bluuebunny/crossref_metadata_2025_split huggingface dataset:
Size-dependent sex allocation and the expression of andromonoecy in a protogynous perennial herb: both size and timing matter
Authors: Chen Kai-Hsiu , Pannell John R 
Published: March 2023

AbstractThe optimal life history and sex allocation of perennial hermaphrodites should depend on both their size and the relative costs and benefits of reproducing through male versus female functions. Theory predicts that insect-pollinated perennials should increase their allocation to female function with size, while the ‘mating environment’ hypothesis predicts that allocation to male function should track mating opportunities over the course of flowering. We test these two predictions by inferring male and female reproductive success in the protogynous perennial herbPulsatilla alpinaby tracking the patterns and dynamics of sex allocation over time for marked individuals over a range of sizes. We found that small individuals tend to produce only male flowers and that both small and larger individuals produced male flowers at the beginning of the flowering season when mating opportunities were high. By considering within-population variation in life history and phenology jointly rather than separately, and by considering both the tradeoff costs and benefits of allocation to male versus female functions, our results provide new insights into the evolution of both gender diphasy and andromonoecy in perennial plants that are constrained by a dichogamous flowering strategy.
Transcending Markov: Non-Markovian Rate Processes of Thermosensitive TRP Ion Channels
Authors: Ben-Abu Yuval , Tucker Stephen J , Contera Sonia 
Published: March 2023

AbstractThe Markov state model (MSM) is a popular theoretical tool for describing the hierarchy of time scales involved in the function of many proteins especially ion channel gating. A MSM is a particular case of the general non-Markovian model, where the rate of transition from one state to another does not depend on the history of state occupancy within the system, i.e., it only includes reversible, non-dissipative processes. However, this requires knowledge of the precise conformational state of the protein and is not predictive when those details are not known. In the case of ion channels, this simple description fails in real (non-equilibrium) situations, for example when local temperature changes, or when energy losses occur during channel gating. Here, we show it is possible to use non-Markovian equations (i.e. offer a general description that includes the MSM as a particular case) to develop a relatively simple analytical model that describes the non-equilibrium behavior of the temperature-sensitive TRP ion channels, TRPV1 and TRPM8. This model accurately predicts asymmetrical opening and closing rates, infinite processes, and the creation of new states, as well as the effect of temperature changes throughout the process. This approach therefore overcomes the limitations of the MSM and allows us to go beyond a mere phenomenological description of the dynamics of ion channel gating towards a better understanding of the physics underlying these processes.Significance StatementModeling ion channel processes has long relied on the Markovian assumption. However, Markov theory cannot translate situations in which the physical state of an ion channel changes during its gating process. By using a non-Markovian approach, we develop a simple analytical model that describes the non-equilibrium behavior of two temperature-sensitive TRP channels, TRPV1 and TRPM8. This model accurately describes and predicts their biophysical behavior as well as their temperature dependence. This approach therefore provides a better understanding of the physics underlying dynamic conformational changes such as those that occur during ion channel gating.
Sensitive, high-throughput HLA-I and HLA-II immunopeptidomics using parallel accumulation-serial fragmentation mass spectrometry
Authors: Phulphagar Kshiti Meera , Ctortecka Claudia , Vaca Jacome Alvaro Sebastian , Klaeger Susan , Verzani Eva K. , Hernandez Gabrielle M. , Udeshi Namrata , Clauser Karl , Abelin Jennifer , Carr Steven A 
Published: March 2023

