bluuebunny/crossref_metadata_2025_split huggingface dataset:
Herbaria provide a valuable resource for obtaining informative mRNA
Authors: Tyszka Alexa S. , Chia Khong-Sam , Bretz Eric C. , Mansour Linda , Larson Drew A. , Carella Philip , Walker Joseph F. 
Published: February 2025

AbstractWhile DNA has built the framework for molecular insights from museum collections, the utility of archival RNA remains largely unexplored. Likely a consequence of the known instability of RNA relative to DNA, this has effectively nullified the use of herbaria for transcriptomics. Here, we challenge the assumption that herbaria cannot be used for transcriptomics by assembling transcriptomes from RNA extracted from herbarium specimens. Through systematic comparison of transcriptomes from fresh-collected, silica-dried, and archival specimens, we demonstrate the suitability of herbarium-derived RNA for transcriptomics. The practical applicability of archival mRNA was further illustrated by the functional validation of a plant immune receptor synthesized from a specimen collected in 1956. These results contradict the community consensus regarding archival RNA and open the door to subsequent transcriptomic explorations in rare and extinct species. Our findings highlight the importance of preserving and utilizing the diversity embedded within herbarium collections.
Lipid packing and local geometry influence septin curvature sensing
Authors: Curtis Brandy N. , Vogt Ellysa J. D. , Edelmaier Christopher , Gladfelter Amy S. 
Published: February 2025

AbstractSeptins assemble into scaffolds that direct cell growth and morphology that are often localized to the plasma membrane. While septins preferentially bind convex membranes via amphipathic helices, their assembly on varied geometries in cells suggests additional localization cues. We tested the hypothesis that lipid composition directs septin assembly through lipid packing properties. Lipid mixtures varying in lipid packing were designed by molecular dynamics simulations and incorporated onto supported lipid bilayers to measure septin adsorption in vitro. Septins strongly favor loosely-packed, disordered lipid bilayers but additional geometry cues act in conjunction with this membrane property. Introducing tighter lipid packing in cells disrupted septin structures in a curvature dependent manner, specifically limiting septin assembly and retention along flat regions of the plasma membrane. This work demonstrates that packing defects and geometry jointly regulate septin localization and highlights how multiple membrane properties are integrated to control organization of the septin cytoskeleton.SummaryLocalization of the septin cytoskeleton is controlled by regulatory factors, membrane curvature, and charge. In this study, changes to lipid composition that modulate lipid packing defects are found to impact septin assemblies in vitro and in cells.
Ribo-seq guided design of enhanced protein secretion inKomagataella phaffii
Authors: Tafrishi Aida , Alva Troy , Chartron Justin , Wheeldon Ian 
Published: February 2025

AbstractThe production of recombinant proteins requires the precise coordination of various biological processes, including protein synthesis, folding, trafficking, and secretion. The overproduction of a heterologous protein can impose various bottlenecks on these networks. Identifying and alleviating these bottlenecks can guide strain engineering efforts to enhance protein production. The methylotrophic yeastKomagataella phaffiiis used for its high capacity to produce recombinant proteins. Here, we use ribosome profiling to identify bottlenecks in protein secretion during heterologous expression of human serum albumin (HSA). Validation of this analysis showed that the knockout of non-essential genes whose gene products target the ER, through co- and post-translational mechanisms, and have high ribosome utilization can increase production of a heterologous protein, HSA. A triple knockout in co-translationally translocated carbohydrate and acetate transporter Gal2p, cell wall maintenance protein Ydr134cp, and the post-translationally translocated cell wall proteinAoa65896.1increased HSA production by 35%. This data-driven strain engineering approach uses cell-level information to identify gene targets for phenotype improvement. This specific case identifies hits and creates strains with improved HSA production, with Ribo-seq and bioinformatic analysis to identify non-essential ER targeted proteins that are high ribosome utilizers.
Defined media reveals the essential role of lipid scavenging to support cancer cell proliferation
Authors: Newsom Oliver J. , Sullivan Lucas B. 
Published: February 2025

