bluuebunny/crossref_metadata_2025 huggingface dataset:
Benchmarking a foundational cell model for post-perturbation RNAseq prediction
Authors: Csendes Gerold , Szalay Kristóf Z. , Szalai Bence
Published: October 2024

Accurately predicting cellular responses to perturbations is essential for understanding cell behaviour in both healthy and diseased states. While perturbation data is ideal for building such predictive models, it is considerably sparser than baseline (non-perturbed) cellular data. To address this limitation, several foundational cell models have been developed using large-scale single-cell gene expression data. These models are fine-tuned after pre-training for specific tasks, such as predicting post-perturbation gene expression profiles, and are considered state-of-the-art for these problems. However, proper benchmarking of these models remains an unsolved challenge.

In this study, we benchmarked a recently published foundational model, scGPT, against baseline models. Surprisingly, we found that even the simplest baseline model - taking the mean of training examples - outperformed scGPT. Furthermore, machine learning models that incorporate biologically meaningful features outperformed scGPT by a large margin. Additionally, we identified that the current Perturb-Seq benchmark datasets exhibit low perturbation-specific variance, making them suboptimal for evaluating such models.

Our results highlight important limitations in current benchmarking approaches and provide insights into more effectively evaluating post-perturbation gene expression prediction models.
CalTrig: A GUI-based Machine Learning Approach for Decoding Neuronal Calcium Transients in Freely Moving Rodents
Authors: Lange Michal A. , Chen Yingying , Fu Haoying , Korada Amith , Guo Changyong , Ma Yao-Ying
Published: October 2024

Advances inin vivoCa2+imaging using miniature microscopes have enabled researchers to study single-neuron activity in freely-moving animals. Tools such as MiniAN and CalmAn have been developed to convertCa2+visual signalsto numerical data, collectively referred to as CalV2N. However, substantial challenges remain in analyzing the large datasets generated by CalV2N, particularly in integrating data streams, evaluating CalV2N output quality, and reliably and efficiently identifying Ca2+transients. In this study, we introduce CalTrig, an open-source graphical user interface (GUI) tool designed to address these challenges at the post-CalV2N stage of data processing. CalTrig integrates multiple data streams, including Ca2+imaging, neuronal footprints, Ca2+traces, and behavioral tracking, and offers capabilities for evaluating the quality of CalV2N outputs. It enables synchronized visualization and efficient Ca2+transient identification. We evaluated four machine learning models (i.e., GRU, LSTM, Transformer, and Local Transformer) for Ca2+transient detection. Our results indicate that the GRU model offers the highest predictability and computational efficiency, achieving stable performance across training sessions, different animals and even among different brain regions. The integration of manual, parameter-based, and machine learning-based detection methods in CalTrig provides flexibility and accuracy for various research applications. The user-friendly interface and low computing demands of CalTrig make it accessible to neuroscientists without programming expertise. We further conclude that CalTrig enables deeper exploration of brain function, supports hypothesis generation about neuronal mechanisms, and opens new avenues for understanding neurological disorders and developing treatments.
Circulatory proteins shape microglia state and boost phagocytosis
Authors: Lu Nannan , Moran-Losada Patricia , Hahn Oliver , Saksena Aryaman , Tapp Emma , Chadarevian Jean Paul , Dong Wentao , Shi Sophia M. , Shuken Steven R. , Guldner Ian , Zeng Wenshu , To Ning-Sum , Wong Pui Shuen , Hasselmann Jonathan , Davtyan Hayk , Sun Jerry , Li Lulin , Luo Jian , Yang Andrew C. , Li Qingyun , Cheung Tom H. , Abu-Remaileh Monther , Blurton-Jones Mathew , Wyss-Coray Tony
Published: October 2024

Microglia, the brain’s immune cells, are highly responsive to their local environment. Given that circulatory proteins can enter the brain, we asked whether microglia are responsive to such proteins. Here, we identify a stable population of microglia specialized to take up circulatory proteins in a region-specific manner under physiological conditions; human hematopoietic stem cell-derived microglia replacing endogenous microglia in chimeric mice show similar regional specialization. Plasma-positive microglia are characterized by prominent expression of genes related to innate immunity and antigen presentation and exhibit high metabolic and phagocytic activity. This activity is dependent, in part, on microglial uptake and accumulation of circulatory Apolipoprotein AI (ApoA-I). Our findings thus identify a new model of communication between brain and periphery through specialized microglia.
Divergence of the Individual repeats in the leucine-rich repeat domains of human Toll-like receptors explain their diversity and functional adaptations
Authors: Takkouche Abraham , Ichii Keita , Qui Xinru , Jaroszewski Lukasz , Godzik Adam
Published: October 2024