AbstractComprehensive, in-depth identification of the human leukocyte antigen HLA-I and HLA-II tumor immunopeptidome can inform the development of cancer immunotherapies. Mass spectrometry (MS) is powerful technology for direct identification of HLA peptides from patient derived tumor samples or cell lines. However, achieving sufficient coverage to detect rare, clinically relevant antigens requires highly sensitive MS-based acquisition methods and large amounts of sample. While immunopeptidome depth can be increased by off-line fractionation prior to MS, its use is impractical when analyzing limited amounts of primary tissue biopsies. To address this challenge, we developed and applied a high throughput, sensitive, single-shot MS-based immunopeptidomics workflow that leverages trapped ion mobility time-of-flight mass spectrometry on the Bruker timsTOF SCP. We demonstrate >2-fold improved coverage of HLA immunopeptidomes relative to prior methods with up to 15,000 distinct HLA-I and HLA-II peptides from 4e7 cells. Our optimized single-shot MS acquisition method on the timsTOF SCP maintains high coverage, eliminates the need for off-line fractionation and reduces input requirements to as few as 1e6 A375 cells for > 800 distinct HLA-I peptides. This depth is sufficient to identify HLA-I peptides derived from cancer-testis antigen, and novel/unannotated open reading frames. We also apply our optimized single-shot SCP acquisition methods to tumor derived samples, enabling sensitive, high throughput and reproducible immunopeptidome profiling with detection of clinically relevant peptides from less than 4e7 cells or 15 mg wet weight tissue.
Switch-like Compaction of Poly(ADP-ribose) Upon Cation Binding
Authors: Badiee Mohsen , Kenet Adam L. , Ganser Laura R. , Paul Tapas , Myong Sua , Leung Anthony K. L. 
Published: March 2023

AbstractPoly(ADP-ribose) (PAR) is a homopolymer of adenosine diphosphate ribose that is added to proteins as a post-translational modification to regulate numerous cellular processes. PAR also serves as a scaffold for protein binding in macromolecular complexes, including biomolecular condensates. It remains unclear how PAR achieves specific molecular recognition. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) to evaluate PAR flexibility under different cation conditions. We demonstrate that, compared to RNA and DNA, PAR has a longer persistence length and undergoes a sharper transition from extended to compact states in physiologically relevant concentrations of various cations (Na+, Mg2+, Ca2+, and spermine). We show that the degree of PAR compaction depends on the concentration and valency of cations. Furthermore, the intrinsically disordered protein FUS also served as a macromolecular cation to compact PAR. Taken together, our study reveals the inherent stiffness of PAR molecules, which undergo switch-like compaction in response to cation binding. This study indicates that a cationic environment may drive recognition specificity of PAR.SignificancePoly(ADP-ribose) (PAR) is an RNA-like homopolymer that regulates DNA repair, RNA metabolism, and biomolecular condensate formation. Dysregulation of PAR results in cancer and neurodegeneration. Although discovered in 1963, fundamental properties of this therapeutically important polymer remain largely unknown. Biophysical and structural analyses of PAR have been exceptionally challenging due to the dynamic and repetitive nature. Here, we present the first single-molecule biophysical characterization of PAR. We show that PAR is stiffer than DNA and RNA per unit length. Unlike DNA and RNA which undergoes gradual compaction, PAR exhibits an abrupt switch-like bending as a function of salt concentration and by protein binding. Our findings points to unique physical properties of PAR that may drive recognition specificity for its function.
Modulating Nucleic Acid Phase Transitions as a Mechanism of Action for Cell-Penetrating Antimicrobial Peptides
Authors: Sneideris Tomas , Erkamp Nadia A. , Ausserwöger Hannes , Saar Kadi L. , Welsh Timothy J. , Qian Daoyuan , Johncock Margaret L. L. Y. , Krainer Georg , Borodavka Alexander , Knowles Tuomas P. J. 
Published: March 2023

AbstractAntimicrobial peptides (AMPs) are a vital part of the immune system that helps combat bacterial infections by disrupting the bacterial cell membrane or interacting with intracellular targets. However, the mechanisms by which AMPs act on intracellular targets are not well understood. Using machine learning-based sequence analysis, we have discovered that a significant number of AMPs have a strong tendency to form liquid-like condensates in the presence of nucleic acids, a process known as phase separation. We have demonstrated that this phase separation propensity is linked to the effectiveness of the AMPs in inhibiting transcription and translation in vitro, as well as their ability to compact nucleic acids and form clusters with bacterial nucleic acids in bacterial cells. We propose that the AMP-driven compaction of nucleic acids and modulation of their phase transitions constitute a previously unrecognised mechanism by which AMPs exert their antibacterial effects. These findings open up exciting possibilities for the development of antimicrobials that target nucleic acid phase transitions.
Asymmetric oligomerization state and sequence patterning can tune multiphase condensate miscibility
Authors: Rana Ushnish , Xu Ke , Narayanan Amal , Walls Mackenzie T. , Panagiotopoulos Athanassios Z. , Avalos José L. , Brangwynne Clifford P. 
Published: March 2023

