bluuebunny/crossref_metadata_2025_split huggingface dataset:
PyPE_RESP: A tool to facilitate and standardize derivation of RESP charges
Authors: Lapsien Marco , Bonus Michele , Gahan Lianne , Raguin Adélaïde , Gohlke Holger 
Published: January 2025

We introduce PyPE_RESP, a tool to facilitate and standardize partial atomic charge derivation using the RESP approach. PyPE_RESP builds upon the open-source Python package RDKit for chemoinformatics and the AMBER suite for molecular simulations. PyPE_RESP provides an easy setup of multi-conformer and multi-molecule Restrained Electrostatic Potential (RESP) fitting while allowing a comprehensive definition of charge constraint groups through multiple methods. As a command line tool, PyPE_RESP can be integrated into batch processes. The software enables the derivation of partial atomic charges for additive and polarizable force fields. It outputs constraint group and non-constraint group charges to give an immediate overview of the fit result. PyPE_RESP will be distributed with AmberTools and compatible with most computing platforms.Table of Contents Graphic
Redox homeostasis in ferroptosis and aging: a causal role forfard-1anddhs-25inCaenorhabditis elegans
Authors: Pensotti Roberta , Sciandrone Barbara , Bovio Federica , Schröter Laura , Maglioni Silvia , Thewes Leonie , Forcella Matilde Emma , Fusi Paola Alessandra , Rossi Andrea , Berndt Carsten , Ventura Natascia , Regonesi Maria Elena 
Published: January 2025

ABSTRACTAging is a natural process characterized by a progressive physiological decline that undermines health and well-being in the elderly population. It is widely accepted that an unbalanced redox state belongs to the hallmarks of aging, but its role as one of the main drivers of ferroptosis is quite recent. Ferroptosis is a form of iron-dependent cell death caused by massive phospholipid peroxidation. The excessive accumulation of intracellular reactive oxygen species and iron, as well as the failure of the main cellular antioxidant systems, cause ferroptotic cell death. While clear roles for ferroptosis in pathological conditions such as cancer or neurodegeneration have been described, its physiological roles and regulators are less clearly understood.Here, usingCaenorhabditis elegansas a powerful model organism for aging studies, we uncover a role for ferroptosis in physiological aging mediated by disturbed redox homeostasis. We evaluated healthspan parameters in aC. eleganswild-type strain highlighting how several age-related features differentially decline during aging. A progressive loss of the capability to contrast external stressors, with an increase in hydroxyl radicals and a failure of the glutathione antioxidant system demonstrated the progressive disruption of redox homeostasis in older age. Moreover, we showed that selected genes involved in redox metabolism are downregulated with aging. Among them, mutant strains of the fatty acyl-CoA reductase,fard-1, and of the dehydrogenase,dhs-25, displayed higher sensitivity to a ferroptosis inducer, increased lipid peroxidation, anticipated drop in total glutathione and reduced lifespan. Accordingly, the expression of one of the closest mammaliansdhs-25homolog, the hydroxysteroid 17-Beta Dehydrogenase 8, was downregulated in cells which are more sensitive to ferroptosis.Our results clearly prove a causal role for ferroptosis inC. elegansaging driven by oxidative stress, unveiling novel genes involved in this connection that may constitute targets for possible interventions to improve healthy aging.
Improving functional protein generation via foundation model-derived latent space likelihood optimization
Authors: Guan Changge , Wan Fangping , Torres Marcelo D. T. , de la Fuente-Nunez Cesar 
Published: January 2025

