bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microtubules coordinate mitochondria transport with myofibril morphogenesis during muscle development
Authors: Avellaneda Jerome , Candeias Duarte , da Rosa Soares Ana , Gomes Edgar R. , Luis Nuno Miguel , Schnorrer Frank 
Published: September 2024

AbstractMuscle morphogenesis creates highly specialised muscle cells containing contractile myofibrils and energy producing mitochondria. Myofibrils are chains of sarcomeres, whose myosin motors slide over actin filaments at the expense of ATP. Thus, myofibrils and mitochondria are in intimate contact in mature muscles. However, how mitochondria morphogenesis is coordinated with myofibrillogenesis during development remains largely unknown. Here, we usedin vivoimaging to investigate myofibril and mitochondria network dynamics in developingDrosophilaflight muscles. We found that mitochondria rapidly intercalate from the surface of actin bundles to their interior; concomitantly, actin filaments condense to individual myofibrils. This ensures that mitochondria are in intimate proximity to each myofibril. Interestingly, antiparallel microtubules bundle in concert with the assembling myofibrils, suggesting a key role in myofibril orientation. Indeed, light-induced microtubule severing directly affects myofibril orientation, whereas knock-down of kinesin heavy chain specifically blocks mitochondria intercalation and long-range transport. Importantly, mitochondria-myofibril intercalation and microtubule-based transport of mitochondria is conserved in developing mammalian muscle. Together, these data identify a key role for microtubules in coordinating mitochondria and myofibril morphogenesis to build functional muscles.
The DNA damage response and RNA Polymerase II regulator Def1 has posttranscriptional functions in the cytoplasm
Authors: Akinniyi O.T. , Kulkarni S , Hribal M.M. , Keller C.A. , Giardine B. , Reese Joseph C. 
Published: September 2024

AbstractYeast Def1 mediates RNA polymerase II degradation and transcription elongation during stress. Def1 is predominantly cytoplasmic, and DNA damage signals cause its proteolytic processing, liberating its N-terminus to enter the nucleus. Cytoplasmic functions for this abundant protein have not been identified. Proximity-labeling (BioID) experiments indicate that Def1 binds to an array of proteins involved in posttranscriptional control and translation of mRNAs. DeletingDEF1reduces both mRNA synthesis and decay rates, indicating transcript buffering in the mutant. Directly tethering Def1 to a reporter mRNA suppressed expression, suggesting that Def1 directly regulates mRNAs. Surprisingly, we found that Def1 interacts with polyribosomes, which requires its ubiquitin-binding domain located in its N-terminus. The binding of Def1 to ribosomes requires the ubiquitylation of eS7a (Rsp7A) in the small subunit by the Not4 protein in the Ccr4-Not complex. Not4 ubiquitylation of the ribosome regulates translation quality control and co-translational mRNA decay. The polyglutamine-rich unstructured C-terminus of Def1 is required for its interaction with decay and translation factors, suggesting that Def1 acts as a ubiquitin-dependent scaffold to link translation status to mRNA decay. Thus, we have identified a novel function for this transcription and DNA damage response factor in posttranscriptional regulation in the cytoplasm and establish Def1 as a master regulator of gene expression, functioning during transcription, mRNA decay, and translation.
Proof of concept study deploying CRISPR inhibition and activation opens key avenues for systematic biological exploration in zebrafish
Authors: Barrientos Nelson B. , Shoppell Elyse A. , Boyd Rachel J. , Culotta Valeria C. , McCallion Andrew S. 
Published: September 2024