AbstractEndogenous biomolecular condensates, comprised of a multitude of proteins and RNAs, can organize into multiphasic structures, with compositionally-distinct phases. This multiphasic organization is generally understood to be critical for facilitating their proper biological function. However, the biophysical principles driving multiphase formation are not completely understood. Here, we utilizein vivocondensate reconstitution experiments and coarse-grained molecular simulations to investigate how oligomerization and sequence interactions modulate multiphase organization in biomolecular condensates. We demonstrate that increasing the oligomerization state of an intrinsically disordered protein region (IDR) results in enhanced immiscibility and multiphase formation. Interestingly, we found that oligomerization tunes the miscibility of IDRs in an asymmetric manner, with the effect being more pronounced when the IDR exhibiting stronger homotypic IDR interactions is oligomerized. Our findings suggest that oligomerization is a flexible biophysical mechanism which cells can exploit to tune the internal organization of biomolecular condensates and their associated biological functions.
Unsupervised discovery of family specific vocal usage in the Mongolian gerbil
Authors: Peterson Ralph E. , Choudhri Aman , Mitelut Catalin , Tanelus Aramis , Capo-Battaglia Athena , Williams Alex H. , Schneider David M. , Sanes Dan H. 
Published: March 2023

AbstractIn nature, animal vocalizations can provide crucial information about identity, including kinship and hierarchy. However, lab-based vocal behavior is typically studied during brief interactions between animals with no prior social relationship, and under environmental conditions with limited ethological relevance. Here, we address this gap by establishing long-term acoustic recordings from Mongolian gerbil families, a core social group that uses an array of sonic and ultrasonic vocalizations. Three separate gerbil families were transferred to an enlarged environment and continuous 20-day audio recordings were obtained. Using a variational autoencoder (VAE) to quantify 583,237 vocalizations, we show that gerbils exhibit a more elaborate vocal repertoire than has been previously reported and that vocal repertoire usage differs significantly by family. By performing gaussian mixture model clustering on the VAE latent space, we show that families preferentially use characteristic sets of vocal clusters and that these usage preferences remain stable over weeks. Furthermore, gerbils displayed family-specific transitions between vocal clusters. Since gerbils live naturally as extended families in complex underground burrows that are adjacent to other families, these results suggest the presence of a vocal dialect which could be exploited by animals to represent kinship. These findings position the Mongolian gerbil as a compelling animal model to study the neural basis of vocal communication and demonstrates the potential for using unsupervised machine learning with uninterrupted acoustic recordings to gain insights into naturalistic animal behavior.
Brain fingerprinting using EEG graph inference
Authors: Miri Maliheh , Abootalebi Vahid , Amico Enrico , Saeedi-Sourck Hamid , Van De Ville Dimitri , Behjat Hamid 
Published: March 2023

AbstractTaking advantage of the human brain functional connectome as an individual’s fingerprint has attracted great research in recent years. Conventionally, Pearson correlation between regional time-courses is used as a pairwise measure for each edge weight of the connectome. Building upon recent advances in graph signal processing, we propose here to estimate the graph structure as a whole by considering all time-courses at once. Using data from two publicly available datasets, we show the superior performance of such learned brain graphs over correlation-based functional connectomes in characterizing an individual.
Metabolic energetics underlying attractors in neural models
Authors: Buxton Richard B. , Wong Eric C. 
Published: March 2023

