bluuebunny/crossref_metadata_2025 huggingface dataset:
Graph perceiver network for lung tumor and bronchial premalignant lesion stratification from histopathology
Authors: Gindra Rushin H. , Zheng Yi , Green Emily J. , Reid Mary E. , Mazzilli Sarah A. , Merrick Daniel T. , Burks Eric J. , Kolachalama Vijaya B. , Beane Jennifer E.
Published: October 2023

Bronchial premalignant lesions (PMLs) precede the development of invasive lung squamous carcinoma (LUSC), posing a significant challenge in distinguishing those likely to advance to LUSC from those that might regress without intervention. In this context, we present a novel computational approach, the Graph Perceiver Network (GRAPE-Net), leveraging hematoxylin and eosin (H&E) stained whole slide images (WSIs) to stratify endobronchial biopsies of PMLs across a spectrum from normal to tumor lung tissues. GRAPE-Net outperforms existing frameworks in classification accuracy predicting LUSC, lung adenocarcinoma (LUAD), and non-tumor (normal) lung tissue on The Cancer Genome Atlas (TCGA) and Clinical Proteomic Tumor Analysis Consortium (CPTAC) datasets containing lung resection tissues while efficiently generating pathologist-aligned, class-specific heatmaps. The network was further tested using endobronchial biopsies from two data cohorts, containing normal to carcinoma in situ histology, and it demonstrated a unique capability to differentiate carcinoma in situ lung squamous PMLs based on their progression status to invasive carcinoma. The network may have utility in stratifying PMLs for chemoprevention trials or more aggressive follow-up.
Female Alms1-deficient mice develop echocardiographic features of adult but not infantile Alström Syndrome cardiomyopathy
Authors: McKay Eleanor J. , Luijten Ineke , Thomson Adrian , Weng Xiong , Gehmlich Katya , Gray Gillian A. , Semple Robert K.
Published: October 2023

Background

Alström Syndrome (AS), a multisystem disorder caused by biallelicALMS1mutations, features major cardiac complications often causing early mortality. These are biphasic, including infantile dilated cardiomyopathy, and distinct adult-onset cardiomyopathy. Cardiomyocyte maturation defects, cardiac fibrosis and early atherosclerosis have all been invoked as contributors to heart failure in AS, but their relative importance and inter-relationships are unknown.

Methods

Cardiac function of globalAlms1knockout mice was assessed by echocardiography at postnatal day 15 (P15) and at 8 and 23 weeks of age. Echocardiography was also undertaken in female mice withPdgfrα-Cre-drivenAlms1deletion in cardiac fibroblasts and a small proportion of cardiomyocytes. Histological and transcriptional analysis of myocardium at P15 and 24 weeks of age was also performed.

Results

Cardiac function was unaltered in knockout mice of both sexes at P15 and 8 weeks of age. At 23 weeks of age female but not male knockout mice showed increased left atrial area, decreased isovolumic relaxation time, and reduced ejection fraction, consistent with early restrictive cardiomyopathy. No histological or transcriptional changes could be identified in myocardium of 23-week old femaleAlms1KO mice, however.Pdgfrα-Cre-drivenAlms1KO in females did not recapitulate the phenotype of global KO at 23 weeks.

Conclusions

Adult female, but not male,Alms1-deficient mice show echocardiographic evidence of cardiac dysfunction, consistent with the restrictive cardiomyopathy of AS. The explanation for sexual dimorphism remains unclear, but may involve metabolic or endocrine differences between sexes. No infantile cardiomyopathy was found in this study.
Selection constraints of plant adaptation can be relaxed by gene editing
Authors: Ruffley Megan , Lutz Ulrich , Leventhal Laura , Hateley Shannon , Yuan Wei , Keck Jakob , Rhee Seung Y. , Weigel Detlef , Exposito-Alonso Moises
Published: October 2023

Climate change has already caused noticeable changes in species-wide traits, such as the well-documented acceleration of spring flowering. Because the evolutionary past has favored certain combinations of traits, some strategies like fast growth with early flowering that are adaptive today are at odds with other plant resilience strategies such as elevated water use efficiency. We know that the evolution of trait combinations is shaped by genomic constraints, but it is unclear whether and how this is affected by natural selection from climate change. Growing hundreds ofArabidopsis thaliananatural populations under different rainfall regimes revealed opposing natural selection on flowering time and water use efficiency, with strong antagonistic genetic correlations and contrasting causal alleles identified by Genome-Wide Association analyses. Inactivation of the central flowering regulatorFLCin multiple, diverse accessions relaxed trait correlations in a genetic background-dependent manner and allowed for the emergence of a novel adaptive trait combination—early flowering and intermediate water use efficiency. Future climates are predicted to escalate conflicts in natural selection among adaptive traits, but our work shows that surprisingly simple genetic changes can help solve these conflicts.
Mapping ovarian cancer spatial organization uncovers immune evasion drivers at the genetic, cellular, and tissue level
Authors: Yeh Christine Yiwen , Aguirre Karmen , Laveroni Olivia , Kim Subin , Wang Aihui , Liang Brooke , Zhang Xiaoming , Han Lucy M. , Valbuena Raeline , Plevritis Sylvia Katina , Bassik Michael C. , Snyder Michael P. , Howitt Brooke E. , Jerby Livnat
Published: October 2023

