bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenological mismatch between trees and wildflowers: Reconciling divergent findings in two recent analyses
Authors: Lee Benjamin R. , Alecrim Evelyn F. , Forrest Jessica R.K. , Heberling J. Mason , Primack Richard B. , Sargent Risa D. 
Published: August 2023

ABSTRACTRecent evidence suggests that community science and herbarium datasets yield similar estimates of species’ phenological sensitivities to temperature. Despite this, two recent studies by Alecrim et al. (2023) and Miller et al. (2022) found contradictory results when investigating an identical ecological mechanism (phenological mismatch of wildflower flowering and of shading by deciduous trees; “phenological escape”) with separate datasets.Here, we investigated whether differences between the two studies’ results could be reconciled by testing four hypotheses related to model design, species selection, spatiotemporal data extent, and phenophase selection.Hybrid model structures brought results from the two datasets closer together but did not fully reconcile the differences between the studies. Cropping the datasets to match spatial and temporal extents appeared to reconcile most differences but only at the cost of much higher uncertainty associated with reduced sample size. Neither species selection nor phenophase selection seemed to be responsible for differences in results.Synthesis:Our analysis suggests that although species-level estimates of phenological sensitivity may be similar between crowd-sourced and herbarium datasets, inherent differences in the types and extent of data may lead to contradictory inference about complex biotic interactions. We conclude that, until community science data repositories grow to match the range of climate conditions present in herbarium collections or until herbarium collections grow to match the spatial extent and temporal frequency of community science repositories, ecological studies should ideally be evaluated using both datasets to test the possibility of biased results from either.
Antibody gene features associated with binding and functional activity in vaccine-derived human mAbs targeting malaria parasites
Authors: Coelho Camila H. , Marquez Susanna , Nguemwo Tentokam Bergeline C. , Berhe Anne D. , Miura Kazutoyo , Long Carole A. , Sagara Issaka , Healy Sara , Kleinstein Steven H. , Duffy Patrick E. 
Published: August 2023

ABSTRACTAdjuvants have been essential to malaria vaccine development, but their impact on the vaccine-induced antibody repertoire is poorly understood. Here, we used cDNA sequences from antigen-specific single memory B cells to express 132 recombinant human anti-Pfs230 monoclonal antibodies (mAbs). Alhydrogel®-induced mAbs demonstrated higher binding to Pfs230D1, although functional activity was similar between adjuvants. All Alhydrogel® mAbs using IGHV1-69 gene bound to recombinant Pfs230D1, but none blocked parasite transmission to mosquitoes; similarly, no AS01 mAb using IGHV1-69 blocked transmission. Functional mAbs from both Alhydrogel® and AS01 vaccines used IGHV3-21 and IGHV3-30 genes. Antibodies with the longest CDR3 sequences were associated with binding but not functional activity. This study assesses adjuvant effects on antibody clonotype diversity during malaria vaccination.
Does late water deficit induce root growth or senescence in wheat?
Authors: Shazadi Kanwal , Christopher John T. , Chenu Karine 
Published: August 2023

AbstractDrought frequently limits productivity in rain-fed systems. To investigate water-stress impacts on post-anthesis root development in wheat, three experiments were conducted with two cultivars, Scout and Mace, grown in 1.5m tubes under well-watered conditions or post-anthesis water-stress. Shallow roots of both genotypes appeared to senesce between heading and maturity under well-watered conditions, whereas moderate water stress tended to increase post-heading shallow-root senescence in Mace but stimulated growth in Scout. For deep roots, net growth in biomass was observed for both genotypes under well-watered conditions between heading and maturity, whereas under moderate water stress, only Scout maintained net growth, with net senescence being observed for Mace. Severe water stress resulted in root senescence at all depths for both genotypes. Above ground, Scout retained leaf greenness for only slightly longer than Mace under well-watered conditions. In contrast, under moderate water stress, Mace showed rapid post-anthesis leaf senescence while Scout was affected little if at all. Grain biomass per plant was similar between genotypes in well-watered conditions but more reduced for Mace under moderate stress. Post-anthesis differences in root growth and senescence can strongly influence water use and grain filling in drought-prone environments. Screening for this could assist breeding for drought tolerant varieties.
Size dependent steady-state saturation limit in biomolecular transport through nuclear membranes
Authors: Shakhi P.K. , Bijeesh M.M. , Hareesh J. , Joseph Toby , Nandakumar P. , Varier Geetha K. 
Published: August 2023

