bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microsecond Molecular Dynamics Simulations and Markov State Models of Mutation-Induced Allosteric Mechanisms for the Light-Oxygen-Voltage 2 Protein : Revealing Structural Basis of Signal Transmission Induced by Photoactivation of the Light Protein State
Authors: Xiao Sian , Ibrahim Mayar Tarek , Verkhivker Gennady M. , Zoltowski Brian D. , Tao Peng 
Published: December 2023

AbstractAvena Sativa phototropin 1 Light-oxygen-voltage 2 domain (AsLOV2) is the model protein of Per-Arnt-Sim (PAS) superfamily, characterized by conformational changes in response to external environmental stimuli. This conformational change is initiated by the unfolding of the N-terminal helix in the dark state followed by the unfolding of the C-terminal helix. The light state is defined by the unfolded termini and the subsequent modifications in hydrogen bond patterns. In this photoreceptor, β-sheets have been identified as crucial components for mediating allosteric signal transmission between the two termini. In this study, we combined microsecond all-atm molecular dynamics simulations and Markov state modeling of conformational states to quantify molecular basis of mutation-induced allostery in the AsLOV2 protein. Through a combination of computational investigations, we determine that the Hβ and Iβ strands are the most critical structural elements involved in the allosteric mechanism. To elucidate the role of these β-sheets, we introduced 13 distinct mutations (F490L, N492A, L493A, F494L, H495L, L496F, Q497A, R500A, F509L, Q513A, L514A, D515V, and T517V) and conducted comprehensive simulation analysis. The results highlighted the role of two hydrogen bond Asn482-Leu453 and Gln479-Val520 in the observed distinct behaviors of L493A, L496F, Q497A, and D515V mutants. The comprehensive atomistic-level analysis of the conformational landscapes revealed the critical functional role of β-sheet segments in the transmission of the allosteric signal upon the photoactivation of the light state.
Comparison of gastric inflammation and metaplasia induced byHelicobacter pyloriorHelicobacter feliscolonization in mice
Authors: Druffner Sara R. , Venkateshwaraprabu Shrinidhi , Khadka Stuti , Duncan Benjamin C. , Morris Maeve T. , Sen-Kilic Emel , Damron Fredrick H. , Liechti George W. , Busada Jonathan T. 
Published: December 2023

AbstractBackgroundGastric cancer is the fifth most diagnosed cancer in the world. Infection by the bacteriaHelicobacter pylori(HP) is associated with approximately 75% of gastric cancer cases. HP infection induces chronic gastric inflammation, damaging the stomach and fostering carcinogenesis. Most mechanistic studies onHelicobacter-induced gastric cancer initiation are performed in mice and utilize either mouse-adapted strains of HP or the natural mouse pathogenHelicobacter felis(HF). Each of these infection models is associated with strengths and weaknesses. Here, we identified the differences in immunogenicity and gastric pathological changes associated with HP and HF infection in mice.Material and MethodsPMSS1 HP strain or with the CS1 HF strain were co-cultured with mouse peritoneal macrophages to assess their immunostimulatory effects. C57BL/6J mice were infected with HP or HF, and gastric inflammation, atrophy, and metaplasia development were assessed 2 months post-infection.ResultsHP and HF induced similar cytokine production from cultured mouse peritoneal macrophages. HP-infected mice caused modest inflammation within both the gastric corpus and antrum and did not induce significant atrophy within the gastric corpus. In contrast, HF induced significant inflammation throughout the gastric corpus and antrum. Moreover, HF infection was associated with significant atrophy of the chief and parietal cell compartments and induced expression of pyloric metaplasia markers.ConclusionsHP is poorly immunogenic compared to HF. HF induces dramatic CD4+ T cell activation, which is associated with increased gastric cancer risk in humans. Thus, HP studies in mice are better suited for studies on colonization, while HF is more strongly suited for pathogenesis and cancer initiation studies.
Effects of parental age and polymer composition on short tandem repeatde novomutation rates
Authors: Goldberg Michael E. , Noyes Michelle D. , Eichler Evan E. , Quinlan Aaron R. , Harris Kelley 
Published: December 2023

