bluuebunny/crossref_metadata_2025_split huggingface dataset:
Marbled Murrelet Habitat Suitability in Redwood Timberlands of Northern Coastal California Utilizing LiDAR-Derived Individual Tree Metrics
Authors: Lamphear David W. , Hamm Keith A. , Early Desiree A. , McDonald Trent L. 
Published: August 2024

AbstractThe marbled murrelet (Brachyramphus marmoratus) is a threatened seabird found from Southern California to Alaska that forages at sea but nests in near coastal forests. Marbled murrelet nesting habitat is generally comprised of old-growth or mature forests with large trees having platforms suitable for nesting. Here, we estimate a habitat suitability model (HSM) that relates evidence of nesting to characteristics of putative trees derived from high resolution light imaging detection and ranging (LiDAR) data. Our study area in Northern California contained stands of old-growth forests on state, federal, and private lands but was predominated by private second-growth redwood and Douglas-fir timberlands. We estimated a two-sample HSM using Maxent software and implemented objective and repeatable covariate selection, model evaluation, and classification methods. Our HSM predicts relative likelihood of occupancy using predicted Habitat Suitability Index (HSI) values that we then classify into five habitat classes based on a novel use the of predicted to expected (P/E) ratio curve. From HSI predictions, we identified patches of murrelet habitat and estimated concave polygons surrounding individual trees within and proximately close to each patch. These methods provide repeatable boundaries for identification of patches and important individual trees based on HSI. Patches with greater relative probability of occupancy were characterized by high densities of 60-meter and taller trees, a large sum of heights for 50-meter and taller trees, and high values of standard deviation of 50-meter and taller trees. During hold-out model evaluations, our HSM showed extremely high fidelity for known patches with indirect evidence of nesting based on occupancy.
A telosma mosaic virus-based vector for foreign gene expression and virus-induced gene silencing in the perennial woody vine, passion fruit (Passiflora edulis)
Authors: Wang Xiaoqing , Qin Li , Shen Wentao , Qiu Wenping , Cui Hongguang , Dai Zhaoji 
Published: August 2024

AbstractPassion fruit (Passiflora edulis) is a perennial, woody, tropical vine crop. It produces edible round to oval fruit that has been increasingly favored for its unique aroma and taste, and richness in antioxidants, vitamins and minerals. However, the functional genomic study of passion fruit lags far behind due to a lack of simple and efficient genetic tools. Here, we report the development of virus-mediated protein overexpression (VOX) and virus-induced gene silencing (VIGS) vector based on telosma mosaic virus (TelMV), an emerging potyvirus infecting passion fruit plants worldwide. This vector, designated pTelMV-GW, incorporates the Gateway-compatible recombination sites for rapid gene cloning. We show that this vector allows for the systemic stable expression of two heterologous proteins, green fluorescent protein (GFP) and bacterial phytoene synthase (crtB) in passion fruit plants, and pTelMV-GW containing different fragments ofGFPcan also induce systemic gene silencing on the GFP-transgenicN. benthamianaplants. Moreover, we demonstrated that in passion fruit plants, this vector can trigger gene silencing of endogenousphytoene desaturase(PDS) to a limited extent. Furthermore, we upgraded the vector by using a mild TelMV strain that does not induce noticeable symptoms in plants. We show that the upgraded vector (pTelMV-R181K-GW) containingPDSorChlIfragments induces the robust silencing of the corresponding endogenous gene in passion fruit plants. Together, we reported the first development of VIGS and VOX vectors in passion fruit plants, as the first step in our endeavor to discover horticulturally important genes for improving passion fruit production and quality.
Synaptic synergy of T cell receptor and interleukin 2 receptor in CD8+T cells
Authors: Capera Jesusa , Jainarayanan Ashwin K , Valvo Salvatore , Chen Lina , Quayle Steven N , Moniz Raymond J , Suri Anish , Dustin Michael L 
Published: August 2024

