settings, light is reflected or refracted from objects with complex shapes that cast shadows and generate highlights. In addition, the illuminating light changes continuously as viewers and targets move through heterogeneous, continually fluctuating, light conditions. Although traditional spectrophotometric approaches for studying colors are objective and repeatable, they fail to document this complexity. Worse, they miss the temporal variation of color signals entirely. Here, we introduce hardware and software that provide ecologists and filmmakers the ability to accurately record animal-perceived colors in motion. Specifically, our Python codes transform photos or videos into perceivable units (quantum catches) for any animal of known photoreceptor sensitivity. We provide the plans, codes, and validation tests necessary for end-users to capture animal-view videos. This approach will allow ecologists to investigate how animals use colors in dynamic behavioral displays, the ways natural illumination alters perceived colors, and other questions that remained unaddressed until now due to a lack of suitable tools. Finally, our pipeline provides scientists and filmmakers with a new, empirically grounded approach for depicting the perceptual worlds of non-human animals.
Drivers of mangrove vulnerability and resilience to tropical cyclones in the North Atlantic Basin
Authors: do Amaral Cibele Hummel , Poulter Benjamin , Lagomasino David , Fatoyinbo Temilola , Taillie Paul , Lizcano Gil , Canty Steven , Herrera Silveira Jorge Alfredo , Teutli-Hernández Claudia , Cifuentes Miguel , Charles Sean Patrick , Moreno Claudia Shantal , González-Trujillo Juan David , Roman-Cuesta Rosa Maria
Published: November 2022

The North Atlantic Basin (NAB) is seeing a significant increase in the frequency and intensity of tropical cyclones since the 1980s, with record-breaking seasons such as 2017 and 2020. However, little is known about how coastal ecosystems, particularly mangroves in the Gulf of Mexico and the Caribbean, are responding to these new “climate normals” at regional and subregional scales. Wind speed, rainfall, pre-cyclone forest structure, and hydro-geomorphology are known to influence mangrove damage and recovery following cyclones in the NAB. However, these studies have focused on site-specific responses and individual cyclonic events. Here, we analyze 25 years (1996-2020) of mangrove vulnerability (damage after a cyclone) and short-term resilience (recovery after damage) for the entire NAB and its subregions, using multi-annual, remote sensing-derived databases. We applied machine learning to characterize the influence of 22 potential drivers that include previously researched variables and new ones such as human development and long-term climate trends. The characteristics of the cyclones mainly drive vulnerability at the regional level, while resilience is largely driven by site-specific conditions. These include long-term climate conditions, such as air temperature and drought trends, pre-cyclone habitat conditions, such as canopy cover and height and soil organic carbon stock, and human interventions on the land. Rates and drivers of mangrove vulnerability and resilience vary across subregions in the NAB, and hotspots for restoration and conservation actions are highlighted within subregions. The impacts of increasing cyclone activity need to be framed in the context of climate change compound effects and heavy human influences in the region. There is an urgent need to value the restoration and conservation of mangroves as fundamental Nature-based Solutions against cyclone impacts in the NAB.
Phylogenomics reveals extensive misidentification of fungal strains from the genusAspergillus
Authors: Steenwyk Jacob L. , Balamurugan Charu , Raja Huzefa A. , Gonçalves Carla , Li Ningxiao , Martin Frank , Berman Judith , Oberlies Nicholas H. , Gibbons John G. , Goldman Gustavo H. , Geiser David M. , Hibbett David S. , Rokas Antonis
Published: November 2022

Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. However, the use of one or few molecular markers can lead to inaccurate inferences of species history and errors in classification. Here, we leverage genome-scale molecular phylogenetics (phylogenomics) of species and populations to reconstruct evolutionary relationships in a dense dataset of 711 fungal genomes from the biomedically and technologically important genusAspergillus. To do so, we generated a novel set of 1,362 high-quality molecular markers specific forAspergillusand provide profile Hidden Markov Models for each, facilitating others to use these molecular markers. Examination of the resulting genome-scale phylogeny: (1) helped resolve ongoing taxonomic controversies and identified new ones; (2) revealed extensive strain misidentification, underscoring the importance of population-level sampling in species classification; and (3) identified novel lineages that may shed light on the early evolution of an important genus. These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the tree of life.
Tau pathology in the dorsal raphe may be a prodromal indicator of Alzheimer’s disease
Authors: Pierson Samantha , Fiock Kimberly L. , Wang Ruixiang , Balasubramanian Nagalakshmi , Reindhardt Jessica , Khan Kanza M. , James Thomas D. , Betters Ryan , Deniz Kaancan , Lee Gloria , Aldridge Georgina , Hefti Marco M. , Marcinkiewcz Catherine A.
Published: November 2022

Protein aggregation in brainstem nuclei is thought to occur in the early stages of Alzheimer’s disease (AD), but its specific role in driving prodromal symptoms and disease progression is largely unknown. The dorsal raphe nucleus (DRN) contains a large population of serotonin (5-hydroxytryptamine; 5-HT) neurons that regulate mood, reward-related behavior, and sleep, which are all disrupted in AD. We report here that tau pathology is present in the DRN of individuals 54-80 years old without a known history of dementia and was found at higher frequency than α-synuclein and TDP-43. Most AD cases had tau pathology in the DRN (90%), whereas only a subset contained TDP-43 or α-synuclein, but not both (30%). To evaluate how early tau pathology impacts behavior, we overexpressed human P301L-tau in the DRN of mice and observed depressive-like behaviors and hyperactivity without any deficits in spatial memory. Tau pathology was predominantly found in neurons relative to glia and colocalized with a significant proportion of Tph2-expressing neurons in the DRN. 5-HT neurons were also hyperexcitable in P301L-tauDRNmice, and there was an increase in the amplitude of excitatory post-synaptic currents (EPSCs), suggestive of increased glutamatergic transmission. Moreover, astrocytic density was elevated in the DRN and accompanied by an increase in IL-1α and Frk expression, which is indicative of inflammation. Additionally, tau pathology was detected in axonal processes in the thalamus, hypothalamus, amygdala, and caudate putamen and a significant proportion of this tau pathology colocalized with the serotonin reuptake transporter (SERT), suggesting that tau may spread in an anterograde manner to regions outside the DRN. Together these results indicate that tau pathology accumulates in the DRN in a subset of individuals over 50 years and may lead to behavioral dysregulation, 5-HT neuronal dysfunction, and activation of local astrocytes which may be prodromal indicators of AD.
Tissue microenvironment dictates the state of human induced pluripotent stem cell-derived endothelial cells of distinct developmental origin in 3D cardiac microtissues
Authors: Cao Xu , Mircea Maria , van den Hil Francijna E. , Mei Hailiang , Neumann Katrin , Anastassiadis Konstantinos , Mummery Christine L. , Semrau Stefan , Orlova Valeria V.
Published: November 2022

Each tissue and organ in the body has its own type of vasculature. Here we demonstrate that organotypic vasculature for the heart can be recreated in a three-dimensional cardiac microtissue (MT) model composed of human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes (CMs), cardiac fibroblasts (CFs) and endothelial cells (ECs). ECs in cardiac MTs upregulated expression of markers enriched in human intramyocardial ECs (iECs), such asCD36, CLDN5, APLNR, NOTCH4, IGFBP3, ARHGAP18, which were previously identified in the single-cell RNA-seq dataset from the human fetal heart (6.5-7 weeks post coitum). We further show that the local microenvironment largely dictates the organ-specific identity of hiPSC-derived ECs: we compared ECs of different developmental origins derived from two distinct mesoderm subtypes (cardiac and paraxial mesoderm) and found that independent of whether the ECs were cardiac or paraxial mesoderm derived, they acquired similar identities upon integration into cardiac microtissues. This was confirmed by single-cell RNA-seq. Overall, the results indicated that whilst the initial gene profile of ECs was dictated by developmental origin, this could be modified by the local tissue environment such that the original identity was lost and the organotypic identity acquired through local environmental signals. This developmental “plasticity” in ECs has implications for multiple pathological and disease states.
IMPASTO: Multiplexed cyclic imaging without signal removalviaself-supervised neural unmixing
Authors: Kim Hyunwoo , Bae Seoungbin , Cho Junmo , Nam Hoyeon , Seo Junyoung , Han Seungjae , Yi Euiin , Kim Eunsu , Yoon Young-Gyu , Chang Jae-Byum
Published: November 2022