AbstractA variety of deep generative models have been adopted to performde novofunctional protein generation. Compared to 3D protein design, sequence-based generation methods, which aim to generate amino acid sequences with desired functions, remain a major approach for functional protein generation due to the abundance and quality of protein sequence data, as well as the relatively low modeling complexity for training. Although these models are typically trained to match protein sequences from the training data, exact matching of every amino acid is not always essential. Certain amino acid changes (e.g., mismatches, insertions, and deletions) may not necessarily lead to functional changes. This suggests that maximizing the training data likelihood beyond the amino acid sequence space could yield better generative models. Pre-trained protein large language models (PLMs) like ESM2 can encode protein sequences into a latent space, potentially serving as functional validators. We propose training functional protein sequence generative models by simultaneously optimizing the likelihood of training data in both the amino acid sequence space and the latent space derived from a PLM. This training scheme can also be viewed as a knowledge distillation approach that dynamically re-weights samples during training. We applied our method to train GPT- like models (i.e., autoregressive transformers) for antimicrobial peptide (AMP) and malate dehydrogenase (MDH) generation tasks. Computational experiments confirmed that our method outperformed various deep generative models (e.g., generative adversarial net, variational autoencoder, and GPT model without the proposed training strategy) on these tasks, demonstrating the effectiveness of our multi-likelihood optimization strategy.
Rational Design and Optimization of a Potent IDO1 Proteolysis Targeting Chimera (PROTAC)
Authors: Monsen Paige J. , Bommi Prashant V. , Grigorescu Arabela A. , Lauing Kristen L. , Mao Yingyu , Berardi Payton , Zhai Lijie , Ojo Oluwatomilayo , Penco-Campillo Manon , Koch Taylor , Egozi Michael , Jha Sonam V. , Dunne Sara F. , Jiang Hong , Song Guiqin , Zhang Fang , Kregel Steven , Vaziri-Gohar Ali , Fanning Sean , Sanchez-Gomez Pilar , Allen Jacob M. , Yamini Bakhtiar , Lukas Rimas V. , Wainwright Derek A. , Schiltz Gary E. 
Published: January 2025

ABSTRACTIndoleamine 2,3-dioxygenase 1 (IDO1) is a potently immunosuppressive protein that inhibits antitumor immunity through both tryptophan metabolism and non-enzymatic functions. Pharmacological therapies targeting IDO1 enzyme activity have generally failed to improve the overall survival of patients with cancer. Developing new therapeutic agents that are capable of neutralizing both enzyme-and non-enzyme-derived immunosuppressive IDO1 effects is therefore of high interest. We previously described the development of a novel Proteolysis Targeting Chimera (PROTAC), NU223612, that degrades IDO1 in cultured human glioblastoma (GBM) cells, as well as in well-established brain tumors,in vivo. In this study, we rationally optimized the composition, rigidity, and linker orientation of the PROTAC structure to create NU227326, which degrades IDO1 with a DC50of 5 nM in human GBM cells. Mechanistic studies showed that IDO1 degradation occurred through the ubiquitin-proteasome system and was sustained for at least 2 days, supporting NU227326 as a highly potent IDO1 PROTAC suitable for further studies in GBM and other human cancers.
Morphological responses of a temperate salt marsh foraminifer,Haynesinasp., to coastal acidification
Authors: Powers Chris , Paz Alberto , Zyck Amaelia , Harri Kaylee , Geraci Madison , Bernhard Joan M. , Zhang Ying 
Published: January 2025

AbstractCoastal acidification leads to widespread impacts on calcifying organisms across the world’s oceans, which could result in decreased calcium carbonate deposition and the dissolution of calcium carbonate. As an abundant group of calcifying organisms, some protists within the phylum Foraminifera demonstrate potential success under elevated partial pressure of carbon dioxide (pCO2) due to their ability to modulate intracellular pH. However, little is known about their responses under more extreme acidification conditions that are already seen in certain coastal environments. Here we exposedHaynesina, a foraminiferal genus that is prevalent in temperate coastal salt marshes, to moderate (pCO2= 2386.05+/-97.14 μatm) and high acidification (pCO2= 4797.64+/-157.82 μatm) conditions through the duration of 28 days. We demonstrate that although this species is capable of withstanding moderate levels of coastal acidification with little impact on their overall test thickness, they could experience deposition deficiency and even dissolution of the calcareous test under highly elevatedpCO2. Interestingly, such a deficit was primarily seen among live foraminifera, as compared to dead specimens, throughout the four-week experiment. We propose that a combination of environmental stress and the physiological process of test formation (i.e., calcite precipitation) could induce thinning of the test surface. Therefore, with the acceleration of coastal acidification due to anthropogenic production of CO2, benthic foraminifera amongst coastal ecosystems could reach a tipping point that leads to thinning and dissolution of their calcareous tests, which in turn, will impair their ecological function as a carbon sink.ImportanceThe calcareous foraminifera protists are responsible for large proportions of calcium carbonate production across the global ocean. Their responses to ocean and coastal acidification are essential for understanding carbon and mineral cycling in diverse marine ecosystems. However, relatively few studies have examined more extreme conditions related to what is seen in coastal habitats (e.g.pCO2> 2,500 μatm), and the response of individual test chambers have never been inspected. Here, we consider the response ofHaynesinasp., a benthic foraminifera obtained from temperate coastal sediments to moderate and high acidification regimes. Comparison of test thicknesses across treatment conditions and among individual chambers ofHaynesinasp. revealed potential tolerance under moderate acidification but demonstrated impaired new chamber formation and test dissolution under high acidification. Our results suggest that with growing anthropogenic CO2production, foraminifera could reach a tipping point that leaves their ecological function as a carbon sink at greater risk.
TGFBR2Highmesenchymal glioma stem cells phenocopy regulatory T cells to suppress CD4+ and CD8+ T cell function
Authors: Johnson Amanda L , Khela Harmon S. , Korleski Jack , Sall Sophie , Li Yunqing , Zhou Weiqiang , Smith-Connor Karen , Lopez-Bertoni Hernando , Laterra John 
Published: January 2025