Immune exclusion and evasion are central barriers to the success of immunotherapies and cell therapies in solid tumors. Here we applied single cell spatial and perturbational transcriptomics alongside clinical, histological, and genomic profiling to elucidate immune exclusion and evasion in high-grade serous tubo-ovarian cancer (HGSC). Using high-plex spatial transcriptomics we profiled more than 1.3 million cells from 95 tumors and 60 patients, revealing generalizable principles in HGSC tumor tissue organization. Our data demonstrates that effector T cells resist stroma-mediated trapping and sequestration. However, upon infiltration into the tumor, T cells, as well as Natural Killer (NK) cells, preferentially co-localize only with a subset of malignant cells that manifest a distinct transcriptional cell state. The latter consists of dozens of co-regulated genes and is repressed under various copy number alterations. Performing CRISPR Perturb-seq screens in ovarian cancer cells, we identified functionally diverse genetic perturbations – including knockout of the insulin sensing repressorPTPN1and the epigenetic regulatorACTR8– that de-repress the proposed immunogenic malignant cell state identified in patients and indeed sensitize ovarian cancer cells to T cell and NK cell cytotoxicity. Taken together, our study uncovered a profound connection between somatic genetic aberrations, malignant cell transcriptional dysregulation, and immune evasion at the cellular and tissue level, allowing us to identify targets that reprogram malignant cell states as an avenue to unleash anti-tumor immune responses.
Towards Interpretable Multitask Learning for Splice Site and Translation Initiation Site Prediction
Authors: Kabanga Espoir , Van Messem Arnout , De Neve Wesley
Published: October 2023

In this study, we investigate the effectiveness of multi-task learning (MTL) for handling three bioinformatics tasks: donor splice site prediction, acceptor splice site prediction, and translation initiation site prediction. As the foundation for our MTL approach, we use the SpliceRover model, which has previously been successful in predicting splice sites. While providing benefits such as efficient resource utilization, reduced complexity, and streamlined model management, our findings show that the newly introduced MTL model performs comparably to the SpliceRover model trained separately for each task (single-task models), with a slight decrease in specificity, sensitivity, F1-score, and Matthews Correlation Coefficient (MCC). However, these differences are statistically insignificant (the specificity decreased with 0.0081 for acceptor splice site prediction and the MCC decreased with 0.0264 for TIS prediction), emphasizing the comparable performance of the MTL model. We further analyze the effectiveness of our MTL model using visualization techniques. The outcomes indicate that our MTL model effectively learns the relevant features associated with each task when compared to the single-task models (presence of nucleotides with a higher contribution to donor splice site prediction, polypyrimidine tracts in the upstream of acceptor splice sites, and the Kozak sequence). In conclusion, our results show that the MTL model generalizes well across all three tasks.
TMPyP binding evokes a complex, tunable nanomechanical response in DNA
Authors: Kretzer Balázs , Herényi Levente , Csík Gabriella , Supala Eszter , Orosz Ádám , Tordai Hedvig , Kiss Bálint , Kellermayer Miklós
Published: October 2023

TMPyP is a porphyrin capable of DNA binding and used in photodynamic therapy and G-quadruplex stabilization. Despite its broad applications, the effect of TMPyP on DNA nanomechanics is unknown. Here we investigated, by manipulating λ-phage DNA with optical tweezers combined with microfluidics, how TMPyP influences DNA nanomechanics across a wide range of TMPyP concentration (5-5120 nM), mechanical force (0-100 pN), NaCl concentration (0.01-1 M) and pulling rate (0.2-20 μm/s). Complex responses were recorded, for the analysis of which we introduced a simple mathematical model. TMPyP binding leads to the lengthening and softening of dsDNA. dsDNA stability, measured as the force of DNA’s overstretch transition, increased at low (<10 nM) TMPyP concentrations, then decreased progressively upon increasing TMPyP concentration. The cooperativity of the overstretch transition decreased, due most likely to mechanical roadblocks of ssDNA-bound TMPyP. TMPyP binding increased ssDNA’s contour length. The addition of NaCl at high (1 M) concentration competed with many of the nanomechanical changes evoked by TMPyP. Because the largest amplitude of the nanomechanical changes are induced by TMPyP in the pharmacologically relevant nanomolar concentration range, this porphyrin derivative may be used to tune DNA’s structure and properties, hence control the myriad of biomolecular processes associated with DNA.
Odorant receptors for floral- and plant-derived volatiles in the yellow fever mosquito,Aedes aegypti(Diptera: Culicidae)
Authors: Pullmann-Lindsley Heidi , Huff Robert , Boyi John , Pitts R. Jason
Published: October 2023

Adult mosquitoes require regular sugar meals, usually floral nectar, to survive and flourish in natural habitats. Both males and females locate potential sugar sources using sensory proteins called odorant receptors activated by plant volatiles that facilitate orientation toward flowers or honeydew. The Yellow Fever mosquito,Aedes aegypti(Linnaeus, 1762), possesses a large repertoire of odorant receptors, many of which are likely to support floral odor detection and nectar-seeking. In this study, we have employed a heterologous expression system and the two-electrode voltage clamping technique to identify environmentally relevant chemical compounds that activate specific odorant receptors. Importantly, we have uncovered ligand-receptor pairings for a suite ofAedes aegyptiodorant receptors likely to mediate appetitive or aversive behavioral responses, thus shaping a critical aspect of the life history of a medically important mosquito. Moreover, the high degree of conservation of these receptors in other disease-transmitting species suggests common mechanisms of floral odor detection. This knowledge can be used to further investigate mosquito foraging behavior to either enhance existing, or develop novel, control strategies, especially those that incorporate mosquito bait-and-kill or attractive toxic sugar bait technologies.
Structural and mechanistic insights intoStreptococcus pneumoniaeNADPH oxidase
Authors: Dubach Victor R. A. , Segundo-Acosta Pablo San , Murphy Bonnie J.
Published: October 2023