ABSTRACTInterleukin 2 (IL2) promotes T cell proliferation and differentiation, making it a central target in immunotherapies. T cells fine-tune their sensitivity to and consumption of IL2 by regulating surface expression and composition of the IL2 receptor. Following antigen recognition, IL2 receptor signaling is shared through polarized interactions in T cell aggregates. However, how IL2 function is integrated during earlier antigen-dependent T cell synapses is unknown. Here, we demonstrate a synergistic effect between the T cell receptor (TCR) and IL2 receptor signaling at the immunological synapse of CD8+T cells with supported lipid bilayers. TCR and IL2 signaling overlapped in space and time, potentiating each other when simultaneously triggered. Immuno-STATs, a safe and effective new class of immunotherapeutics, which fuse IL2 and peptide-major histocompatibility complex (pMHC) in a single molecule to expand antigen-specific CD8+T cells, enhanced both TCR and IL2 signaling and promoted antigen specific T-T immunological synapses.
Paradoxical Activation of GCN2 by ATP-competitive inhibitors via allosteric activation and autophosphorylation
Authors: Neill Graham , Vinciauskaite Vanesa , Paul Marilyn , Gilley Rebecca , Cook Simon J. , Masson Glenn R. 
Published: August 2024

AbstractRecently it has been found that General Control Non-derepressible 2 (GCN2) can be activated by an array of small molecule ATP-competitive inhibitors, including clinically relevant compounds such as Ponatinib, and compounds specifically designed to be GCN2 inhibitors, such as GCN2iB. Furthermore, we recently showed that GCN2 can be activated in cells by clinically approved small molecule RAF inhibitors. GCN2 is a drug target, specifically in cancers such as mesothelioma, and a better understanding of this paradoxical activation is required to develop drugs which truly inhibit the enzyme. Using biochemical assays and structural mass spectrometry, we present a model for how GCN2 is activated by these compounds by promoting an active conformation in the HisRS domain while competitively inhibiting the kinase domain. This conformation promotes activating phosphorylation of GCN2, potentially through phosphorylation of other activated GCN2 molecules which are not bound to compound. Together this model suggests that efforts to inhibit GCN2 would benefit from exploring allosteric routes rather than targeting the ATP-binding pocket of the kinase domain.
Structural Analyses of a GABARAP∼ATG3 Conjugate Uncover a Novel Non-covalent Ubl-E2 Backside Interaction
Authors: Ohashi Kazuto , Otomo Takanori 
Published: August 2024

ABSTRACTMembers of the ATG8 family of ubiquitin-like proteins (Ubls) are conjugated to phosphatidylethanolamine (PE) in the autophagosomal membrane, where they recruit degradation substrates and facilitate membrane biogenesis. Despite this well-characterized function, the mechanisms underlying the lipidation process, including the action of the E2 enzyme ATG3, remain incompletely understood. Here, we report the crystal structure of human ATG3 conjugated to the mammalian ATG8 protein GABARAP via an isopeptide bond, mimicking the Ubl∼E2 thioester intermediate. In this structure, the GABARAP∼ATG3 conjugate adopts an open configuration with minimal contacts between the two proteins. Notably, the crystal lattice reveals non-covalent contacts between GABARAP and the backside of ATG3’s E2 catalytic center, resulting in the formation of a helical filament of the GABARAP∼ATG3 conjugate. While similar filament formations have been observed with canonical Ub∼E2 conjugates, the E2 backside-binding interface of GABARAP is distinct from those of Ub/Ubl proteins and overlaps with the binding site for LC3 interacting region (LIR) peptides. NMR analysis confirms the presence of this non-covalent interaction in solution, and mutagenesis experiments demonstrate the involvement of the E2 backside in PE conjugation. These findings highlight the critical role of the E2 backside in the lipidation process and suggest evolutionary adaptations in the unique E2 enzyme ATG3.
Human footprint and forest disturbance reduce space use of brown bears (Ursus arctos) across Europe
Authors: Hertel Anne G. , Parres Aida , Frank Shane C. , Renaud Julien , Selva Nuria , Zedrosser Andreas , Balkenhol Niko , Maiorano Luigi , Fedorca Ancuta , Dutta Trishna , Bogdanović Neda , Bragalanti Natalia , Chiriac Silviu , Ćirović Duško , Ciucci Paolo , Domokos Csaba , Fedorca Mihai , Filacorda Stefano , Finďo Slavomir , Groff Claudio , Hernando Miguel de Gabriel , Huber Djuro , Ionescu Georgeta , Jerina Klemen , Karamanlidis Alexandros A. , Kindberg Jonas , Kojola Ilpo , Mertzanis Yorgos , Palazon Santiago , Pop Mihai I. , Psaralexi Maria , Quenette Pierre Yves , Sergiel Agnieszka , Skuban Michaela , Zlatanova Diana , Zwijacz-Kozica Tomasz , De Barba Marta 
Published: August 2024