The receptor domains of Toll-like receptors (TLRs) are characterized by a solenoid-like structure composed of tandem repeats of α/β units known as Leucine Rich Repeats (LRRs). LRR proteins form large paralogous families, with nearly 400 in the human genome alone, all sharing similar semi-regular solenoid-like structures. Despite this structural similarity, they exhibit remarkable diversity in binding specificity. For TLR receptors, this includes a range of pathogen-associated molecular patterns (PAMPs), while other LRR proteins bind an extensive array of ligands, including proteins, DNA, RNA, and small molecules. The LRR domains contain repeats that have similar, yet not identical, 3D structures and patterns of conserved residues. Through in-depth analysis of sequence and structural conservation in individual repeats of human TLRs, we demonstrate that even subtle variations between these repeats alter the local solenoid structure, leading to significant functional changes. Variations in repeat length and defining patterns result in local changes in curvature and the emergence of structural features such as loops, cavities, or specific interaction interfaces. Understanding how divergence in LRR repeats influences their functional roles can provide deeper insights into their binding mechanisms, including interactions with unknown ligands, both in humans and across the diverse phylogenetic spectrum of animals that rely on their TLR repertoires for immune activation.
Metabolic vulnerabilities in Down syndrome B-cell acute lymphoblastic leukemia can be targeted using Venetoclax
Authors: Jones Dallas , Woods Elena , Li Zhenhua , Schaller Kristin L. , Hoffmeyer Eric , Kooiman Ben , Fernandez Joseph , Wharton Tegan , Tufa Dejene , Hall Spencer C. , Trahan George , Maloney Kelly W. , Pacenta Holly , Sullivan Kelly , Espinosa Joaquin , Roede James R. , Marentette John , Stevens Brett , Inguva Anagha , Stephenson Daniel , Reisz Julie A. , D’Alessandro Angelo , Jordan Craig T. , Yang Jun J. , Verneris Michael R.
Published: October 2024

Children with Down syndrome (DS) and B-cell acute lymphoblastic leukemia (B-ALL) are at increased risk for treatment-related mortality and relapse, highlighting the need for new therapies. Leukemia cell lines (CLs) have been fundamental to understanding therapeutic responses to pharmacological agents. We generated three DS B-ALL CLs characterized with diverse genomic alterations, includingIGH::CRLF2rearrangement (BCR::ABL1 like), mutations inFLT3andTP53, and a novelERG::CEBPDrearrangement. DS CLs had diminished proliferation, metabolism, and mitochondrial function when compared to non-DS (NDS) CLs and interestingly, these findings were similar to NDS Philadelphia chromosome-like (Ph-like) B-ALL CLs. Based on similar mitochondrial defects and prior preclinical data using Venetoclax for Ph-like B-ALL, we hypothesized that Venetoclax would be effective in DS. Intriguingly, Venetoclax was more effective in DS when compared to both NDS and Ph-like CLs. Efficacy was observed in DS patient derived xenografts (PDXs) and diagnostic/relapsed patient samples treated with Venetoclax, which synergized with Trametinib and Vincristine. Mass spectrometry-based multiomics analyses in DS and NDS B-ALL patient samples revealed an enriched metabolite profile in DS, particularly in the hubs of glucose metabolism and polyunsaturated phosphatidylcholines and phosphatidylinositols. Transcriptome analyses in DS B-ALL patients (n=249) supported enhanced glucose and fatty acid metabolism. Glucose regulated B-ALL viability throughde novoserine biosynthesis. Targeting serine synergized with Venetoclax in DS B-ALL CLs. In summary, we have generated novel tools for studying DS B-ALL and identify altered metabolism in DS that responds to Venetoclax.
Quantitative 2D J-resolved metabolite-cycled semiLASER spectroscopy of metabolites and macromolecules in the human brain at 9.4 T
Authors: Murali-Manohar Saipavitra , Borbath Tamas , Wright Andrew Martin , Avdievich Nikolai I. , Henning Anke
Published: October 2024

Purpose

While two-dimensional (2D) in vivo spectroscopy yields rich information and has been successfully used in clinical trials, it requires a localization scheme that minimizes the impact of chemical shift displacement on J-coupling evolution, a robust frequency drift correction and dedicated processing and quantification methods. Considering these needs this study demonstrates a novel data acquisition and an analysis pipeline to quantify 16 metabolites in mmol/kg in the human brain using a 2D J-resolved metabolite-cycled (MC) semiLASER localization sequence at 9.4 T in the human brain.

Methods

Metabolite spectra were acquired in vivo using the newly developed J-resolved MC semiLASER localization sequence with maximum echo sampling (MES) at 9.4 T. In order to account for the underlying macromolecular (MM) spectra in the acquired metabolite spectra, J-resolved MM spectra were acquired using a double inversion recovery (DIR) J-resolved MC semiLASER. Spectral fitting was performed with ProFit 2.0 using a simulated basis set from VesPA tailored to 2D J-resolved semiLASER with MES. Finally, metabolite concentrations were calculated using internal water referencing.

Results

Tissue concentrations for 16 metabolites in mmol/kg are reported after correcting for number of protons, tissue content, and relaxation effects of both water and metabolites at 9.4T. Quantification results of spectra considering 8 and 2 averages per TE did not show any significant differences.

Conclusion

2D spectra of metabolites acquired at 9.4T and 2D MMs acquired at any field strength are presented for the first time. Basis set simulation and quantification of metabolites for metabolite spectra acquired using maximum-echo-sampled 2D J-resolved semiLASER was performed for the first time. The sensitivity in the detection of J-coupled metabolites such as glutamine, glucose or lactate. At ultra-high field, the acquisition duration of 2D MRS can be also substantially reduced since only a very low number of averages per TE are needed.
Biologically grounded brain-on-chip model identifies selective topographic reorganization within hyperexcitable neural networks
Authors: Poinsot Maxime , Dos Santos Marine , Marthy Baptiste , Borges-Correia Ana , Gascon-Gonzalo Eduardo , Charlot Benoit , Cazorla Maxime
Published: October 2024