AbstractAttempts to activate an anti-tumor immune response in glioblastoma (GBM) have been met with many challenges due to its inherently immunosuppressive tumor microenvironment. The degree and mechanisms by which molecularly and phenotypically diverse tumor-propagating glioma stem cells (GSCs) contribute to this state are poorly defined. In this study, our multifaceted approach combining bioinformatics analyses of clinical and experimental datasets, single-cell sequencing, and molecular and pharmacologic manipulation of patient-derived cells identified GSCs expressing immunosuppressive effectors mimicking regulatory T cells (Tregs). We show that thisImmunosuppressiveTreg-Like (ITL) GSC state is specific to the mesenchymal GSC subset and is associated with and driven specifically by TGF-β type II receptor (TGFBR2) in contrast to TGFBR1. Transgenic TGFBR2 expression in patient-derived GBM neurospheres promoted a mesenchymal transition and induced a 6-gene ITL signature consisting of CD274 (PD-L1), NT5E (CD73), ENTPD1 (CD39), LGALS1 (galectin-1), PDCD1LG2 (PD-L2), and TGFB1. This TGFBR2-driven ITL signature was identified in clinical GBM specimens, patient-derived GSCs and systemic mesenchymal malignancies. TGFBR2HighGSCs inhibited CD4+ and CD8+ T cell viability and their capacity to kill GBM cells, effects reversed by pharmacologic and shRNA-based TGFBR2 inhibition. Collectively, our data identify an immunosuppressive GSC state that is TGFBR2-dependent and susceptible to TGFBR2-targeted therapeutics.
Cullin-RING ligase BioE3 reveals molecular-glue-induced neosubstrates and rewiring of the endogenous Cereblon ubiquitome
Authors: Merino-Cacho Laura , Barroso-Gomila Orhi , Pozo-Rodríguez Mónica , Muratore Veronica , Guinea-Pérez Claudia , Serrano Álvaro , Pérez Coralia , Cano-López Sandra , Urcullu Ainhoa , Azkargorta Mikel , Iloro Ibon , Galdeano Carles , Juárez-Jiménez Jordi , Mayor Ugo , Elortza Felix , Barrio Rosa , Sutherland James D. 
Published: January 2025

AbstractBackgroundThe specificity of the ubiquitination process is mediated by the E3 ligases. Discriminating genuine substrates of E3s from mere interacting proteins is one of the major challenges in the field. We previously developed BioE3, a biotin-based approach that uses BirA-E3 fusions together with ubiquitin fused to a low-affinity AviTag to obtain a site-specific and proximity-dependent biotinylation of the substrates. We proved the suitability of BioE3 to identify targets of RING and HECT-type E3 ligases.MethodsBioE3 experiments were performed in HEK293FT and U2OS stable cell lines expressing TRIPZ-bioGEFUb transiently transfected with BirA-cereblon (CRBN). Cells were seeded using biotin-free media, adding a short-biotin pulse. We evaluated the applicability of the BioE3 system to CRBN and molecular glues by western blot and confocal microscopy, blocking the proteasome with bortezomib, inhibiting NEDDylation with MLN4924 and treating the cells with pomalidomide. For the identification of endogenous substrates and neosubstrates we analyzed the eluates of streptavidin pull-downs of BioE3 experiments by LC-MS/MS. Analysis of targets which ubiquitination changes significantly upon treatment was done using two-sided Student’s t-test. Orthogonal validations were performed by histidine pull-down, GFP-trap and computational modelling.ResultsHere we demonstrate that BioE3 is suitable for the multi-protein complex Cullin-RING E3s ligases (CRLs), the most utilized by targeted protein degradation strategies. Choosing CRBN as proof of concept, one of the substrate receptors of CRL4 E3 ligase, we identified both endogenous substrates and novel neosubstrates upon pomalidomide treatment, including CSDE1 which contains a G-loop motif potentially involved in the binding to CRBN in presence of pomalidomide. Importantly, we observed a major rearrangement of the endogenous ubiquitination landscape upon treatment with this molecular glue.ConclusionsThe ability of BioE3 to detect and compare both substrates and neosubstrates, as well as how substrates change in response to treatments, will facilitate both target and off-target identifications and offer a broader characterization and validation of targeted protein degradation degraders, like molecular glues and PROTACs.
KilR ofE. coliRac prophage is a dual morphogenetic inhibitor of bacterial cell shape
Authors: Marepalli Anusha , Nandhakumar Muruganandam , Govindarajan Sutharsan 
Published: January 2025