Spatially resolved proteomics requires a highly multiplexed imaging modality. Cyclic imaging techniques, which repeat staining, imaging, and signal erasure, have been adopted for this purpose. However, due to tissue distortion, it is challenging to obtain high fluorescent signal intensities and complete signal erasure in thick tissue with cyclic imaging techniques. Here, we propose an “erasureless” cyclic imaging method named IMPASTO. In IMPASTO, specimens are iteratively stained and imaged without signal erasure. Then, images from two consecutive rounds are unmixed to retrieve the images of single proteins through self-supervised machine learning without any prior training. Using IMPASTO, we demonstrate 30-plex imaging from brain slices in 10 rounds, and when used in combination with spectral unmixing, in five rounds. We show that IMPASTO causes negligible tissue distortion and demonstrate 3D multiplexed imaging of brain slices. Further, we show that IMPASTO can shorten the signal removal processes of existing cyclic imaging techniques.
CASBERT: BERT-Based Retrieval for Compositely Annotated Biosimulation Model Entities
Authors: Munarko Yuda , Rampadarath Anand , Nickerson David P.
Published: November 2022

Maximising FAIRness of biosimulation models requires a comprehensive description of model entities such as reactions, variables, and components. The COmputational Modeling in BIology NEtwork (COMBINE) community encourages the use of RDF with composite annotations that semantically involve ontologies to ensure completeness and accuracy. These annotations facilitate scientists to find models or detailed information to inform further reuse, such as model composition, reproduction, and curation. SPARQL has been recommended as a key standard to access semantic annotation with RDF, which helps get entities precisely. However, SPARQL is not suitable for most repository users who explore biosimulation models freely without adequate knowledge regarding ontologies, RDF structure, and SPARQL syntax. We propose here a text-based information retrieval approach, CASBERT, that is easy to use and can present candidates of relevant entities from models across a repository’s contents. CASBERT adapts Bidirectional Encoder Representations from Transformers (BERT), where each composite annotation about an entity is converted into an entity embedding for subsequent storage in a list-like structure. For entity lookup, a query is transformed to a query embedding and compared to the entity embeddings, and then the entities are displayed in order based on their similarity. The simple list-like structure makes it possible to implement CASBERT as an efficient search engine product, with inexpensive addition, modification, and insertion of entity embedding. To demonstrate and test CASBERT, we created a dataset for testing from the Physiome Model Repository and a static export of the BioModels database consisting of query-entities pairs. Measured using Mean Average Precision and Mean Reciprocal Rank, we found that our approach can perform better than the traditional bag-of-words method.
Evolution of drug resistance drives progressive destabilizations in functionally conserved molecular dynamics of the flap region of the HIV-1 protease
Authors: Rajendran Madhusudan , Ferran Maureen C. , Mouli Leora , Everingham Eric , Babbitt Gregory A. , Lynch Miranda L.
Published: November 2022