Connectomics has revolutionized our understanding of brain function by emphasizing the importance of neural networks and their topographical organization. Corticostriatal circuits, which play a critical role in cognition and emotion, follow a precise topographic architecture essential for integrating and processing cortical information within the basal ganglia. Disruptions to this connectivity are often implicated in neurodevelopmental and psychiatric disorders such as obsessive compulsive disorders, schizophrenia, epilepsy, and autism spectrum disorders. However, studying network disruptionsin vivopresents significant challenges due to their intricate architecture and early developmental onset. To address this, we employed a brain-on-chip microfluidic platform to recreate a biologically relevant model of topographically organized corticostriatal networks. By mimicking the directional control of neuronal projections using Tesla valve-inspired microchannels, we demonstrate that genetic perturbations affecting neuronal excitability during development lead to selective alterations of local versus long-range network topology, resulting in the formation of new convergent nodes. This model offers critical insights into how early perturbations contribute to circuit-specific pathologies, providing a valuable tool for understanding neurodevelopmental disorders and advancing therapeutic strategies.
Hierarchical Patterns of Soil Biodiversity in the Atacama Desert: Insights Across Biological Scales
Authors: Villegas Laura , Pettrich Laura , Acevedo-Trejos Esteban , Suwanngam Arunee , Wassey Nadim , Allende Miguel L , Stoll Alexandra , Holovachov Oleksandr , Waldvogel Ann-Marie , Schiffer Philipp H.
Published: October 2024

Species diversity and distribution, in relation to how they interact with their environment is a major focus of ecological research. Particularly for soil ecosystems, information about geographical patterns of biota is scarce despite the pivotal role of soils as ecosystem service providers. The Atacama is the driest non-polar desert on earth: water is scarce, high salinity patches are frequent and water bodies have high concentrations of metals. It is believed that only specialized taxa can survive in this Desert. Accordingly, only some microbial life-forms and few plants, and vertebrates are present. Above ground invertebrates have been reported in the desert but its soils have not been comprehensively analyzed. By studying different areas in the Atacama, we aim to better understand resilience of soil organisms in times of global aridification. Nematodes are one of the most important groups of soil organisms in abundance and biodiversity. Here, we investigated diversity of soil nematodes at the genetic, taxonomic, community and life-cycle levels. We find distinct patterns and assemblages along the different habitats in the desert: dune systems, high altitude mountains, saline lakes, river valleys and fog oases. We also find that distribution of asexual taxa appears to be in the marginal ranges of high altitudes, and that the distribution of genera richness in the Atacama follows a latitudinal diversity gradient, as well as an increase with increasing precipitation. Our work shows that even under extreme environmental conditions stable, healthy soil communities can persist, but we see indicatives of poor soil food webs.
Mapping the attractor landscape of Boolean networks
Authors: Trinh Van-Giang , Park Kyu Hyong , Pastva Samuel , Rozum Jordan C
Published: October 2024

Boolean networks are popular dynamical models of cellular processes in systems biology. Their attractors model phenotypes that arise from the interplay of key regulatory subcircuits. A succession diagram describes this interplay in a discrete analog of Waddington’s epigenetic attractor landscape that allows for fast identification of attractors and attractor control strategies. We present a new approach to succession diagram construction for asynchronously updated Boolean networks, implemented in the biologist’s Boolean attractor landscape mapper,biobalm, a Python 3 library. We compare the performance ofbiobalmto similar tools and find a substantial performance increase in succession diagram construction, attractor identification, and attractor control. To illustrate the utility ofbiobalm, we perform the most comprehensive comparative analysis to date of the succession diagram structure in experimentally-validated Boolean network models of cell processes and random ensembles. We find that random models (including critical Kauffman networks) have relatively small succession diagrams, indicating simple decision structures. In contrast, non-random models from the literature are enriched in extremely large succession diagrams, indicating an abundance of decision points in their dynamics and suggesting the presence of complex Waddington landscapes in nature.
Brain-wide connectivity and novelty response of the dorsal endopiriform nucleus in mice
Authors: Manjila Steffy B. , Son Seoyoung , Kline Hannah , Betty Rebecca , Wu Yuan-ting , Pi Hyun-Jae , Parmaksiz Deniz , Shin Donghui , Liwang Josephine K. , Kronman Fae N. , Paul Anirban , Kim Yongsoo
Published: October 2024

The dorsal endopiriform nucleus (EPd) is an enigmatic cortical subplate structure located inside the piriform cortex that shares a similar developmental origin with the claustrum. Although the EPd has been previously implicated in epilepsy and olfactory processing, its anatomical organization, connectivity patterns, and function remain largely unclear due to a lack of specific molecular markers. Our previous mapping study serendipitously identified that the Oxt receptor (Oxtr) is densely expressed in the EPd. Subsequent immunohistochemical and spatial transcriptomic analyses confirmed that Oxtr expression is enriched in the EPd, revealing distinct molecular organization compared to the neighboring claustrum. Whole brain input-output mapping of EPd Oxtr-positive neurons unveils extensive bidirectional connections to the ventral half of the brain, orchestrating functional circuits regulating olfaction, internal state, and emotion. Furthermore, our in-vivo miniscope recordings show that EPd Oxtr neurons exhibit high baseline activity during exploratory behavior, with a sharp decrease in activity in response to novel stimuli. This suggests that the EPd regulates interoceptive states and likely plays a role in adapting to novel exteroceptive cues.
rDNA copy number variation in yeast alters response to environmental conditions
Authors: Thornton Kevin , Kwan Elizabeth X. , Bubb Kerry , Paleologu Luana , Raghuraman M. K. , Brewer Bonita J. , Cuperus Josh T. , Queitsch Christine
Published: October 2024