AbstractThe nucleus preserves the genomic DNA of eukaryotic organisms and maintains the integrity of the cell by regulating the transport of molecules across the nuclear membrane. It is hitherto assumed that small molecules having a size below the passive permeability limit are allowed to diffuse freely to the nucleus while the transport of larger molecules are regulated via an active mechanism involving energy. Here we report on the kinetics of nuclear import and export of a model system of dextran molecules having a size below the passive permeability limit. The studies carried out using time-lapse confocal fluorescence microscopy show a clear deviation from the passive diffusion model. In particular, it is observed that the steady-state concentration of dextran molecules inside the nucleus is consistently less than the concentration outside, in contradiction to the predictions of the passive diffusion model. Detailed analysis and modeling of the transport show that the nuclear export rates significantly differ from the import rates and the difference in rates is dependent on the size of the molecules. The nuclear export rates are further confirmed by an independent experimental study where we observe the diffusion of dextran molecules from the nucleus directly. Our experiments and transport model would suggest that the nucleus actively rejects exogenous macromolecules even below the passive permeability limit. This result can have significant impact on biomedical research especially in areas related to targeted drug delivery and gene therapy.
Optimal antimicrobial response to a changing microbial background at a mucus interface
Authors: Bossa Guilherme Volpe , Bel Shai , Mugler Andrew , Erez Amir 
Published: August 2023

AbstractComplex lifeforms host microbiota, microbes that live synergistically with their host. Accordingly, hosts have mechanisms to defend against and tolerate the microbiota. The intestinal mucus, where these systems collide, plays a pivotal role in managing this relationship, yet lacks an integrative theoretical framework. We propose a minimal model to elucidate dynamics at this interface, focusing on the ileum’s mucus defense. The model considers the effect of delay in host antimicrobial peptide secretion and how the host can use two different signals, from the bulk microbiota and from segmented filamentous bacteria (SFB). Our theory suggests the host can optimize defense by minimizing antimicrobial peptide production and controlling bacterial exposure. Integrating two recent experiments, we show host dynamics are consistent with sensing both bulk and SFB, supporting our ‘optimal defense’ hypothesis. Therefore, we propose that similar mechanisms could prove advantageous to other species and applicable beyond the ileum’s mucus barrier.
Dynamic instability of force-generating bacterial microtubules
Authors: Amini H. Reza , Volkov Vladimir A. , Dogterom Marileen 
Published: August 2023

SummaryDynamic instability refers to the ability of cytoskeletal polymers to switch between growing and shrinking phases. This phenomenon has been extensively studied for eukaryotic microtubules which consist of 13 protofilaments. Here we report on the dynamic properties of prokaryotic microtubules found inProsthecobacterbacteria, which consist of 4-5 protofilaments and, like their eukaryotic counterparts, display dynamic instability. Using microfabricated barriers we show that the catastrophe rate of bacterial microtubules increases when their growth is stalled by a rigid barrier. We find that the lifetime distributions of both free and stalled bacterial microtubules can be fitted using the same phenomenological model that we previously introduced for eukaryotic microtubules, suggesting that bacterial microtubules may be considered a model system for eukaryotic microtubules. We further use cryo-electron tomography to reveal structural details of dynamic ends and show that bacterial microtubules may form doublets similar to axonemal microtubules in eukaryotes.
Molecular Studies of Phages-Klebsiella pneumoniaein a Mucoid Environment: Innovative use of mucolytic agents prior to the administration of lytic phages
Authors: Pacios Olga , Blasco Lucía , Ortiz-Cartagena Concha , Bleriot Inés , Fernández-García Laura , López María , Barrio-Pujante Antonio , Pascual Álvaro , Cuenca Felipe Fernández , Martínez-Martínez Luis , Aracil Belén , Oteo-Iglesias Jesús , Tomás María 
Published: August 2023