ABSTRACTThe application of CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) technologies in zebrafish has the potential to expand its capacity for the study of gene function significantly. We report proof-of-principle data evaluating transient expression of a codon optimized CRISPRi/a system for zebrafish across established pigmentary and growth phenotypes. A codon-optimized and catalytically inactivecas9gene (dcas9) was cloned upstream of codon-optimized Krüppel associated box (KRAB) and methyl-CpG binding protein 2 (MeCP2) for CRISPRi, and VP64 for CRISPRa. To validate CRISPRi, we targeted key genes in melanocyte differentiation (sox10, mitfa,andmitfb); and melanin production (tyrosinase;tyr). Microinjection of CRISPRi mRNA and single guide RNAs (sgRNAs) targeting thetyrpromoter or 5’-UTR resulted in larvae with hypopigmented epidermal melanocytes. CRISPRi-mediated targeting of the promoters or 5’-UTR of transcription factors mitfa and mitfb also results in pronounced hypopigmentation of epidermal melanocytes (mitfa), and RPE (mitfb). Also, CRISPRi targeting of thesox10promoter results in hypopigmentation of both epidermal melanocytes and RPE consistent with its role upstream ofmitfaandmitfb, andtyr. Finally, we tested both CRISPRi/a to modulate a single gene to yield hypomorphic and hypermorphic effects, selectingmrap2aas our target. This gene regulates energy homeostasis and somatic growth via inhibition of the melanocortin 4 receptor gene (mc4r). We demonstrate that inactivating or activatingmrap2awith CRISPRi/a significantly decreases or increases larval body length, respectively. We demonstrate that CRISPRi/a can modulate control of zebrafish gene expression, facilitating efficient assay of candidate gene function and disease relevance.
Manipulating attentional priority creates a trade-off between memory and sensory representations in human visual cortex
Authors: Rademaker Rosanne L. , Serences John T. 
Published: September 2024

AbstractPeople often remember visual information over brief delays while actively engaging with ongoing inputs from the surrounding visual environment. Depending on the situation, one might prioritize mnemonic contents (i.e., remembering details of a past event), or preferentially attend sensory inputs (i.e., minding traffic while crossing a street). Previous fMRI work has shown that early sensory regions can simultaneously represent both mnemonic and passively viewed sensory information. Here we test the limits of such simultaneity by manipulating attention towards sensory distractors during a working memory task performed by human subjects during fMRI scanning. Participants remembered the orientation of a target grating while a distractor grating was shown during the middle portion of the memory delay. Critically, there were several subtle changes in the contrast and the orientation of the distractor, and participants were cued to either ignore the distractor, detect a change in contrast, or detect a change in orientation. Despite sensory stimulation being matched in all three conditions, the fidelity of memory representations in early visual cortex was highest when the distractor was ignored, intermediate when participants attended distractor contrast, and lowest when participants attended the orientation of the distractor during the delay. In contrast, the fidelity of distractor representations was lowest when ignoring the distractor, intermediate when attending distractor-contrast, and highest when attending distractor-orientation. These data suggest a trade-off in early sensory representations when engaging top-down feedback to attend both seen and remembered features and may partially explain memory failures that occur when subjects are distracted by external events.
Shared selection and genetic architecture drive strikingly repeatable evolution in long-term experimental hybrid populations
Authors: Owens Gregory L. , Caseys Celine , Mitchell Nora , Hübner Sariel , Whitney Kenneth D. , Rieseberg Loren H. 
Published: September 2024

AbstractThe degree to which evolution repeats itself has implications regarding the major forces driving evolution and the potential for evolutionary biology to be a predictive (versus solely historical) science. To understand the factors that control evolutionary repeatability, we experimentally evolved four replicate hybrid populations of sunflowers at natural sites for up to 14 years and tracked ancestry across the genome. We found that there was very strong negative selection against introgressed ancestry in several chromosomes, but positive selection for introgressed ancestry in one chromosome. Further, the strength of selection was influenced by recombination rate. High recombination regions had lower selection against introgressed ancestry due to more frequent recombination away from incompatible backgrounds. Strikingly, evolution was highly parallel across replicates, with shared selection driving 88% of variance in introgressed allele frequency change. Parallel evolution was driven by both high levels of sustained linkage in introgressed alleles and strong selection on large-effect quantitative trait loci. This work highlights the repeatability of evolution through hybridization and confirms the central roles that natural selection, genomic architecture, and recombination play in the process.
HP1α-driven Phase Separation and Repair Pathway Choice in Response to Heterochromatin Damage
Authors: Bohra Darshika , Mazumder Aprotim 
Published: September 2024