The HIV-1 protease is one of several common key targets of combination drug therapies for human immunodeficiency virus infection and acquired immunodeficiency syndrome (HIV/AIDS). During the progression of the disease, some individual patients acquire -drug resistance due to mutational hotspots on the viral proteins targeted by combination drug therapies. It has recently been discovered that drug-resistant mutations accumulate on the ‘flap region’ of the HIV-1 protease, which is a critical dynamic region involved in non-specific polypeptide binding during invasion and infection of the host cell. In this study, we utilize machine learning assisted comparative molecular dynamics, conducted at single amino acid site resolution, to investigate the dynamic changes that occur during functional dimerization and polypeptide binding of the main protease. We use a multi-agent machine learning model to identify conserved dynamics of the HIV-1 main protease that are preserved across simian and feline protease orthologs (SIV and FIV). We also investigate changes in dynamics due to common drug-resistant mutations in many patients. We find that a key functional site in the flap region, a solvent-exposed isoleucine (ILE50) and surrounding sites that control flap dynamics is often targeted by drug-resistance mutations, likely leading to malfunctional molecular dynamics affecting the overall flexibility of the flap region. We conclude that better long term patient outcomes may be achieved by designing drugs that target protease regions which are less dependent upon single sites with large functional binding effects.
Fatty acid elongases 1-3 have distinct roles in mitochondrial function, growth and lipid homeostasis inTrypanosoma cruzi
Authors: Pagura Lucas , Dumoulin Peter C. , Ellis Cameron C. , Estevao Igor L. , Mendes Maria T. , Almeida Igor C. , Burleigh Barbara A.
Published: November 2022

Trypanosomatids are a diverse group of uniflagellate protozoa that include globally important pathogens such asTrypanosoma cruzi, the causative agent of Chagas disease. Trypanosomes lack the fatty acid synthase (FAS)-I system typically used forde novosynthesis of long chain fatty acids (LCFA) in other eukaryotes. Instead, these microbes have evolved a modular fatty acid elongase (ELO) system comprised of individual ELO enzymes that operate processively. The role of the ELO system in maintaining lipid homeostasis in trypanosomes has not been determined. Here we demonstrate that ELO2 and ELO3 are required for global lipidome maintenance in the insect stage ofT. cruziwhereas ELO1 is dispensable for this function. Instead, ELO1 activity is needed to sustain mitochondrial activity and normal growth. The cross-talk between microsomal ELO1 and the mitochondrion is a novel finding that merits examination of the trypanosomatid ELO pathway as critical for central metabolism.
Modulatory effect of non-invasive prefrontal brain stimulation on risk-taking behaviours in humans: preliminary insight on the influence of personality traits
Authors: de la Torre Ona Martin , Valero-Cabré Antoni , Gallardo-Pujol David , Redolar-Ripoll Diego
Published: November 2022

We investigated the modulatory effects of cathodal High-Definition transcranial Direct Current Stimulation (HD-tDCS) on the left dorsolateral prefrontal cortex (DLPFC) and the left ventrolateral prefrontal cortex (VLPFC) on risk-taking.

Methods

Thirty-four healthy adults underwent 3 independent cathodal HD-tDCS interventions (DLPFC, VLPFC, sham) delivered in counterbalanced order during the performance of the balloon analogue risk task (autoBART). Participants were clustered post-hoc in 3 separate personality profiles according to the HEXACO-60 and the Dark Triad dirty dozen and we reanalysed the data.

Results

Dorsal prefrontal cathodal HD-tDCS significantly modulated autoBART performance rendering participants less prone to risk-taking (i.e., more conservative) under left DLPFC HD-tDCS compared to left VLPFC or sham stimulation. The re-analysis of the same dataset, taking into consideration personality traits, suggested specific effects in impulsive-disinhibited and normative participants for DLPFC and VLPFC stimulation, respectively. Specifically, we saw that participants classified as impulsive-disinhibited were more affected by HD-tDCS left DLPFC stimulation than other profiles.

Conclusions

Both, dorsal and ventral prefrontal active HD-tDCS decrease risk-taking behaviour compared to sham stimulation. Importantly, such effects are likely influenced by personality traits (impulsive disinhibited vs normative) exhibited by the participants.

Highlights

We investigated the effect of dorsal and ventral prefrontal HD-tDCS on risk-taking.

We considered post-hoc, the influence of individual personality differences.

Dorsal and ventral Prefrontal cathodal HD-tDCS decreased risk-taking behaviour.

