bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of RNA-Binding Protein Targets with HyperTRIBE inSaccharomyces cerevisiae
Authors: Piao Weilan , Li Chong , Sun Pengkun , Yang Miaomiao , Ding Yansong , Song Wei , Jia Yunxiao , Yu Liqun , Jin Hua 
Published: March 2023

AbstractAs a mater regulator in cells, RNA-binding protein (RBP) plays critical roles in organismal development, metabolism and various diseases. It controls gene expression at multiple levels mostly by specific recognition of target RNA. The traditional CLIP-seq method to detect transcriptome-wide RNA targets of RBP is less efficient in yeasts due to their cell walls. Here, we established an efficient HyperTRIBE (Targets of RNA-binding proteins Identified By Editing) in yeast, by fusing a RBP to the hyper active catalytic domain of human RNA editing enzyme ADAR2 and expressing the fusion protein in yeast cells. The target transcripts of RBP were marked with new RNA editing events and identified by high-throughput sequencing. We successfully applied TRIBE to identifying the RNA targets of two yeast RBPs, KHD1 and BFR1. The antibody-free HyperTRIBE has competitive advantages including low background, high sensitivity and reproducibility, and a simple library preparation procedure, which provides a reliable strategy for RBP target identification inSaccharomyces cerevisiae.
Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments
Authors: Rasmussen Torben Sølbeck , Mao Xiaotian , Forster Sarah , Larsen Sabina Birgitte , Von Münchow Alexandra , Tranæs Kaare Dyekær , Brunse Anders , Larsen Frej , Castro Mejia Josue Leonardo , Adamberg Signe , Hansen Axel Kornerup , Adamberg Kaarel , Hansen Camilla Hartmann Friis , Nielsen Dennis Sandris 
Published: March 2023

ABSTRACTBackgroundFecal microbiota transplantation (FMT) and fecal virome transplantation (FVT, sterile filtrated donor feces) have been effective in treating recurrentClostridioides difficileinfections, possibly through bacteriophage-mediated modulation of the gut microbiome. However, challenges like donor variability, costly screening, coupled with concerns over pathogen transfer (incl. eukaryotic viruses) with FMT or FVT hinders their wider clinical application in treating less acute diseases.MethodsTo overcome these challenges, we developed methods to broaden FVT’s clinical application while maintaining efficacy and increasing safety. Specifically, we employed the following approaches: 1) Chemostat-fermentation to reproduce the bacteriophage FVT donor component and remove eukaryotic viruses (FVT-ChP), 2) solvent-detergent treatment to inactivate enveloped viruses (FVT-SDT), and 3) pyronin-Y treatment to inhibit RNA-virus replication (FVT-PyT). We assessed the efficacy of these processed FVTs in aC. difficileinfection mouse model and compared them with untreated FVT (FVT-UnT), FMT, and saline.ResultsFVT-SDT, FVT-UnT, and FVT-ChP reduced the incidence of mice reaching the humane endpoint (0/8, 2/7, and 3/8, respectively) compared to the FMT, FVT-PyT, and saline control (5/8, 7/8, and 5/7, respectively) and significantly reduced the load of colonizingC. difficilecells and toxin A/B levels. There was a potential elimination ofC. difficilecolonization, with 7 out of 8 mice treated with FVT-SDT testing negative with qPCR. In contrast, all other treatments exhibited the continued presence ofC. difficile. Moreover, the results were supported by changes in the gut microbiome profiles, cecal cytokine levels and histopathological findings. Assessment of viral engraftment following FMT/FVT treatment and host-phage correlations analysis suggested that transfer of phages likely were an important contributing factor associated with treatment efficacy.ConclusionsThis proof-of-concept study show that specific modifications to FVT hold promise in addressing challenges related to donor variability and infection risks. Two strategies lead to treatments significantly limitingC. difficilecolonization in mice, with solvent/detergent treatment and chemostat-propagation emerging as promising approaches.
Combining cancer chemotherapeutics with bacterial DNA repair inhibitors to develop novel antimicrobials
Authors: Bernacchia Lorenzo , Gupta Arya , Paris Antoine , Moores Alexandra A. , Kad Neil M 
Published: March 2023