AbstractDouble-strand breaks (DSBs) pose significant threat to genomic stability and need immediate attention from DNA Damage Response (DDR) machinery involved in Homologous Recombination (HR) or Non-homologous end joining (NHEJ). DDR in heterochromatin is challenging owing to the distinct chromatin organization. Heterochromatin Protein 1 (HP1) isoforms that contribute significantly to the organization of heterochromatin, have been shown to be involved in DDR. Mammalian HP1 has three isoforms, HP1α, HP1β, and HP1γ, which possess significant homology and yet have distinct functions. HP1α is the only isoform known to undergo liquid-liquid phase separation. We show that the minute-scale dynamics of HP1α and HP1β differ dramatically and they promote differential recruitment of HR vs. NHEJ factors at the sites of laser-induced clustered DSBs. Perturbing HP1α phase-separation abrogates both the recruitment of HR factors and readouts of HR. Our study provides a link between phase-separation and DDR-centric roles of HP1α and hints at spatial partitioning of repair pathways in response to damage in heterochromatin.
Humoral Immune Responses in German Dialysis Patients after mRNA Omicron JN.1 Vaccination
Authors: Stankov Metodi V. , Hoffmann Markus , Happle Christine , Lürken Karsten , Kempf Amy , Nehlmeier Inga , Stölting Andrea , Pöhlmann Stefan , Dopfer-Jablonka Alexandra , Behrens Georg M. N. 
Published: September 2024

AbstractTo assess the effect of the updated mRNA JN.1 omicron vaccine (bretovameran, BioNTech/Pfizer, Mainz, Germany) in an immunocompromised and elderly population, we measured humoral immune responses after mRNA omicron JN.1 vaccination in 37 haemodialysis patients before and 21 days after vaccination.We observed a 3-fold change in anti-S IgG, and a 4·7-fold change in anti-S omicron IgG. Memory B cells (MBC) exclusively binding the receptor binding domain (RBD) of JN.1 displayed a median frequency of 0·11% before vaccination and changed significantly 3·9-fold to a median of 0·43%. Cross reactive JN.1 RBD and Wuhan-Hu-1 S-binding MBCs and MBCs only binding to Wuhan-Hu-1 S changed 2·3-fold and 1·8-fold, respectively. Using a vesicular stomatitis virus-based pseudovirus particle (pp) neutralisation assay, baseline response rates were 86% for XBB.1.5pp, 78% for JN.1pp, 73% for and KP.2pp, 65% for KP.2.3ppand KP.3pp, and 68% for LB.1pp. After vaccination, the response rates for all pseudoviruses increased significantly, and we observed a mean increase in neutralisation of XBB.1.5pp, JN.1pp, KP.2pp, KP.2.3pp, KP.3pp, and LB.1ppof 8·3-fold, 18·7-fold, 22·5-fold, 18·7-fold, 25·5-fold, and 23·5-fold, respectively. In summary, our report provides first evidence for a firm humoral immune response in dialysis patients after mRNA omicron JN.1 vaccination.Our data suggest that the vaccine could be highly effective at enhancing protection of vulnerable populations against evolving SARS-CoV-2 variants.
DNA-PK controls cyclic dinucleotide-associated type I Interferon responses
Authors: Taffoni Clara , Vila Isabelle K. , Jardine Jane , Schussler Moritz , McKellar Joe , Chemarin Morgane , Re Joanna , Messaout-Nacer Yasmine , El Mansouri Insaf , Chrousos George P , Bidère Nicolas , Majzoub Karim , Vlachakis Dimitrios , Laguette Nadine 
Published: September 2024