AbstractNeural population modeling, including the role of neural attractors, is a promising tool for understanding many aspects of brain function. We propose a modeling framework to connect the abstract variables used in modeling to recent cellular level estimates of the bioenergetic costs of different aspects of neural activity, measured in ATP consumed per second per neuron. Based on recent work, an empirical reference for brain ATP use for the awake resting brain was estimated as ∼2×109ATP/s-neuron across several mammalian species. The energetics framework was applied to the Wilson-Cowan (WC) model of two interacting populations of neurons, one excitatory (E) and one inhibitory (I). Attractors were considered exhibiting steady-state behavior and limit cycle behavior, both of which end when the excitatory stimulus ends, and sustained activity that persists after the stimulus ends. The general finding was that the energy cost essentially follows the firing rate (average spikes/s) of theE-population, and firing rates of 8-10 spikes/s are in good agreement with the empirical reference value of ATP use. Self-sustained firing driven by recurrent excitation, though, involves higher firing rates and a higher energy cost. By considering a network in which each node is a WC model, we found that a combination of three nodes can serve as a circuit element that turns on when input passes a threshold and then persists after the input ends (an ‘on-switch’), with moderate overall ATP use. The proposed framework can serve as a guide for anchoring neural population models to plausible bioenergetics requirements.
Assessment and validation of enrichment and target capture approaches to improveMycobacterium tuberculosisWGS from direct patient samples
Authors: Mann B.C. , Jacobson K.R. , Ghebrekristos Y. , Warren R.M. , Farhat M.R. 
Published: March 2023

AbstractBackgroundWithin-hostM. tuberculosis(Mtb) diversity may capture antibiotic resistance or predict tuberculosis treatment failure and is best captured through sequencing directly from sputum. Here we compared three sample preprocessing steps for DNA decontamination and studied the yield of a new target enrichment protocol for optimal whole-genome sequencing (WGS) from direct patient samples.Design/MethodsMtb positive NALC - NaOH treated patient sputum sediments were pooled, and heat inactivated, split in replicates, and treated by either a wash, DNase I or Benzonase digestion. Levels of contaminating host DNA and target Mtb DNA was assessed by Quantitative PCR (qPCR), followed by WGS with and without custom dsDNA target enrichment.ResultsThe pre-treatment sample has a high host-to-target ratio of DNA (6 168 ± 1 638 host copies/ng to 212,3 ± 59,4 Mtb copies/ng) that significantly decreased with all three treatments. Benzonase treatment resulted in the highest enrichment of Mtb DNA at 100-fold compared with control (3 422 ± 2 162 host copies/ng to 11 721 ± 7 096 Mtb copies/ng). The custom dsDNA probe panel successfully enriched libraries from as little as 0.45 pg of Mtb DNA (100 genome copies). Applied to direct sputum after benzonase treatment the dsDNA target enrichment panel increased the percent of sequencing reads mapping to the Mtb to 90,95% from 1,18 % compared with benzonase treatment without enrichment.ConclusionWe demonstrate a low limit of detection (LoD) for a new custom dsDNA Mtb target enrichment panel that has a favourable cost profile. The results also demonstrate that pre-processing to remove contaminating extracellular DNA prior to cell lysis and DNA extraction improves the host-to-Mtb DNA ratio but is not adequate to support average coverage WGS without target capture.
First report of a successful development of yam hybrids (Dioscorea alataL.) from lyophilized and long-term stored pollens
Authors: Malédon Erick , Nudol Elie , Perrot Christophe , Gravillon Marie-claire , Rivallan Ronan , Cornet Denis , Chair Hâna , Dossa Komivi 
Published: March 2023