AbstractCancer chemotherapeutics kill rapidly dividing cells, which includes cells of the immune system. The resulting neutropenia predisposes patients to infection, which delays treatment and is a major cause of morbidity and mortality. Here we have exploited the cytotoxicity of the anti-cancer compound cisplatin to screen for FDA-approved drugs that impair bacterial nucleotide excision DNA repair (NER), the primary mechanism bacteria use to repair cisplatin lesions. Five compounds have emerged of which three possess ideal antimicrobial properties including cell penetrance, specific activity for NER, and the ability to kill a multi-drug resistant clinically relevantE. colistrain. Targeting NER offers a new therapeutic approach for infections in cancer patients by combining antimicrobial activity with cancer chemotherapy.
A CUG-initiated CATSPERθ functions in the CatSper channel assembly and serves as a checkpoint for flagellar trafficking
Authors: Huang Xiaofang , Miyata Haruhiko , Wang Huafeng , Mori Giulia , Iida-Norita Rie , Ikawa Masahito , Percudani Riccardo , Chung Jean-Ju 
Published: March 2023

AbstractCalcium signaling is critical for successful fertilization. In spermatozoa, calcium influx into the sperm flagella mediated by the sperm specific CatSper calcium channel is necessary for hyperactivated motility and male fertility. CatSper is a macromolecular complex and is repeatedly arranged in zigzag rows within four linear nanodomains along the sperm flagella. Here, we report that theTmem249-encoded transmembrane domain containing protein, CATSPERθ, is essential for the CatSper channel assembly during sperm tail formation. CATSPERθ facilitates the channel assembly by serving as a scaffold for a pore forming subunit CATSPER4. CATSPERθ is specifically localized at the interface of a CatSper dimer and can self-interact, suggesting its potential role in CatSper dimer formation. Male mice lacking CATSPERθ are infertile because the sperm lack the entire CatSper channel from sperm flagella, rendering sperm unable to hyperactivate, regardless of their normal expression in the testis. In contrast, genetic abrogation of any of the other CatSper transmembrane subunits results in loss of CATSPERθ protein in the spermatid cells during spermatogenesis. CATSPERθ might acts as a checkpoint for the properly assembled CatSper channel complex to traffic to sperm flagella. This study provides insights into the CatSper channel assembly and elucidates the physiological role of CATSPERθ in sperm motility and male fertility.
THE RIBOREGULATION MECHANISM OF HUMAN SERINE HYDROXYMETHYLTRANSFERASE IS ROOTED IN AN ALLOSTERIC SWITCH
Authors: Spizzichino Sharon , Di Fonzo Federica , Marabelli Chiara , Tramonti Angela , Chaves-Sanjuan Antonio , Parroni Alessia , Boumis Giovanna , Liberati Francesca Romana , Paone Alessio , Montemiglio Linda Celeste , Ardini Matteo , Jakobi Arjen J. , Bharadwaj Alok , Swuec Paolo , Tartaglia Gian Gaetano , Paiardini Alessandro , Contestabile Roberto , Rinaldo Serena , Bolognesi Martino , Giardina Giorgio , Cutruzzolà Francesca 
Published: March 2023

SUMMARYRNA can directly control protein activity in a process called riboregulation; only a few mechanisms of riboregulation have been described in detail, none of these being characterized on structural grounds. Here we present a comprehensive structural, functional, and phylogenetic analysis of riboregulation of cytosolic serine hydroxymethyltransferase (SHMT1), the enzyme interconverting serine and glycine in one-carbon metabolism. We show that the RNA modulator competes with polyglutamylated folates and acts as an allosteric switch, selectively altering the enzyme’s reactivity vs. serine. In addition, we identify the tetrameric assembly and a flap structural motif as key structural elements necessary for binding of RNA to eukaryotic SHMT1. The results presented here suggest that riboregulation may have played a role in the evolution of eukaryotic SHMT1 and the compartmentalization of one-carbon metabolism. The findings also provide insights for RNA-based therapeutic strategies targeting this cancer-linked metabolic pathway.
BCL7 proteins, metazoan-specific subunits of the mammalian SWI/SNF complex, bind the nucleosome core particle
Authors: Diaz Dana , Kazrani Asgar Abbas , Martin Franck , Lafouge Julie , Siebert Stéphanie , Birck Catherine , Blais Alexandre , Bergamin Elisa 
Published: March 2023