ABSTRACTBacterial cryptic prophages encode genes that reduce the viability of the host, upon induction, but also contribute to host survival during stress conditions. Rac is a cryptic prophage ofEscherichia coliand it encodes a toxic protein KilR which causes morphological defects to the host. But the mechanistic basis of its action is not well understood. In this study, we provide evidence that KilR is a dual morphogenetic inhibitor that affects cell division and cytoskeletal organization. We show that KilR expression is highly toxic, as demonstrated previously, and its predicted C-terminal unstructured region plays a crucial role in its function via a length-dependent manner. Low levels of KilR expression lead to cell filamentation and disruption of Z-rings, while high levels result in rod-shaped defects and mislocalization of the MreB cytoskeletal protein. Using fluorescent fusions, we observed that KilR is diffusively localized in the cytoplasm. When MreBCD proteins are overexpressed, KilR co-localizes with them, forming membrane-associated filaments, indicating a physical association. However, overexpressed MreBCD proteins does not alleviate the KilR-associated growth defect, unlike FtsZ. Finally, we present evidence that chromosomal KilR contributes to the co-inhibition of FtsZ and MreB localization in response to oxidative stress. Our data indicate that KilR inhibits MreB-associated cytoskeletal system, in addition to its effect on FtsZ-associated cell division system. We propose that dual inhibition activity of KilR contributes to its high level of toxicity and to its function in SOS-independent DNA damage tolerance during oxidative stress.IMPORTANCEKilR is a Rac cryptic prophage encoded toxic protein which contributes to host survival during oxidative stress conditions. It is known to inhibit cell division by targeting the tubulin homolog, FtsZ. In this study, we show that KilR is a dual morphogenetic inhibitor that affects FtsZ-mediated cell division and MreB-mediated cell elongation. Simultaneous inhibition of cell division and cell elongation are known to be crucial for bacterial survival during stress conditions like oxidative stress. Our study identifies KilR as a dual morphogenetic inhibitor, offering insights into how bacterial-phage coevolution drives the emergence of cryptic prophage elements, with specific genes enhancing bacterial fitness.
CSDE1 regulates miR-20a-5p/ TMBIM6 axis in melanoma
Authors: Ramakrishna Sushmitha , Guitart Tanit , Gebauer Fatima , Kakumani Pavan Kumar 
Published: January 2025

ABSTRACTRNA-binding proteins (RBPs) and microRNAs (miRNAs) play crucial roles in regulating gene expression at the post-transcriptional level in tumorigenesis. They primarily target the 3′UTRs of mRNAs to control their translation and stability. However, their co-regulatory effects on specific mRNAs in the pathogenesis of particular cancers are yet to be fully explored. CSDE1 is an RBP that promotes melanoma metastasis, and the mechanisms underlying its function in melanoma development are yet to be fully understood. In the current study, we report that CSDE1 enhances TMBIM6 protein expression without altering its mRNA levels in melanoma cells, indicating post-transcriptional regulation. CSDE1 and AGO2 competitively bind to TMBIM6 mRNA, and we identify miR-20-5p, which represses TMBIM6 expression, regulates the binding of CSDE1 to TMBIM6 mRNA. Further, the RNA-binding mutant of CSDE1 foregoes its competitive binding to the mRNA, allowing AGO2-mediated silencing of TMBIM6 expression. Our study highlights the pivotal role of CSDE1 in regulating miR-20a-5p function and the expression of TMBIM6 in melanoma cells, thus unveiling the potential of therapeutic strategies targeting this regulatory pathway in treating malignant skin cancers.
Probabilities of finding trace profile donors and their paternal relatives in Y-STR reference databases
Authors: Olsen Tóra Oluffa Stenberg , Morling Niels , Eriksen Poul Svante , Kampmann Marie-Louise , Mogensen Helle Smidt , Andersen Mikkel Meyer 
Published: January 2025

