bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA Polymerase II Degradation Triggered by DNA Repair OccursIn Transand Independently of how the Lesion is Recognised
Authors: Choudhary Ramveer , Muñoz Juan Cristobal , Beckerman Inés , Bastianello Giulia , Bouvier León Alberto , Foiani Marco , Muñoz Manuel J. 
Published: September 2024

SummaryIn response to DNA damage, RPB1, the catalytic subunit of RNA Polymerase II (RNAPII), is degraded by the ubiquitin-proteasome system. Degradation models only consider transcriptionally engaged molecules, where a stalled RNAPII complex functions as a lesion recognition factor and its RPB1 subunit is proposed to be subsequently degraded to facilitate access of core Nucleotide Excision Repair (NER) factors. This Transcription Coupled repair is complemented by the Global Genome repair (GG-NER) system, where lesions are recognized by the XPE and XPC factors. Here we show that RPB1 degradation is controlledin transby a pathway that depends on NER activity, irrespectively of whether the lesion is recognized by RNAPII itself or by GG-NER factors. Incomplete lesion repair due to absence of any core NER factor enhances RPB1 degradation, indicating that the signal controlling RPB1 abundance is started by lesion recognition and continues until DNA repair is completed. Consistent with anin transmechanism, damage-induced RPB1 degradation is not restricted to active nor phosphorylated RPB1 molecules and depends on Cullin-RING ubiquitin ligases. These findings uncover a repair-dependent mechanism controlling RPB1 levels and provide a rationale for the control of gene expression under stress, where more damage implies more repair and less RPB1 levels, hence restricting RNAPII activity.
Alzheimer-mutant γ-secretase complexes stall amyloid β-peptide production
Authors: Arafi Parnian , Devkota Sujan , Williams Emily , Maesako Masato , Wolfe Michael S. 
Published: September 2024

AbstractMissense mutations in the amyloid precursor protein (APP) and presenilin-1 (PSEN1) cause early-onset familial Alzheimer’s disease (FAD) and alter proteolytic production of secreted 38-to-43-residue amyloid β-peptides (Aβ) by the PSEN1-containing γ-secretase complex, ostensibly supporting the amyloid hypothesis of pathogenesis. However, proteolysis of APP substrate by γ-secretase is processive, involving initial endoproteolysis to produce long Aβ peptides of 48 or 49 residues followed by carboxypeptidase trimming in mostly tripeptide increments. We recently reported evidence that FAD mutations in APP and PSEN1 cause deficiencies in early steps in processive proteolysis of APP substrate C99 and that this results from stalled γ-secretase enzyme-substrate and/or enzyme-intermediate complexes. These stalled complexes triggered synaptic degeneration in aC. elegansmodel of FAD independently of Aβ production. Here we conducted full quantitative analysis of all proteolytic events on APP substrate by γ-secretase with six additional PSEN1 FAD mutations and found that all six are deficient in multiple processing steps. However, only one of these (F386S) was deficient in certain trimming steps but not in endoproteolysis. Fluorescence lifetime imaging microscopy in intact cells revealed that all six PSEN1 FAD mutations lead to stalled γ-secretase enzyme-substrate/intermediate complexes. The F386S mutation, however, does so only in Aβ-rich regions of the cells, not in C99-rich regions, consistent with the deficiencies of this mutant enzyme only in trimming of Aβ intermediates. These findings provide further evidence that FAD mutations lead to stalled and stabilized γ-secretase enzyme-substrate and/or enzyme-intermediate complexes and are consistent with the stalled process rather than the products of γ-secretase proteolysis as the pathogenic trigger.
A Novel Approach to Reducing Spinal Implant-Associated Infections
Authors: Nishizawa Mitsuhiro , Hu Diane , Serhan Hassan , Saleh Bahram , Marcucio Ralph S , Morioka Kazuhito 
Published: September 2024