Left cathodal DLPFC HD-tDCS decreased risk propensity in impulsive-disinhibited participants.

Left cathodal VLPFC HD-tDCS decreased risk propensity in normative personality participants.
A ubiquitination-mediated degradation system to target phospho-14-3-3-binding-motif embedded proteins
Authors: Li Zhaokai , Huang Xiaoqiang , Li Mohan , Sabry Ziad , Chen Y. Eugene , Wang Zhong , Liu Liu
Published: November 2022

The phosphorylation of 14-3-3 binding motif is involved in many cellular processes. A strategy that enables targeted degradation of phospho-14-3-3-binding-motif embedded (P-14-3-3-BME) proteins for studying their functions is highly desirable for basic research. Here, we report a phosphorylation-induced, ubiquitin-proteasome-system-mediated targeted protein degradation (TPD) strategy that allows specific degradation of P-14-3-3-BME proteins. Specifically, by ligating a modified von Hippel-Lindau E3-ligase with an engineered 14-3-3 bait, we generated a protein chimera referred to as Targeted Degradation of P-14-3-3-BME Protein (TDPP). TDPP can serve as a universal degrader for P-14-3-3-BME proteins based on the specific recognition of the phosphorylation in 14-3-3 binding motifs. TDPP shows high efficiency and specificity to a difopein-EGFP reporter, general and specific P-14-3-3-BME proteins. TDPP can also be applied for the validation of P-14-3-3-BME proteins. These results strongly support TDPP as a powerful tool for 14-3-3 related research.
Deficits in integrative NMDA receptors caused byGrin1disruption can be rescued in adulthood
Authors: Venkatesan S. , Binko M.A. , Mielnik C.A. , Ramsey A.J. , Lambe E.K.
Published: November 2022

Glutamatergic NMDA receptors (NMDAR) are critical for cognitive function, and their reduced expression leads to intellectual disability. Since subpopulations of NMDARs exist in distinct subcellular environments, their functioning may be unevenly vulnerable to genetic disruption. Here, we investigate synaptic and extrasynaptic NMDARs on the major output neurons of the prefrontal cortex in mice deficient for the obligate NMDAR subunit encoded byGrin1and wild-type littermates. With whole-cell recording in brain slices, we find that single, low-intensity stimuli elicit surprisingly-similar glutamatergic synaptic currents in both genotypes. By contrast, clear genotype differences emerge with manipulations that recruit extrasynaptic NMDARs, including stronger, repetitive, or pharmacological stimulation. These results reveal a disproportionate functional deficit of extrasynaptic NMDARs compared to their synaptic counterparts. To probe the repercussions of this deficit, we examine an NMDAR-dependent phenomenon considered a building block of cognitive integration, basal dendrite plateau potentials. Since we find this phenomenon is readily evoked in wild-type but not inGrin1-deficient mice, we ask whether plateau potentials can be restored by an adult intervention to increaseGrin1expression. This genetic manipulation, previously shown to restore cognitive performance in adulthood, successfully rescues electrically-evoked basal dendrite plateau potentials after a lifetime of NMDAR compromise. Taken together, our work demonstrates NMDAR subpopulations are not uniformly vulnerable to the genetic disruption of their obligate subunit. Furthermore, the window for functional rescue of the more-sensitive integrative NMDARs remains open into adulthood.
Mutations in Complex I of the mitochondrial electron-transport chain sensitize the fruit fly (Drosophila melanogaster) to ether and non-ether volatile anesthetics
Authors: Borchardt Luke , Scharenbrock Amanda R. , Olufs Zachariah P. G. , Wassarman David A. , Perouansky Misha
Published: November 2022