AbstractForensic investigative genetic genealogy using Y-chromosome short tandem repeat (Y-STR) DNA profiles can give investigative leads in criminal cases by searching for the Y-STR trace profile or similar but not identical Y-STR profiles in relevant Y-STR databases. We conducted a simulation study with Yfiler™Plus and PowerPlex®Y23 Y-STR profiles to estimate the probabilities of finding matches and near-matches in Y-STR databases. The success rate of finding the trace profile donors or their close relatives was quantified. We used the malan R software package to simulate the populations based on the Wright-Fisher model with the YHRD Y-STR mutation rates where uncertainties were incorporated in a Bayesian manner, a variance in reproductive success of 0.2, and a constant size for 100 generations followed by a 2% growth for 150 generations. Y-STR databases were generated by randomly drawing Y-STR profiles from a Yfiler™Plus and PowerPlex®Y23 Y-STR population data set, respectively.In a population of 500,066 individuals, a database size of 0.5% of the population resulted in a Y-STR database match probability of ca. 6% and 10% for Yfiler™Plus and PowerPlex®Y23, respectively. Increasing the database size to 5% of the population resulted in a Y-STR match probability of ca. 41% and 54% for Yfiler™Plus and PowerPlex®Y23, respectively. When a Y-STR match was found in the database, the probability of one of the individuals with the matching profiles being related within five meioses to the trace donor was ca. 64% and 56% for Yfiler™Plus and PowerPlex®Y23, respectively, including the cases where the Y-STR profile originated from the donor. In this case, the closest relative in the database was found among the matching individuals with a probability of ca. 91%.
Assessing the inference of single-cell phylogenies and population dynamics from genetic lineage tracing data
Authors: Pilarski Julia , Stadler Tanja , Seidel Sophie 
Published: January 2025

AbstractBackgroundMulticellular organisms develop from a single cell by repeated rounds of cell division, differentiation and apoptosis, which can be displayed in a single-cell phylogenetic tree. Genetic lineage tracing allows us to investigate this development by tracking the ancestry of individual cells as populations grow and change over time. However, accurate reconstruction of the cell phylogeny and quantification of the corresponding phylodynamic parameters - division, differentiation and apoptosis rate - from this tracking data remains challenging and needs to be systematically evaluated.ResultsWe perform simulations and assess, using the Bayesian framework, the joint inference of time-scaled cell phylogenies and phylodynamic parameters from CRISPR lineage recordings with random or sequential edits. Principally, we characterize the inference improvement as the recorder capacity increases. Further, we characterize the increase of accuracy of phylogenetic reconstruction when using sequential compared to random recordings, i.e. when using the additional information contained in the order of edits. Moreover, we find that CRISPR lineage recordings carry a strong signal on the rates of cell division. When the phylodynamic parameters are inferred under models that match the true dynamics and when sufficiently many cells of each type are sampled, also cell death and differentiation rates can be estimated from the data.ConclusionIn this study, we evaluate how much information on cellular development can be extracted from genetic lineage tracing data using phylogenetic and phylodynamic methodology. We identify important experimental, conceptual, and computational limitations for the inference which can guide future advancements in the field.
Single-cell sequencing reveals psilocybin induces sustained cell-type specific plasticity in mouse medial prefrontal cortex
Authors: Zhou Delong , Schuler Heike , Cvetkovska Vedrana , Meccia Juliet , Harutyunyan Ashot S. , Ragoussis Jiannis , Bagot Rosemary C. 
Published: January 2025

SUMMARYThe ever-increasing burden of psychiatric disorders and limitations of current treatments have fueled enormous interest in the therapeutic potential of psychedelics. Yet how psychedelics, such as psilocybin, produce lasting therapeutic effects is unclear. Using scRNA-sequencing we identify a type of deep layer near projecting neuron that is most robustly regulated in the medial prefrontal cortex of female mice 24h after psilocybin. We show that this cell-type specificity does not align with 5-HT2Areceptor expression but is consistent with the integrated signaling via cell-type specific 5-HT receptor co-expression patterns. Cell-cell communication reveals that psilocybin also broadly suppresses GABAergic inhibition. Ultimately, psilocybin induces plasticity-related genes in subsets of excitatory neurons suggesting that psilocybin induces sustained increases in neuroplasticity in the mouse mPFC. Our findings point to L5/6NP neurons as a key mediator of psilocybin’s neuroplastic effects.