AbstractShort tandem repeats (STRs) are hotspots of genomic variability in the human germline because of their high mutation rates, which have long been attributed largely to polymerase slippage during DNA replication. This model suggests that STR mutation rates should scale linearly with a father’s age, as progenitor cells continually divide after puberty. In contrast, it suggests that STR mutation rates should not scale with a mother’s age at her child’s conception, since oocytes spend a mother’s reproductive years arrested in meiosis II and undergo a fixed number of cell divisions that are independent of the age at ovulation. Yet, mirroring recent findings, we find that STR mutation rates covary with paternal and maternal age, implying that some STR mutations are caused by DNA damage in quiescent cells rather than the classical mechanism of polymerase slippage in replicating progenitor cells. These results also echo the recent finding that DNA damage in quiescent oocytes is a significant source ofde novoSNVs and corroborate evidence of STR expansion in postmitotic cells. However, we find that the maternal age effect is not confined to previously discovered hotspots of oocyte mutagenesis, nor are post-zygotic mutations likely to contribute significantly. STR nucleotide composition demonstrates divergent effects on DNM rates between sexes. Unlike the paternal lineage, maternally derived DNMs at A/T STRs display a significantly greater association with maternal age than DNMs at GC-containing STRs. These observations may suggest the mechanism and developmental timing of certain STR mutations and are especially surprising considering the prior belief in replication slippage as the dominant mechanism of STR mutagenesis.Author SummaryWe have long known that tandem repeats are hypermutable and attributed that hypermutability to slippage during DNA replication. Contradicting this long-held theory, we show that tandem repeats accumulate mutations in maternal germ cells during periods when these cells do not replicate. This bolsters a new consensus that DNA replication is not the only driver of mutagenesis, even at loci where replicative slippage is possible. Patterns shared by certain loci enriched for mutations from older mothers may hint at mechanisms.
RNA polymerases reshape chromatin and coordinate transcription on individual fibers
Authors: Tullius Thomas W. , Isaac R. Stefan , Ranchalis Jane , Dubocanin Danilo , Churchman L. Stirling , Stergachis Andrew B. 
Published: December 2023

AbstractDuring eukaryotic transcription, RNA polymerases must initiate and pause within a crowded, complex environment, surrounded by nucleosomes and other transcriptional activity. This environment creates a spatial arrangement along individual chromatin fibers ripe for both competition and coordination, yet these relationships remain largely unknown owing to the inherent limitations of traditional structural and sequencing methodologies. To address these limitations, we employed long-read chromatin fiber sequencing (Fiber-seq) to visualize RNA polymerases within their native chromatin context at single-molecule and near single-nucleotide resolution along up to 30 kb fibers. We demonstrate that Fiber-seq enables the identification of single-molecule RNA Polymerase (Pol) II and III transcription associated foot-prints, which, in aggregate, mirror bulk short-read sequencing-based measurements of transcription. We show that Pol II pausing destabilizes downstream nucleosomes, with frequently paused genes maintaining a short-term memory of these destabilized nucleosomes. Furthermore, we demonstrate pervasive direct coordination and anti-coordination between nearby Pol II genes, Pol III genes, transcribed enhancers, and insulator elements. This coordination is largely limited to spatially organized elements within 5 kb of each other, implicating short-range chromatin environments as a predominant determinant of coordinated polymerase initiation. Overall, transcription initiation reshapes surrounding nucleosome architecture and coordinates nearby transcriptional machinery along individual chromatin fibers.
Multiple performance peaks for scale-biting in an adaptive radiation of pupfishes
Authors: Tan Anson , St. John Michelle , Chau Dylan , Clair Chloe , Chan HoWan , Holzman Roi , Martin Christopher H. 
Published: December 2023

AbstractThe physical interactions between organisms and their environment ultimately shape their rate of speciation and adaptive radiation, but the contributions of biomechanics to evolutionary divergence are frequently overlooked. Here we investigated an adaptive radiation ofCyprinodonpupfishes to measure the relationship between feeding kinematics and performance during adaptation to a novel trophic niche, lepidophagy, in which a predator removes only the scales, mucus, and sometimes tissue from their prey using scraping and biting attacks. We used high-speed video to film scale-biting strikes on gelatin cubes by scale-eater, molluscivore, generalist, and hybrid pupfishes and subsequently measured the dimensions of each bite. We then trained the SLEAP machine-learning animal tracking model to measure kinematic landmarks and automatically scored over 100,000 frames from 227 recorded strikes. Scale-eaters exhibited increased peak gape and greater bite length; however, substantial within-individual kinematic variation resulted in poor discrimination of strikes by species or strike type. Nonetheless, a complex performance landscape with two distinct peaks best predicted gel-biting performance, corresponding to a significant nonlinear interaction between peak gape and peak jaw protrusion in which scale-eaters and their hybrids occupied a second performance peak requiring larger peak gape and greater jaw protrusion. A bite performance valley separating scale-eaters from other species may have contributed to their rapid evolution and is consistent with multiple estimates of a multi-peak fitness landscape in the wild. We thus present an efficient deep-learning automated pipeline for kinematic analyses of feeding strikes and a new biomechanical model for understanding the performance and rapid evolution of a rare trophic niche.
Unexplored regions of the protein sequence-structure map revealed at scale by a library of foldtuned language models
Authors: Subramanian Arjuna M. , Martinez Zachary A. , Lourenço Alec L. , Liu Shichen , Thomson Matt 
Published: December 2023