Ribosomal DNA (rDNA) in eukaryotes is maintained in hundreds of copies with rDNA copy number varying greatly among individuals within a species. In the budding yeastSaccharomyces cerevisiae, the rDNA copy number across wild isolates ranges from 90 to 300 copies. Previous studies showed that 35 rDNA copies are sufficient for ribosome biogenesis in this yeast and enable wild-type-like growth in standard laboratory growth conditions. We addressed two major questions concerning rDNA copy number variation in this yeast: (1) What are the fitness consequences of rDNA copy number variation outside and within the natural range in standard laboratory growth conditions? (2) Do these fitness effects change in different growth conditions? We used growth competitions to compare the fitness effects of rDNA copy number variation in otherwise isogenic strains whose rDNA copy number ranged from 35 to 200. In standard growth conditions, we found that fitness gradually increases from 35 rDNA copies until reaching a plateau that spans from 98 to 160 rDNA copies, well within the natural range. However, rDNA copy number-dependent fitness differed across environments. Compared to standard growth conditions, strains with higher rDNA copy numbers showed improved fitness when grown at increased temperature or in glycerol media. Moreover, the gradual fitness increase with increasing rDNA copy number in standard growth conditions gave way to a markedly lower fitness of strains with copy numbers below the natural range in these two stress conditions. These results suggest that selective pressures drive rDNA copy number in this yeast to at least ~100 copies and that a higher number of copies buffers against environmental stress. The similarity of theS. cerevisiaerDNA copy number range to the ranges reported inC. elegans, D. melanogaster, and humans points to conserved selective pressures maintaining the range of natural rDNA copy number in these highly diverse species.
Sociality shapes mitochondrial adaptations supporting hypoxia tolerance
Authors: Rossi Alice , Ruwolt Max , Kakouri Paraskevi , Kosten Tetiana , Kunz Severine , Puchkov Dmytro , Reznick Jane , Purfürst Bettina , Omerbašić Damir , Aranda Daniel Méndez , Carai Giorgia , Mastrobuoni Guido , Hart Daniel W. , Carraro Michela , Tommasin Ludovica , Bennett Nigel C. , Bégay Valérie , Faelber Katja , Daumke Oliver , Bernardi Paolo , Park Thomas J. , Kempa Stefan , Liu Fan , Lewin Gary R.
Published: October 2024

Oxygen deprivation or hypoxia is poorly dealt with by most terrestrial species and often leads to permanent tissue damage and death. One prominent exception is the naked mole-rat (Heterocephalus glaber) which is remarkably adapted to withstand prolonged periods (∼18 mins) of severe hypoxia, a trait likely driven by its crowded underground lifestyle. Other African mole-rat species are less social or entirely solitary like the Cape mole-rat (Georychus capensis). Here, we asked whether cellular and molecular adaptations to hypoxia map to social traits. We discovered that at the cellular level naked mole-rat fibroblasts survive >30 hours in 1% oxygen, while fibroblasts from terrestrial or non-social mole-rat species (human, mouse and Cape mole-rat) die rapidly under hypoxic conditions. We further show that naked mole-rat mitochondria have evolved morphological, functional and proteomic adaptations crucial for hypoxia resistance, remaining unaffected after long periods of severe hypoxia. We identify the mitochondrial protein Optic Atrophy 1 (OPA1) as a key player in naked mole-rat hypoxia resilience. Naked mole-rat mitochondria not only express more protective forms of OPA1, but also harbor a structurally unique isoform that likely protects cells from hypoxic damage. We show that evolutionary changes including the functionalization of a uniqueOpa1exon support mitochondrial mediated cellular protection. Indeed, knockdown of OPA1 in naked mole-rat cells is sufficient to render them equally susceptible to hypoxia as human cells or cells from non-social African species. Our study demonstrates how molecular evolution drives unique adaptations that enable cells to achieve unprecedented resistance to hypoxic damage. We also show that molecular changes at the level of mitochondria are crucial in conferring hypoxia resistance. Our results thus chart a novel molecular path to understand how robust cellular hypoxia resistance can be achieved. Such knowledge may eventually inspire novel strategies to circumvent the consequences of hypoxic-damage in humans.
Mutant IDH uncouples p53 from target gene regulation to disable tumor suppression
Authors: Martin Cole , Sullivan William B. , Brinkman Jacqueline , Scoville Deena , Yashinskie Jossie J , Tian Sha , Mezzadra Riccardo E. , Ho Yu-Jui , Koche Richard P. , Baslan Timour , Raab Jesse , Corcoran David , Finley Lydia W.S. , Lowe Scott W. , Morris John P.
Published: October 2024

p53 prevents tumor initiation and progression via transcriptional regulation of target gene networks. Here, we find that cancer-associated mutations in isocitrate dehydrogenase (IDH) can uncouple p53 activity from tumor suppression by perturbing chromatin states that determine target gene expression. Mutant IDH impairs tumor regressions and promotes the outgrowth of cancer cells with transcriptionally active, wild-type p53 in a mouse model of liver cancer where restoration of p53 activity results in tumor clearance. Mutant IDH alters p53 target gene expression through the oncometabolite 2-hydroxyglutarate (2-HG), an inhibitor of alpha-ketoglutarate (αKG)-dependent chromatin remodeling enzymes, without preventing p53 accumulation or global genomic binding. Rather, mutant IDH alters chromatin accessibility landscapes that dictate target gene expression, resulting in disabled upregulation of targets that execute tumor suppression. Specifically, mutant IDH disrupts the expression of pro-apoptotic p53 targets that enable p53-dependent tumor regressions, including the death ligand receptor Fas. Pharmacological inhibition of mutant IDH in TP53 wild-type cholangiocarcinoma cells, a tumor type where p53 and IDH mutations are mutually exclusive, potentiates p53 target gene expression and sensitizes cells to Fas ligand and chemotherapy-induced apoptosis. Therefore, we implicate the disruption of p53 target gene regulation as a reversible, oncogenic feature of cancer-associated IDH mutations.

