bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractTMPyP 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

AbstractAdult 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

AbstractNADPH 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

AbstractThe 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

AbstractGlioblastoma (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

AbstractThe 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

AbstractPulmonary 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

AbstractAccurate 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

ABSTRACTBackgroundGenomic 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.ResultsUsing 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.ConclusionsWe 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

ABSTRACTMonitoring 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

AbstractBotulinum 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

AbstractMechanical 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

AbstractAlternative 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.