AbstractThe combinatorial scale of amino-acid sequence-space has traditionally precluded substantive study of the full protein sequence-structure map. It remains unknown, for instance, how much of the vast uncharted landscape of far-from-natural sequences encodes the familiar ensemble of natural folds in a fashion consistent with the laws of biophysics but seemingly untouched by evolution on Earth. The scale of sequence perturbations required to access these spaces exceeds the reach of even gold-standard experimental approaches such as directed evolution. We surpass this limitation guided by the innate capacity of protein language models (pLMs) to explore sequences outside their natural training data through generation and self-feedback. We recast pLMs as probes that explore into regions of protein “deep space” that possess little-to-no detectable homology to natural examples, while enforcing core structural constraints, in a novel sequence design approach that we term “foldtuning.” We build a library of foldtuned pLMs for >700 natural folds in the SCOP database, covering numerous high-priority targets for synthetic biology, including GPCRs and small GTPases, composable cell-surface-receptor and DNA-binding domains, and small signaling/regulatory domains. Candidate proteins generated by foldtuned pLMs reflect distinctive new “rules of language” for sequence innovation beyond detectable homology to any known protein and sample subtle structural alterations in a manner reminiscent of natural structural evolution and diversification. Experimental validation of two markedly different fold targets; the tyrosine-kinase- and small-GTPase-regulating SH3 domain and the bacterial RNase inhibitor barstar demonstrates that fold-tuning proposes protein variants that express and fold stablyin vitroand functionin vivo. Foldtuning reveals protein sequence-structure information at scale out-side of the context of evolution and promises to push forward the redesign and reconstitution of novel-to-nature synthetic biological systems for applications in health and catalysis.
DrugHIVE: Target-specific spatial drug design and optimization with a hierarchical generative model
Authors: Weller Jesse A. , Rohs Remo 
Published: December 2023

ABSTRACTRapid advancement in the computational methods of structure-based drug design has led to their widespread adoption as key tools in the early drug development process. Recently, the remarkable growth of available crystal structure data and libraries of commercially available or readily synthesizable molecules have unlocked previously inaccessible regions of chemical space for drug development. Paired with improvements in virtual ligand screening methods, these expanded libraries are having a significant impact on the success of early drug design efforts. However, screening-based methods are limited in their scalability due to computational limits and the sheer scale of drug-like space. An approach within the quickly evolving field of artificial intelligence (AI), deep generative modeling, is extending the reach of molecular design beyond classical methods by learning the fundamental intra- and inter-molecular relationships in drug-target systems from existing data. In this work we introduce DrugHIVE, a deep hierarchical structure-based generative model that enables fine-grained control over molecular generation. Our model outperforms state of the art autoregressive and diffusion-based methods on common benchmarks and in speed of generation. Here, we demonstrate DrugHIVE’s capacity to accelerate a wide range of common drug design tasks such as de novo generation, molecular optimization, scaffold hopping, linker design, and high throughput pattern replacement. Our method is highly scalable and can be applied to high confidence AlphaFold predicted receptors, extending our ability to generate high quality drug-like molecules to a majority of the unsolved human proteome.
The PROVIDE Study: Primary care assessment of the ROche IPDM tools for Validation and Implementation in Diabetes management and Evaluation
Authors: Roshan Simran , Hunter Elena , Marriott Claire , Carruthers Ross , Poulton Barnaby , Gibson Linda , Cummin Jeremy , Rizvi Fahad , Jaspal Rusi , Wilson Philippe B. 
Published: December 2023

