bluuebunny/crossref_metadata_2025_split huggingface dataset:
Entomopathogen-host evolution and implications for biopesticide resistance management
Authors: Roberts Jeremy P. , Northfield Tobin D. 
Published: November 2022

AbstractInsecticide resistance evolution is becoming increasingly problematic globally. With chemical insecticides, attempts to combat resistance involves developing compounds with novel modes of action, or increasing rates to overcome partial resistance. While pests can develop resistance to pathogens used as biopesticides, these “pesticides” can be subjected to evolutionary selection pressure as well and may be able to adapt countermeasures to overcome pest resistance. Here, we consider two scenarios: 1) a single trait governs an arms race between pest and parasite, and 2) an epidemiological scenario where each, pathogen transmission and virulence, are governed by host and pathogen traits. Considering the single-trait parasite attack scenario, the evolving parasite is able to overcome resistance in the pest population and effectively suppress host population abundance. In this case, overcoming biopesticide resistance may be possible from parasite evolution to resistant hosts. In contrast, when transmission and abundance are allowed to vary independently in an epidemiological model, different pathogen traits promote different types of resistance development in the host – more contagious pathogens promote pathogen-tolerant (low mortality susceptibility) hosts, while less contagious pathogens promote pathogen-resistant (low transmission susceptibility) hosts. Pathogen-tolerant hosts are particularly detrimental to control programs, because they can quickly outcompete wild types by promoting infection in wild type populations. Furthermore, because evolution of pathogen-tolerance in pests can benefit pathogens through increasing infection prevalence, we do not expect pathogen evolution to improve control. Thus, the keys to biopesticide management depend on the virulence-transmission trade-off and whether hosts evolve to better prevent or survive infection.
Self-Assembly of Tunable Intrinsically Disordered Peptide Amphiphiles
Authors: Ehm Tamara , Shinar Hila , Jacoby Guy , Meir Sagi , Koren Gil , Segal Asher Merav , Korpanty Joanna , Thompson Matthew P. , Gianneschi Nathan C. , Kozlov Michael M. , Azoulay-Ginsburg Salome Emma , Amir Roey J. , Rädler Joachim O. , Beck Roy 
Published: November 2022

AbstractIntrinsically disordered peptide amphiphiles (IDPAs) present a novel class of synthetic conjugates that consist of short hydrophilic polypeptides anchored to hydrocarbon chains. These hybrid polymer-lipid block constructs spontaneously self-assemble into dispersed nanoscopic aggregates or ordered mesophases in aqueous solution due to hydrophobic interactions.Yet, the possible sequence variations and their influence on the self-assembly structures is vast and have hardly been explored.Here, we measure the nanoscopic self-assembled structures of four IDPA systems that differ by their amino acid sequence. We show that permutations in the charge pattern along the sequence remarkably alter the headgroup conformation and consequently alters the pH-triggered phase transitions between spherical, cylindrical micelles and hexagonal condensed phases. We demonstrate that even a single amino acid mutation is sufficient to tune structural transitions in the condensed IDPA mesophases, while peptide conformations remain unfolded and disordered. Furthermore, alteration of the peptide sequence can render IDPAs to become susceptible to enzymatic cleavage and induces enzymatically activated phase transitions.These results hold great potential for embedding multiple functionalities into lipid nanoparticle delivery systems by incorporating IDPAs with desired properties.
SUB-OPTIMAL ENVIRONMENTAL CONDITIONS PROLONG PHAGE EPIDEMICS IN BACTERIAL POPULATIONS
Authors: Goehlich Henry , Roth Olivia , Sieber Michael , Chibani Cynthia M. , Poehlein Anja , Rajkov Jelena , Liesegang Heiko , Wendling Carolin C. 
Published: November 2022