SummaryCytosolic dsDNAs are potent immune-stimulatory molecules that trigger inflammation in several human pathologies1,2. A major pathway for the detection of cytosolic dsDNA relies on the cyclic GMP-AMP (cGAMP) synthase (cGAS) that produces the 2’3’-cGAMP cyclic dinucleotide (CDN) for activation of the Stimulator of Interferon Genes (STING) adaptor protein that subsequently drives type I Interferon (IFN) responses3,4. Here, we investigated the mechanism regulating intracellular 2’3’-cGAMP levels. We show that the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a major player in the repair of double-strand breaks, directly regulates intracellular levels of 2’3’-cGAMP, thereby reducing STING activation. We describe that the binding of 2’3’-cGAMP to DNA-PKcs occurs in its catalytic cleft, impeding its kinase function. Contrary to other CDN regulatory mechanisms that have been shown to primarily regulate extracellular 2’3’-cGAMP, we show that DNA-PKcs also interacts with the 3’3’-cGAMP bacterial CDN, limiting its capacity to activate STING signaling. Furthermore, we found that DNA-PKcs decreases the potency of pharmacological STING activators. As STING is a major target for therapeutic interventions aiming to boost inflammatory responses in immunosuppressed contexts5, our data bear important implications for drug development and deepens our understanding of inflammatory regulation in response to CDNs.
The predominant binding mode of Palmatine to DNA
Authors: Gentile Marziogiuseppe , Talotta Francesco , Tremblay Jean Christophe , González Leticia , Monari Antonio 
Published: September 2024

AbstractPalmatine is a protoberberine alkaloid, which may produce singlet oxygen under visible light irradiation and binds to DNA. The fact that singlet oxygen activation in palmatine may be triggered by environmental conditions, and in particular its interaction with nucleic acids, makes it a most suitable candidate for photodynamic therapy and DNA-targeted non-invasive anticancer strategies. Despite these remarkable properties the actual binding mode between palmatine and DNA has not been resolved, yet. Its elucidation has, indeed, led to contrasting hypothesis. In this contribution by using long-range molecular dynamic simulations and enhanced sampling approaches, we unequivocally identify that intercalation is the dominant binding mode of palmatine with DNA, from either a thermodynamic and kinetic point of view.TOC Graphic
On the Analysis of Protein Genetic Architecture: Response to “Protein sequence landscapes are not so simple”
Authors: Park Yeonwoo , Metzger Brian P.H. , Thornton Joseph W. 
Published: September 2024

ABSTRACTWe recently reanalyzed 20 combinatorial mutagenesis datasets using a novel reference-free analysis (RFA) method and showed that high-order epistasis contributes negligibly to protein sequence-function relationships in every case. Dupic, Phillips, and Desai (DPD) commented on a preprint of our work. In our published paper, we addressed all the major issues they raised, but we respond directly to them here. 1) DPD’s claim that RFA is equivalent to estimating reference-based analysis (RBA) models by regression neglects fundamental differences in how the two formalisms dissect the causal relationship between sequence and function. It also misinterprets the observation that using regression to estimate any truncated model of genetic architecture will always yield the same predicted phenotypes and variance partition; the resulting estimates correspond to those of the RFA formalism but are inaccurate representations of the true RBA model. 2) DPD’s claim that high-order epistasis is widespread and significant while somehow explaining little phenotypic variance is an artifact of two strong biases in the use of regression to estimate RBA models: this procedure underestimates the phenotypic variance explained by RBA epistatic terms while at the same time inflating the magnitude of individual terms. 3) DPD erroneously claim that RFA is “exactly equivalent” to Fourier analysis (FA) and background-averaged analysis (BA). This error arises because DPD used an incorrect mathematical definition of RFA and were misled by a simple numerical relationship among the models that only holds only for the simplest kinds of datasets. 4) DPD argue that using a nonlinear transformation to account for global nonlinearities in sequence-function relationships is often unnecessary and may artifactually absorb specific epistatic interactions. We show that nonspecific epistasis caused by a limited dynamic range affects datasets of all types, even when the phenotype is represented on a free-energy scale. Moreover, using a nonlinear transformation in a joint fitting procedure does not underestimate specific epistasis under realistic conditions, even if the data are not affected by nonspecific epistasis. The conclusions of our work therefore hold: the genetic architecture of all 20 protein datasets we analyzed can be efficiently and accurately described in an RFA framework by first-order amino acid effects and pairwise interactions with a simple model of global nonlinearity. We are grateful for DPD’s commentary, which helped us improve our paper.
Patient-specificin silicoprediction of outcomes of partial continuous-flow LVAD treatment in peripartum cardiomyopathy
Authors: Nagawa Juliet , Sack Kevin L. , Nchejane N. John , Motchon Y. Dodzi , Sirry Mazin S. , Kraus Sarah , Davies Neil H. , Ntusi Ntobeko A.B. , Franz Thomas 
Published: September 2024