NADPH oxidases (NOXs) play a major role in the physiology of eukaryotic cells by mediating the production of reactive oxygen species (ROS). Evolutionarily distant proteins sharing the NOX catalytic core have been recently described in Bacteria. Among them, theStreptococcus pneumoniae NOX (SpNOX) has been proposed as a model for the study of NOXs due to its high activity and stability in detergent micelles. Here, we report high-resolution cryo-EM structures of substrate-free and stably reduced NADH-bound SpNOX, and of the NADPH-bound SpNOX and a Phe397Ala mutant under turnover conditions. In combination with structure-guided mutagenesis and biochemical analyses, we provide the structural basis for constitutive activity, the lack of substrate specificity towards NADPH and the electron transfer pathway. Additionally, we shed light on the catalytic regulation by the C-terminal tail residue Phe397 and the potentialin vivofunction of this protein.
Fast and universal single molecule localization using multi-dimensional point spread functions
Authors: Li Mengfan , Shi Wei , Liu Sheng , Fu Shuang , Fei Yue , Zhou Lulu , Li Yiming
Published: October 2023

The recent development of single molecule imaging techniques has enabled not only high accuracy spatial resolution imaging but also information rich functional imaging. Abundant information of the single molecules can be encoded in its diffraction pattern and be extracted precisely (e.g. 3D position, wavelength, dipole orientation). However, sophisticated high dimensional point spread function (PSF) modeling and analyzing methods have greatly impeded the broad accessibility of these techniques. Here, we present a graphics processing unit (GPU)-based B-spline PSF modeling method which could flexibly model high dimensional PSFs with arbitrary shape without greatly increasing the model parameters. Our B-spline fitter achieves 100 times speed improvement and minimal uncertainty for each dimension, enabling efficient high dimensional single molecule analysis. We demonstrated, both in simulations and experiments, the universality and flexibility of our B-spline fitter to accurately extract the abundant information from different types of high dimensional single molecule data including multicolor PSF (3D + color), multi-channel four-dimensional 4Pi-PSF (3D + interference phase) and five-dimensional vortex PSF (3D + dipole orientation).
Interactions between ploidy and resource availability shape clonal interference at initiation and recurrence of glioblastoma
Authors: Nowicka Zuzanna , Rentzeperis Frederika , Beck Richard , Tagal Vural , Pinto Ana Forero , Scanu Elisa , Veith Thomas , Cole Jackson , Ilter Didem , Viqueira William Dominguez , Teer Jamie K. , Maksin Konstantin , Pasetto Stefano , Abdalah Mahmoud A. , Fiandaca Giada , Prabhakaran Sandhya , Schultz Andrew , Ojwang Maureiq , Barnholtz-Sloan Jill S. , Farinhas Joaquim M. , Gomes Ana P. , Katira Parag , Andor Noemi
Published: October 2023

Glioblastoma (GBM) is the most aggressive form of primary brain tumor. Complete surgical resection of GBM is almost impossible due to the infiltrative nature of the cancer. While no evidence for recent selection events have been found after diagnosis, the selective forces that govern gliomagenesis are strong, shaping the tumor’s cell composition during the initial progression to malignancy with late consequences for invasiveness and therapy response. We present a mathematical model that simulates the growth and invasion of a glioma, given its ploidy level and the nature of its brain tissue micro-environment (TME), and use it to make inferences about GBM initiation and response to standard-of-care treatment. We approximate the spatial distribution of resource access in the TME through integration of in-silico modelling, multi-omics data and image analysis of primary and recurrent GBM. In the pre-malignant setting, our in-silico results suggest that low ploidy cancer cells are more resistant to starvation-induced cell death. In the malignant setting, between first and second surgery, simulated tumors with different ploidy compositions progressed at different rates. Whether higher ploidy predicted fast recurrence, however, depended on the TME. Historical data supports this dependence on TME resources, as shown by a significant correlation between the median glucose uptake rates in human tissues and the median ploidy of cancer types that arise in the respective tissues (Spearman r = -0.70; P = 0.026). Taken together our findings suggest that availability of metabolic substrates in the TME drives different cell fate decisions for cancer cells with different ploidy and shapes GBM disease initiation and relapse characteristics.
MCHelper automatically curates transposable element libraries across eukaryotic species
Authors: Orozco-Arias Simon , Sierra Pío , Durbin Richard , González Josefa
Published: October 2023