AbstractImplant-associated infection is a severe complication of instrumented spinal surgery. Preventive measures against biofilm formation, such as chemical modifications of devices with antibiotics or bactericidal substances, have been explored to decrease infection rates and enhance therapeutic outcomes. However, this approach remains challenging, and the safety issues associated with antibiotic resistance and cellular toxicity need to be addressed. Hence, there is an unmet clinical need for implants that resist biofilm formation. Ultrafine-grained material (UFG), which has a nanoscale grain structure, is a novel form of metal with exceptional mechanical and biocompatibility properties that may also have antimicrobial activity. This study investigates the extent to which UFG stainless steel implants resist biofilm formation byStaphylococcus aureus in vitroandin vivo. The results show that the UFG stainless steel wire significantly reduced biofilm formation at early time points after bacterial infection compared to a standard wire. In mouse models of implant-associated infection below the skin or the fascia, the UFG wire had significantly less biofilm formation at early time points. The UFG wire appeared to delay initial bacterial adhesion and biofilm maturation. These findings suggest that UFG implants may resist initial biofilm formation and maturation, leading to promising antibacterial materials for patients.
Temporal control of acute protein aggregate turnover by UBE3C and NRF1-dependent proteasomal pathways
Authors: Hickey Kelsey L. , Panov Alexandra , Whelan Enya Miguel , Schäfer Tillman , Mizrak Arda , Kopito Ron R. , Baumeister Wolfgang , Fernández-Busnadiego Rubén , Harper J. Wade 
Published: September 2024

AbstractA hallmark of neurodegenerative diseases is the progressive loss of proteostasis, leading to the accumulation of misfolded proteins or protein aggregates, with subsequent cytotoxicity. To combat this toxicity, cells have evolved degradation pathways (ubiquitin-proteasome system and autophagy) that detect and degrade misfolded proteins. However, studying the underlying cellular pathways and mechanisms has remained a challenge, as formation of many types of protein aggregates is asynchronous, with individual cells displaying distinct kinetics, thereby hindering rigorous time-course studies. Here, we merge a kinetically tractable and synchronous agDD-GFP system for aggregate formation with targeted gene knockdowns, to uncover degradation mechanisms used in response to acute aggregate formation. We find that agDD-GFP forms amorphous aggregates by cryo-electron tomography at both early and late stages of aggregate formation. Aggregate turnover occurs in a proteasome-dependent mechanism in a manner that is dictated by cellular aggregate burden, with no evidence of the involvement of autophagy. Lower levels of misfolded agDD-GFP, enriched in oligomers, utilizes UBE3C-dependent proteasomal degradation in a pathway that is independent of RPN13 ubiquitylation by UBE3C. Higher aggregate burden activates the NRF1 transcription factor to increase proteasome subunit transcription, and subsequent degradation capacity of cells. Loss or gain of NRF1 function alters the turnover of agDD-GFP under conditions of high aggregate burden. Together, these results define the role of UBE3C in degradation of this class of misfolded aggregation-prone proteins and reveals a role for NRF1 in proteostasis control in response to widespread protein aggregation.
Neuronal firing rate diversity lowers the dimension of population covariability
Authors: Tian Gengshuo John , Zhu Ou , Shirhatti Vinay , Greenspon Charles M. , Downey John E. , Freedman David J. , Doiron Brent 
Published: September 2024

AbstractPopulations of neurons produce activity with two central features. First, neuronal responses are very diverse – specific stimuli or behaviors prompt some neurons to emit many action potentials, while other neurons remain relatively silent. Second, the trial-to-trial fluctuations of neuronal response occupy a low dimensional space, owing to significant correlations between the activity of neurons. These two features define the quality of neuronal representation. We link these two aspects of population response using a recurrent circuit model and derive the following relation: the more diverse the firing rates of neurons in a population, the lower the effective dimension of population trial-to-trial covariability. This surprising prediction is tested and validated using simultaneously recorded neuronal populations from numerous brain areas in mice, non-human primates, and in the motor cortex of human participants. Using our relation we present a theory where a more diverse neuronal code leads to better fine discrimination performance from population activity. In line with this theory, we show that neuronal populations across the brain exhibit both more diverse mean responses and lower-dimensional fluctuations when the brain is in more heightened states of information processing. In sum, we present a key organizational principle of neuronal population response that is widely observed across the nervous system and acts to synergistically improve population representation.
Prodrug activation in malaria parasites mediated by an imported erythrocyte esterase, acylpeptide hydrolase (APEH)
Authors: Sundararaman SA , Miller JJ , Daley EC , O’Brien KA , Kasak P , Daniels AM , Edwards RL , Heidel KM , Bague DA , Wilson MA , Koelper AJ , Kourtoglou EC , White AD , August SA , Apple GA , Rouamba RW , Durand AJ , Esteb JJ , Muller FL , Johnson RJ , Hoops GC , Dowd CS , Odom John AR 
Published: September 2024