AbstractFetal bovine serum (FBS) is a nearly ubiquitous, yet undefined additive in mammalian cell culture media whose functional contributions to promoting cell proliferation remain poorly understood. Efforts to replace serum supplementation in culture media have been hindered by an incomplete understanding of the environmental requirements fulfilled by FBS in culture. Here, we use a combination of live-cell imaging and liquid chromatography-mass spectrometry to elucidate the role of serum in supporting proliferation. We show that serum provides consumed factors that enable proliferation and demonstrate that the serum metal and lipid components are crucial to sustaining proliferation in culture. Importantly, despite access to a wide range of lipid classes, albumin-bound lipids are the primary species consumed during cancer cell proliferation. Furthermore, we find that combinations of the additive ITS, containing necessary metals, and albumin-associated lipid classes are sufficient to replace FBS in culture media. We show that serum-free media enables sensitive quantification of lipid consumption dynamics during cell proliferation, which indicate that fatty acids (FA) are consumed through a mass-action mechanism, with minimal competition from other lipid classes. Finally, we find that pharmacologic disruption of FA activation and incorporation into the cellular lipidome reduces uptake from the environment and impairs cell proliferation. This work therefore identifies metabolic contributions of serum in cell culture settings and provides a framework for building cell culture systems that sustain cell proliferation without the variable and undefined contributions of FBS.
Expression of MMP-11, an estrogen-suppressed gene in MCF-7 cells, is elevated upon acquisition of tamoxifen resistance
Authors: Sonia Ningthoujam , Mondal Sreeja , Limaye Anil Mukund 
Published: February 2025

AbstractMatrix metalloproteinase-11 (MMP-11), also known as stromelysin-3, is a member of a large family of zinc-dependent proteinases. Known to be expressed in breast tumor stroma, the epithelium, and the associated mononuclear inflammatory cells, its expression is associated with invasion, metastasis, and poor clinical outcomes and survival rates. Despite the known effects of estrogen on extracellular matrix remodeling, and breast cancer metastasis, the role of MMP-11 therein is not understood. Here, we show that estrogen suppresses MMP-11 expression in MCF-7 breast cancer cells via a mechanism that involves binding of the estrogen receptor α (ERα) to an estrogen response element located in the intron-1 of MMP-11. ERαknockdown alone upregulates MMP-11 expression, highlighting its crucial role in this regulatory axis. Additionally, the anti-estrogen tamoxifen (4-OHT) blocks estrogen-mediated MMP-11 suppression. However, prolonged 4-OHT exposure or 4-OHT resistance leads to increased MMP-11 expression. This suggests that MMP-11 may play a role in 4-OHT resistance, potentially leading to a more aggressive tumor phenotype. Our study underscores the importance of estrogen-ERαsignaling in breast cancer progression, emphasizing the need for further investigation into MMP-11’s role in 4-OHT resistance and cancer metastasis.
Laboratory yeast strains are highly diverse in lipid metabolism
Authors: Renne Mike F. , Bachmann Richard , Klose Christian , Hentrich Thomas , Schulze-Hentrich Julia M. , Ernst Robert 
Published: February 2025

AbstractThe impact of the genetic background on the lipidome of yeast strains remains underexplored. This study systematically compares the lipidomes of five commonly used laboratory yeast strains: BY4741, W303, D273-10B, RM11-1a, and CEN.PK2-1c. Shotgun lipidomics reveals significant variations in lipid class and acyl chain composition down to the level of molecular species. Notably, the most abundant lipid class differed between the strains: phosphatidylinositol (PI) lipids are predominant in BY4741, while phosphatidylethanolamine (PE) lipids are in D273. Ergosterol esters, which are the storage form of the major yeast sterol ergosterol, are at higher levels in all strains other than BY4741, correlating with a low gene expression of lipid metabolic enzymes Hmg1 and Are2 in BY4741. Despite these lipidomic differences, transcriptomic analysis did not show significant changes in most genes related to lipid metabolism, suggesting post-transcriptional modifications, protein abundance, and metabolic flux as potential regulatory mechanisms. This study underscores the complexity of lipidome regulation and the need for further investigation into the underlying mechanisms.
Predicting hybrid fitness: the effects of ploidy and complex ancestry
Authors: Schneemann Hilde , Welch John J. 
Published: February 2025