The number of species with high quality genome sequences continues to increase, in part due to scaling up of multiple large scale biodiversity sequencing projects. While the need to annotate genic sequences in these genomes is widely acknowledged, the parallel need to annotate transposable element sequences that have been shown to alter genome architecture, rewire gene regulatory networks, and contribute to the evolution of host traits is becoming ever more evident. However, accurate genome-wide annotation of transposable element sequences is still technically challenging. Severalde novotransposable element identification tools are now available, but manual curation of the libraries produced by these tools is needed to generate high quality genome annotations. Manual curation is time-consuming, and thus impractical for large-scale genomic studies, and lacks reproducibility. In this work, we present the Manual Curator Helper tool MCHelper, which automates the TE library curation process. By leveraging MCHelper’s fully automated mode with the outputs from three de novo transposable element identification tools, RepeatModeler2, EDTA and REPET, in fruit fly, rice, hooded crow, zebrafish, maize, and human, we show a substantial improvement in the quality of the transposable element libraries and genome annotations. MCHelper libraries are less redundant, with up to 65% reduction in the number of consensus sequences, have up to 11.4% fewer false positive sequences, and up to ∼48% fewer “unclassified/unknown” transposable element consensus sequences. Genome-wide transposable element annotations were also improved, including larger unfragmented insertions. Moreover, MCHelper is an easy to install and easy to use tool.
Aberrant macrophage activation and failed regeneration of pulmonary epithelium promote tuberculosis progression uniquely in lung tissue
Authors: Yabaji Shivraj M. , Lo Ming , Lata Suruchi , Gavrish Igor , Tseng Anna E. , O’Connell Aoife K , Gertje Hans P , Mazzilli Sarah , Tan Shumin , Thurman Colleen E , Bishai William R , Crossland Nicholas , Kobzik Lester , Kramnik Igor
Published: October 2023

Pulmonary TB that develops in immunocompetent adult humans is responsible for approximately 85% of the disease burden and is central for Mtb transmission. Most humans contain Mtb infection within primary granulomatous lesions, but in certain immunocompetent humans, containment fails, leading to hematogenous spread and active pulmonary disease with the formation of necrotic lesions and cavities that enable Mtb transmission via aerosols. To reveal lung-specific microenvironments conducive for Mtb survival and replication despite systemic immunity, we use fluorescence multiplex immunohistochemistry and spatial transcriptomic analyses of heterogenous TB lesions that uniquely form in the lungs of immunocompetent but TB-susceptible B6.Sst1S mice after hematogenous spread from the primary lesion. Initially, these secondary lung lesions manifested local adoptive immunity featuring tertiary lymphoid follicles similar to resistant B6 mice and contained primarily non-replicating bacilli. Following these early events, however, the B6.Sst1S mice uniquely demonstrate expansion of myeloid cell populations with the appearance of alternatively activated macrophages, dissolution of lymphoid follicles, and the accumulation of de-differentiated lung epithelial cells. These processes led to bronchogenic expansion, broncho-occlusion, and necrosuppurative pneumonia closely resembling advanced pulmonary tuberculosis in humans. To determine whether lung parenchymal cells or lung oxygenation were necessary for the pulmonary TB progression, we implanted lung and spleen fragments subcutaneously prior to the infection. The lung implants uniquely displayed the formation of the characteristic organized granulomas with necrosis and Mtb replication that paralleled TB progression in native lungs, demonstrating that the cellular composition of inflamed lung tissue, not oxygenation, is a critical determinant of pulmonary TB progression. Our data demonstrate that deleterious bi-directional interactions of aberrantly activated macrophages with the inflammation-injured lung resident cells determine lung vulnerability to virulent Mtb in immunocompetent hosts. Because these mechanisms enable Mtb transmission among humans via aerosols, they are likely evolutionary conserved and, therefore, represent appealing targets for host-directed TB therapies.
Centromere-Proximal Suppression of Meiotic Crossovers inDrosophilais Robust to Changes in Centromere Number and Repetitive DNA Content
Authors: Pazhayam Nila M. , Frazier Leah K. , Sekelsky Jeff
Published: October 2023

Accurate segregation of homologous chromosomes during meiosis depends on both the presence and regulated placement of crossovers (COs). The centromere effect (CE), or CO exclusion in pericentromeric regions of the chromosome, is a meiotic CO patterning phenomenon that helps prevent nondisjunction (NDJ), thereby protecting against chromosomal disorders and other meiotic defects. Despite being identified nearly a century ago, the mechanisms behind this fundamental cellular process remain unknown, with most studies of theDrosophilaCE focusing on local influences of the centromere and pericentric heterochromatin. In this study, we sought to investigate whether dosage changes in centromere number and repetitive DNA content affect the strength of the CE, using phenotypic recombination mapping. Additionally, we also studied the effects of repetitive DNA function on CE strength using satellite-DNA binding protein mutants shown to have defective centromere clustering. Despite what previous studies suggest, our results show that theDrosophilaCE is robust to dosage changes in centromere number and repetitive DNA content, and potentially also to repetitive DNA function. Our study suggests that the CE is unlikely to be spatially controlled, providing novel insight into the mechanisms behind theDrosophilacentromere effect.
A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus ‘fossil record’
Authors: Blanco-Melo Daniel , Campbell Matthew A. , Zhu Henan , Dennis Tristan P.W. , Modha Sejal , Lytras Spyros , Hughes Joseph , Gatseva Anna , Gifford Robert J.
Published: October 2023

Background

Genomic regions that remain poorly understood, often referred to as the “dark genome,” contain a variety of functionally relevant and biologically informative genome features. These include endogenous viral elements (EVEs) - virus-derived sequences that can dramatically impact host biology and serve as a virus “fossil record”. In this study, we introduce a database-integrated genome screening (DIGS) approach to investigating the dark genomein silico, focusing on EVEs found within vertebrate genomes.