ABSTRACTBCL7 proteins are among the most recently identified subunits of the mammalian SWI/SNF (mSWI/SNF) chromatin remodeling complex and are absent from the unicellular version of the complex. Mutations in BCL7 proteins are associated with different kind of cancers including blood malignancies. The information on the molecular function and on the structure of BCL7 proteins is to date very limited. Here we report that BCL7 proteins directly bind the nucleosome core particle (NCP) and free DNA with high affinity. We demonstrate that BCL7 proteins form defined complexes with the NCP and we identify the conserved N-terminal part of BCL7 proteins as sufficient to nucleosome binding. We further characterize the impact of BCL7 protein mutations reported in cancer patients on NCP binding and show that the R11S driver mutation reduces the affinity for the nucleosome. Our findings clarify the molecular function of BCL7 proteins and help rationalize the impact of cancer-associated mutations.
ZIP4is required for normal progression of synapsis and for over 95% of crossovers in wheat meiosis
Authors: Draeger Tracie N. , Rey María-Dolores , Hayta Sadiye , Smedley Mark , Alabdullah Abdul Kader , Moore Graham , Martín Azahara C. 
Published: March 2023

AbstractTetraploid and hexaploid wheat have multiple genomes, with successful meiosis and preservation of fertility relying on synapsis and crossover only taking place between homologous chromosomes. In hexaploid wheat, the major meiotic geneTaZIP4-B2(Ph1) on chromosome 5B, promotes crossover between homologous chromosomes, whilst suppressing crossover between homeologous (related) chromosomes. Tetraploid wheat has threeZIP4copies:TtZIP4-A1on chromosome 3A,TtZIP4-B1on 3B andTtZIP4-B2on 5B. Previous studies showed thatZIP4mutations eliminate approximately 85% of crossovers, consistent with loss of the class I crossover pathway. Here, we show that disruption of twoZIP4gene copies inTtzip4-A1B1double mutants, results in a 76-78% reduction in crossovers when compared to wild-type plants. Moreover, when all three copies are disrupted inTtzip4-A1B1B2triple mutants, crossover is reduced by over 95%, suggesting that theTtZIP4-B2copy is also affecting class II crossovers. This implies that, in wheat, the class I and class II crossover pathways may be interlinked. WhenZIP4duplicated and diverged from chromosome 3B on wheat polyploidization, the new 5B copy,TaZIP4-B2, may have acquired an additional function to stabilize both crossover pathways. In plants deficient in all threeZIP4copies, synapsis is delayed and does not complete, consistent with our previous studies in hexaploid wheat, when a similar delay in synapsis was observed in a 59.3Mb deletion mutant,ph1b, encompassing theTaZIP4-B2gene on chromosome 5B. These findings confirm the requirement ofZIP4-B2for efficient synapsis, and suggest thatTtZIP4genes have a stronger effect on synapsis than previously described in Arabidopsis and rice. Thus,ZIP4-B2accounts for the two major phenotypes reported forPh1, promotion of homologous synapsis and suppression of homeologous crossover.Key messageIn tetraploid wheat,ZIP4is required for efficient chromosome synapsis and for over 95% of crossovers, involving both the class I and class II crossover pathways.Author contribution statementTD grew and maintained the plants, made the crosses, carried out the KASP genotyping and sequencing, carried out the meiotic metaphase I studies and produced the corresponding figure, and wrote the manuscript. M-DR scored chromosome crossover, performed the statistical analysis and produced the graphs. AM selected the TILLING mutant, carried out the immunolocalization and FISH experiments and produced the immunolocalization figure; SH and MS developed theTtzip4-B2CRISPR mutant in Kronos using RNA-guided Cas9 and produced the CRISPRTtzip4-B2sequence figure; AKA designed the KASP primers; AM and GM provided the concept, provided thoughts and guidance, and revised and edited the manuscript.Conflict of interestThe authors declare that they have no conflict of interest.
Reduction of Spermine Synthase Suppresses Tau Accumulation Through Autophagy Modulation in Tauopathy
Authors: Tao Xianzun , Liu Jiaqi , Diaz-Perez Zoraida , Foley Jackson R , Stewart Tracy Murray , Casero Robert A , Zhai R. Grace 
Published: March 2023