AbstractIntroductionThe adoption of digital tools in diabetes care has transformed the way people with diabetes (PwD) and healthcare professionals (HCPs) manage the condition. Digital tools allow for remote management, improved accuracy in blood glucose readings, and enhanced education for patients. This paper presents the results of a 12-month service evaluation of the Roche Diabetes Care Platform, a diabetes data management platform that was implemented into a primary care network (PCN). The aim of the implementation of the RocheDiabetes Care Platform was to address the current challenges faced by clinicians and PwD in diabetes care, such as reducing complications, improving diabetes education, and the delivery of health care to PwD. Semi-structured interviews were conducted virtually to capture the views of HCPs on their experiences with these digital tools.MethodologyInterviews were conducted with individuals in a range of roles, intrinsic to the diabetes service management in the Leicester PCN, at each stage of implementation. This included pre-implementation, implementation, and post-implementation phases. The data was analysed using thematic analysis.ResultsThe use of the RocheDiabetes Care Platform in the Leicester PCN has advanced HCPs’ management of PwD, demonstrably improving patient outcomes and enhancing interactions. There were two themes identified in the pre-implementation stage, including pre-appointment activities and challenges, and appointment activities and challenges. A further six themes were identified in the post-implementation results, including the optimisation of appointments, time and cost savings, enhanced engagement with PwD, the centralisation of resources, challenges in the PCN’s pathway of care that the RocheDiabetes Care Platform addressed and the future vision of the PCN with the RocheDiabetes Care Platform. Overall, available and accessible data helped to reduce the number of appointments efficiency. Additionally, where PwD were onboarded onto the RocheDiabetes Care Platform, and there was no specific need for the PwD to attend the practice, the number of face-to-face appointments was reduced, improving overall clinic efficiency. Over the period of the evaluation there were no (0) Did Not Attend (DNAs).
PTPRZ1-targeting RNA CAR-T cells exert antigen-specific and bystander antitumor activity in glioblastoma
Authors: Martinez Bedoya Darel , Marinari Eliana , Davanture Suzel , Cantero Castillo Luis , Erraiss Sarah , Dockerill Millicent , Barluenga Badiola Sofia , Winssinger Nicolas , Schaller Karl , Bijlenga Philippe , Momjian Shahan , Hammel Philippe , Cosson Pierre , Walker Paul R. , Dutoit Valérie , Migliorini Denis 
Published: December 2023

AbstractThe great success of chimeric antigen receptor (CAR)-T cell therapy in B-cell malignancies has prompted its translation to solid tumors. In the case of glioblastoma (GBM), clinical trials have shown modest efficacy, but anti-GBM CAR-T cells are being intensely developed. In this study, we selected PTPRZ1 as an attractive new target for GBM treatment. We isolated six anti-human PTPRZ1 scFv from a human phage display library and produced 2ndgeneration CAR-T cells in an RNA format. Patient-derived GBM PTPRZ1-knock-in cell lines were used to select the CAR construct (471_28z), which showed high cytotoxicity while consistently displaying high CAR expression. CAR-T cells incorporating 471_28z were able to release IFN-γ, IL-2, TNF-α, Granzyme B, IL-17A, IL-6, and soluble FasL, and displayed low tonic signaling. Additionally, they maintained an effector memory phenotype afterin vitrokilling. Importantly, 471_28z CAR-T cells displayed strong bystander killing against PTPRZ1-negative cell lines after pre-activation by PTPRZ1-positive tumor cells, but did not kill antigen-negative non-tumor cells. In an orthotopic xenograft tumor model using NSG mice, a single dose of anti-PTPRZ1 CAR-T cells significantly delayed tumor growth. Taken together, these results validate the use of PTPRZ1 as a new GBM target and prompt the use of anti-PTPRZ1 CAR-T cells for clinical translation.
Expanding RNA editing toolkit using an IDR-based strategy
Authors: Di Minghui , Lv Junjun , Jing Zhengyu , Dickinson Bryan , Chi Tian 
Published: December 2023