Results

Using DIGS on 874 vertebrate species genomes, we uncovered approximately 1.1 million EVE sequences, with over 99% originating from endogenous retroviruses or transposable elements that contain EVE DNA. We show that the remaining 6038 sequences represent over a thousand distinct horizontal gene transfer events across ten virus families, including some that have not previously been reported as EVEs. We explore the genomic and phylogenetic characteristics of non-retroviral EVEs and determine their rates of acquisition during vertebrate evolution. Our study uncovers novel virus diversity, broadens knowledge of virus distribution among vertebrate hosts, and provides new insights into the ecology and evolution of vertebrate viruses.

Conclusions

We comprehensively catalogue and analyse EVEs within 874 vertebrate genomes, shedding light on the distribution, diversity and long-term evolution of viruses, and revealing their extensive impact on vertebrate genome evolution. Our results demonstrate the power of linking a relational database management system to a similarity search-based screening pipeline forin silicoexploration of the dark genome.
Estimates of Fall-run Chinook Salmon Escapement in Two San Joaquin River Tributaries from Device-based and Survey-based Methods
Authors: Pilger Tyler J. , Jonagan Emily , Peterson Matthew L. , Guignard Jason , Demko Doug , Fuller Andrea
Published: October 2023

Monitoring the escapement (i.e., spawner abundance) of adult salmonids is a fundamental component of fisheries stock assessment and evaluating recovery goals. Whereas multiple methods exist for estimating escapement, they exhibit trade-offs between degree of accuracy and implementation expenses and effort. Various methods are used throughout the Central Valley to estimate escapement of the four runs of Chinook Salmon (Oncorhynchus tshawytscha), but few rivers have more than one escapement monitoring program. Fall-run Chinook Salmon escapement to the Stanislaus and Tuolumne rivers is estimated by two independent monitoring programs on each river. Since 1952, California Department of Fish and Wildlife has performed carcass surveys that provide an index of escapement. Beginning in 2003 (Stanislaus River) and 2009 (Tuolumne River), private contractors have seasonally installed and operated weirs with fish counting devices to enumerate returning adults. We used the overlapping time series to evaluate the relationship between estimates from carcass surveys and the counting weirs. With few exceptions, estimates from counting adult salmon at the weirs as they entered the spawning grounds were greater than estimates from carcass surveys on both rivers. Escapement estimates from the Stanislaus weir were on average 1.7 (SE = 0.07) times greater than estimates from carcass surveys, while estimates at the Tuolumne weir were 2.5 (SE = 0.17) times greater than estimates from carcass surveys. Estimates from both methods were highly correlated, withr2values > 96% for both rivers. The high degree of covariation between methods indicates escapement estimates are robust and can be used in population models that incorporate additional data sources, such as estimates of juvenile production. Having multiple sources of data on fall-run Chinook Salmon will be increasingly useful for guiding and evaluating management actions in these heavily managed rivers.
Botulinum toxin intoxication requires retrograde transport and membrane translocation at the ER in RenVM neurons
Authors: Yeo Jeremy C. , Tay Felicia P. , Bennion Rebecca , Loss Omar , Maignel Jacquie , Pons Laurent , Foster Keith , Beard Matthew , Bard Frederic
Published: October 2023

Botulinum neurotoxin A (BoNT/A) is a highly potent proteolytic toxin specific for neurons with numerous clinical and cosmetic uses. After uptake at the synapse, the protein is proposed to translocate from synaptic vesicles to cytosol through a self-formed channel. Surprisingly, we found that after intoxication proteolysis of a fluorescent reporter occurs in the neuron soma first and then centrifugally in neurites. To investigate the molecular mechanisms at play, we use a genome-wide siRNA screen in genetically engineered neurons and identify over three hundred genes. An organelle-specific split-mNG complementation indicates BoNT/A traffic from the synapse to the soma-localised Golgi in a retromer dependent fashion. The toxin then moves to the ER and appears to require the Sec61 complex for retro-translocation to the cytosol. Our study identifies genes and trafficking processes hijacked by BoNT/A, revealing a complex route for efficient intoxication that contradicts the currently accepted model of BonT intoxication.
Nanomechanics of wild-type and mutant dimers of the tip-link protein protocadherin 15
Authors: Villasante Camila M. , Deng Xinyue , Cohen Joel E. , Hudspeth A. J.
Published: October 2023

Mechanical force controls the opening and closing of mechanosensitive ion channels atop the hair bundles of the inner ear. The filamentous tip link connecting transduction channels to the tallest neighboring stereocilium modulates the force transmitted to the channels and thus changes their probability of opening. Each tip link comprises four molecules: a dimer of protocadherin 15 and a dimer of cadherin 23, all of which are stabilized by Ca2+binding. Using a high-speed optical trap to examine dimeric PCDH15, we find that the protein’s configuration is sensitive to Ca2+and that the molecule exhibits limited unfolding at a physiological Ca2+concentration. PCDH15 can therefore modulate its stiffness without undergoing large unfolding events in physiological Ca2+conditions. The experimentally determined stiffness of PCDH15 accords with published values for the stiffness of the gating spring, the mechanical element that controls the opening of mechanotransduction channels. When PCDH15 has a point mutation, V507D, associated with non-syndromic hearing loss, unfolding events occur more frequently under tension and refolding events occur less often than in the wild-type protein. Our results suggest that the maintenance of appropriate tension in the gating spring is critical to the appropriate transmission of force to transduction channels, and hence to hearing.
Investigating RNA splicing as a source of cellular diversity using a binomial mixture model
Authors: Isaev Keren , Knowles David A
Published: October 2023