AbstractThe continued emergence of antimalarial drug resistance highlights the need to develop new antimalarial therapies. Unfortunately, new drug development is often hampered by poor drug-like properties of lead compounds. Prodrugging temporarily masks undesirable compound features, improving bioavailability and target penetration. We have found that lipophilic diester prodrugs of phosphonic acid antibiotics, such as fosmidomycin, exhibit significantly higher antimalarial potency than their parent compounds (1). However, the activating enzymes for these prodrugs were unknown. Here, we show that an erythrocyte enzyme, acylpeptide hydrolase (APEH) is the major activating enzyme of multiple lipophilic ester prodrugs. Surprisingly, this enzyme is taken up by the malaria parasite,Plasmodium falciparum, where it localizes to the parasite cytoplasm and retains enzymatic activity. Using a novel fluorogenic ester library, we characterize the structure activity relationship of APEH, and compare it to that ofP. falciparumesterases. We show that parasite-internalized APEH plays an important role in the activation of substrates with branching at the alpha carbon, in keeping with its exopeptidase activity. Our findings highlight a novel mechanism for antimicrobial prodrug activation, relying on a host-derived enzyme to yield activation at a microbial target. Mutations in prodrug activating enzymes are a common mechanism for antimicrobial drug resistance (2–4). Leveraging an internalized host enzyme would circumvent this, enabling the design of prodrugs with higher barriers to drug resistance.SignificanceRising antimalarial drug resistance threatens current gains in malaria control. New antimalarial drugs are urgently needed. Unfortunately, many drug candidates have poor drug-like properties, such as poor absorbability in the gastrointestinal tract, or poor accumulation at the site of action. This can be overcome by prodrugging, the addition of prodrug groups which mask poor drug features until they are removed by an activating enzyme. Here, we show that a red blood cell enzyme, acylpeptide hydrolase, is taken up by malaria parasites and serves as the activating enzyme for multiple lipophilic ester prodrugs. Our findings highlight a novel mechanism for prodrug activation, which could be leveraged to design novel prodrugs with high barriers to drug resistance.
The human hippocampus is involved in implicit motor learning
Authors: Griffa Guillermina , Deleglise Alvaro , Solano Agustín , Jacobacci Florencia , De Pino Gabriela , Della-Maggiore Valeria 
Published: September 2024

ABSTRACTRecent evidence suggests that the human hippocampus, traditionally associated with declarative memory, plays a role in motor sequence learning (MSL). However, the classic MSL paradigm depends initially on declarative learning. Therefore, it is critical to discern whether the participation of the hippocampus relates to its canonical role or to processing a general aspect of learning that transcends the declarative/non-declarative distinction. To address this issue, here we turn to visuomotor adaptation -a type of motor learning involving skill recalibration-which unlike MSL can be easily manipulated to eliminate the explicit component. Here, we examined the broader involvement of the hippocampus in procedural motor learning by using diffusion MRI to indirectly assess structural plasticity associated with memory consolidation in visuomotor adaptation (VMA) and an implicit-only version (IVMA). We found that both VMA and IVMA engaged the left posterior hippocampus in a learning-specific manner. Remarkably, while VMA induced only transient hippocampal alterations, IVMA elicited structural changes that persisted overnight, underscoring the reliance on implicit learning for enduring neuroplasticity. As expected, training on both visuomotor tasks impacted the microstructure of the cerebellum, the motor and the posterior parietal cortex. Notably, the temporal dynamics of changes in these regions closely paralleled those of the left hippocampus, suggesting that motor and limbic regions operate in a coordinated manner as part of the same neural network. Collectively, our findings support an active role of the hippocampus in procedural motor memory and argue for a unified function in memory encoding regardless of the declarative or non-declarative nature of the task.
Limosilactobacillus reuteripromotes the expression and secretion of enteroendocrine- and enterocyte-derived hormones
Authors: Di Rienzi Sara C. , Danhof Heather A. , Forshee Micah D. , Roberts Ari , Britton Robert A. 
Published: September 2024