AbstractMucins are important glycoproteins that form a protective layer throughout the gastrointestinal and respiratory tracts. There is scientific evidence of increase in phage-resistance in the presence of mucin for some bacterial pathogens. Manipulation in mucin composition may ultimately influence the effectiveness of phage therapy. In this work, two clinical strains ofK. pneumoniae(K3574 and K3325), were exposed to the lytic bacteriophage vB_KpnS-VAC35 in the presence and absence of mucin on a long-term co-evolution assay, in an attempt to mimicin vitrothe exposure to mucins that bacteria and their phages facein vivo. Enumerations of the bacterial and phage counts at regular time intervals were conducted, and extraction of the genomic DNA of co- evolved bacteria to the phage, the mucin and both was performed. We determined the frequency of phage-resistant mutants in the presence and absence of mucin and including a mucolytic agent (N-acetyl L-cysteine, NAC), and sequenced these conditions using Nanopore. We phenotypically demonstrated that the presence of mucin induces the emergence of bacterial resistance against lytic phages, effectively decreased in the presence of NAC. In addition, the genomic analysis revealed some of the genes relevant to the development of phage resistance in long-term co- evolution, with a special focus on the mucoid environment. Genes involved in the metabolism of carbohydrates were mutated in the presence of mucin. In conclusion, the use of mucolytic agents prior to the administration of lytic phages could be an interesting therapeutic option when addressingK. pneumoniaeinfections in environments where mucin is overproduced.
Dissecting Mechanisms of Ligand Binding and Conformational Changes in the Glutamine-Binding Protein
Authors: Han Zhongying , Panhans Sabrina , Brameyer Sophie , Bilgen Ecenaz , Ram Marija , Herr Anna , Narducci Alessandra , Isselstein Michael , Harris Paul D. , Brix Oliver , Jung Kirsten , Lamb Don C. , Lerner Eitan , Griffith Douglas , Weikl Thomas R. , Zijlstra Niels , Cordes Thorben 
Published: August 2023

AbstractLigand binding and conformational changes of biomacromolecules play a central role in the regulation of cellular processes. It is important to understand how both are coupled and what their role is in biological function. The biochemical properties, conformational states, and structural dynamics of periplasmic substrate-binding proteins (abbreviated SBPs or PBPs), which are associated with a wide range of membrane proteins, have been extensively studied over the past decades. Their ligand-binding mechanism, i.e., the temporal order of ligand-protein interactions and conformational changes, however, remains a subject of controversial discussion. We here present a biochemical and biophysical analysis of theE. coliglutamine-binding protein GlnBP concerning ligand binding and its coupling to conformational changes. For this, we used a combination of experimental techniques including isothermal titration calorimetry, single-molecule Förster resonance energy transfer, and surface-plasmon resonance spectroscopy. We found that both apo- and holo-GlnBP show no detectable exchange between open and (semi-)closed conformations on timescales between 100 ns and 10 ms. Furthermore, we also demonstrate that ligand binding and conformational changes in GlnBP are highly correlated. A global analysis of our results is consistent with a dominant induced-fit mechanism, where the ligand binds GlnBP prior to conformational rearrangements. Importantly, we suggest that the rigorous experimental and theoretical framework used here can be applied to other protein systems where the coupling mechanism of conformational changes and ligand binding is yet unclear or where doubts prevail.
Endocytosis gated by emergent properties of membrane-clathrin interactions
Authors: Wang Xinxin , Li Yueping , Liu Ailing , Padilla Ronnin , Lee Donghoon M. , Kim Daehwan , Mettlen Marcel , Chen Zhiming , Schmid Sandra L. , Danuser Gaudenz 
Published: August 2023

