bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromatin regulator HELLS mediates SSB repair and responses to DNA alkylation damage
Authors: Joseph Joyous T , Wright Christine M , Peixoto Estanislao , Khan Asad , Li Yong , Neidigk Jason S Romero , Decker Olivia , Imtiaz Azait , Jones Brianna A , Zhang Yangfeng , Shiabata Etsuko , Gradilone Sergio A , Lewis Zachary A , Contreras-Galindo Rafael , Sen Arko , Dutta Anindya , Czaja Wioletta 
Published: December 2024

SummaryThe SNF2 family chromatin remodeler HELLS has emerged as an important regulator of cell proliferation, genome stability, and several cancer pathways. Significant upregulation of HELLS has been reported in 33 human cancer types. While HELLS has been implicated in DNA damage response, its function in DNA repair is poorly understood. Here we report a new regulatory link between HELLS and single-strand break (SSB) repair in cellular responses to DNA alkylation damage. We found that loss of HELLS impairs SSB repair, and selectively sensitizes cells to DNA alkylating agents and PARP inhibitors (PARPi). Furthermore, we found that HELLS is co-expressed with PARP1 in cancer cells, and its loss is synthetic lethal with homologous recombination deficiency (HRD). This work unveils new functions of HELLS in modulating SSB repair and responses to clinically relevant DNA alkylation damage, thus offering new insights into the potential therapeutic value of targeting HELLS in cancer.Graphical Abstract
Solution biophysics identifies lipid nanoparticle non-sphericity, polydispersity, and dependence on internal ordering for efficacious mRNA delivery
Authors: Padilla Marshall S. , Shepherd Sarah J. , Hanna Andrew R. , Kurnik Martin , Zhang Xujun , Chen Michelle , Byrnes James , Joseph Ryann A. , Yamagata Hannah M. , Ricciardi Adele S. , Mrksich Kaitlin , Issadore David , Gupta Kushol , Mitchell Michael J. 
Published: December 2024

AbstractLipid nanoparticles (LNPs) are the most advanced delivery system currently available for RNA therapeutics. Their development has accelerated since the success of Patisiran, the first siRNA-LNP therapeutic, and the mRNA vaccines that emerged during the COVID-19 pandemic. Designing LNPs with specific targeting, high potency, and minimal side effects is crucial for their successful clinical use. However, our understanding of how the composition and mixing method influences the structural, biophysical, and biological properties of the resulting LNPs remains limited, hindering the development of LNPs. Our lack of structural understanding extends from the physical and compositional polydispersity of LNPs, which render traditional characterization methods, such as dynamic light scattering (DLS), unable to accurately quantitate the physicochemical characteristics of LNPs. In this study, we address the challenge of structurally characterizing polydisperse LNP formulations using emerging solution-based biophysical methods that have higher resolution and provide biophysical data beyond size and polydispersity. These techniques include sedimentation velocity analytical ultracentrifugation (SV-AUC), field-flow fractionation followed by multi-angle light scattering (FFF-MALS), and size-exclusion chromatography in-line with synchrotron small-angle X-ray scattering (SEC-SAXS). Here, we show that the LNPs have intrinsic polydispersity in size, RNA loading, and shape, and that these parameters are dependent on both the formulation technique and lipid composition. Lastly, we demonstrate that these biophysical methods can be employed to predict transfection in human primary T cells, intravenous administration, and intramuscular administration by examining the relationship between mRNA translation and physicochemical characteristics. We envision that employing solution-based biophysical methods will be essential for determining LNP structure-function relationships, facilitating the creation of new design rules for LNPs.
Neurons and molecules involved in noxious light sensation inCaenorhabditis elegans
Authors: Dunkel Eva , Aoki Ichiro , Gottschalk Alexander 
Published: December 2024