SIGNIFICANCE

We find that chromatin states altered by cancer-associated IDH mutations intersect with transcriptional regulation of p53 target genes. This reversible interaction may represent a strategy to reinvigorate latent tumor suppression in IDH mutant, p53 wild-type tumors.
Age dependency of neurometabolite T1relaxation times
Authors: Murali-Manohar Saipavitra , Zöllner Helge J. , Hupfeld Kathleen E. , Song Yulu , Carter Emily E. , Yedavalli Vivek , Hui Steve C. N. , Simicic Dunja , Gudmundson Aaron T. , Simegn Gizeaddis Lamesgin , Davies-Jenkins Christopher W. , Oeltzschner Georg , Porges Eric C. , Edden Richard A. E.
Published: October 2024

Purpose

To measure T1relaxation times of metabolites at 3T in a healthy aging population and investigate age dependence.

Methods

A cohort of 101 healthy adults were recruited with approximately 10 male and 10 female participants in each ‘decade’ band: 18-29, 30-39, 40-49, 50-59, and 60+ years old. Inversion-recovery PRESS data (TE/TR: 30/2000 ms) were acquired at 8 inversion times (TIs) (300, 400, 511, 637, 780, 947, 1148 and 1400 ms) from voxels in white-matter-rich centrum semiovale (CSO) and gray-matter-rich posterior cingulate cortex (PCC). Modeling of TI-series spectra was performed in Osprey 2.5.0. Quantified metabolite amplitudes for total N-acetylaspartate (tNAA2.0), total creatine at 3.0 ppm (tCr3.0) and 3.9 ppm (tCr3.9), total choline (tCho), myo-inositol (mI), and the sum of glutamine and glutamate (Glx) were modeled to calculate T1relaxation times of metabolites.

Results

T1relaxation times of tNAA2.0in CSO and tNAA2.0, tCr3.0, mI and Glx in PCC decreased with age. These correlations remained significant when controlling for cortical atrophy. T1relaxation times were significantly different between PCC and CSO for all metabolites except tCr3.0. We also propose linear models for predicting metabolite T1s at 3T to be used in future aging studies.

Conclusion

Metabolite T1relaxation times change significantly with age, an effect that will be important to consider for accurate quantitative MRS, particularly in studies of aging.
A sustainable and bee-pollinated coffee to start your day
Authors: Alves Denise Araujo , Ramos Jenifer Dias , dos Santos Charles Fernando , Moure-Oliveira Diego , Almeida-Dias Joyce Mayra Volpini , Santos Gustavo Souza , Kaminski Thamires Sá de Oliveira , Cione Ana Paola , Quenzer Fernando Celso Longhim , Campbell Alistair John , Berretta Andresa Aparecida , Sousa Guilherme Jorge Gomes e , Pereira Andrigo Monroe , Thompson Helen , Vasconcelos Natalia Bottan de Toledo , Cruz Rafael , de Queiroz Ana Carolina Martins , Bento José Maurício Simões , Menezes Cristiano
Published: October 2024

The integration of managed pollinators into agricultural systems represents a practical strategy for boosting crop production, optimising sustainable farming practices, and improving rural livelihoods. However, the use of managed bees to supplement the contribution of wild pollinators still faces challenges, such as over-reliance on pesticides in intensively managed agroecosystems. Here, we placed managed bee colonies on conventional farms to assess their impact on arabica coffee yield, quality and market value, while also to evaluate colony health in coffee fields treated with field rates of thiamethoxam-based products. We show that supplementing farms with managed bees increased farmer income by enhancing coffee yield and beverage quality, which is rewarded by specialty coffee markets. Moreover, our field-based study reveals that, even when exposed to field-realistic levels of the neonicotinoid thiamethoxam, managed bee colonies exhibited no significant adverse effects on their health within coffee fields. Our results underline that pollination is a key input on intensively managed coffee farms, and that agricultural production and environmental conservation interact synergically to maximize profitability, which is fundamental to encourage farmers to be good stewards of their croplands by adopting nature-positive practices.
Multiplexed functional analysis of TAP2 variants in regulating MHC-I cell surface abundance reveals overexpression of PLK1 downregulates antigen presentation
Authors: Nagy Gregory , Presley Rebecca , Jeon Hyeongseon , Moreira Lynn , Dhar Shruti , Tull Olivia , Soysal Burak , Yadati Anika S. , Cook Kayleigh D. , Schnell Laura E. , Gupta Arkobrato , Banerjee Tapahsama , Chung Dongjun , Tsichlis Philip N. , Parvin Jeffrey D.
Published: October 2024