AbstractObservations that intestinal microbes can beneficially impact host physiology have prompted investigations into the therapeutic usage of such microbes in a range of diseases. For example, the human intestinal microbeLimosilactobacillus reuteristrains ATCC PTA 6475 and DSM 17938 are being considered for use for intestinal ailments including colic, infection, and inflammation as well as non- intestinal ailments including osteoporosis, wound healing, and autism spectrum disorder. While many of their beneficial properties are attributed to suppressing inflammatory responses in the gut, we postulated thatL. reuterimay also regulate hormones of the gastrointestinal tract to affect physiology within and outside of the gut. To determine ifL. reuterisecreted factors impact the secretion of enteric hormones, we treated an engineered jejunal organoid line,NGN3-HIO, which can be induced to be enriched in enteroendocrine cells, withL. reuteri6475 or 17938 conditioned medium and performed transcriptomics. Our data suggest that theseL. reuteristrains affect the transcription of many gut hormones, including vasopressin and luteinizing hormone subunit beta, which have not been previously recognized as being produced in the gut epithelium. Moreover, we find that these hormones appear to be produced in enterocytes, in contrast to canonical gut hormones which are produced in enteroendocrine cells. Finally, we show thatL. reutericonditioned media promotes the secretion of several enteric hormones including serotonin, GIP, PYY, vasopressin, and luteinizing hormone subunit beta. These results supportL. reuteriaffecting host physiology through intestinal hormone secretion, thereby expanding our understanding of the mechanistic actions of this microbe.
Programmed ribosomal frameshifting duringPLEKHM2mRNA decoding generates a constitutively active proteoform that supports myocardial function
Authors: Loughran Gary , Pace Raffaella De , Ding Ningyu , Zhang Jianchao , Jungreis Irwin , Carancini Gionmattia , Mudge Jonathan M. , Wang Ji , Kellis Manolis , Atkins John F. , Baranov Pavel V. , Firth Andrew E. , Li Xiaowei , Bonifacino Juan S. , Khan Yousuf A. 
Published: September 2024

AbstractProgrammed ribosomal frameshifting is a process where a proportion of ribosomes change their reading frame on an mRNA1, rephasing the ribosome relative to the mRNA. While frameshifting is commonly employed by viruses2, very few phylogenetically conserved examples are known in nuclear encoded genes and some of the evidence is controversial3,4. Here we report a +1 frameshifting event during decoding of the human genePLEKHM25. This frameshifting occurs at the sequence UCC_UUU_CGG, which is conserved in vertebrates and is similar to an influenza virus sequence that frameshifts with similar efficiency6,7. The new C-terminal domain generated by this frameshift forms an α-helix, which relieves PLEKHM2 from autoinhibition and allows it to move to the tips of cellsviaassociation with kinesin-1 without requiring activation by ARL8. Reintroducing both the canonically-translated and frameshifted protein are necessary to restore normal contractile function ofPLEKHM2-knockout cardiomyocytes, demonstrating the necessity of frameshifting for normal cardiac activity.
Engineering pathogen-inducible promoters for conferring disease resistance in tomato
Authors: Wei Wei , Kim Doogie , Koehler Naio , Bendl Ashley , Cho Myeong-Je , Krasileva Ksenia 
Published: September 2024

AbstractPlant diseases pose a significant threat to global crop production. Most disease resistance genes used in crop breeding programs encode nucleotide-binding leucine-rich repeat receptors (NLRs) that are limited in pathogen specificity and durability. In this study, we leveraged synthetic biology to develop an inducible broad-spectrum resistance in tomatoes. Constitutive expression of autoactive NLRs in plants leads to robust resistance against multiple pathogens but significantly stunts growth. We expressed autoactive NLRs under the control of pathogen-inducible (PI) promoters to mitigate the fitness costs. Taking advantage of extensive, new genomic and transcriptomic resources, we identified PI promoters that responded to multiple pathogens but not abiotic stress. We further validated functionality of predicted elements through a promoter luciferase assay. We generated significant resistance in transgenic tomatoes but we also encountered unwanted expression induction of the native promoter regions in flowers which led to lethal fruit development. Thus, we pursued promoter engineering for fine-tuning the induction. We identified cis-regulatory regions responsible for pathogen-inducibility through promoter bashing experiments and recombined the native promoter with the inducible part and the core promoter. Furthermore, we rationally created synthetic promoters showing a gradient of expression levels, which will allow for selection for transgenic tomatoes with the best performance. We found that the spacing between functional sequences, repeat number of inducible sequences, and core promoters all influence the outcome of engineering. Our study outlines a framework for developing broad-spectrum synthetic immune constructs with reduced fitness cost and provides examples of pathogen-inducible promoter engineering.
Decreasing ZAP Poly(ADP-ribose) Binding Enhances Antiviral Activity Against Alphaviruses
Authors: Cheng Shang-Jung , Griffin Diane E. , Leung Anthony K. L. , Abraham Rachy 
Published: September 2024