AbstractHybridization between divergent populations places alleles in novel genomic contexts. This can inject adaptive variation – which is useful for breeders and conservationists – or reduce fitness, leading to reproductive isolation. Most theoretical work on hybrids involves haploid or diploid hybrids between two parental lineages, but real-world hybridization is often more complex. We introduce a simple fitness landscape model to predict hybrid fitness with arbitrary ploidy and an arbitrary number of hybridizing lineages. We test our model on published data from maize (Zea mays) and rye (Secale cereale), including hybrids between multiple inbred lines, both as diploids and synthetic tetraploids. Quantitative predictions for the effects of inbreeding, and the strength of progressive heterosis, are well supported. This suggests that the model captures the important properties of dosage and genetic interactions, and may help to unify theories of heterosis and reproductive isolation.
Non-Canonical Role of DNA Mismatch Repair on Sensory Processing in Mice
Authors: Rahman Sadia N. , Neophytou Demetrios , Oviedo-Gray Siboney , Vuong Bao Q. , Oviedo Hysell V. 
Published: February 2025

AbstractDNA repair mechanisms are essential for cellular development and function. This is particularly true in post-mitotic neurons, where deficiencies in DNA damage response proteins can result in severe neurodegenerative and neurodevelopmental disorders. One highly conserved factor involved in DNA repair is Mut-S Homolog 2 (Msh2), which is responsible for correcting base-base mismatches and insertion/deletion loops during cell proliferation. However, its role in mature neuronal function remains poorly understood. This study investigates the impact ofMsh2loss on sensory processing in a mouse model. Using electrophysiological and molecular assays, we identified significant deficits in cortical and thalamic sound processing inMsh2-/-mice. These deficits were linked to dysfunction of the thalamic reticular nucleus (TRN), a brain region that critically regulates corticothalamic and thalamocortical activity. Our findings revealed increased oxidative damage, aberrant neuronal activity, and elevated parvalbumin (PV) expression in PV+interneurons in the TRN ofMsh2-/-mice. Additionally, we observed the presence of connexin plaques, indicating that disrupted gap junction formation may contribute to impaired TRN function. These results underscore the critical role ofMsh2in supporting the functionality of PV+interneurons in the TRN, thereby profoundly influencing sensory processing pathways. This study provides new insights into the importance of DNA repair mechanisms in neuronal development and function, potentially contributing to our understanding of their role in neurological disorders.
Planetary-scale marine community modeling predicts metabolic synergy and viral impacts
Authors: Régimbeau A. , Tian F. , Smith G. , Riddell J. , Andreani C. , Bordron P. , Budinich M. , Howard-Varona C. , Larhlimi A. , Ser-Giacomi E. , Trottier C. , Guidi L. , Hallam S.J. , Iudicone D. , Karsenti E. , Maass A. , Sullivan M.B. , Eveillard D. 
Published: February 2025

AbstractThe oceans buffer against climate change via biogeochemical cycles underpinned by microbial metabolic networks. While planetary-scale surveys provide baseline microbiome data, inferring metabolic and biogeochemical impacts remains challenging. Here, we constructed a metabolic model for each TARA Ocean metagenome or metatranscriptome, quantified the importance of each metabolic reaction, and used this to assess planetary-scale heterotrophic prokaryotic metabolic phenotypes as a proxy for marine biogeochemistry. This revealed metabolism-inferred ecological zones that matched taxonomy- and function-inferred ones, connections between microbial metabolism and diversity, and predictions about long-sought virus ecological roles, including that virus-encoded metabolic genes target important reactions and identify viral shunt- or shuttle-enriched ocean regions. Together, this framework is agile and resolves planetary-scale community metabolic features to better incorporate microbes and viruses into future predictive ecosystem and climate models.
Identifying a logical specification and a program for an LLM-based generator of lead molecules
Authors: Srinivasan Ashwin , Dash Tirtharaj , Baskar A , Dey Sanjay Kumar , Banerjee Mainak 
Published: February 2025