The abundance of MHC-I on the cell surface depends on its association with antigenic peptides transported to the endoplasmic reticulum by the Transporter Associated with Antigen Processing (TAP), a peptide channel composed of TAP1 and TAP2. We functionally screened over 1400 TAP2 variants for effects on MHC-I cell surface abundance. Amino-acid substitutions of loss of function (LOF) variants clustered in the NTP-binding domain and along the TAP1-TAP2 binding interface, suggesting that these variants interfered with TAP conformational changes associated with peptide transport. Some LOF variants carried potential phosphomimetic substitutions; one such substitution at Ser251 was embedded in a sequence context consistent with the phosphorylation motif of PLK kinases. Inhibition of PLK kinases increased MHC-I surface expression, while overexpression of PLK1 in cells decreased MHC-I in wild type TAP2, but not in TAP2-S251A-expressing cells. Importantly, site-specific phosphorylation of TAP2 in human tumor samples correlated with alterations of gene expression in the cell cycle and antigen presentation pathways, consistent with the notion that phosphorylation downregulates antigenic peptide transport in human tumors. These data strongly support the hypothesis that in cancer cells, TAP2 phosphorylation by PLK1, and perhaps other kinases, can downregulate the antigen presentation process.
De novodesign of proteins that bind naphthalenediimides, powerful photooxidants with tunable photophysical properties
Authors: Mann Samuel I. , Lin Zhi , Tan Sophia K. , Zhu Jiaqi , Widel Zachary X. W. , Bakanas Ian , Mansergh Jarrett P. , Liu Rui , Kelly Mark J. S. , Wu Yibing , Wells James A. , Therien Michael J. , DeGrado William F.
Published: October 2024

De novoprotein design provides a framework to test our understanding of protein function and to build proteins with cofactors and functions not found in nature. Here, we report the design of proteins designed to bind powerful photooxidants and the evaluation of the use of these proteins to generate diffusible small molecule reactive species for applications in proximity labeling. Because excited state dynamics are influenced by the dynamics and hydration of a photo-oxidant’s environment, it was important to not only design a binding site, but also to evaluate its dynamic properties. Thus, we used computational design in conjunction with molecular dynamics (MD) simulations to design a protein, designated NBP (NDIBindingProtein) that held a naphthalenediimide (NDI), a powerful photooxidant, in a programable molecular environment. Solution NMR confirmed the structure of the complex. We evaluated two NDI cofactors in thisde novoprotein, using ultra-fast pump-probe spectroscopy to evaluate light-triggered intra- and intermolecular electron transfer function. Moreover, we demonstrated the utility of this platform to activate multiple molecular probes for protein proximity labeling.
Loss of SARM1 protects against retinal ganglion cell degeneration in Autosomal Dominant Optic Atrophy
Authors: Ding Chen , Ndiaye Papa S. , Campbell Sydney R. , Fry Michelle Y. , Gong Jincheng , Wienbar Sophia R. , Gibbs Whitney , Morquette Philippe , Chao Luke H. , Do Michael Tri H. , Schwarz Thomas L.
Published: October 2024

Autosomal Dominant Optic Atrophy (ADOA), the most prevalent inherited optic neuropathy, leads to retinal ganglion cell (RGC) degeneration and vision loss. ADOA is primarily caused by mutations in theOPA1gene, which encodes a conserved GTPase important for mitochondrial inner membrane dynamics. To date, the disease mechanism remains unclear, and no therapies are available. Here, we present a novel mouse model carrying the pathogenicOpa1R290Q/+allele that recapitulates key features of human ADOA, including mitochondrial defects, age-related RGC loss, optic nerve degeneration, and reduced RGC functions. We identify SARM1, a neurodegeneration switch, as a key driver of RGC degeneration in these mice.Sarm1knockout nearly completely suppresses all the degeneration phenotypes. Additionally, we show that SARM1 is located within the mitochondrial intermembrane space (IMS). These findings indicate that SARM1 is activated downstream of mitochondrial dysfunction in ADOA, highlighting it as a promising therapeutic target.
Creased ciliary flocks shape unfolding dynamics via information bottlenecks in an aneural animal
Authors: Brannon Charlotte M. , Prakash Manu
Published: October 2024

Multicellular organisms utilize thin sheet folding to achieve functional three-dimensional forms. During embryonic development, stereotypical epithelial folds emerge from active cellular and molecular processes including cell shape change and differential cell growth. Active thin sheet folding promises to be a powerful design technique in the fields of active solids, soft robotics, and synthetic biology. However, the general principles of active thin sheet folding remain poorly understood. Here we discover a non-canonical cilia-driven thin sheet folding behavior exhibited by basal animalTrichoplax adhaerens. Through volumetric imaging, we found that, despite having no nervous system,T. adhaerenshas the remarkable ability to resolve complex body folding states in a non-stereotypical fashion using a carpet of collectively flocking cilia. Cilia-resolved imaging revealed that folds create crease defects in the animal’s ciliary carpet, which act as information bottlenecks to break collective behavior of cilia. In turn, these bottlenecks enable the disjointed locomotion required for fold removal. These findings point to a two-way coupling mechanism, wherein ciliary activity shapes the animal’s folding state and vice versa. Our work demonstrates the broad configuration space of non-stereotypical active folding and highlights the power of distributed activity to drive folding and unfolding of a thin multicellular sheet. We anticipate our study to be a starting point for the establishment of a new class of distributed active origami wherein fold lines themselves are dynamic and motile, with implications in engineering of self-folding materials. Additionally, our work reveals a new facet of the Placozoan behavioral repertoire, which extends our understanding of mechanical intelligence in the absence of a nervous system.
Single-cell RNA-seq Reveals Early Transcriptional Programs of the Maternal to Zygote Transition in Mice and Rats
Authors: Su Yangqi , Kouranova Evguenia , Shea Jonathan , Cui Xiaoxia , Su Zhengchang
Published: October 2024