AbstractClathrin-mediated endocytosis (CME), the major cellular entry pathway, starts when clathrin assembles on the plasma membrane into clathrin-coated pits (CCPs). Two populations of CCPs are detected within the same cell: ‘productive’ CCPs that invaginate and pinch off, forming clathrin-coated vesicles (CCVs) [1, 2], and ‘abortive’ CCPs [3, 4, 5] that prematurely disassemble. The mechanisms of gating between these two populations and their relations to the functions of dozens of early-acting endocytic accessory proteins (EAPs) [5, 6, 7, 8, 9] have remained elusive. Here, we use experimentally-guided modeling to integrate the clathrin machinery and membrane mechanics in a single dynamical system. We show that the split between the two populations is an emergent property of this system, in which a switch between anOpenstate and aClosedstate follows from the competition between the chemical energy of the clathrin basket and the mechanical energy of membrane bending.In silicoexperiments revealed an abrupt transition between the two states that acutely depends on the strength of the clathrin basket. This critical strength is lowered by membrane-bending EAPs [10, 11, 12]. Thus, CME is poised to be shifted between abortive and productive events by small changes in membrane curvature and/or coat stability. This model clarifies the workings of a putative endocytic checkpoint whose existence was previously proposed based on statistical analyses of the lifetime distributions of CCPs [4, 13]. Overall, a mechanistic framework is established to elucidate the diverse and redundant functions of EAPs in regulating CME progression.
Trichinella spiralis secretes stage-specific extracellular vesicles for modulating host microenvironment for parasitism
Authors: Khueangchiangkhwang Sukhonthip , Wu Zhiliang , Hosoda-Yabe Ritsuko , Yabe Tomio , Okamoto Toru , Takada Chihiro , Okada Hideshi , Ogura Shinji , Maekawa Yoichi 
Published: August 2023

AbstractExtracellular vesicles (EVs) regulate cell-to-cell communication by transferring biomolecules within individuals or between different organisms. Trichinella spiralis is thought to secrete EVs to establish parasitism, but the detailed mechanisms of EV-mediated parasitic strategies have remained unclear. We identified EVs of T. spiralis as stage-specific in adult worms in host intestine (AW-EVs) and larvae in host muscles (ML-EVs). Stage-specific EVs exhibited unique functions, such as suppressing the expression of mucin-related genes only in AW-EVs and inducing genes associated with myoblast differentiation found in nurse cell formation in ML-EVs. Both EVs also suppressed IL-6 expression. These functions corelated with the contents of each EV, as confirmed by proteomics and whole microRNA sequencing. One of the microRNAs common to both EVs, tsp-miR-1, was involved in the suppression of IL-6 expression. These results suggest that Trichinella spiralis secretes stage-specific EVs containing unique as well as common biomolecules to regulate the host microenvironment for parasitism.
Heterologous expression of influenza hemagglutinin leads to early and transient activation of the unfolded protein response inNicotiana benthamiana
Authors: Hamel Louis-Philippe , Comeau Marc-André , Tardif Rachel , Gravel Francis Poirier- , Paré Marie-Ève , Lavoie Pierre-Olivier , Goulet Marie-Claire , Michaud Dominique , D’Aoust Marc-André 
Published: August 2023

SummaryThe unfolded protein response (UPR) allows cells to cope with endoplasmic reticulum (ER) stress induced by the accumulation of misfolded proteins in the ER. Due to its sensitivity toAgrobacterium tumefaciens, model plantNicotiana benthamianais widely employed for the transient expression of recombinant proteins of biopharmaceutical interest, including therapeutic antibodies and virus surface proteins used for vaccine production. As such, study of the plant UPR is of practical significance, since enforced expression of complex secreted proteins often results in ER stress. After 6 days of expression, we recently reported that influenza hemagglutinin (HA) induces accumulation of UPR proteins. Since the upregulation of corresponding UPR genes was not detected at this time point, accumulation of UPR proteins was hypothesized to either be independent of transcriptional regulation, or associated with early but transient UPR gene upregulation. Using time course sampling, we here show that HA expression does result in early and transient activation of the UPR, as inferred from unconventional splicing ofNbbZIP60transcripts and induction of UPR genes with varied functions. The transient nature of HA-induced UPR suggests that this response was sufficient to cope with ER stress provoked by expression of the secreted protein, as opposed to an antibody that triggered a stronger and more sustained UPR. As defense-related genes were induced after the peak of UPR activation and correlated with high increase in HA protein accumulation, we hypothesize that these immune responses, rather than the UPR, were responsible for the onset of necrotic symptoms on HA-expressing leaves.One-sentence summaryAgrobacterium-mediated expression of influenza hemagglutinin results in early and transient activation of the unfolded protein response, preventing deleterious effects caused by unresolved endoplasmic reticulum stress.
A Phosphoproteomics Data Resource for Systems-level Modeling of Kinase Signaling Networks
Authors: Feng Song , Sanford James A. , Weber Thomas , Hutchinson-Bunch Chelsea M. , Dakup Panshak P. , Paurus Vanessa L. , Attah Kwame , Sauro Herbert M. , Qian Wei-Jun , Wiley H. Steven 
Published: August 2023