AbstractUltraviolet (UV) light is a danger to unpigmented organisms, inducing photodamage of cells and DNA. The transparent nematodeCaenorhabditis elegans, despite having no eyes, detects light and exhibits negative phototaxis in order to evade sunlight. UV absorption is detected by the photosensor protein LITE-1, that also responds to reactive oxygen species. We investigated which neurons express LITE-1 and act as noxious photosensors and how they transmit this sensation to the nervous system to evoke escape behavior. We identified the interneuron AVG as a main focus of LITE-1 function in mediating the noxious light evoked escape behavior, with minor roles of the interneuron PVT, the sensory ASK neurons and touch receptor neurons. AVG is activated by blue light, and also its optogenetic stimulation causes escape behavior. Signaling from AVG involves chemical neurotransmission, likely directly to premotor interneurons, and to other cells, by extrasynaptic signaling through the neuropeptide NLP-10. NLP-10 signaling is not required for the acute response, but for maintaining responsiveness to repeated noxious stimuli. The source of NLP-10 in this context is largely AVG, however, also other cells contribute, possibly PVT. This work uncovers entry points of sensory information to the neuronal circuits mediating behavioral responses to noxious UV/blue light.Article SummaryC. eleganssenses noxious light and induces escape behavior to avoid damage. The photosensor protein LITE-1 mediates this sensation but understanding responsible neural circuits is incomplete. We identified neurons expressing LITE-1 and identify AVG as the main site of action. The neurotransmitter GABA plays a role in acuteness of the response. AVG, and other cells, need to release the neuropeptide NLP-10 to maintain responsiveness to repeated noxious stimuli. These findings help understanding theC. elegansphotophobic response and will guide future work delineating the precise circuit pathways, as an example of how similar photosensation can evoke protective behavior in invertebrates.
Evaluating Genome Sequencing Strategies: Trio, Singleton, and Standard Testing in Rare Disease Diagnosis
Authors: Kaschta Daniel , Post Christina , Gaass Franziska , Greiten Bianca , Liegmann Anna-Sophie , Gembicki Rebecca , Pozojevic Jelena , Meyenborg Michelle , Wehnert Janne , Schau-Römer Katharina , Rust Franka , Salewski Maj-Britt , Schulz Kristin , Sreenivasan Varun , Balachandran Saranya , Händler Kristian , Yumiceba Veronica , Rösler Laelia , Dalski Andreas , Hoff Kirstin , Hornig Nadine , Köhler Juliane , Arriens Vincent , Utermann-Thüsing Caroline , Roberts Kimberly , Murga Penas Eva Maria , Zühlke Christine , Kautza-Lucht Monika , Dittmar Maike , Hüning Irina , Hellenbroich Yorck , Hanker Britta , Berge Valerie , Birgel Friederike , Rosenstiel Philip , Franke Andre , Fuß Janina , Löscher Britt-Sabina , Franzenburg Sören , Papingi Dzhoy , van der Ven Amelie , Wilson Sandra , Woitschach Rixa , Lisfeld Jasmin , Volk Alexander E. , Herget Theresia , Schlein Christian , Möllring Anna , Hoffmann Birga , Poggenburg Imke , Nommels Henning , Al-Tawil Milad , Herrmann Gloria , Recke Andreas , Toutouna Louiza , Hiort Olaf , Margraf Nils , Gehring Bettina , Muhle Hiltrud , Bäumer Tobias , Harder Lana , Münchau Alexander , Brüggemann Norbert , Vater Inga , Caliebe Almuth , Nagel Inga , Spielmann Malte 
Published: December 2024

AbstractPurposeShort-read genome sequencing (GS) is a comprehensive genetic testing method capable of detecting multiple variant types. Despite its technical advantages, systemic comparisons of singleton GS (sGS), trio GS (tGS), and exome sequencing-based standard-of-care (SoC) in real-world diagnostics remain limited.MethodsWe systematically compared sGS, tGS, and SoC genetic testing in 448 patients with rare diseases in a blinded, prospective study. Three independent teams evaluated the diagnostic yield, variant detection capabilities, and clinical feasibility of GS as a first-tier test. Diagnostic yield was assessed through both prospective and retrospective analyses.ResultsIn prospective analyses, tGS achieved the highest diagnostic yield for likely pathogenic/pathogenic variants (36.8%) in a newly trained team, outperforming the experienced SoC team (36.0%) and the sGS team (30.4%). Retrospective analyses, accounting for technical variant detection and team experience differences, reported diagnostic yields of 38.6% for SoC, 41.3% for sGS, and 42.2% for tGS. GS excelled in identifying deep intronic, non-coding, and small copy-number variants missed by SoC. Notably, tGS additionally identified three de novo variants classified as likely pathogenic based on recent GeneMatcher collaborations and newly published gene-disease association studies.ConclusionGS, particularly tGS, demonstrated superior diagnostic performance, supporting its use as a first-tier genetic test. sGS offers a cost-effective alternative, enabling faster, more efficient diagnoses for rare disease patients.
LEF1-AS1 deregulation in the peripheral blood of patients with persistent post-COVID symptoms
Authors: Madè Alisia , Piella Santiago Nicolas , Ranucci Marco , Gaetano Carlo , Renna Laura Valentina , Cardani Rosanna , Spinetti Gaia , Martelli Fabio 
Published: December 2024