AbstractThree-quarters of the planet’s land surface has been altered by humans, with consequences for animal ecology, movements and related ecosystem functioning. Species often occupy wide geographical ranges with contrasting human disturbance and environmental conditions, yet, limited data availability across species’ ranges has constrained our understanding of how human impact and resource availability jointly shape intraspecific variation of animal space use. Leveraging a unique dataset of 752 annual GPS movement trajectories from 370 brown bears (Ursus arctos) across the species’ range in Europe, we investigated the effects of human impact (i.e., human footprint index), resource availability, forest cover and disturbance, and area-based conservation measures on brown bear space use. We quantified space use at different spatio-temporal scales during the growing season (May - September): home range size; representing general space requirements, 10-day long-distance displacement distances, and routine 1-day displacement distances. We found large intraspecific variation in brown bear space use across all scales, which was profoundly affected by human footprint index, vegetation productivity, and recent forest disturbances creating opportunity for resource pulses. Bears occupied smaller home ranges and moved less in more anthropized landscapes and in areas of higher resource availability. Forest disturbances reduced space use while contiguous forest cover promoted longer daily movements. The amount of strictly protected and roadless areas within bear home ranges were too small to affect space use. Anthropized landscapes may hinder the expansion of small and isolated populations, such as the Apennine and Pyrenean, and obstruct population connectivity, for example between the Alpine or Carpathian with the Dinaric Pindos populations. Our findings call for actions to maintain bear movements across landscapes with high human footprint, for example by maintaining forest integrity, to support viable bear populations and their ecosystem functions.
Increased chloroplast area in the rice bundle sheath through cell specific perturbation of brassinosteroid signalling
Authors: Cackett Lee , Luginbuehl Leonie H. , Hendron Ross-William , Plackett Andrew R. G. , Stanley Susan , Kelly Steven , Hibberd Julian M. 
Published: August 2024

AbstractIn the leaves of C3species such as rice, mesophyll cells contain the largest compartment of photosynthetically active chloroplasts. In contrast, plants that use the derived and more efficient C4photosynthetic pathway have a significant chloroplast compartment in both bundle sheath and mesophyll cells. Accordingly, the evolution of C4photosynthesis from the ancestral C3state requires an increase in the chloroplast compartment of the bundle sheath. Here we investigated the potential to increase chloroplast compartment size in rice bundle sheath cells by manipulating brassinosteroid signalling. Treatment with brassinazole, a brassinosteroid biosynthesis inhibitor, increased leaf chlorophyll content and increased the number but decreased the area of chloroplasts in bundle sheath cells. Constitutive overexpression of theBRASSINAZOLE RESISTANT 1(OsBZR1) transcription factor increased bundle sheath chloroplast area by up to 45% but plants became chlorotic. However, whenOsBZR1was placed under the control of a bundle sheath specific promoter, the negative effects on growth and viability were removed whilst chloroplast area still increased. In summary, we report a role for brassinosteroids in controlling chloroplast area and number in rice and conclude that cell-specific manipulation of brassinosteroid signalling can be used to manipulate the chloroplast compartment in rice bundle sheath cells.
Hemin binding causes structural rearrangements in HRI to inhibit activation via autophosphorylation
Authors: Kanta Shivani , Vinciauskaite Vanesa , Neill Graham , Muqit Miratul M.K. , Masson Glenn R. 
Published: August 2024