The maternal to zygote transition in mammals has been an area of intensive research over the past few decades, with an ever-changing landscape of understanding that has accompanied the rapid development of cell-profiling technology. Utilizing a full-length single cell RNA-seq protocol, we profiled mature oocytes and zygotes of mice and rats to uncover elusive transcriptomic dynamics during the maternal to zygote transition. We confirm the existence of early gene expression in the mouse zygote while revealing a similar chain of events occurring in the rat zygote. We observe an increase in nascent transcription in both species. Moreover, we find subtle but pervasive signals of differential splicing of genes related to key early zygotic activities occurring in both species. Meanwhile, we find distinct profiles of alternative polyadenylation between zygotes and oocytes in both species, particularly, in genes related to major processes within the zygotes. Finally, although a more dynamic transcriptomic landscape exists in the mouse zygote, the rat zygote also displays similar transcriptomic features, suggesting that minor zygotic activation in rat occurs earlier than originally thought.
N-Acetyl-2-Aminofluorene (AAF):In vivotemporal expression patterns of growth cycle-dependent macromolecular binding constants KD[APPARENT]and BMAX[APPARENT]are revealed by primary cultures of premalignant hepatocytes derived from a multi-cyclic hepatocarcinogenic feeding regimen
Authors: Koch K.S. , Moran T. , Sell S. , Leffert H.L.
Published: October 2024

Biochemical investigations of the hepatoprocarcinogen N-acetyl-2-aminofluorene (AAF) have shown that normal adult rat hepatocytes in primary culture express two sets of pharmacokinetic constants – designated Systems I and II, and Sites I and II – associated respectively with themetabolism(System I [high-affinity Km[APPARENT]and low-velocity VMAX[APPARENT]] and System II [low-affinity Km APPARENT]and high-velocity VMAX[APPARENT]]), and the macromolecular binding(Site I [high-affinityKD[APPARENT]and low capacityBMAX[APPARENT]] and Site II ([low-affinityKD[APPARENT]and high-capacityBMAX[APPARENT]]) of AAF. Additional findings – that genomically saturating levels of AAF-DNA adducts form far below reported extracellular AAF concentrations required to block replicative and repair DNA synthesis; and, that biphasic Site I and Site II BMAX[APPARENT]and KD[APPARENT]expression curves varied inversely with respect to time and magnitude during hepatocyte growth – led us to wonder how macromolecular binding constants are expressed during chemical hepatocarcinogenesis. These questions were addressed by Scatchard analysis measurements through five consecutive AAF feeding cycles. Notably, cultured premalignant hepatocytes displayed reduced and elevated BMAX[APPARENT]and KD[APPARENT]levels, respectively, akin to the Site I and Site II expression curves observed during hepatocyte growth transitionsin vitro. In contrast, prominent hepatocellular functions such as N-OH-AAF production, DNA replication, cell aggregation and resistance to AAF toxicity displayed different temporal trajectories.

Impact Statement

Striking similarities are observed between both Site I and Site II BMAXand KDexpression curves duringin vitroandin vivopremalignant growth transitions. These new findings fit earlier ones that hepatocytes growing during carcinogen exposure manifest fewer intranuclear AAF-DNA adducts. How this phenomenon leads to malignancy remains unclear.
The c-di-GMP effector FleQ controls alginate production by repressing transcription of thealgDgene inAzotobacter vinelandii
Authors: Barrios-Rafael Víctor V. , Ahumada-Manuel Carlos L. , Orgaz-Hidalgo Scherezada , Nava-Galeana Jessica , Guzmán Josefina , Moreno Soledad , Bustamente Victor , Núñez Cinthia
Published: October 2024

Azotobacter vinelandii, belonging to thePsedomonadaceaefamily, produces the exopolysaccharide alginate during its vegetative growth and also during its differentiation process to form desiccation resistant cysts. The second messenger c-di-GMP regulates a vast array of cellular processes. It is produced by diguanylate cyclases (DGC) and degraded by phosphodiesterases (PDE). InA. vinelandiithe absence of the AvgReg DGC impairs alginate synthesis while the absence of the PDE MucG increased alginate production. The effect of the different c-di-GMP levels was solely attributed to its essential role in activating the alginate polymerase complex. Here in we investigated the possible role of c-di-GMP in the control ofalgDtranscription, encoding the key enzyme of the alginate biosynthetic pathway. At artificially high or reduced levels of c-di-GMPalgDtranscription was increased, or almost abrogated, respectively. Therefore, the role of the transcriptional regulator FleQ, one of the best characterized c-di-GMP effectors, was investigated. Alginate production increased in the ΔfleQrelative to the wt strain, which agreed with increasedalgDtranscription. These phenotypes were rescued in the ΔfleQ/fleQ+ complemented strain indicating a FleQ repressing effect. EMSA assay showed that FleQ was able to directly bind to the regulatory region ofalgDwhich agreed with the presence of a FleQ binding site overlapping its RpoS-dependent promoter. InA. vinelandiithe c-di-GMP is also necessary for expression of alginate C-5 epimerase genes, essential for structuring mature cysts. Out data revealed that FleQ is not an intermediary in this regulation since its absence did not impair mature cyst formation nor affected expression ofalgE1-6genes. Collectively, our results support a model in which FleQ is the intermediary in the regulation ofalgDby c-di-GMP, exerting a direct repressing effect and reveal the existence of a FleQ-independent regulatory mechanism for the control ofA. vinelandiiencystment.
In silicomodelling and characterization of Epstein–Barr virus LMP1 protein
Authors: Salam Dayang-Sharyati D.A. , Juliyan Gunasinghe Kavinda Kashi , San Hwang Siaw , Henry Ginjom Irine Runnie , Wezen Xavier Chee , Rahman Taufiq
Published: October 2024