AbstractLong COVID denotes the persistence of symptoms after acute SARS-CoV-2 infection lasting for at least two months without another identifiable cause. Affecting an estimated 15% of COVID-19 patients, long COVID manifests in a wide range of symptoms. Despite extensive research on its one-year effects, limited data exist beyond 12 months. Due to the different manifestations of long COVID, its diagnosis can be challenging. Identifying potential mechanistic contributors and biomarkers would be highly valuable. Recent studies have highlighted the potential of noncoding RNAs (ncRNAs) as biomarkers for disease stratification in COVID-19. Specifically, we have recently identified miR-144-3p and a subset of lncRNAs as candidates for assessing disease severity and outcomes in COVID-19. This study extends such investigations to 98 long COVID patients recruited 18 months after hospitalization, exploring the relationship between circulating ncRNA expression and persistent symptoms. While miR-144-3p, HCG18, and lncCEACAM21 expression did not differ between symptomatic and asymptomatic patients, LEF1-AS1 was downregulated in peripheral blood mononuclear cells (PBMCs) of symptomatic patients. Of note, multiple LEF1-AS1 isoforms and LEF1 sense transcript levels were reduced and negatively correlated with relevant clinical markers. While further studies are needed, our discoveries offer new perspectives for the diagnosis and management of persistent long COVID.
Unexpected Activities of CYP152 Peroxygenases towards Non-carboxylic Substrates Reveal Novel Substrate Recognition Mechanism and Catalytic Versatility
Authors: Jiang Yuanyuan , Gong Piqian , Li Zhong , Li Yuxuan , Wang Binju , Peng Wei , Gao Xiang , Li Shengying 
Published: December 2024

AbstractExploring and exploiting the catalytic promiscuity of enzymes is a central topic and captivating challenge in enzymology. CYP152 peroxygenases are attractive biocatalysts for diverse reactions under mild conditions using H2O2as cofactor. However, their substrate scope is limited by a carboxyl group required for acid-base catalysis, following the well-accepted principle that heme-dependent H2O2-utilizing enzymes employ a carboxyl group within their active sites to facilitate H2O2activation. Herein, we reveal for the first time that several CYP152 family members can directly degrade various aromatic pollutants without any carboxyl group, exhibiting novel aromatic hydroxylation and dehalogenation activities. Through crystal structure analysis, isotope tracing experiments, and QM/MM calculations, we elucidate that the phenolic hydroxyl group activated by electron-withdrawing substituent(s) functionally replaces the carboxyl group, forming hydrogen bonds with the conserved arginine leading to Compound I formation. The oxygen atom of the newly formed hydroxyl group originates from water, bypassing the conventional oxygen rebound step. These findings provide first insights into the mechanisms of P450 peroxygenases towards non-carboxylic substrates, expanding our knowledge of biological C-H activation and C-halogen bond cleavage beyond canonical P450 reactions. This discovery holds immense potential for harnessing these enzymes in innovative strategies for industrial biocatalysis and environmental remediation.
MCL-1 regulates cellular transitions during oligodendrocyte development
Authors: Gil Melanie , Hanna Marina R , Gama Vivian 
Published: December 2024