AbstractHeme-Regulated Inhibitor (HRI) is one of the four mammalian kinases which phosphorylates eIF2α to facilitate a cellular response to stress through the regulation of mRNA translation. Originally identified for its role as a heme sensor in erythroid progenitor cells, it has since materialised as a potential therapeutic target in both cancer and neurodegeneration. Here we characterise two modes of HRI inhibition of using structural mass spectrometry, biochemical and biophysical techniques. We demonstrate that several ATP-mimetic compounds, including BRAF inhibitors and a compound, GCN2iB, thought to be specific to GCN2, are capable of potently inhibiting HRI. We demonstrate that hemin, a haem-like molecule, inactivates HRI structurally using hydrogen-deuterium exchange mass spectrometry (HDX-MS), and this results in wide-spread structural rearrangement of the protein and how that impacts on the kinase domain through a series of allosteric interactions. This inhibition mainly impacts autophosphorylation, which includes tyrosine phosphorylation, not observed before in the eIF2α kinases.
Live imaging in zebrafish reveals tissue-specific strategies for amoeboid migration
Authors: Robertson Tanner F. , Schrope Jon , Zwick Zoe , Rindy Julie K. , Horn Adam , Huttenlocher Anna 
Published: August 2024

SummaryAmoeboid cells like leukocytes can enter and migrate within virtually every tissue of the body, even though tissues vary widely in their chemical and mechanical composition. Here, we imaged motile T cells as they colonized peripheral tissues during zebrafish development to ask if cells tailor their migration strategy to their local tissue environment. We found that T cells in most sites migrated with f-actin-rich leading-edge pseudopods, matching how they migratein vitro. T cells notably deviated from this strategy in the epidermis, where they instead migrated using a rearward concentration of f-actin and stable leading-edge blebs. This mode of migration occurs under planar confinementin vitro, and we correspondingly found the stratified keratinocyte layers of the epidermis impose planar-like confinement on leukocytesin vivo. By imaging the same cell type across the body, our data collectively indicates that cells adapt their migration strategy to navigate different tissue geometriesin vivo.
Multi-strategies embedded framework for neoantigen vaccine maturation
Authors: Zhang Guanqiao , Fu Yaqi , Chan Kevin C. , Jin Ruofan , Yang Yuxuan , Zhou Ruhong 
Published: August 2024

AbstractEffective cancer immunotherapy hinges on the precise recognition of neoantigens, presented as binary complexes with major histocompatibility complex (MHC) molecules, by T cell receptors (TCR). The development of immunogenic peptide predictors and generators plays a central role in personalizing immunotherapies while reducing experimental costs. However, the current methods often fall short in leveraging structural data efficiently and providing comprehensive guidance for neoantigen selection. To address these limitations, we introduce NEOM, a novel neoantigen maturation framework encompassing five distinct modules: “policy”, “structure”, “evaluation”, “selection” and “filter”. This framework is designed to enhance precision, interpretability, customizability and cost-effectiveness in neoantigen screening. We evaluated NEOM using a set of random synthetic peptides, followed by available clinically-derived peptides. NEOM achieved higher performance on generated peptide quality compared to other baseline models. Using established predictors for filtering revealed a substantial number of peptides with immunogenic potential. Subsequently, a more rigorous binding affinity evaluation using free energy perturbation methods identified 6 out of 38 candidates showing superior binding characteristics. MHC tetramer peptide exchange assays and flow cytometry experiments further validate five of them. These results demonstrate that NEOM not only excels in identifying diverse peptides with enhanced binding stability and affinity for MHC molecules but also augments their immunogenic potential, showcasing its utility in advancing personalized immunotherapies.
Dual CRISPRi-Seq for genome-wide genetic interaction studies identifies key genes involved in the pneumococcal cell cycle
Authors: Dénéréaz Julien , Eray Elise , Jana Bimal , de Bakker Vincent , Todor Horia , van Opijnen Tim , Liu Xue , Veening Jan-Willem 
Published: August 2024