ABSTRACTZinc finger antiviral protein (ZAP), also known as PARP13, is an antiviral factor effective against several virus families. ZAP contains three major protein domains: N-terminal zinc fingers, central WWE domains, and a C-terminal inactive ADP-ribosyltransferase domain, which is present only in the longer isoform ZAPL. While both the zinc finger and ADP-ribosyltransferase domains inhibit viral replication, the role of the WWE domains remains unclear. WWE domains bind poly(ADP-ribose) (PAR). In this study, we focus on ZAPS, the shorter isoform comprised of the minimal unit that confers antiviral activity and lacking the ADP-ribosyltransferase domain, to investigate how PAR-binding contributes to antiviral defense against alphaviruses. We identified the Y659 residue on the second WWE domain as essential for PAR-binding both in vitro and in cells. When infected with Chikungunya or Sindbis virus, cells with the Y659A mutant of ZAPS had reduced formation of replication complexes, decreased levels of viral genomic and subgenomic transcripts, and fewer infectious virions released compared to cells with the unmutated ZAPS, suggesting enhanced antiviral activity of the PAR-binding mutant. These findings suggest that inhibiting PAR-binding in ZAPS could potentiate host antiviral functions, offering a novel therapeutic strategy against alphavirus infections.
BayeSMART: Bayesian Clustering of Multi-sample Spatially Resolved Transcriptomics Data
Authors: Guo Yanghong , Zhu Bencong , Tang Chen , Rong Ruichen , Ma Ying , Xiao Guanghua , Xu Lin , Li Qiwei 
Published: September 2024

AbstractThe field of spatially resolved transcriptomics (SRT) has greatly advanced our understanding of cellular microenvironments by integrating spatial information with molecular data collected from multiple tissue sections or individuals. However, methods for multi-sample spatial clustering are lacking, and existing methods primarily rely on molecular information alone. This paper introduces BayeSMART, a Bayesian statistical method designed to identify spatial domains across multiple samples. BayeSMART leverages artificial intelligence (AI)-reconstructed single-cell level information from the paired histology images of multi-sample SRT datasets while simultaneously considering the spatial context of gene expression. The AI integration enables BayeSMART to effectively interpret the spatial domains. We conducted case studies using four datasets from various tissue types and SRT platforms and compared BayeSMART with alternative multi-sample spatial clustering approaches and a number of state-of-the-art methods for single-sample SRT analysis, demonstrating that it surpasses existing methods in terms of clustering accuracy, interpretability, and computational efficiency. BayeSMART offers new insights into the spatial organization of cells in multi-sample SRT data.
Fluctuating chromatin facilitates enhancer-promoter communication by regulating transcriptional clustering dynamics
Authors: Zhu Tao , Li Chunhe , Chu Xiakun 
Published: September 2024

AbstractEnhancers regulate gene expression by forming contacts with distant promoters. Phase-separated condensates or clusters formed by transcription factors (TFs) and co-factors are thought to facilitate these enhancer-promoter (E-P) interactions. Using polymer physics, we developed distinct coarse-grained chromatin models that produce similar ensemble-averaged Hi-C maps but with “stable” and “dynamic” characteristics. Our findings, consistent with recent experiments, reveal a multi-step E-P communication process. The dynamic model facilitates E-P proximity by enhancing TF clustering and subsequently promotes direct E-P interactions by destabilizing the TF clusters through chain flexibility. Our study promotes physical understanding of the molecular mechanisms governing E-P communication in transcriptional regulation.Graphical TOC Entry