The mitochondrial electron transport chain (mETC) contains molecular targets of volatile general anesthetics (VGAs), which places carriers of mutations at risk for anesthetic complications. TheND-2360114andmt:ND2del1lines of fruit flies (Drosophila melanogaster) that carry mutations in core subunits of Complex I of the mETC, replicate numerous characteristics of Leigh syndrome (LS) caused by orthologous mutations in mammals and serve as models of LS.ND-2360114flies are behaviorally hypersensitive to volatile anesthetic ethers and develop an age- and oxygen-dependent anesthetic-induced neurotoxicity (AiN) phenotype after exposure to isoflurane but not to the related anesthetic sevoflurane. The goal of this paper was to investigate whether the alkane volatile anesthetic halothane and other mutations in Complex I and in Complexes II-V of the mETC cause AiN. We found that (i)ND-2360114andmt:ND2del1were susceptible to toxicity from halothane; (ii) in wildtype flies halothane was toxic under anoxic conditions; (iii) alleles of accessory subunits of Complex I predisposed to AiN; and (iv) mutations in Complexes II-V did not result in an AiN phenotype. We conclude AiN is neither limited to ether anesthetics nor exclusive to mutations in core subunits of Complex I.

Previous presentations

parts of the data were presented in abstract form at the 63rdAnnual Drosophila Research Conference in San Diego, March 2022.
Accuratede novodetection of somatic mutations in high-throughput single-cell profiling data sets
Authors: Muyas Francesc , Li Ruoyan , Rahbari Raheleh , Mitchell Thomas J. , Hormoz Sahand , Cortés-Ciriano Isidro
Published: November 2022

Characterization of somatic mutations at single-cell resolution is essential to study cancer evolution, clonal mosaicism, and cell plasticity. However, detection of mutations in single cells remains technically challenging. Here, we describe SComatic, an algorithm designed for the detection of somatic mutations in single-cell transcriptomic and ATAC-seq data sets without requiring matched bulk or single-cell DNA sequencing data. Using >1.5M single cells from 383 single-cell RNAseq and single-cell ATAC-seq data sets spanning cancer and non-neoplastic samples, we show that SComatic detects mutations in single cells, even in differentiated cells from polyclonal tissues not amenable to mutation detection using existing methods. In addition, SComatic permits the estimation of mutational burdens andde novomutational signature analysis at single-cell and cell-type resolution. Notably, using matched exome and single-cell RNAseq data, we show that SComatic achieves a 20 to 40-fold increase in precision as compared to existing algorithms for somatic SNV calling without compromising sensitivity. Overall, SComatic opens the possibility to study somatic mutagenesis at unprecedented scale and resolution using high-throughput single-cell profiling data sets.
Structure of LRRK1 and mechanisms of autoinhibition and activation
Authors: Reimer Janice M. , Dickey Andrea M. , Lin Yu Xuan , Abrisch Robert G. , Mathea Sebastian , Chatterjee Deep , Fay Elizabeth J. , Knapp Stefan , Daugherty Matthew D. , Reck-Peterson Samara L. , Leschziner Andres E.
Published: November 2022

Leucine Rich Repeat Kinase 1 and 2 (LRRK1 and LRRK2) are homologs in the ROCO family of proteins in humans. Despite their shared domain architecture and involvement in intracellular trafficking, their disease associations are strikingly different: LRRK2 is involved in familial Parkinson’s Disease (PD) while LRRK1 is linked to bone diseases. Furthermore, PD-linked mutations in LRRK2 are typically autosomal dominant gain-of-function while those in LRRK1 are autosomal recessive loss-of-function. To understand these differences, we solved cryo-EM structures of LRRK1 in its monomeric and dimeric forms. Both differ from the corresponding LRRK2 structures. Unlike LRRK2, which is sterically autoinhibited as a monomer, LRRK1 is sterically autoinhibited in a dimer-dependent manner. LRRK1 has an additional level of autoinhibition that prevents activation of the kinase and is absent in LRRK2. Finally, we place the structural signatures of LRRK1 and LRRK2 in the context of the evolution of the LRRK family of proteins.
A novel crosstalk between Nrf2 and Smad2/3 bridged by two nuanced Keap1 isoforms
Authors: Chen Feilong , Wang Qing , Xiao Mei , Lou Deshuai , Wufur Reziyamu , Hu Shaofan , Zhang Zhengwen , Wang Yeqi , Zhang Yiguo
Published: November 2022