ABSTRACTTauopathy, including Alzheimer Disease (AD), is characterized by Tau protein accumulation and autophagy dysregulation. Emerging evidence connects polyamine metabolism with the autophagy pathway, however the role of polyamines in Tauopathy remains unclear. In the present study we investigated the role of spermine synthase (SMS) in autophagy regulation and tau protein processing inDrosophilaand human cellular models of Tauopathy. Our previous study showed thatDrosophila spermine synthase(dSms) deficiency impairs lysosomal function and blocks autophagy flux. Interestingly, partial loss-of-function of SMS in heterozygousdSmsflies extends lifespan and improves the climbing performance of flies with human Tau (hTau) overexpression. Mechanistic analysis showed that heterozygous loss-of-function mutation ofdSmsreduces hTau protein accumulation through enhancing autophagic flux. Measurement of polyamine levels detected a mild elevation of spermidine in flies with heterozygous loss ofdSms. SMS knock-down in human neuronal or glial cells also upregulates autophagic flux and reduces Tau protein accumulation. Proteomics analysis of postmortem brain tissue from AD patients showed a significant albeit modest elevation of SMS protein level in AD-relevant brain regions compared to that of control brains consistently across several datasets. Taken together, our study uncovers a correlation between SMS protein level and AD pathogenesis and reveals that SMS reduction upregulates autophagy, promotes Tau clearance, and reduces Tau protein accumulation. These findings provide a new potential therapeutic target of Tauopathy.
Pten, Pi3K and PtdIns(3,4,5)P3dynamics modulate pulsatile actin branching inDrosophilaretina morphogenesis
Authors: Malin Jacob , Birriel Christian Rosa , Hatini Victor 
Published: March 2023

ABSTRACTEpithelial remodeling of theDrosophilaretina depends on the pulsatile contraction and expansion of apical contacts between the cells that form its hexagonal lattice. Phosphoinositide PI(3,4,5)P3(PIP3) accumulates around tricellular adherens junctions (tAJs) during contact expansion and dissipates during contraction, but with unknown function. Here we found that manipulations of Pten or Pi3K that either decreased or increased PIP3resulted in shortened contacts and a disordered lattice, indicating a requirement for PIP3dynamics and turnover. These phenotypes are caused by a loss of protrusive branched actin, resulting from impaired activity of the Rac1 Rho GTPase and the WAVE regulatory complex (WRC). We additionally found that during contact expansion, Pi3K moves into tAJs to promote the cyclical increase of PIP3in a spatially and temporally precise manner. Thus, dynamic regulation of PIP3by Pten and Pi3K controls the protrusive phase of junctional remodeling, which is essential for planar epithelial morphogenesis.Graphical Abstract: Control of contact length by Pi3K, Pten and PIP3.Pi3K regulates the transition from contraction to expansion through its tension-dependent localization to tAJs and modulation of its lipid phosphatase activity. Pten localizes uniformly to regulate PIP3turnover and attenuate PIP3production. (A) Tension shortens contacts, concentrates Pi3K at four spots at a distance from tAJs, and inhibits Pi3K’s lipid phosphatase function. (B) High tension ultimately disassembles contractile networks allowing Pi3K to flow toward tAJs, produce PIP3and activate the WRC to promote actin branching and contact expansion. (C) High protrusion in expanded contacts disperses the WRC and disassembles the branched actin network. (D) Branched actin disassembly allows the assembly and contraction of an actomyosin network, which increases tension and contracts the contact leading to the flow of Pi3K away from tAJs and inhibition of its lipid phosphatase function, thus completing the cycle.
Sensory cortical ensembles exhibit differential coupling to ripples in distinct hippocampal subregions
Authors: Jeong Huijeong , Namboodiri Vijay Mohan K , Jung Min Whan , Andermann Mark L. 
Published: March 2023