AbstractOligodendrocytes are the myelinating cells of the central nervous system. Regulation of the early stages of oligodendrocyte development is critical to the function of the cell. Specifically, myelin sheath formation is an energetically demanding event that requires precision, as alterations may lead to dysmyelination. Recent work has established that fatty acid β-oxidation is required for the function of oligodendrocytes. We have shown that MCL-1, a well-characterized anti-apoptotic protein, is required for the development of oligodendrocytesin vivo. Further, it was recently uncovered that MCL-1 regulates long- chain fatty acid β-oxidation through its interaction with acyl-CoA synthetase long-chain family member 1 (ACSL1), an enzyme responsible for the conversion of long-chain fatty acids into acyl-CoA. Here, we introduce anin vitrosystem to isolate human stem cell- derived oligodendrocyte progenitor cells and investigate the involvement of MCL-1 during human oligodendrocyte development. Using this system, we pharmacologically inhibited MCL-1 in oligodendrocyte progenitor cells (OPCs) to elucidate the non-apoptotic function of the protein at this developmental stage. Additionally, we used a motor neuron co-culture system to investigate the downstream effects that MCL-1 inhibition has at later developmental stages when oligodendrocytes begin to contact axons and generate myelin basic protein. We demonstrate that the mitochondrial network changes in human oligodendrocyte development resemble those reportedin vivo. Our findings point to MCL-1 as a critical factor essential at the OPC stage for proper oligodendrocyte morphogenesis.
Heterologous Expression of the carbon monoxide dehydrogenase Gene fromClostridiumsp. to Enhance Acetic Acid and Alcohol Production from CO₂
Authors: Tharak Athmakuri , Suresh G , Kaveti Sreeram , Jain Nishant , Mohan S Venkata 
Published: December 2024

AbstractThis study evaluates the performance of carbon monoxide dehydrogenase (codh) embedded strains in bench-scale microbial electrochemical systems (MES) for CO₂ reduction to biofuels and biochemicals. CO2fermentation efficiency was evaluated by comparing the wild-typeClostridium acetobutylicum(Wild), a negative controlE. colistrain lacking thecodhgene (NC-BL21), and engineeredE. colistrain (Eng) alone and with IPTG induction (Eng+IPTG). Four electrochemical systems were used viz. Wild+E, NC-BL21+E, Eng+E, and Eng+IPTG+E, with a poised potential of 0.6 V applied to the working electrode. CO₂ and bicarbonate were supplemented to a total inorganic carbon (IC) concentration of 40 g/L, with a retention time of 60 h. The engineered strains demonstrated enhanced metabolic performance compared to the wild-type and negative control strains, yielding a maximum formic acid concentration of 2.1 g/L and acetic acid concentration of 7.8 g/L under the Eng+IPTG condition. Ethanol yield was highest at 3.9 g/L under the Eng+IPTG+E condition, substantially exceeding the 2.4 g/L acetic acid yield observed in the wild-type strain. The engineered strains showed superior cumulative yields (0.4075 g/g), improvedcodhcharge flux stability (60 vs. 5 for Wild), and upregulated expression of genes in the Wood-Ljungdahl pathway. Bioelectrochemical performance analysis demonstrated elevated reductive catalytic currents, enhanced CO₂ reduction, and optimal charge transfer kinetics. This study highlights the effectiveness of genetic and process engineering, particularlycodhoverexpression and IPTG induction, in optimizing microbial electrosynthesis for biofuel and biochemical production from C1 gases.
Restriction on Ku’s Inward Translocation Caps Telomere Ends
Authors: Mattarocci Stefano , Baconnais Sonia , Roisné-Hamelin Florian , Pobiega Sabrina , Alibert Olivier , Morin Vincent , Deshayes Alice , Veaute Xavier , Ropars Virginie , Chevreuil Maelenn , Mehringer Johannes , Busso Didier , Mazon Gerard , Fernandez Varela Paloma , Le Cam Éric , Charbonnier Jean-Baptiste , Cuniasse Philippe , Marcand Stéphane 
Published: December 2024