AbstractBackgroundGreater yam,Dioscorea alataL., is a significant food security crop in tropical areas. However, low genetic diversity and various biological constraints, including susceptibility to viruses, ploidy, erratic and low flowering intensity, and asynchronous flowering hinder successful hybrid development and genetic gains in greater yam breeding programs. Therefore, pollen storage has gained much attention to facilitate genetic material exchanges, artificial pollinations and to increase the genetic gains in breeding programs. This 4-year study aimed at developing a practical long-term pollen storage technique for the successful development of yam hybrids. Fresh pollens were collected from twoD. alatamales, then lyophilized (two lyophilization treatments were applied), followed by storage at room temperature (24-25 °C) for 12 months. Moreover, the lyophilized and stored pollens were tested for viability by crossing with four female varieties.ResultsOur results showed that lyophilization is effective for achieving viable pollens after 12 months of storage. Treatment 1 (48 h drying) showed higher pollen germination and fertility rates than Treatment 2 (72 h drying). Although we observed a reduction in viability of lyophilized pollens after 12 months of storage, we generated hybrid seedlings with success rates from 12 to 21% compared to 21-31% when using fresh pollens. Paternity testing based on molecular genotyping confirmed the hybrid status of the obtained seedlings, which grew well in a greenhouse.ConclusionsThe results signify the importance of pollen lyophilization for yam breeding programs.
Direct determination of oligomeric organization of integral membrane proteins and lipids from intact customizable bilayer
Authors: Panda Aniruddha , Giska Fabian , Duncan Anna L. , Welch Alexander J. , Brown Caroline , McAllister Rachel , Parameswaran Hariharan , Goder Jean N. D. , Coleman Jeff , Ramakrishnan Sathish , Pincet Frédéric , Guan Lan , Krishnakumar Shyam , Rothman James E. , Gupta Kallol 
Published: March 2023

ABSTRACTHierarchical organization of integral membrane proteins (IMP) and lipids at the membrane is essential for regulating myriad downstream signaling. A quantitative understanding of these processes requires both detections of oligomeric organization of IMPs and lipids directly from intact membranes and determination of key membrane components/properties that regulate them. Addressing this, we have developed a platform that enables native mass spectrometry (nMS) analysis of IMP-lipid complexes directly from intact and customizable lipid membranes. Both the lipid composition and membrane properties (such as curvature, tension, fluidity) of these bilayers can be precisely customized to a target membrane. Subsequent direct nMS analysis of these intact proteo-lipid vesicles can yield the oligomeric states of the embedded IMPs, identify bound lipids, and determine the membrane properties that can regulate the observed IMP-lipid organization. Applying this, we show how lipid binding regulates neurotransmitter release and how membrane composition regulates the functional oligomeric state of a transporter.
Dimensionality reduction reveals separate translation and rotation populations in the zebrafish hindbrain
Authors: Feierstein Claudia E. , de Goeij Michelle H.M. , Ostrovsky Aaron D. , Laborde Alexandre , Portugues Ruben , Orger Michael B. , Machens Christian K. 
Published: March 2023

AbstractIn many brain areas, neuronal activity is associated with a variety of behavioral and environmental variables. In particular, neuronal responses in the zebrafish hindbrain relate to oculomotor and swimming variables, as well as sensory information. However, the precise functional organization of the neurons has been difficult to unravel since neuronal responses are heterogeneous. Here we used dimensionality reduction methods on neuronal population data to reveal the role of the hindbrain in visually-driven oculomotor behavior and swimming. We imaged neuronal activity in zebrafish expressing GCaMP6s in the nucleus of almost all neurons, while monitoring the behavioral response to gratings that rotated with different speeds. We then used reduced-rank regression, a method that condenses the sensory and motor variables into a smaller number of ‘features’, to predict the fluorescence traces of all ROIs (regions of interest). Despite the potential complexity of the visuo-motor transformation, our analysis revealed that the bulk of population activity can be explained by only two features. Based on the contribution of these features to each ROI’s activity, ROIs formed three clusters. One cluster was related to vergent movements and swimming, whereas the other two clusters related to leftward and rightward rotation. Voxels corresponding to these clusters were segregated anatomically, with leftward and rightward rotation clusters located selectively to the left and right hemispheres, respectively. Just as described in many cortical areas, our analysis revealed that single neuron complexity co-exists with a simpler population-level description, thereby providing insights into the organization of visuo-motor transformations in the hindbrain.