The Keap1-Nrf2 signalling to transcriptionally regulate antioxidant response element (ARE)-driven target genes has been accepted as key redox-sensitive pathway governing a vast variety of cellular stresses during healthy survival and disease development. Herein, we identified two nuanced isoforms α and β of Keap1, arising from its first and another in-frame translation starting codons, respectively. In identifying those differential expression genes monitored by Keap1α and/or Keap1β, an unusual interaction of Keap1 with Smad2/3 was discovered by parsing transcriptome sequencing, Keap1-interacting protein profiling and relevant immunoprecipitation data. Further examination validated that Smad2/3 enable physical interaction with Keap1, as well as its isoforms α and β, by both EDGETSD and DLG motifs in the linker regions between their MH1 and MH2 domains, such that the stability of Smad2/3 and its transcriptional activity are enhanced with the prolonged half-lives and signalling responses from the cytoplasmic to nuclear compartments. The activation of Smad2/3 by Keap1, Keap1α or Keap1β was likely contributable to a coordinative or another competitive effect of Nrf2, particularly in distinct Keap1-based cellular responses to its cognate growth factor or redox stress. Overall, this discovery presents a novel functional bridge crossing both the Keap1-Nrf2 redox signalling and the TGF-β1-Smad2/3 pathways in healthy growth and development.
PilD mutant is a new cheater inPseudomonas aeruginosaquorum-sensing evolution
Authors: Qiu Huifang , Dai Weijun
Published: November 2022

Pathogen virulence is largely driven by the evolution and adaptation of the genome. LasR is a master regulator of quorum-sensing (QS) system. The QS-inactive LasR-null mutant regains QS activation in a laboratory evolution experiment through obtaining mutations inmexT, a gene encoding transcriptional regulator. How the QS-active LasR-MexT mutant continuously evolves is still unknown. Here we passaged the LasR-MexT mutant in casein broth and monitored its evolutionary trajectory. By examining the proteolytic phenotype of isolated single colonies, we found a protease-negative subpopulation arising from the parental population. The whole genome sequencing analysis revealed that these protease-negativ colonies bear mutations inpilDgene. In accordance with its role as a prepilin peptidase of type IV system, PilD mutants are defective in twitching motility. In conclusion, we identified a new PilD mutant cheater that evolved from the parental LasR-MexT mutant population. Our work demonstrates that population evolution is highly dynamics, with arising of distinct subpopulations containing different social behaviors.
OPUS-DSD: Deep Structural Disentanglement for cryo-EM Single Particle Analysis
Authors: Luo Zhenwei , Ni Fengyun , Wang Qinghua , Ma Jianpeng
Published: November 2022

Many Cryo-EM datasets contain structural heterogeneity due to functional or nonfunctional dynamics that conventional reconstruction methods may fail to resolve. Here we propose a new method, OPUS-DSD (Deep Structural Disentanglement), which can reliably reconstruct the structural landscape of cryo-EM data by directly translating the 2D cryo-EM images into 3D structures. The method adopts a convolutional neural network and is regularized by a latent space prior that encourages the encoding of structural information. The performance of OPUS-DSD was systematically compared to a previously reported method, cryoDRGN, on synthetic and real cryo-EM data. It consistently outperformed existing methods, resolved large or small structural heterogeneity, and improved the final reconstructions of tested systems even on highly noisy cryo-EM data. The results have shown that OPUS-DSD should be particularly suitable for cases in which the high structural flexibilities cannot easily be represented by rigid-body movements. Therefore, OPUS-DSD represents a valuable tool that can not only recover functionally-important structural dynamics missed in a traditional cryo-EM refinement, but also improve the final reconstruction by increasing homogeneity in a dataset. OPUS-DSD is available athttps://github.com/alncat/opusDSD.