Latent membrane protein 1 (LMP1) plays a crucial role in Epstein-Barr virus (EBV)’s ability to establish latency and is involved in the development and progression of EBV-associated cancers. Additionally, EBV-infected cells affect the immune responses, making it challenging for immune system to eliminate. Due to the aforementioned reasons, it is important to understand the structural features of LMP1 which is essential for the development of novel cancer therapies that target its signaling pathways. To date, there is no complete LMP1 protein structure therefore in our work, we modeled the full-length LMP1 containing the short cytoplasmic N-terminus, six transmembrane domains and a long-simulated C-terminus. Our model showed good stability and protein compactness evaluated through accelerated-Molecular Dynamics where the conformational ensemble exhibited compact folds, particularly in the transmembrane domains. Our results suggest that specific domains or motifs, predominantly in the C-terminus domain of LMP1 show promise as potential drug targets. As a whole, our work provides insights on key strucutral features of LMP1 that will allow the development of novel LMP1 therapies.
Subendothelial Calcification Increases Surface Roughness and Promotes Lipid Deposition into the Arterial Wall
Authors: Kosciuszek Nina D. , Petrosian David , Voleti Navya , Dave Param , Kelly Ian , Moussouros Daniel , Davidov Josef , Mararenko Anton , Borges Kelly A. , Nasruddin Saud A. , Padalkar Mugdha V. , Plummer Maria M. , Millan Jose Luis , Carka Dorinamaria , Beatty Brian L. , Savinova Olga V.
Published: October 2024

Objective

We have previously demonstrated that subendothelial calcification accelerates atherosclerosis in mice. This study addresses a mechanism by which subendothelial calcifications can increase low-density lipoprotein (LDL) uptake into the arterial wall.

Methods

Mice overexpressing tissue-nonspecific alkaline phosphatase (TNAP) in endothelial cells (eTNAP mice) were used as a model of calcification. Calcification and atherosclerosis were detected by micro-computed tomography (micro-CT) and histology. The endothelial roughness was characterized by surface metrology. A fluid-structure interaction model was used to calculate wall shear stress (WSS). The uptake of fluorescent LDL was tracedin vitroandin vivo. Human arteries were assessed for the prevalence of internal elastic lamina (IEL) calcification.

Results

eTNAP mice developed more severe aortic atherosclerosis than controls on the LDL receptor mutant background (p<0.01). Subendothelial calcifications in eTNAP mice were confirmed by micro-CT. An increase in aortic surface area roughness, including the height, volume, and steepness parameters, was observed in eTNAP mice compared to controls (p<0.01). Calcifications affected near-wall hemodynamics, creating pockets of reduced WSS. Endothelial cells cultured on rough surfaces showed increased LDL uptake compared to cells cultured on smooth collagen (p<0.0001). Fluorescent LDLs were traced to subendothelial calcifications in eTNAP mice but not in controls. In humans, IEL calcification was prevalent in older adults and inversely correlated with arterial diameter (p<0.05).

Conclusion

Subendothelial calcification is sufficient to perturb near-wall hemodynamics, creating localized areas of reduced WSS, consistent with increased LDL uptake near calcified lesions. Subendothelial calcification may represent an alternative or concurrent mechanism for the initiation of atherosclerosis.

Research perspective

What is new?

We tested a novel hypothesis that subendothelial microcalcification can initiate atherosclerosis.

The study demonstrated that micron-sized subendothelial calcifications, induced by the overexpression of tissue-nonspecific alkaline phosphatase in the endothelium, are sufficient to perturb local hemodynamics, creating pockets of low wall shear stress, consistent with an increase in low-density lipoprotein uptake and deposition into the arterial wall in juxtaposition to calcified lesions.

What are the clinical implications?

We suggest that calcification of internal elastic lamina of medium-sized arteries may represent early lesions initiating atherosclerosis; however, the epidemiologic evidence for this theory is currently unavailable.
Delicate tuning of H2O2by salicylic acid, catalase 2, and AtSAP5 incites plant immunity
Authors: Chang Li , Chiu Yi-Shu , Chiang Shang-Huan , Cheng An-Po , Tzean Yuh , Yeh Hsin-Hung
Published: October 2024

Salicylic acid (SA) triggers plant immunity through redox state changes, initially oxidizing and then reducing. SA binds and inhibits the H2O2-scavenging enzyme catalase 2 (CAT2), promoting an initial oxidative state. However, a reduced state is crucial for a robust immune response. InArabidopsis, the SA-induced A20/AN1 zinc finger protein, AtSAP5, competes with SA for CAT2 binding, maintaining CAT2 activity. This reduces H2O2levels and prevents CAT2 degradation through inhibition of H2O2-induced autophagy formation, which forms a positive feedback loop to CAT2 accumulation. Consequently, cells shift to a more reduced state, activating immune responses. Our findings reveal a nuanced regulatory mechanism through which H2O2levels are controlled by SA with cross-kingdom conserved proteins AtSAP5 and CAT2, managing redox states and plant immunity.