ABSTRACTInfections by filamentous phages influence bacterial fitness in various ways. While phage-encoded accessory genes, e.g., virulence genes, can be highly beneficial, the production of viral particles is energetically costly and often reduces bacterial growth. Consequently, if costs outweigh benefits, bacteria evolve resistance which can shorten phage epidemics. Abiotic conditions are known to influence the net-fitness effect for infected bacteria. Their impact on the dynamics and trajectories of host resistance evolution, however, remains yet unknown. To address this, we experimentally evolved the bacteriumVibrio alginolyticusin the presence of a filamentous phage at three different salinity levels, i.e., (1) ambient (2) 50% reduction, and (3) fluctuations between reduced and ambient. In all three salinities, bacteria rapidly acquired resistance through super infection exclusion (SIE), whereby phage-infected cells acquired immunity at the cost of reduced growth. Over time, SIE was gradually replaced by evolutionary fitter surface receptor mutants (SRM). This replacement was significantly faster at ambient and fluctuating conditions compared to the low saline environment. Our experimentally parameterized mathematical model explains that suboptimal environmental conditions, in which bacterial growth is slower, slow down phage resistance evolution ultimately prolonging phage epidemics. Our results imply that, if filamentous phages encode virulence genes, these may persist longer in bacterial populations at sub-optimal environmental conditions, which, in times of climate change, are becoming more frequent. Thus, our future ocean may favour the emergence of phage-born pathogenic bacteria, and impose a greater risk for disease outbreaks, impacting not only marine animals but also humans.
Different biological effects of exposure to far-UVC (222 nm) and near-UVC (254 nm) irradiation
Authors: Napoleão Tavares Renata Spagolla , Adamoski Douglas , Girasole Alessandra , Lima Ellen Nogueira , Justo-Junior Amauri da Silva , Domingues Romênia , Caznok Silveira Ana Clara , Marques Rafael Elias , de Carvalho Murilo , Ambrosio Andre Luis Berteli , Paes Leme Adriana Franco , Dias Sandra Martha Gomes 
Published: November 2022

AbstractUltraviolet C (UVC) light has long been used as a sterilizing agent, primarily through devices that emit at 254 nm. Depending on the dose and duration of exposure, UV 254 nm can cause erythema and photokeratitis and potentially cause skin cancer since it directly modifies nitrogenated nucleic acid bases. Filtered KrCl excimer lamps (emitting mainly at 222 nm) have emerged as safer germicidal tools and have even been proposed as devices to sterilize surgical wounds. All the studies that showed the safety of 222 nm analyzed cell number and viability, erythema generation, epidermal thickening, the formation of genetic lesions such as cyclobutane pyrimidine dimers (CPDs) and pyrimidine-(6-4)-pyrimidone photoproducts (6-4PPs) and cancer-inducing potential. Although nucleic acids can absorb and be modified by both UV 254 nm and UV 222 nm equally, compared to UV 254 nm, UV 222 nm is more intensely absorbed by proteins (especially aromatic side chains), causing photooxidation and cross-linking. Here, in addition to analyzing DNA lesion formation, for the first time, we evaluated changes in the proteome and cellular pathways, reactive oxygen species formation, and metalloproteinase (MMP) levels and activity in full-thicknessin vitroreconstructed human skin (RHS) exposed to UV 222 nm. We also performed the longest (40 days)in vivostudy of UV 222 nm exposure in the HRS/J mouse model at the occupational threshold limit value (TLV) for indirect exposure (25 mJ/cm2) and evaluated overall skin morphology, cellular pathological alterations, CPD and 6-4PP formation and MMP-9 activity. Our study showed that processes related to reactive oxygen species and inflammatory responses were more altered by UV 254 nm than by UV 222 nm. Our chronicin vivoexposure assay using the TLV confirmed that UV 222 nm causes minor damage to the skin. However, alterations in pathways related to skin regeneration raise concerns about direct exposure to UV 222 nm.
One-stop analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform
Authors: Yu Fengchao , Teo Guo Ci , Kong Andy T. , Li Ginny Xiaohe , Demichev Vadim , Nesvizhskii Alexey I. 
Published: November 2022

