bluuebunny/crossref_metadata_2025 huggingface dataset:
Dominant Malignant Clones Leverage Lineage Restricted Epigenomic Programs to Drive Ependymoma Development
Authors: Kardian Alisha , Sun Hua , Ippagunta Siri , Laboe Nicholas , Chen Hsiao-Chi , Emanus Erik , Varadharajan Srinidhi , Zheng Tuyu , Holcomb Blake , Connelly Patrick , Connelly Jon P. , Wang Michael , Lowe Kimberley , Pruett-Miller Shondra M. , Bertrand Kelsey C. , Deneen Benjamin , Mack Stephen C.
Published: August 2024

ZFTA-RELA is the most recurrent genetic alteration seen in pediatric supratentorial ependymoma (EPN) and is sufficient to initiate tumors in mice. Despite ZFTA-RELA’s potent oncogenic potential,ZFTA-RELAgene fusions are observed exclusively in childhood EPN, with tumors located distinctly in the supratentorial region of the central nervous system (CNS). We hypothesized that specific chromatin modules accessible during brain development would render distinct cell lineage programs at direct risk of transformation by ZFTA-RELA. To this end, we performed combined single cell ATAC and RNA-seq analysis (scMultiome) of the developing mouse forebrain as compared to ZR-driven mouse and human EPN. We demonstrate that specific developmental lineage programs present in radial glial cells and regulated by Plagl family transcription factors are at risk of neoplastic transformation. Binding of this chromatin network byZFTA-RELAor other PLAGL family motif targeting fusion proteins leads to persistent chromatin accessibility at oncogenic loci and oncogene expression. Cross-species analysis of mouse and human EPN reveals significant cell type heterogeneity mirroring incomplete neurogenic and gliogenic differentiation, with a small percentage of cycling intermediate progenitor-like cells that establish a putative tumor cell hierarchy.In vivolineage tracing studies reveal single neoplastic clones that aggressively dominate tumor growth and establish the entire EPN cellular hierarchy. These findings unravel developmental epigenomic states critical for fusion oncoprotein driven transformation and elucidate how these states continue to shape tumor progression.

HIGHLIGHTS

1. Specific chromatin modules accessible during brain development render distinct cell lineage programs at risk of transformation by pediatric fusion oncoproteins.

2. Cross-species single cell ATAC and RNA (scMultiome) of mouse and human ependymoma (EPN) reveals diverse patterns of lineage differentiation programs that restrain oncogenic transformation.

3. Early intermediate progenitor-like EPN cells establish a tumor cell hierarchy that mirrors neural differentiation programs.

4. ZFTA-RELA transformation is compatible with distinct developmental epigenetic states requiring precise ‘goldilocks’ levels of fusion oncoprotein expression.

5. Dominant tumor clones establish the entire EPN cellular hierarchy that reflects normal gliogenic and neurogenic differentiation programs.
Changes in Proteome Profiles Linked to Hormonal Contraceptive Use Among African American Women with untreated high blood pressure
Authors: DeRoo Lisa , Abbas Malak , Goodney Gabriel , Gaye Amadou
Published: August 2024

Background

The use of oral contraceptives among women with pre-existing cardiometabolic risk factors has been associated with increased risk of cardiovascular events but the underlying mechanisms are not well understood. Analyzing the proteome enables the identification and quantification of proteins involved in various cellular processes, including those affected by oral contraceptives.

Objective

The objective of this study was to investigate if current oral contraceptive use was associated with alterations in the plasma proteome among pre-menopausal African American women with hypertension in the Genomics, Environmental Factors, and the Social Determinants of Cardiovascular Disease in African Americans Study (GENE-FORECAST).

Study Design

We evaluated 2,941 serum proteins measured on the Olink platform to assess the associations between oral contraception use and protein levels among 51 pre-menopausal women with untreated Stage 2 hypertension (13 oral contraception users and 38 non-users). A generalized linear model was fitted for each protein, adjusting for age, body mass index, alcohol consumption, level of education, and physical activity. Pathway enrichment analysis was carried out to identify common pathways among the proteins associated with oral contraceptive use. Gene Ontology enrichment analysis was conducted to gain insight into the functional characteristics of the proteins and the underlying biology.

Results

We identified 44 proteins significantly associated with oral contraceptive use. Among those, 31 showed decreased levels among oral contraceptive users, while 13 exhibited an increase in users. Fourteen proteins were enriched in potentially relevant pathways for the pathogenesis of cardiovascular disease including complement and coagulation cascades, cholesterol metabolism and Notch signaling. There were 25 enriched Gene Ontology terms encompassing 39 of the 44 proteins linked to oral contraceptive use; several of these are involved in peptidase inhibitor activity.