ABSTRACTSafeguarding chromosome ends against fusions via nonhomologous end joining (NHEJ) is essential for preserving genome integrity. Paradoxically, the conserved NHEJ core factor Ku binds telomere ends. How it is prevented from promoting NHEJ remains unclear, as does the mechanism that allows Ku to coexist with telomere-protective DNA binding proteins, e.g., Rap1 inSaccharomyces cerevisiae. Here, we reveal a direct role for Rap1 in the inhibition of Ku’s NHEJ function at telomeres. A single Rap1 molecule bound near a DNA end inhibits NHEJin vivowithout disrupting Ku presence. Consistent with this, Rap1 and Ku form a complex on short DNA duplexesin vitro. Cryo-EM and molecular modelling analysis of this complex shows that Rap1 obstructs Ku’s inward translocation on DNA – an essential step for NHEJ at broken ends. Nanopore sequencing of telomere fusions confirms the importance of this pathway in protecting native telomere ends. Collectively, our findings uncover a mechanism of telomere end protection mediated by restricting Ku’s inward translocation, a functional switch that prevents promiscuous NHEJ repair at telomeres.
Spatially ordered zygotic genome activation fulfills embryo quality control
Authors: Qian Wenchao , Chen Hui , Lee Hongju , Good Matthew C. 
Published: December 2024

AbstractEarly embryo development features autonomous, maternally-driven cell divisions that self- organize the multicellular blastula or blastocyst tissue. Maternal control cedes to the zygote starting with the onset of widespread zygotic genome activation (ZGA), which is essential for subsequent cell fate determination and morphogenesis. Intriguingly, although the onset of ZGA is highly regulated at the level of an embryo, it can be non-homogenous and precisely patterned at the single-cell level. We previously demonstrated a stereotyped spatial and temporal ordering of ZGA in a model vertebrate embryo. Unknown, however, was whether this precise ZGA patterning was required for development. To address this fundamental question, we devised a strategy to spatially control cell divisions in the embryo that perturb blastula embryo organization. We demonstrate the feasibility of spatially inverting the cell size pattern of embryos and find that these inverted embryos undergo a flipped pattern of ZGA. Mispatterned ZGA along the animal-vegetal axis causes embryo apoptosis, revealing that gastrula embryos have a built-in quality control system to sense inappropriate ZGA patterning, including regional defects in transcriptional onset. The quality control response is non-autonomous which may depend on anti-apoptotic signals that repress cell death outside of the animal hemisphere. These results reveal the requirement of properly patterned ZGA for normal development and the existence of an embryo quality control response exquisitely tuned to the spatial and temporal ordering of genome activation and zygotic gene expression.
Structural maturation of the matrix lattice is not required for HIV-1 particle infectivity
Authors: Chen Long , Hikichi Yuta , Rey Juan S. , Akil Caner , Zhu Yanan , Veler Hana , Shen Yao , Perilla Juan R. , Freed Eric O. , Zhang Peijun 
Published: December 2024

AbstractHIV-1 assembly is initiated by the binding of Gag polyproteins to the inner leaflet of the plasma membrane, mediated by the myristylated matrix (MA) domain of Gag. Subsequent to membrane binding, Gag oligomerizes and buds as an immature, non-infectious virus particle, which, upon cleavage of the Gag precursor by the viral protease, transforms into a mature, infectious virion. During maturation, the MA lattice underlying the viral membrane undergoes a structural rearrangement and the newly released capsid (CA) protein forms a mature capsid that encloses the viral genome. While it is well established that formation of the mature capsid is essential to particle infectivity, the functional role of MA structural maturation remains unclear. Here, we examine MA maturation of an MA triple mutant, L20K/E73K/A82T, which exhibits distinct biochemical behaviours. The L20K/E73K/A82T mutant is a revertant derived by propagating the L20K mutant, which exhibits reduced infectivity and increased association of the Gag polyprotein with membranes. L20K/E73K/A82T replicates similarly to wild type but retains the increased Gag membrane binding properties of L20K. L20K/E73K/A82T MA also sediments to high-density fractions in sucrose gradients after detergent treatment under conditions that fully solubilize WT MA, suggesting enhanced MA-MA interactions. Cryo-electron tomography with subtomogram averaging reveals that the immature MA lattice of L20K/E73K/A82T closely resembles the wild type. However, mature virions of the triple mutant lack a detectable MA lattice, in stark contrast to both the wild type and L20K mutant. All-atom molecular dynamics simulations suggest that this absence results from destabilized inter-trimer interactions in the mature L20K/E73K/A82T MA. Furthermore, introducing additional mutations designed to disrupt the mature MA lattice does not impair particle infectivity. These findings suggest that an ordered, membrane-associated mature MA lattice is not essential for HIV-1 infectivity, providing new insights into the structural plasticity of the matrix during maturation and its functional role in the viral lifecycle.