AbstractLiquid chromatography (LC) coupled with data-independent acquisition (DIA) mass spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we present a fast and sensitive approach for direct peptide identification from DIA data, MSFragger-DIA, which leverages the unmatched speed of the fragment ion indexing-based search engine MSFragger. MSFragger-DIA conducts a database search of the DIA tandem mass (MS/MS) spectra prior to spectral feature detection and peak tracing across the LC dimension. We have integrated MSFragger-DIA into the FragPipe computational platform for seamless support of peptide identification and spectral library building from DIA, data dependent acquisition (DDA), or both data types combined. We compared MSFragger-DIA with other DIA tools, such as DIA-Umpire based workflow in FragPipe, Spectronaut, andin silicolibrary-based DIA-NN and MaxDIA. We demonstrated the fast and sensitive performance of MSFragger-DIA across a variety of sample types and data acquisition schemes, including single-cell proteomics, phosphoproteomics, and large-scale tumor proteome profiling studies.
Landscape variation in defense traits along gradients of multiple resources and mammalian herbivory
Authors: Mohanbabu Neha , Veldhuis Michiel P , Jung Dana , Ritchie Mark E 
Published: November 2022

AbstractVariation in defense traits likely depends on access to different resources and risk from herbivory. Plant defense theories have predicted both positive and negative associations between defense traits and access to resources, but relatively few studies have explored intraspecific variation in defense traits along multiple resource and mammalian herbivory risk gradients. We assessed relationships between herbivory intensity, multiple resources, and plant defense traits using a widely distributed tropical savanna herb,Solanum incanum. As independent measures of risk from large mammal herbivores are rare, we used a satellite-based vegetation index to predict herbivory intensity at the landscape scale. We found that the satellite-based estimate of herbivory intensity was positively associated with browser abundance and total soil P, but negatively associated with rainfall. Intraspecific defense traits too varied substantially across sites (n=43) but only variation in spine density was associated with herbivory intensity and plant resources, such that spine density was positively associated with both rainfall and soil P, but bimodally associated with herbivory intensity. Taken together, it suggests that defenses maybe favored either where resources for defense are abundant under low but still present risk (i.e, at high rainfall sites) or where resource-expensive plant tissue is at high risk (i.e, at high soil P sites). This hints at the possibility of a shift from a resource-associated (bottom-up) to an herbivory-associated (top-down) control of allocation to defenses along an environmental gradient. Additionally, the independent effect of soil P on a carbon-based defense, spine density, suggests potential for resources that are not components of defenses to also influence allocation to defense traits. Thus, our study provides evidence for the influence of multiple drivers, resources, and herbivory intensity, on anti-herbivore defenses and their shifting relative importance on allocation to defenses along an environmental gradient.
Single-cell transcriptomic atlas reveals increased regeneration in diseased human inner ears
Authors: Wang Tian , Ling Angela H. , Billings Sara E. , Hosseini Davood K. , Vaisbuch Yona , Kim Grace S. , Atkinson Patrick J. , Sayyid Zahra N. , Aaron Ksenia A. , Wagh Dhananjay , Pham Nicole , Scheibinger Mirko , Ishiyama Akira , Maria Peter Santa , Blevins Nikolas H. , Jackler Robert K. , Heller Stefan , Lopez Ivan A. , Grillet Nicolas , Jan Taha A. , Cheng Alan G. 
Published: November 2022

AbstractMammalian inner ear hair cell loss leads to permanent hearing and balance dysfunction. In contrast to the cochlea, vestibular hair cells of the murine utricle have some regenerative capacity. Whether human utricular hair cells regenerate remains unknown. Here we procured live, mature utricles from organ donors and vestibular schwannoma patients, and present a validated single-cell transcriptomic atlas at unprecedented resolution. We describe previously unknown markers of 25 sensory and non-sensory cell types, with genes of hair cell and supporting cell subtypes displaying striking divergence between mice and humans. We further uncovered transcriptomes unique to hair cell precursors, which we validated to be 14-fold more robust in vestibular schwannoma utricles, representing ongoing regeneration in humans. Lastly, trajectory analysis of the supporting cell-hair cell axis revealed 5 distinct patterns of dynamic gene expression and associated pathways, including mTOR signaling and synaptogenesis. Our dataset constitutes a foundational resource, accessible via a web-based interface, serving to advance knowledge of the normal and diseased human inner ears and tools to stimulate human inner ear regeneration.
Cell Dynamic Mechanics Regulates Large-spatial Isotropic Matrix Modeling with Computational Simulations
Authors: Ouyang Mingxing , Hu Yanling , Chen Weihui , Li Hui , Ji Yingbo , Qiu Linshuo , Zhu Linlin , Ji Baohua , Bu Bing , Deng Linhong 
Published: November 2022