Conclusions

This study provides novel insights into the proteomic landscape associated with oral contraceptive use among African American women with uncontrolled hypertension.
Graphical Representation of Landscape Heterogeneity Identification through Unsupervised Acoustic Analysis
Authors: Guerrero Maria J. , Sánchez-Giraldo Camilo , Uribe Cesar A. , Martínez Victor , Isaza Claudia
Published: August 2024

Changes in land use and global warming pose an increasing threat to global biodiversity and ecosystems, calling for the urgent development of effective conservation strategies. Recognizing landscape heterogeneity, which refers to the variation in natural features within an area, is crucial for these strategies. While remote sensing images quantify landscape heterogeneity, they might fail to detect ecological patterns in moderately disturbed areas, particularly at minor spatial scales. This is partly because satellite imagery may not effectively capture undergrowth conditions due to its resolution constraints. In contrast, soundscape analysis, which studies environmental acoustic signals, emerges as a novel tool for understanding ecological patterns, providing reliable information on habitat conditions and landscape heterogeneity in complex environments across diverse scales and serving as a complement to remote sensing methods.

We propose an unsupervised approach using passive acoustic monitoring data and network inference methods to analyze acoustic heterogeneity patterns based on biophony composition and richness. This method uses sonotypes, unique acoustic entities characterized by their specific time-frequency spaces, to establish the acoustic structure of a site through sonotype occurrences, focusing on general biophony rather than specific species and providing information on the acoustic footprint of a site. From a sonotype composition matrix, we use the Graphical Lasso method, a sparse Gaussian graphical model, to identify acoustic similarities across sites, map ecological complexity relationships through the nodes (sites) and edges (similarities) and transform acoustic data into a graphical representation of ecological interactions and landscape acoustic diversity.

We implemented the proposed method across 17 sites within an oil palm plantation in Santander, Colombia. The resulting inferred graphs visualize the acoustic similarities among sites, reflecting the biophony achieved by characterizing the landscape through its acoustic structures. Correlating our findings with ecological metrics like the Bray-Curtis dissimilarity index and satellite imagery indices reveals significant insights into landscape heterogeneity.

This unsupervised approach offers a new perspective on understanding ecological and biological interactions and advances soundscape analysis. The soundscape decomposition into sonotypes underscores the method’s advantage, offering the possibility to associate sonotypes with species and identify their contribution to the similarity proposed by the graph.
Male and female mice respectively form stronger social aversive memories with same and different sex conspecifics
Authors: Beaver Jasmin N. , Nicodemus Marissa M. , Spalding Isabella R. , Dutta Sohini , Jasnow Aaron M. , Gilman T. Lee
Published: August 2024

Mice offer a wealth of opportunities for investigating brain circuits regulating multiple behaviors, largely due to their genetic tractability. Social behaviors are of translational relevance, considering both mice and humans are highly social mammals, and disruptions in human social behavior are key symptoms of myriad neuropsychiatric disorders. Stresses related to social experiences are particularly influential in the severity and maintenance of neuropsychiatric disorders like anxiety disorders, and trauma and stressor-related disorders. Yet, induction and study of social stress in mice is disproportionately focused on males, influenced heavily by their natural territorial nature. Conspecific-elicited stress (i.e., defeat), while ethologically relevant, is quite variable and predominantly specific to males, making rigorous and sex-inclusive studies challenging. In pursuit of a controllable, consistent, high throughput, and sex-inclusive paradigm for eliciting social stress, we have discovered intriguing sex-specific social aversions that are dependent upon the sex of both experimental and conspecific mice. Specifically, we trained male and female F1 129S1/SvlmJ × C57BL/6J mice to associate (via classical conditioning) same or different sex C57BL/6J conspecifics with a mild, aversive stimulus. Upon subsequent testing for social interaction 24 h later, we found that males socially conditioned better to male conspecifics by exhibiting reduced social interaction, whereas females socially conditioned better to male conspecifics. Serum corticosterone levels inversely corresponded to social avoidance after different sex, but not same sex, conditioning, suggesting corticosterone-mediated arousal could influence cross sex interactions. While our paradigm has further optimization ahead, these current findings reveal why past pursuits to develop same sex female social stress paradigms may have met with limited success. Future research should expand investigation of utilizing male mouse conspecifics to instigate social stress across sexes.
Protamine protects against Vancomycin Induced Kidney Injury
Authors: Shiau Justin , Engel Patti , Olsen Mark , Pais Gwendolyn , Chang Jack , Scheetz Marc H.
Published: August 2024

Introduction

Vancomycin causes kidney injury by accumulating in the proximal tubule, likely mediated by megalin uptake. Protamine is a putative megalin inhibitor that shares binding sites with heparin and is approved for heparin overdose in patients.