AbstractOur interest is in the generation of “lead” molecules in early-stage drug design. Leads are small molecules (ligands) that can bind to a part of pre-specified target and also satisfy multiple physico-chemical constraints. We propose using techniques developed in Inductive Logic Programming (ILP) to identify a logical specification of feasible molecules; and then using this specification to construct a program that uses a large language model (LLM) to generate new molecules. We ensure the program constructed is correct, in the sense that every molecule generated by the program is feasible according the specification. Our focus is on contributing to on-going drug-discovery research on novel inhibitors for Dopamineβ-hydroxylase (DBH), an enzyme that plays a pivotal role in several diseases related to the brain and the heart. We find molecules comparable in affinity to the latest generation drugs currently in clinical trials, and chemical assessment of synthesisablity of the molecules generated. For completeness, we also provide results obtained on the classic benchmark datasets used in recent work reported in [1].
Recombination and retroprocessing in broomrapes reveal a universal roadmap for mitochondrial evolution in heterotrophic plants
Authors: Cai Liming , Havird Justin C , Jansen Robert K 
Published: February 2025

ABSTRACTThe altered life history strategies of heterotrophic organisms often leave a profound genetic footprint on energy metabolism related functions. In parasitic plants, the reliance on host-derived nutrients and loss of photosynthesis in holoparasites have led to highly degraded to absent plastid genomes, but its impact on mitochondrial genome (mitogenome) evolution has remained controversial. By examining mitogenomes from 45 Orobanchaceae species including three independent transitions to holoparasitism and key evolutionary intermediates, we identified measurable and predictable genetic alterations in genomic shuffling, RNA editing, and intracellular (IGT) and horizontal gene transfer (HGT) en route to a nonphotosynthetic lifestyle. In-depth comparative analyses revealed DNA recombination and repair processes, especially RNA-mediated retroprocessing, as significant drivers for genome structure evolution. In particular, we identified a novel RNA-mediated IGT and HGT mechanism, which has not been demonstrated in cross-species and inter-organelle transfers. Based on this, we propose a generalized dosage effect mechanism to explain the biased transferability of plastid DNA to mitochondria across green plants, especially in heterotrophic lineages like parasites and mycoheterotrophs. Evolutionary rates scaled with these genomic changes, but the direction and strength of selection varied substantially among genes and clades, resulting in high contingency in mitochondrial genome evolution. Finally, we describe a universal roadmap for mitochondrial evolution in heterotrophic plants where increased recombination and repair activities, rather than relaxed selection alone, lead to differentiated genome structure compared to free-living species.
A Potent Nonapeptide Inhibitor for the CXCL12/HMGB1 heterocomplex: A Computational and Experimental Approach
Authors: Fassi Enrico Mario Alessandro , Pirani Edisa , Cecchinato Valentina , Cavalli Andrea , Roda Gabriella , Uguccioni Mariagrazia , Sgrignani Jacopo , Grazioso Giovanni 
Published: February 2025

AbstractInflammation is a vital defense mechanism activated in response to injury or infection, which induces the release of cytokines and chemokines to promote tissue repair. However, persistent inflammation may result in the development of autoimmune diseases.During pathological conditions such as rheumatoid arthritis, HMGB1 is kept in its reduced isoform and can complex with CXCL12 enhancing cell migration and exacerbating the immune responses. Small organic compounds selective for HMGB1 have been previously reported to be able to disrupt the CXCL12/HMGB1 heterocomplex, but due to their low affinity, they are unsuitable for further development as novel anti-inflammatory drugs.We previously reported a peptide (HBP08) that binds to HMGB1 with high affinity (Kd= 0.8 µM), and blocks the activity of the heterocomplex, in line with a wide literature that supports the use of peptides to design protein-protein interaction inhibitors. In the present work, we computationally optimized the HBP08 peptide sequence, finding new analogues endowed with improved affinity for HMGB1. In particular, HBP08-2 inhibited the activity of the CXCL12/HMGB1 heterocomplex with an IC5010-fold lower (3.31 µM) and displayed a Kd28-fold lower (28.1 ± 7.0 nM) than the parent peptide HBP08.
Molecular Mechanisms Limiting the Therapeutic Window of AAV Gene Therapy in Mouse Models of Blue Cone Monochromacy
Authors: Brothers Brooke A. , Sechrest Emily R. , Ma Li , Ashcraft Madyson , Guan Tongju , Barbera Robert J. , Cahill Marion E. , Shaw Lee M. , Chen Becky , Baehr Wolfgang , Hu Gangqing , Stoilov Peter , Deng Wen-Tao 
Published: February 2025