AbstractTissues are often isotropic and heterogeneous organizations, which developmental processes are coordinated by cells and extracellular matrix modeling. Cells have the capability of modeling matrix in distance, however, the biophysical mechanism is largely unknown. We investigated underlying mechanism of large collagen I (COL) fibrillary modeling by cell mechanics with designed arrays of cell clusters. By incorporating dynamic contractions, Molecular Dynamics simulations yielded highly matching isotropic outcomes with observed COL clustering in experiments from variable geometrical arrays without spatial limitation. Further designed single polygons from triangles to hexagons resulted in predicted structural assembly which showed maintained spatial balance. Cell cytoskeletal integrity (actin filaments, microtubules), actomyosin contractions, and endoplasmic reticulum calcium channels were essential for remote fiber inductions, while membrane mechanosensitive integrin and Piezo showed coordinative role in regulating the fiber assembly. The study provides new insights on cell mechanics-induced isotropic matrix modeling with dynamic large-spatial scales and the associated cellular mechanism. The assembled biomechanical scaffolds with pre-designs may lead to applications in micro-tissue engineering. This work implicates heterogeneous tissue structures maybe partially derived from isotropic cell mechanics.
Antigen presentation by discrete class I molecules on brain endothelium dynamically regulates T-cell mediated neuropathology in experimental cerebral malaria
Authors: Fain CE , Zheng J , Jin F , Ayasoufi K , Wu Y , Lilley MT , Dropik AR , Wolf DM , Rodriguez RC , Aibaidula A , Tritz ZP , Bouchal SM , Pewe LL , Urban SL , Chen Y , Chang S , Hansen MJ , Kachergus JM , Shi J , Thompson EA , Harty JT , Parney IF , Sun J , Wu LJ , Johnson AJ 
Published: November 2022

AbstractCD8 T cell engagement of brain vasculature is a putative mechanism of neuropathology in human cerebral malaria. To define contributions of brain endothelial cell MHC class I antigen-presentation to CD8 T cells in establishing this pathology, we developed novel H-2KbLoxP and H-2DbLoxP mice crossed with Cdh5-Cre mice to achieve targeted deletion of discrete class I molecules on brain endothelium. Using thePlasmodium bergheiANKA model of experimental cerebral malaria (ECM), we observe that H-2Kband H-2Dbregulate distinct patterns of disease onset, CD8 T cell infiltration, targeted cell death, and regional blood-brain barrier (BBB) disruption. Strikingly, ablation of H-2Kbor H-2Dbfrom brain endothelial cells resulted in reduced CD8 T cell activation, attenuated T cell interaction with brain vasculature, lessened targeted cell death, preserved BBB integrity, and prevented ECM and the death of the animal. These data demonstrate that interactions of CD8 T cells with discrete MHC class I molecules on brain endothelium regulate development of ECM neuropathology. Therefore, targeting MHC class I interactions therapeutically may hold potential for treatment of cases of severe malaria.
Unique features of the arterial Blood-Brain Barrier
Authors: Bell Batia , Anzi Shira , Sasson Esther , Ben-Zvi Ayal 
Published: November 2022

AbstractCNS vasculature differs from vascular networks of peripheral organs by its ability to tightly control selective material exchange across capillary barriers. Capillary permeability is mostly defined by unique cellular components of the endothelium. While capillaries are extensively investigated, the barrier properties of larger vessels are understudied. Here, we investigate barrier properties of CNS arterial walls. Using tracer challenges and various imaging modalities, we discovered that at the mouse cortex, the arterial barrier does not reside at the classical level of the endothelium. The arterial wall’s unique permeability acts bi-directionally; CSF substances travel along the glymphatic path and can penetrate from the peri-vascular space through arteriolar walls towards the lumen. We found that caveolae vesicles in arteriole endothelial and smooth-muscle cells are functional transcytosis machinery components, and that a similar mechanism is evident in the human brain. Our discoveries highlight vascular heterogeneity investigations as a potent approach to uncover new barrier mechanisms.
An iterative search algorithm to identify oscillatory dynamics in neurophysiological time series
Authors: Beck Amanda M. , He Mingjian , Gutierrez Rodrigo G. , Hotan Gladia C. , Purdon Patrick L. 
Published: November 2022