Methods

We employed a well characterized Sprague Dawley rat model to assess kidney injury and function in animals that received vancomycin, protamine alone, or vancomycin plus protamine over 5 days. Urinary KIM-1 was used as the primary measure for kidney injury while iohexol clearance was calculated to assess kidney function. Animals had samples drawn pre-treatment to serve as their own controls. Additionally, since protamine is not a known nephrotoxin, the protamine group also served as a control. Cellular inhibition studies were performed to assess the ability of protamine to inhibit OAT1, OAT3, and OCT2.

Results

Rats that received vancomycin had significantly increased urinary KIM-1 on day 2 (24.9 ng/24h, 95% CI 1.87 to 48.0) compared to the protamine alone group. By day 4, animals that received protamine with vancomycin had urinary KIM-1 amounts that were elevated compared to protamine alone (KIM-1 29.0 ng/24h, 95% CI 5.0 to 53.0). No statistically significant differences were identified for iohexol clearance changes between drug groups or when comparing clearance change from baseline (P>0.05). No substantial inhibition of OAT1, OAT3, or OCT2 was observed with protamine. IC50values for protamine were 1e-4 M for OAT1 and OAT3 and 4.3e-5 M for OCT2.

Conclusion

Protamine, when added to vancomycin therapy, delays vancomycin induced kidney injury as defined by urinary KIM-1 in the rat model by one to three days. Protamine putatively acts through blockade of megalin and does not appear to have significant inhibition on OAT1, OAT3, or OCT2. Since protamine is an approved FDA medication, it has clinical potential as a therapeutic to reduce vancomycin related kidney injury; however, greater utility may be found by pursuing compounds with fewer adverse event liabilities.
Variable responses of alpine-plant communities to warming and loss of dominant species
Authors: Marraffini ML , Sanders NJ , Sundquist MK , Classen AT , Deslippe JR , He JS , McLaren JR , Rixen C , Wipf S , Chisholm C , Giejsztowt J , Prager C , Stouffer DB
Published: August 2024

Responses of ecological communities to perturbations are inherently variable because responses of their constituent populations also vary. Species within a single community may show combinations of no response, positive responses, and negative responses to any given perturbation often canceling each other out resulting in small or no signal that the community level. Here we explore the impacts of warming and loss of the dominant species on alpine ecosystems in a global study. We investigate warming and species-loss treatments on population- and community-level dynamics across alpine-plant communities at two elevations in five globally-distributed mountain locations. Communities showed varied responses to treatments; no community showed strong responses to a single treatment. Rather, most sites were influenced by both perturbations. Populations within these communities responded idiosyncratically, suggesting that constituent species are not all equally robust to perturbations even when community-level effects appear weak. Our results highlight the challenge of making general predictions about population- and community-level responses of alpine ecosystems in the face of present and future perturbations.
Iron homeostasis in the annual and perennial stem zones ofArabis alpina
Authors: Sergeeva Anna , Mai Hans-Jörg , Bauer Petra
Published: August 2024

Plants serve as reservoirs for vital micronutrients, including iron, which they store in bioavailable forms to support growth in subsequent seasons. The perennial life style is preponderant in nature. Annual species allocate iron towards their seeds. However, our understanding of iron homeostasis in perennial plants remains limited.Arabis alpinais a perennial model organism. Its perenniating branches undergo secondary growth where they store carbon-rich macromolecules.

In this study, we investigated iron homeostasis in the perennial and annual stem zones (PZ, AZ) ofA. alpina. We found that both, the wild-type Pajares (Paj) andperpetual flowering 1mutant accumulated iron at various developmental stages in the PZ as well as in the AZ. Notably, iron levels in the PZ were found to be approximately two-fold higher than those in the AZ, underscoring the PZ’s enhanced capacity for iron storage, irrespective of flowering status. Iron was predominantly located within plastid-bound ferritin, providing insight into its storage mechanism. Furthermore, gene expression analyses supported the significance of ferritin and demonstrated an enrichment of transcripts related to iron homeostasis within the stems. Distinct patterns of expression among iron homeostasis genes were observed in relation to iron contents in the PZ and AZ, indicating tissue-specific regulatory mechanisms governing iron accumulation.