Alternative splicing (AS) contributes significantly to RNA and protein variability yet its role in defining cellular diversity is not fully understood. While Smart-seq2 offers enhanced coverage across transcripts compared to 10X single cell RNA-sequencing (scRNA-seq), current computational methods often miss the full complexity of AS. Most approaches for single cell based differential splicing analysis focus on simple AS events such as exon skipping, and rely on predefined cell type labels or low-dimensional gene expression representations. This limits their ability to detect more complex AS events and makes them dependent on prior knowledge of cell classifications. Here, we present Leaflet, a splice junction centric approach inspired by Leafcutter, our tool for quantifying RNA splicing variation with bulk RNA-seq. Leaflet is a probabilistic mixture model designed to infer AS-driven cell states without the need for cell type labels. We detail Leaflet’s generative model, inference methodology, and its efficiency in detecting differentially spliced junctions. By applying Leaflet to the Tabula Muris brain cell dataset, we highlight cell-state specific splicing patterns, offering a deeper insight into cellular diversity beyond that captured by gene expression alone.
Impaired embryo sac cellularization byPMEIgene mutation affects gamete specification and twin plants in Arabidopsis
Authors: Sharma Isha , Malathi Pinninti , Srinivasan Ramamurthy , Bhat Shripad Ramachandra , Sreenivasulu Yelam
Published: October 2023

Arabidopsislines with loss-of-function mutations in the gene encodingEmbryo sacPectinMethylEsteraseInhibitor(Atepmei) were found to have short silique and high seed sterility. Examination of tissue-cleared mature ovules (FG7-stage) revealed irregularly positioned nuclei within the embryo sacs. Instead of horse-shoe-shaped ovules, defective globular ovules without proper micropylar and chalazal ends were found. Embryo sac cell-type-specific GFP marker expression studies confirmed gamete and accessory cell identity alterations. Egg cell-specific marker (DD45) expression analysis confirmed the presence of multiple egg cells in the mutant embryo sacs, possibly due to defect in embryo sac cellularization. These supernumerary egg cells were functional as evident from the production of twin embryos when supernumerary sperm cells were provided. The results of Ruthenium red and tannic acid-ferric chloride staining ofAtepmeimutant developing ovules, conferred its interaction with the specific PME in proper cell wall formation and maintenance around embryo sac nuclei which also coincide with its fate as a specific gamete. This is the first report implicating role of cell wall in gamete cell fate determination by altering cell-cell communication. Our analysis of the twin-embryo phenotype ofepmeimutants also sheds light on the boundary conditions for double fertilization in plant reproduction.
Integrative analysis of the methylome and transcriptome of tomato fruit (Solanum lycopersicumL.) induced by postharvest handling
Authors: Zhou Jiaqi , Zhou Sitian , Chen Bixuan , Sangsoy Kamonwan , Luengwilai Kietsuda , Albornoz Karin , Beckles Diane M.
Published: October 2023

Tomato fruit ripening is triggered by the demethylation of key genes, which alters their transcriptional levels thereby initiating and propagating a cascade of physiological events. What is unknown, is how these processes are altered when fruit are ripened using postharvest practices to extend shelf-life, as these practices often reduce fruit quality. To address this, postharvest handling-induced changes in the fruit DNA methylome and transcriptome, and how they correlated with ripening speed, and ripening indicators such as ethylene, ABA, and carotenoids, were assessed. This study comprehensively connected changes in physiological events with dynamic molecular changes. Ripening fruit that reached ‘Turning’ (T) after storage under dark at 20°C, 12.5°C, or 5°C chilling (followed by 20°C rewarming), were compared to fresh-harvest fruit ‘FHT’. Fruit stored at 12.5°C, had the biggest epigenetic marks and alterations in gene expression, exceeding changes induced by postharvest chilling. Fruit physiological and chronological age were uncoupled at 12.5°C, as the time-to-ripening was longest. Fruit ripening at 12.5°C was not climacteric; there was no respiratory or ethylene burst, rather, fruit were high in ABA. Clear differentiation between postharvest-ripened and ‘FHT’ was evident in the methylome and transcriptome. Higher expression of photosynthetic genes and chlorophyll levels in ‘FHT’ fruit, pointing to light as influencing the molecular changes in fruit ripening. Finally, correlative analyses of the -omics data putatively identified genes regulated by DNA methylation. Collectively these data improve our interpretation of how tomato fruit ripening patterns are altered by postharvest practices, and long-term are expected to help improve fruit quality.
Do Domain-Specific Protein Language Models Outperform General Models on Immunology-Related Tasks?
Authors: Deutschmann Nicolas , Pelissier Aurelien , Weber Anna , Gao Shuaijun , Bogojeska Jasmina , Martínez María Rodríguez
Published: October 2023