AbstractNeural oscillations have long been recognized for their mechanistic importance in coordinating activity within and between brain circuits. Co-occurring broad-band, non-periodic signals are also ubiquitous in neural data and are thought to reflect the characteristics of populationlevel neuronal spiking activity. Identifying oscillatory activity distinct from broadband signals is therefore an important, yet surprisingly difficult, problem in neuroscience. Commonly-used bandpass filters produce spurious oscillations when applied to broad-band noise and may be illinformed by canonical frequency bands. Curve-fitting procedures have been developed to identify peaks in the power spectrum distinct from broadband noise. Unfortunately, these ad hoc methods are prone to overfitting and are difficult to interpret in the absence of generative models to formally represent oscillatory behavior. Here we present a novel method to identify and characterize neural oscillations distinct from broad-band noise. First, we propose a new conceptual construct that makes clear, from a dynamical systems perspective, when oscillations are present or not. We then use this construct to develop generative models for neural oscillations. We show through extensive analyses of simulated and human EEG data that our approach identifies oscillations and their characteristics far more accurately than widely used methods, achieving near-perfect recovery of the number of oscillations when the SNR exceeds a very modest threshold. We also show that our method can automatically identify subject-level variations in frequency to overcome the limitations of fixed canonical frequency bands. Finally we demonstrate how our method can extract clinically-relevant neurophysiological features with greater statistical efficiency other established methods.
Mineral phase analysis of various marine-species shells and skeletons collected in Japan: Implications for marine biominerals
Authors: Mitsuguchi Takehiro , Minakata Keiji , Sugihara Kaoru , Hiraoka Masanori , Yoshida Masa-aki , Saito-Kokubu Yoko 
Published: November 2022

AbstractMineral phase analysis was performed, using X-ray diffractometry (XRD), for marine-organism shell/skeleton samples of 146–148 extant species of the following 10 phyla (18 classes) collected in Japan: Rhodophyta (Florideophyceae), Foraminifera (Globothalamea and Tubothalamea), Porifera (Hexactinellida), Cnidaria (Anthozoa and Hydrozoa), Bryozoa (Gymnolaemata), Brachiopoda (Lingulata and Rhynchonellata), Mollusca (Bivalvia, Cephalopoda, Gastropoda and Polyplacophora), Annelida (Polychaeta), Arthropoda (Cirripedia), and Echinodermata (Asteroidea, Crinoidea and Echinoidea). Some of the species were analyzed for each specific part of their shells/skeletons. Almost all the samples exhibited any of calcite, aragonite or their mixed phase, predominantly depending on their taxonomy and shell/skeletal structures. For samples containing significant amounts of calcite, the MgCO3wt % of calcite has been determined from their XRD data, which ranges from ∼0 to ∼15 wt % and indicates clear inter-taxonomic differences. Low MgCO3values (∼0–4 wt %) are observed for Rhynchonellata, Bivalvia, Gastropoda and Cirripedia; intermediate values (∼4–8 wt %) for Cephalopoda; high values (∼8–15 wt %) for Florideophyceae, Globothalamea, Tubothalamea, Polychaeta, Asteroidea and Crinoidea; low-to-high values for Gymnolaemata; intermediate-to-high values for Anthozoa and Echinoidea. These MgCO3data show broad trends mostly consistent with general phylogenetic evolution (i.e. very similar patterns for each phylogenetic group). Distinct within-individual variability of the MgCO3content is found for regular Echinoidea species (i.e. their teeth and spines have lower MgCO3values than the other skeletal parts). Correlation of the MgCO3content with seawater temperature is also examined/discussed for most of the above calcite-containing classes. In order to interpret our XRD-based observations of various marine-species shells/skeletons, detailed discussions are presented by comparing with previous studies and also by using knowledge of taxonomy, shell/skeletal structures, habitats, living modes and so on. The comprehensive dataset and discussions will provide useful implications for biomineralization studies.