AbstractBuilding mechanistic models of kinase-driven signaling pathways requires quantitative measurements of protein phosphorylation across physiologically relevant conditions, but this is rarely done because of the insensitivity of traditional technologies. By using a multiplexed deep phosphoproteome profiling workflow, we were able to generate a deep phosphoproteomics dataset of the EGFR-MAPK pathway in non-transformed MCF10A cells across physiological ligand concentrations with a time resolution of <12 min and in the presence and absence of multiple kinase inhibitors. An improved phosphosite mapping technique allowed us to reliably identify >46,000 phosphorylation sites on >6600 proteins, of which >4500 sites from 2110 proteins displayed a >2-fold increase in phosphorylation in response to EGF. This data was then placed into a cellular context by linking it to 15 previously published protein databases. We found that our results were consistent with much, but not all previously reported data regarding the activation and negative feedback phosphorylation of core EGFR-ERK pathway proteins. We also found that EGFR signaling is biphasic with substrates downstream of RAS/MAPK activation showing a maximum response at <3ng/ml EGF while direct substrates, such as HGS and STAT5B, showing no saturation. We found that RAS activation is mediated by at least 3 parallel pathways, two of which depend on PTPN11. There appears to be an approximately 4-minute delay in pathway activation at the step between RAS and RAF, but subsequent pathway phosphorylation was extremely rapid. Approximately 80 proteins showed a >2-fold increase in phosphorylation across all experiments and these proteins had a significantly higher median number of phosphorylation sites (~18) relative to total cellular phosphoproteins (~4). Over 60% of EGF-stimulated phosphoproteins were downstream of MAPK and included mediators of cellular processes such as gene transcription, transport, signal transduction and cytoskeletal arrangement. Their phosphorylation was either linear with respect to MAPK activation or biphasic, corresponding to the biphasic signaling seen at the level of the EGFR. This deep, integrated phosphoproteomics data resource should be useful in building mechanistic models of EGFR and MAPK signaling and for understanding how downstream responses are regulated.
Migrasome formation is initiated preferentially in tubular junctions by alternations of membrane tension or intracellular pressure
Authors: Zucker Ben , Dharan Raviv , Wang Dongju , Yu Li , Sorkin Raya , Kozlov Michael M. 
Published: August 2023

AbstractMigrasomes, the transient vesicle-like cellular organelles, arise on the retraction fibers (RFs), the branched tubular extensions of the plasma membrane generated during cell migration. Migrasomes form in two steps: a local RF swelling is followed by a protein-dependent stabilization of the emerging spherical bulge. Here we approached experimentally and theoretically the previously unaddressed mechanism of the initial RF swelling. We hypothesized that the swelling can be driven by alterations of the generic mechanical factors, the RF’s luminal pressure and membrane tension. To examine the effects of pressure, we exposed migrating RF-producing cells to a hypotonic medium and observed the formation of migrasome-like bulges with a preferential location in the RF branching sites. To test the results of tension variations, we developed a biomimetic system of three membrane tubules connected by a junction and subjected to controlled membrane tension. An abrupt increase of tension resulted in a migrasome-like bulge formation in the junction and in the tubular regions. Following the formation, the tubule’s bulges moved toward and merged with the junctional bulge. To understand the physical forces behind the observations, we considered theoretically the mechanical energy of a membrane system consisting of a three-way tubular junction with emerging tubular arms connected to a membrane reservoir. The energy minimization predicted the membrane bulging, preferably, in the junction site as a result of both an increase in the luminal pressure and an abrupt rise of the membrane tension. We discuss the common physical background of the two phenomena.