Deciphering the antigen recognition capabilities by T cell and B cell receptors (antibodies) is essential for advancing our understanding of adaptive immune system responses. In recent years, the development of protein language models (PLMs) has facilitated the development of bioinformatic pipelines where complex amino acid sequences are transformed into vectorized embeddings, which are then applied to a range of downstream analytical tasks. With their success, we have witnessed the emergence of domain-specific PLMs tailored to specific proteins, such as immune receptors. Domain-specific models are often assumed to possess enhanced representation capabilities for targeted applications, however, this assumption has not been thoroughly evaluated. In this manuscript, we assess the efficacy of both generalist and domain-specific transformer-based embeddings in characterizing B and T cell receptors. Specifically, we assess the accuracy of models that leverage these embeddings to predict antigen specificity and elucidate the evolutionary changes that B cells undergo during an immune response. We demonstrate that the prevailing notion of domain-specific models outperforming general models requires a more nuanced examination. We also observe remarkable differences between generalist and domain-specific PLMs, not only in terms of performance but also in the manner they encode information. Finally, we observe that the choice of the size and the embedding layer in PLMs are essential model hyperparameters in different tasks. Overall, our analyzes reveal the promising potential of PLMs in modeling protein function while providing insights into their information-handling capabilities. We also discuss the crucial factors that should be taken into account when selecting a PLM tailored to a particular task.
AnophelesModel: An R package to interface mosquito bionomics, human exposure and intervention effects with models of malaria intervention impact
Authors: Golumbeanu Monica , Briët Olivier , Champagne Clara , Lemant Jeanne , Winkel Munir , Zogo Barnabas , Gerhards Maximilian , Sinka Marianne , Chitnis Nakul , Penny Melissa , Pothin Emilie , Smith Tom
Published: October 2023

In recent decades, field and semi-field studies of malaria transmission have gathered geographic-specific information about mosquito ecology, behaviour and their sensitivity to interventions. Mathematical models of malaria transmission can incorporate such data to infer the likely impact of vector control interventions and hence guide malaria control strategies in various geographies. To facilitate this process and make model predictions of intervention impact available for different geographical regions, we developed AnophelesModel. AnophelesModel is an online, open-access, R package that directly allows incorporating generated entomological data for adjustment of models to assess intervention scenarios according to species and location-specific characteristics. In addition, it includes a previously published, comprehensive, curated database of field entomological data from over 50Anophelesspecies, field data on mosquito and human behaviour, and on estimates of vector control effectiveness. Using the input data, the package parameterizes a discrete-time, state transition model of the mosquito oviposition cycle and infers species-specific impacts of various interventions on vectorial capacity. In addition, it offers formatted outputs ready to use in downstream analyses and by other models of malaria transmission for accurate representation of the vector-specific components. Using AnophelesModel, we show how the key implications for intervention impact change for various vectors and locations. The package facilitates quantitative comparisons of likely intervention impacts in different geographical settings varying in vector compositions, and can thus guide towards more robust and efficient malaria control recommendations. The AnophelesModel R package is available under a GPL-3.0 license athttps://github.com/SwissTPH/AnophelesModel.
Targeted Acidosis Mediated Delivery of Antigenic MHC-Binding Peptides
Authors: Kelly Joey J. , Ankrom Emily , Thévenin Damien , Pires Marcos M.
Published: October 2023

Cytotoxic T lymphocytes are the primary effector immune cells responsible for protection against cancer, as they target peptide neoantigens presented through the major histocompatibility complex (MHC) on cancer cells, leading to cell death. Targeting peptide-MHC (pMHC) complexes offers a promising strategy for immunotherapy due to its specificity and effectiveness against cancer. In this work, we exploit the acidic tumor micro-environment to selectively deliver antigenic peptides to cancer cells using pH(low) insertion peptides (pHLIP). We demonstrated that the delivery of MHC binding peptides directly to the cytoplasm of melanoma cells resulted in the presentation of antigenic peptides on MHC, and subsequent activation of T cells. This work highlights the potential of pHLIP as a vehicle for targeted delivery of antigenic peptides and their presentationviaMHC-bound complexes on cancer cell surfaces for activation of T cells with implications for enhancing anti-cancer immunotherapy.
The Synaptic Architecture of Layer 5 Thick Tufted Excitatory Neurons in the Visual Cortex of Mice
Authors: Bodor Agnes L. , Schneider-Mizell Casey M , Zhang Chi , Elabbady Leila , Mallen Alex , Bergeson Andi , Brittain Derrick , Buchanan JoAnn , Bumbarger Daniel J. , Dalley Rachel , Gamlin Clare , Joyce Emily , Kapner Daniel , Kinn Sam , Mahalingam Gayathri , Seshamani Sharmishtaa , Suckow Shelby , Takeno Marc , Torres Russel , Yin Wenjing , Bae J. Alexander , Castro Manuel A. , Dorkenwald Sven , Halageri Akhilesh , Jia Zhen , Jordan Chris , Kemnitz Nico , Lee Kisuk , Li Kai , Lu Ran , Macrina Thomas , Mitchell Eric , Mondal Shanka Subhra , Mu Shang , Nehoran Barak , Popovych Sergiy , Silversmith William , Turner Nicholas L. , Yu Szi-chieh , Wong William , Wu Jingpeng , Celii Brendan , Campagnola Luke , Seeman Stephanie C , Jarsky Tim , Ren Naixin , Arkhipov Anton ,   The MICrONS Consortium, Reimer Jacob , Seung H Sebastian , Reid R. Clay , Collman Forrest , Maçarico da Costa Nuno
Published: October 2023

The neocortex is one of the most critical structures that makes us human, and it is involved in a variety of cognitive functions from perception to sensory integration and motor control. Composed of repeated modules, or microcircuits, the neocortex relies on distinct cell types as its fundamental building blocks. Despite significant progress in characterizing these cell types1–5, an understanding of the complete synaptic partners associated with individual excitatory cell types remain elusive.