AbstractCortical neurons activated during recent experiences often reactivate with dorsal hippocampal CA1 sharp-wave ripples (SWRs) during subsequent rest. Less is known about cortical interactions with intermediate hippocampal CA1, whose connectivity, functions, and SWRs differ from those of dorsal CA1. We identified three clusters of visual cortical excitatory neurons that are excited together with either dorsal or intermediate CA1 SWRs, or suppressed before both SWRs. Neurons in each cluster were distributed across primary and higher visual cortices and co-active even in the absence of SWRs. These ensembles exhibited similar visual responses but different coupling to thalamus and pupil-indexed arousal. We observed a consistent activity sequence: (i) suppression of SWR-suppressed cortical neurons, (ii) thalamic silence, and (iii) activation of the cortical ensemble preceding and predicting intermediate CA1 SWRs. We propose that the coordinated dynamics of these ensembles relay visual experiences to distinct hippocampal subregions for incorporation into different cognitive maps.
Scaling models of visual working memory to natural images
Authors: Bates Christopher J. , Alvarez George A. , Gershman Samuel J. 
Published: March 2023

AbstractOver the last few decades, psychologists have developed precise quantitative models of human recall performance in visual working memory (VWM) tasks. However, these models are tailored to a particular class of artificial stimulus displays and simple feature reports from participants (e.g., the color or orientation of a simple object). Our work has two aims. The first is to build models that explain people’s memory errors in continuous report tasks with natural images. Here, we use image generation algorithms to generate continuously varying response alternatives that differ from the stimulus image in natural and complex ways, in order to capture the richness of people’s stored representations. The second aim is to determine whether models that do a good job of explaining memory errors with natural images also explain errors in the more heavily studied domain of artificial displays with simple items. We find that: (i) features taken from state-of-the-art deep encoders predict trial-level difficulty in natural images better than several reasonable baselines; and (ii) the same visual encoders can reproduce set-size effects and response bias curves in the artificial stimulus domains of orientation and color. Moving forward, our approach offers a scalable way to build a more generalized understanding of VWM representations by combining recent advances in both AI and cognitive modeling.
The power and limitations of species tree-aware phylogenetics
Authors: Williams Tom A. , Davin Adrian A. , Morel Benoit , Szánthó Lénárd L. , Spang Anja , Stamatakis Alexandros , Hugenholtz Philip , Szöllősi Gergely J. 
Published: March 2023

AbstractSpecies tree-aware phylogenetic methods model how gene trees are generated along the species tree by a series of evolutionary events, including the duplication, transfer and loss of genes. Over the past ten years these methods have emerged as a powerful tool for inferring and rooting gene and species trees, inferring ancestral gene repertoires, and studying the processes of gene and genome evolution. However, these methods are complex and can be more difficult to use than traditional phylogenetic approaches. Method development is rapid, and it can be difficult to decide between approaches and interpret results. Here, we review ALE and GeneRax, two popular packages for reconciling gene and species trees, explaining how they work, how results can be interpreted, and providing a tutorial for practical analysis. It was recently suggested that reconciliation-based estimates of duplication and transfer frequencies are unreliable. We evaluate this criticism and find that, provided parameters are estimated from the data rather than being fixed based on prior assumptions, reconciliation-based inferences are in good agreement with the literature, recovering variation in gene duplication and transfer frequencies across lineages consistent with the known biology of studied clades. For example, published datasets support the view that transfers greatly outnumber duplications in most prokaryotic lineages. We conclude by discussing some limitations of current models and prospects for future progress.Significance statementEvolutionary trees provide a framework for understanding the history of life and organising biodiversity. In this review, we discuss some recent progress on statistical methods that allow us to combine information from many different genes within the framework of an overarching phylogenetic species tree. We review the advantages and uses of these methods and discuss case studies where they have been used to resolve deep branches within the tree of life. We conclude with the limitations of current methods and suggest how they might be overcome in the future.