ABSTRACTRNA base editors should ideally be free of immunogenicity, compact, efficient and specific, which has not been achieved for C>U editing. Here we first describe a compact C>U editor entirely of human origin, created by fusing the human C>U editing enzyme RESCUE-S to CIRTS, a tiny, human-originated programmable RNA binding domain. This editor, CIRTS-RESCUEv1 (V1), was inefficient. Remarkably, a short Histidine-Rich Domain (HRD), which is derived from the Internal Disordered Region (IDR) in the human CYCT1, a protein capable of liquid-liquid phase separation (LLPS), enhanced V1 editing at on-targets as well as off-targets, the latter effect being minor. The V1-HRD fusion protein formed puncta characteristic of LLPS, and various other IDRs (but not an LLPS-impaired mutant) could replace HRD to effectively induce puncta and potentiate V1, suggesting that the diverse domains acted via a common, LLPS-based mechanism. Importantly, the HRD fusion strategy was applicable to various other types of C>U RNA editors. Our study expands the RNA editing toolbox and showcases a general method for stimulating C>U RNA base editors.
Netrin4 is a new target specific factor, ensuring adult sympathetic neuron survival via promoting protein synthesis
Authors: Zhu Zhu , Zhou Lili , Wang Yuanjiao , Zhang Xiaoxuan , Zhang Dongdong , Li Xuzhao , Zhao Bingrui , Jia Jie-Min 
Published: December 2023

AbstractHow mature neurons survive under homeostasis is a question of utmost importance and is known to be different from developing neurons. However, the understanding of this regard remains largely unknown. Here, based on the relationship between the sympathetic cervical ganglia (SCG) and the arterial networks of projecting and targeting organs, we report that the secretome of cerebral, but not peripheral, arterial smooth muscles (SMC) was required for the survival of sympathetic neurons. Among the secretome, we further identified that netrin-4, encoded by the ntn-4 gene, only entered neurons and not glia and played a crucial role both in vitro and in vivo. This was demonstrated with three independent lines of tamoxifen-inducible SMC-specific conditional knockout mice (cKO). Notably, in cKO mice, the local supply of exogenous netrin-4 confined to SCG selectively rescued neuronal necroptosis, which otherwise consistently occurred in a specific subgroup of SCG neurons that innervate cerebral SMCs. Mechanistically, we demonstrated that cerebral netrin-4 was endocytosed at the neurovascular interface and retrogradely long transported to peripheral soma in SCG, where it differentially regulated mRNA translations. This regulation suppressed vacuolization and neuronal necrosis, both of which took place spontaneously in cKO mice. The former is immediately followed by the latter when we injured axons using two-photon laser ablation. The findings revealed a new principle of neurovascular interactions vital for mature neuron survival, implying that under circumstances of cerebral SMC insufficient secretion, such as natural aging, may initiate mature neuronal loss due to uncontrolled vacuolization.
The expression of congenital Shoc2 variants induces AKT-dependent feedback activation of the ERK1/2 pathway
Authors: Wilson Patricia , Abdelmoti Lina , Gao Tianyan , Galperin Emilia 
Published: December 2023

ABSTRACTThe Shoc2 scaffold protein is crucial in transmitting signals within the Epidermal Growth Factor Receptor (EGFR)-mediated Extracellular signal-regulated Kinase (ERK1/2) pathway. While the significance of Shoc2 in this pathway is well-established, the precise mechanisms through which Shoc2 governs signal transmission remain to be fully elucidated. Hereditary mutations in Shoc2 are responsible for Noonan Syndrome with Loose anagen Hair (NSLH). However, due to the absence of known enzymatic activity in Shoc2, directly assessing how these mutations affect its function is challenging. ERK1/2 phosphorylation is used as a primary parameter of Shoc2 function, but the impact of Shoc2 mutants on the pathway activation is unclear. This study investigates how the NSLH-associated Shoc2 variants influence EGFR signals in the context of the ERK1/2 and AKT downstream signaling pathways. We show that when the ERK1/2 pathway is a primary signaling pathway activated downstream of EGFR, Shoc2 variants cannot upregulate ERK1/2 phosphorylation to the level of the WT Shoc2. Yet, when the AKT and ERK1/2 pathways were activated, in cells expressing Shoc2 variants, ERK1/2 phosphorylation was higher than in cells expressing WT Shoc2. We found that, in cells expressing the Shoc2 NSLH mutants, the AKT signaling pathway triggers the PAK activation, followed by phosphorylation and Raf-1/MEK1/2 /ERK1/2 signaling axis activation. Hence, our studies reveal a previously unrecognized feedback regulation downstream of the EGFR and provide evidence for the Shoc2 role as a “gatekeeper” in controlling the selection of downstream effectors within the EGFR signaling network.