ABSTRACTBlue cone monochromacy (BCM) is an X-linked retinal disorder caused by mutations in theOPN1LW/OPN1MWgene locus, resulting in impaired cone function and structural degeneration. We conducted a comparative analysis of AAV-mediated gene therapy inOpn1lw/Opn1mwdouble knockout (DKO) andOpn1mwC198R/Opn1sw-/-(C198R) BCM mouse models and evaluated the therapeutic window, efficacy, and longevity. Our results demonstrate that the AAV8-Y733F capsid achieved superior cone rescue compared to AAV5. While both DKO and C198R models showed similar therapeutic windows and rescue longevity, treatment efficacy decreased markedly in older mutant mice. Structural analysis revealed that aged cones in both models displayed degenerative changes, including mislocalized mitochondria and compromised connecting cilia. At the molecular level, we observed reduced AAV-mediated transgene expression in DKO and C198R older cones, which may result from decreased transduction efficiency, decreased circular episome stability, genome-wide transcription/translation downregulation, targeted mRNA/protein degradation, or overall cone degeneration. Notably, the cone-specific promoters forPde6candCngb3maintained robust activity in degenerating cones. These findings suggest that combining an efficient AAV serotype with an optimized cone promoter could be a viable approach to extend the therapeutic window and enhance treatment longevity for BCM patients.
cxcl18b-defined transitional state-specific nitric oxide drives injury-induced Müller glia cell-cycle re-entry in the zebrafish retina
Authors: Ye Aojun , Yu Shuguang , Du Meng , Zhou Dongming , He Jie , Chen Chang 
Published: February 2025

AbstractIn lower vertebrates, retinal Müller glia (MG) exhibit a life-long capacity of cell-cycle re-entry to regenerate neurons following the retinal injury. However, the mechanism driving such injury-induced MG cell-cycle re-entry remains incompletely understood. Combining single-cell transcriptomic analysis andin-vivoclonal analysis, we identified previously undescribedcxcl18b-defined MG transitional states as essential routes towards MG proliferation following green/red cone (G/R cone) ablation. Microglial inflammation was necessary for triggering these transitional states, which expressed the gene modules shared by cells of the ciliary marginal zone (CMZ) where life-long adult neurogenesis takes place. Functional studies of the redox properties of these transitional states further demonstrated the regulatory role of nitric oxide (NO) produced byNos2bin injury-induced MG proliferation. Finally, we developed a viral-based strategy to specifically disruptnos2bincxcl18b-defined MG transitional states and revealed the effect of transitional state-specific NO signaling. Our findings elucidate the redox-related mechanism underlying injury-induced MG cell-cycle re-entry, providing insights into species-specific mechanisms for vertebrate retina regeneration.
Predicting Non-Covalent Interactions Between Antioxidants In Biological Membranes Through Molecular Dynamics
Authors: Martin Marving , Chantemargue Benjamin , Fabre Gabin , Gierschner Johannes , Trouillas Patrick 
Published: February 2025

AbstractThe synergistic association of different polyphenols has gained much interest in the food industry to develop efficient antioxidant cocktails, reducing the concentration of active agents and subsequently potential toxicity. The theoretical description and prediction of such processes is of central interest in this development. This study aims at benchmarking the performance of molecular dynamics (MD) to predict the formation of non-covalent complexes between π-conjugated antioxidants, including two prototypes (quercetin and vitamin E), in a pure 1,2-dipalmitoylphosphatidylcholine (DOPC) lipid bilayer. To reproduce the experimentally observed quenching of vitamin E fluorescence by quercetin, a sphere-of-action quenching model was applied. The predictive capability of MD simulations at capturing this non-covalent association was evaluated with five other π-conjugated potential partners of vitamin E, namely catechin, caffeic acid, myricetin, kaempferol, and galangin. The observed trend agreed with experimental studies, validating again the use of MD simulations as a tool to measure the potential synergism between natural antioxidants.