AbstractPatients with severe peripartum cardiomyopathy (PPCM) often receive mechanical circulatory support with good outcomes. However, the mechanisms underlying the functional improvements are poorly understood. This study investigated the effects of partial, continuous-flow left ventricular assist device (LVAD) support on cardiac function and mechanics in patients with PPCM of different severity. Patient-specific biventricular finite element models of six PPCM patients (four recovered, two non-recovered) were developed from magnetic resonance images and combined with a circulatory system model, including variable LVAD support. Ventricular function and myocardial mechanics were predicted, and changes due to LVAD support were quantified. The LVAD support decreased myofiber stress and increased ejection fraction (EF) of the LV. EF increased steadily (two patients), fluctuated (two patients), or peaked before a steady decrease (two patients) with increasing LVAD speed. Improvement due to LVAD support was greater for PPCM patients with higher disease severity than those with lower disease severity. The LVAD and native LV jointly generated stroke volume (SV) in four patients, and the LV contribution diminished with increasing LVAD speed. In the two patients with the lowest EF, the LVAD was the sole source of SV. The improvement of cardiac function and mechanics due to LVAD support in PPCM exceeds that reported for chronic heart failure due to ischemia. However, the predicted variability of the LVAD benefits with PPCM severity and mechanical support level suggests the need and potential for further studies to guide clinicians in selecting personalised treatment parameters required for optimised LVAD therapy for each PPCM patient.Key points summaryPartial continuous-flow left ventricular assist device (LVAD) therapy has presented positive outcomes for critically ill patients with peripartum cardiomyopathy (PPCM), but the underlying LVAD mechanisms are poorly understood.This study showed greater functional improvement for patients who did not recover than those who recovered from PPCM.In patients with severe functional impairment, the LVAD provides the entire ventricular output at all speeds, whereas the LVAD and left ventricle generate the output jointly in patients with mild impairment, and the contribution of the left ventricle decreases with increasing LVAD speed.The variability of the LVAD benefits with disease severity and device speeds emphasises the need for patient-specific treatment to achieve optimal therapy outcomes.The developed patient-specific computational models offer a tool for further research and the potential for developing a clinical decision guide for personalised treatment of PPCM.
Associations between RetNet gene polymorphisms and efficacy of orthokeratology for myopia control : sample from a clinical retrospective study
Authors: Xia Ruijing , Yu Xiangyi , Peng Lulu , Du Zhenlin , Yu Xiaoguang , Xing Shilai , Lu Fan , Mao Xinjie 
Published: September 2024

BackgroundTo study how clinical and genetic factors control the effectiveness of orthokeratology lenses in myopia.MethodsIn this study, we conducted a retrospective clinical study of 545 children aged 8–12 years with myopia who were wearing orthokeratology lenses for one year and performed whole-genome sequencing (WGS) for 60 participants in two groups, one with rapid axial length progression of larger than 0.33 mm and the other with slow axial length progression of less than 0.09 mm. Genes in the RetNet database were used to screen candidate genes that may contribute to the effectiveness of orthokeratology lenses in controlling myopia.ResultsWe found that children with a greater baseline eye axial length, greater spherical equivalent (SE) and greater age had better myopia control with orthokeratology. We observed a significant excess of nonsynonymous variants among those with slow myopia progression, which were prominently enriched in retinal disease related genes. We subsequently identifiedRIMS2(OR=0.01,p=0.0075) andLCA5(OR=6.96,p=0.0080) harboring an excess number of nonsynonymous variants in patients with slow progression of high myopia. Two intronic common variants rs36006402 inSLC7A14and rs2285814 inCLUAP1 were strongly associated with axial length growth. Together, our finding identified novel genes associated with the effectiveness of orthokeratology lenses therapy in myopic children and provide insight into the genetic mechanism of orthokeratology treatment.ConclusionThe effectiveness of orthokeratology lenses treatment involved interindividual variability in controlling axial length growth in myopic eyes. The efficacy increased when patients carried more nonsynonymous variants in retinal disease-related gene sets. Our data will serve as a well-founded reference for genetic counseling and better management of patients who choose orthokeratology lenses to control myopia.