These findings collectively emphasize the critical function of secondary growth and the PZ as an important site for iron storage in perennial plants, suggesting thatfuture research should further explore the nuances of iron homeostasis signaling in perennial plants.

Highlight

‐ Iron accumulates in the perennial stem zone, and ferritin is a storage form for iron there.

‐ Transcripts of iron homeostasis genes are enriched among genes expressed in the annual and perennial stem zones, yet iron accumulation correlates with different gene expression patterns.
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

The 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

Passion 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.
Larger diet particle sizes cause crickets to grow faster with no effect on final body size
Authors: Muzzatti Matthew J , Kong Jacinta D , McColville Emily R , Brzezinski Hunter , Stabile Cassandra C , MacMillan Heath A , Bertram Susan M
Published: August 2024

Artificial diets are costly to produce, so diet efficiency is critically important to the success of mass rearing insects. One way to improve feed efficiency is through dietary particle size optimization. We used a commercially reared species,Gryllodes sigillatus, to test whether individual crickets reared from hatch to adulthood on diets of different particle sizes would grow differently. Crickets fed a diet ≥0.5 mm grew heavier during the first three weeks but weighed the same after six weeks regardless of diet size. We then provided crickets with a choice of particle size throughout development to test for dietary size preference. Given a choice, crickets consumed the most food from the 1.0-1.4 mm diet. Crickets also preferentially select ingredients from mixed diets, so to test whether grinding a conventional diet to a finer particle size could influence performance traits, we ran a large-scale group rearing experiment and found no effect of further grinding on colony mass gain or development time. Pelleting diet is another method for eliminating self-selection of ingredients, and so we tested whether pelleting finely ground conventional cricket feed would result in any substantial changes to the developmental life history of individual crickets. Crickets fed a 2 mm pelleted diet grew larger body size but were not significantly heavier. Overall, our results demonstrate that particle size optimization can be leveraged to enhance cricket life history traits important to mass production, as growth was accelerated on larger particle size diets and crickets preferred to eat larger-sized diets. Researchers focusing on physical properties of insect diets should carefully consider the timing of growth and development through which diet particle size may influence feed efficiency.
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

Interleukin 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.
Monsoonal climate and asymmetric heating facilitate the slope-aspect to influence landscape-scale tree structure in the Western Ghats, India
Authors: Maheshwori Devi , Managave Shreyas , Jathar Girish , Davande Sham
Published: August 2024

The regional variation of rainfall and length of the rainy season are identified to control the vegetation distribution in the Western Ghats (WG) of India, one of the important biodiversity hotspots. Here we demonstrate the existence of two new modes related to monsoonal climate and asymmetric solar heating that influence the vegetation structure at the landscape-scale in the WG: (i) the north-facing slopes have a higher tree cover (TC) and canopy height (CH) than the south-facing slopes and (ii) higher TC and CH on the west-facing slopes than the east-facing slopes. The asymmetry associated with these modes increases with the slope angle. The interaction of these modes often leads northwest and southeast aspects to have the highest and lowest TC (and CH), respectively. We thus demonstrate that even in low-latitude regions, the slope-aspect plays an important role in determining the TC and CH if the relief is higher. This fundamental driver of vegetation structure needs to be considered while formulating and executing programs aimed at increasing tree cover and conserving biodiversity, especially in the high relief areas in the tropics having seasonal rainfall, such as in the WG.
alpha-Actinin-3 deficiency protects from the effects of acute cold exposure through altered skeletal muscle Ca2+ and OXPHOS signaling.
Authors: Houweling Peter J , Tiong Chrystal F , Kiriaev Leonit , Diaz-Pena Roberto , Albers Patrick K , Wood Harrison , Wyckelsma Victoria , Stait Tegan , Venckunas Tomas , Valenzuela Pedro , Castillo-Garcia ADRIAN , Brazaitis Marius , Berman Yemima , Seto Jane T , Westerblad Hakan , Lek Monkol , Thorburn David , Lucía Alejandro , Head Stewart , North Kathryn N
Published: August 2024