Here, we investigate the connectivity of arguably the most well recognized and studied excitatory neuron in the neocortex: the thick tufted layer 5 pyramidal cell6–10also known as extra telencephalic (ET)11neurons. Although the synaptic interactions of ET neurons have been extensively explored, a comprehensive characterization of their local connectivity remains lacking. To address this knowledge gap, we leveraged a 1 mm3electron microscopic (EM) dataset.

We found that ET neurons primarily establish connections with inhibitory cells in their immediate vicinity. However, when they extend their axons to other cortical regions, they tend to connect more with excitatory cells. We also find that the inhibitory cells targeted by ET neurons are a specific group of cell types, and they preferentially inhibit ET cells. Finally, we observed that the most common excitatory targets of ET neurons are layer 5 IT neurons and layer 6 pyramidal cells, whereas synapses with other ET neurons are not as common.

These findings challenge current views of the connectivity of ET neurons and suggest a circuit design that involves local competition among ET neurons and collaboration with other types of excitatory cells. Our results also highlight a specific circuit pattern where a subclass of excitatory cells forms a network with specific inhibitory cell types, offering a framework for exploring the connectivity of other types of excitatory cells.
Highly pathogenic Avian Influenza A (H5N1) Clade 2.3.4.4b in Wild Birds, Ecuador
Authors: Carrazco-Montalvo Andrés , Luje Lucia , Rodríguez-Pólit Cristina , Ampuño Antonio , Patiño Leandro , Gutiérrez-Pallo Diana , Alava Daniel , Alarcón-Vallejo Damaris , Arguello Natali , Echeverría-Garcés Gabriela , De La Torre David
Published: October 2023

Highly pathogenic avian influenza A(H5N1) virus clade 2.3.4.4b was detected in four wild birds of two species,Fregata magnificensandSula nebouxii, on the Ecuadorian Coast. This report highlights the importance of intersectoral collaboration and timely genotyping for monitoring this zoonotic pathogen, especially in regions with a rich biodiversity.
Amyloidogenic regions in beta-strands II and III modulate the aggregation and toxicity of SOD1 in living cells
Authors: McAlary Luke , Nan Jeremy R , Shyu Clay , Sher Mine , Plotkin Steven S. , Cashman Neil R.
Published: October 2023

Mutations in the protein superoxide dismutase-1 (SOD1) promote its misfolding and aggregation, ultimately causing familial forms of the debilitating neurodegenerative disease amyotrophic lateral sclerosis (ALS). Currently, over 220 (mostly missense) ALS-causing mutations in the SOD1 protein have been identified throughout the primary sequence, indicating that common structural features responsible for aggregation and toxicity may be present. Here, we usedin silicotools to predict amyloidogenic regions in the ALS-associated SOD1-G85R mutant, finding 7 regions spread throughout the protein structure. We found that the introduction of proline residues into β-strands II (I18P) or III (I35P) reduced the aggregation propensity and toxicity of SOD1-G85R in living cells, significantly more so than proline mutations in other amyloidogenic regions. The I18P and I35P mutations also reduced the capability of SOD1-G85R to template onto previously formed non-proline mutant SOD1 aggregates as measured by fluorescence recovery after photobleaching. Finally, we found that, while the I18P and I35P mutants are less structurally stable than SOD1-G85R, the proline mutants are less aggregation-prone during proteasome inhibition, and less toxic overall. Our research highlights the importance of a previously underappreciated SOD1 amyloidogenic region in β-strand II (15QGIINF20) to the aggregation and toxicity of SOD1 in ALS mutants, and suggests that β-strands II and III may be good targets for the development of SOD1-associated ALS therapies.
SELECTIVELY MANIPULATING SOFTNESS PERCEPTION OF MATERIALS THROUGH SOUND SYMBOLISM
Authors: Nalbantoğlu H. , Hazır B. M. , Dövencioğlu D. N.
Published: October 2023

Cross-modal interactions between auditory and haptic perception manifest themselves in language, such as sound symbolic words: crunch, splash, and creak. Several studies have shown strong associations between sound symbolic words, shapes (e.g., Bouba/Kiki effect), and materials. Here, we identified these material associations in Turkish sound symbolic words and then tested for their effect on softness perception. First, we used a rating task in a semantic differentiation method to extract the perceived softness dimensions from words and materials. We then tested whether Turkish onomatopoeic words can be used to manipulate the perceived softness of everyday materials such as honey, silk, or sand across different dimensions of softness. In the first preliminary study, we used 40 material videos and 29 adjectives in a rating task with a semantic differentiation method to extract the main softness dimensions. A principal component analysis revealed 7 softness components, including Deformability, Viscosity, Surface Softness, and Granularity, in line with the literature. The second preliminary study used 47 Turkish onomatopoeic words and 31 adjectives in the same rating task. Again, the findings aligned with the literature, revealing dimensions such as Fluidity, Granularity, and Surface Softness. However, no factors related to Deformability were found due to the absence of sound symbolic words in this category. Next, we paired the onomatopoeic words and material videos based on their associations with each softness dimension. We conducted a new rating task, synchronously presenting material videos and spoken onomatopoeic words. We hypothesized that congruent word-video pairs would produce significantly higher ratings for dimension-related adjectives, while incongruent word-video pairs would decrease these ratings, and the ratings of unrelated adjectives would remain the same. Our results revealed that onomatopoeic words selectively alter the perceived material qualities, providing evidence and insight into the cross-modality of perceived softness.