AbstractA major goal in biology is to uncover the relationship between genotype and phenotype. However, identifying gene function is often hampered by genetic redundancy. For example, under standard laboratory conditions, three-quarters of the genes in the human pathogenStreptococcus pneumoniaeare non-essential. A powerful approach to unravel genetic redundancy is by identifying gene-gene interactions. To uncover genetic interactions (GIs) inS. pneumoniaeon a genome-wide scale, a generally applicable dual CRISPRi-Seq method and associated analysis pipeline was developed. Specifically, we created a library of 869 dual sgRNAs targeting high-confidence operons that encode essential and non-essential genes, covering over 70% of the genetic elements in the pneumococcal genome. Testing these 378,015 unique combinations, 4,026 significant GIs were identified, including 1,935 negative and 2,091 positive interactions. Besides known GIs, we found and confirmed previously unknown interactions involving genes responsible for fundamental cellular processes such as cell division, cell shape maintenance, and chromosome segregation. The presented methods and bioinformatic approaches can serve as a roadmap for genome-wide gene interaction studies in other organisms. Lastly, all interactions are available for exploration via the Pneumococcal Genetic Interaction Network (PneumoGIN) athttps://veeninglab.shinyapps.io/PneumoGIN, which can serve as a starting point for new biological discoveries and translational research.
Distinct bacterial and protist plankton diversity dynamics uncovered through DNA-based monitoring in the Baltic Sea area
Authors: Jurdzinski Krzysztof T , Latz Meike AC , Torstensson Anders , Brugel Sonia , Hedblom Mikael , Hu Yue O O , Lindh Markus , Andersson Agneta , Karlson Bengt , Andersson Anders F 
Published: August 2024

AbstractPlanktonic microorganisms in coastal waters form the base of food web and biogeochemical cycles. The Baltic Sea area, with its pronounced environmental gradients, serves as a model coastal environment. Yet, microbial diversity assessment across these environmental gradients has so far lacked either taxonomic scope or the integration of spatial and temporal scales. Here, we analyzed protist and bacterial diversity using DNA metabarcoding across 398 samples synchronized with national monitoring of the Baltic Sea and the Kattegat-Skagerrak. We show that salinity, unlike other environmental factors, had a stronger effect on bacterial than on protist community composition. Likewise, Bayesian modeling showed that bacterial lineages were less likely than protists to occur in both lower (<9 PSU) and higher (>15 PSU) brackish salinities. Nonetheless, protist alpha diversity increased with salinity. Changes in bacterial alpha diversity were primarily seasonal and linked to influx of deepwater taxa through vertical mixing in winter. We propose that protists are ecologically less sensitive to salinity because compartmentalization allows them to disconnect basic metabolic processes from the cell membrane. Additionally, further and more frequent dispersal of bacteria might impede local adaptation. Ultimately, DNA-based environmental monitoring expands our understanding of microbial diversity patterns and the underlying factors.
A leaf-expressedTERMINAL FLOWER1ortholog from coffee with alternate splice forms alters flowering time and inflorescence branching inArabidopsis
Authors: Cardon Carlos Henrique , Lesy Victoria , Fust Catherine , Cherubino Ribeiro Thales Henrique , Hebb Owen , Ricon de Oliveira Raphael , Minow Mark , Chalfun Junior Antonio , Colasanti Joseph 
Published: August 2024

ABSTRACTPerennial, polycarpic species, such asCoffeasp L. (coffee), exhibit asynchronous flowering while maintaining concomitant vegetative growth. This growth dichotomy is associated directly with fruit development and maturation time. To identify molecular components that underlie asynchronous flowering, we isolated phosphatidylethanolamine binding protein (PEBP) homologs expressed in coffee and identified a gene with high similarity to ArabidopsisTERMINAL FLOWER1-like. In Arabidopsis, interaction of TFL1 (AtTFL1) with bZIP transcription factor floral regulator FD (AtFD) forms a floral repressor complex that maintains inflorescence meristems in an indeterminate state. UnlikeAtTFL1, which is expressed only in the shoot apical meristem,CaTFL1transcript was detected exclusively in coffee leaves. Moreover, this transcript retained an intron, which was not reported forAtTFL1. CaTFL1 was characterized through heterologous expression inArabidopsisand protein interaction analysis. Ectopic overexpression ofCaTFL1in transgenicArabidopsisplants caused extreme late flowering or prevented flowering. However, the most severe floral repressive activity occurred in transgenic plants that spliced out the extra intron fromCaTFL1. Yeast two hybrid assay revealed that CaTFL1 protein encoded by the spliced mRNA interacts with AtFD, as well asArabidopsis14-3-3 protein. These findings suggest thatCaTFL1acts as a leaf-expressed floral repressor, whose activity is controlled by alternate splicing, and may contribute to asynchronous flowering in coffee.