A nonsense polymorphism in the ACTN3 gene (R577X, rs1815739) results in the loss of the fast skeletal muscle fiber protein α-actinin-3 in an estimated 1.5 billion humans worldwide. Homozygosity for this common polymorphism (ACTN3 577XX) does not cause disease but is detrimental to sprint performance in elite athletes. Recently, we reported that ACTN3 577XX humans and Actn3 knockout mice show improved cold tolerance. This was not due to an increase in brown adipose tissue activity or a greater muscle shivering response, but was associated with an increased abundance of slow myosin heavy chain muscle fibers in XX individuals, which in turn increased muscle tone to improve cold tolerance. Using the Actn3 knockout mouse we have now analyzed the molecular and physiological impacts of acute cold exposure (4oC, for 5 hours) on skeletal muscle. In addition, we used statistical inference of publicly available archaic (Neanderthal and Denisovan) and modern human DNA data to estimate the age of the ACTN3 X-allele and to identify a novel haplotype associated with this variant that provides support for genetic selection in some populations of modern humans. Our results indicate that skeletal muscle of Actn3 knockout mice exhibit higher mitochondrial oxidative phosphorylation abundance and activity than wild-type controls. Following acute cold exposure, we identified reductions in gene ontology pathways associated with metabolism and protein breakdown, which impact muscle mass loss and improved muscle fatigue resistance. Together this provides further evidence for improved cold tolerance in Actn3 knockout mice and ACTN3 577XX individuals. Furthermore, we confirm that the X-allele first appeared in modern humans ~135,000 years ago, with this variant increasing in frequency in European and Asian populations from as early as 42,000 years ago, which aligns with modern human migration out of Africa. Taken together these data provide additional molecular and functional evidence for a protective advantage of α-actinin-3 deficiency following cold exposure, highlighting the importance of skeletal muscle in mammalian thermogenesis and its potential role in the evolution of modern-day humans.
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

Recently 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

Members 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

Three-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

In 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

Heme-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

Amoeboid 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

Effective 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

A 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

Planktonic 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

Perennial, 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.
Surfactin facilitates the establishment ofBacillus subtilisin synthetic communities
Authors: Lozano-Andrade Carlos N. , Dinesen Caja , Wibowo Mario , Bach Nil Arenos , Hesselberg-Thomsen Viktor , Jarmusch Scott A. , Strube Mikael Lenz , Kovács Ákos T.
Published: August 2024

Soil bacteria are prolific producers of a myriad of biologically active secondary metabolites. These natural products play key roles in modern society, finding use as anti-cancer agents, as food additives, and as alternatives to chemical pesticides. As for their original role in interbacterial communication, secondary metabolites have been extensively studied underin vitroconditions, revealing a multitude of roles including antagonism, effects on motility, niche colonization, signaling, and cellular differentiation. Despite the growing body of knowledge on their mode of action, biosynthesis, and regulation, we still do not fully understand the role of secondary metabolites on the ecology of the producers and resident communitiesin situ.Here, we specifically examine the influence ofBacillus subtilis-produced cyclic lipopeptides (LPs) during the assembly of a bacterial synthetic community (SynCom), and simultaneously, explore the impact of LPs onB. subtilisestablishment success in a SynCom propagated in an artificial soil microcosm. We found that surfactin production facilitatesB. subtilisestablishment success within multiple SynComs. Surprisingly, while neither a wild type nor a LP non-producer mutant had major impact on the SynCom composition over time, theB. subtilisand the SynCom metabolomes are both altered during co-cultivation. Overall, our work demonstrates the importance of surfactin production in microbial communities, suggesting a broad spectrum of action of this natural product.
Farmyard Mulching in Regenerative Agriculture Enhances Saprotrophs and Concomitantly Reduces Pathogenic Fungal Genera
Authors: Naresh Pratyusha , Singh Indira
Published: August 2024

Regenerative agriculture (RA) using nature-friendly methods nurtures soil microbial communities. Indian RA farmers use diverse practices to manage their soil. This study compared the fungal communities in RA plots with those in conventional agriculture (CA) and barren land (BL) plots (comprising completely barren-BL and with Eucalyptus - BL-Euc). Two crops were considered - Finger millets and Vegetables (Tomato/ beans) for this study. ITS metagenomic analysis of soil DNA samples obtained from RA, CA and BL plots was done to identify fungal composition in each of the study plots. The fungal communities in RA finger millet and RA vegetable were compared with respective CA finger millet and CA vegetable and with BL plots. Vegetable RA plots observed higher abundances of fungal Operational Taxonomic Units (OTUs) than in CA vegetable and BL plots. Whereas the RA finger millet plots had similar fungal OTUs as in CA finger millet and BL plots. The vegetable RA plot carrying out natural farming for 12 years (maximum length in our samples) recorded the highest fungal OTU (13707) levels while the CA plots had average OTU abundance of (7416). RA plots in both crops showed a significant reduction in plant pathogenic fungal genuses -BipolarisandPyrenochaetopsis. Furthermore, RA finger millet plots showed an enhanced representation of saprotrophs while CA (finger millets) had pathotroph-saprotrophs suggesting a favorable increase in decomposer populations in RA.