bluuebunny/crossref_metadata_2025_split huggingface dataset:
Binding of SARS-CoV-2 non-structured protein 1 to 40S ribosome inhibits mRNA translation
Authors: Nguyen Hung , Nguyen Hoang Linh , Li Mai Suan 
Published: February 2023

AbstractExperiments have shown that non-structural protein 1 (NSP1) of SARS-CoV-2 is a factor that restricts cellular gene expression and prevents mRNA translation in the ribosome 40S subunit. However, the molecular mechanism of this phenomenon remains unclear. To clarify this issue, all-atom steered molecular dynamics and coarse-grained alchemical simulations were used to compare the binding affinity of mRNA to 40S ribosome in the absence and presence of NSP1. We found that NSP1 binding to the 40S ribosome dramatically increases the binding affinity of mRNA, which, in agreement with experiment, suggests that NSP1 can stall mRNA translation. The mRNA translation has been found to be driven by electrostatic mRNA-40S ribosome interactions. Water molecules have been demonstrated to play an important role in stabilizing the mRNA-40S ribosome complex. The NSP1 residues that are critical in triggering a translation arrest have been identified.
Cell Surface Nucleocapsid Protein Expression: A Betacoronavirus Immunomodulatory Strategy
Authors: López-Muñoz Alberto Domingo , Santos Jefferson J.S. , Yewdell Jonathan W. 
Published: February 2023

ABSTRACTWe recently reported that SARS-CoV-2 Nucleocapsid (N) protein is abundantly expressed on the surface of both infected and neighboring uninfected cells, where it enables activation of Fc receptor-bearing immune cells with anti-N antibodies (Abs) and inhibits leukocyte chemotaxis by binding chemokines (CHKs). Here, we extend these findings to N from the seasonal human coronavirus (HCoV)-OC43, which is also robustly expressed on the surface of infected and non-infected cells by binding heparan-sulfate/heparin (HS/H). HCoV-OC43 N binds with high affinity to the same set of 11 human CHKs as SARS-CoV-2 N, but also to a non-overlapping set of 6 cytokines (CKs). As with SARS-CoV-2 N, HCoV-OC43 N inhibits CXCL12β-mediated leukocyte migration in chemotaxis assays, as do all highly pathogenic and endemic HCoV N proteins. Together, our findings indicate that cell surface HCoV N plays important evolutionary conserved roles in manipulating host innate immunity and as a target for adaptive immunity.
Premarital sex and its association with child marriage among ever-married women: a study of national representative survey
Authors: Billah Md Arif , Khan Md. Mostaured Ali , Hanifi Syed Manzoor Ahmed , Islam M Mofizul , Khan Md. Nuruzzaman 
Published: February 2023

AbstractBackgroundSexual engagement before marriage (premarital sex) can influence child marriage; however, the evidence is scarce in low- and middle-income countries (LMICs), including Bangladesh. This study aimed to explore the association between premarital sex and child marriage among ever-married women aged 15-24 years.MethodsWe analysed data of ever-married women aged 15-24 years after extracting from the 2017/18 Bangladesh Demographic Health Survey (BDHS). Premarital sex (yes, no) was the primary exposure in this study, and child marriage was the outcome variable. Multilevel mixed-effect logistic regression models were used to determine the extent to which premarital sex influences the occurrence of child marriage.ResultsThe prevalence of premarital sex and child marriage was 27% and 76.6%, respectively. Ever-married women who experienced child marriage had higher odds of reporting that they had engaged in premarital sex (aOR: 2.68; 95% CI: 2.20-3.26). The odds of premarital sex for women who experienced child marriage were higher in both urban (aOR: 2.67; 95% CI: 1.88-3.80) and rural areas (aOR: 2.69; 95% CI: 2.11-3.43). Child marriage was more common among women of relatively poor households who had premarital sex than those from other wealth quintiles.ConclusionPremarital sex significantly impacts girls’ child marriage in Bangladesh, and it varies greatly depending on the household’s socioeconomic status. Expanding existing school and community-based programmes aimed at reducing girls’ child marriage, abstinence from early premarital-sexual intercourse and context-specific multi-component interventions for at-risk young people may reduce these practices.
Factors associated with the utilisation of mosquito nets amongst rural adults: A cross-sectional study in East Nusa Tenggara Province Indonesia
Authors: Guntur Robertus Dole , Lobo Maria , Islam Fakir M Amirul 
Published: February 2023

AbstractBackgroundsThe use of mosquito nets has shown a significant impact on the reduction to malaria burden; however, the utilisation of this kind prevention measures greatly depend on the community behaviour which is limited to be studied in Indonesia. This study explored the factors associated with the use of mosquito nets in the rural of East Nusa Tenggara Province (ENTP) Indonesia.MethodsThe community-based cross-sectional study to 1503 rural adults was carried out from October to December 2019. Data on the ownership and the utilisation of mosquito nets were collected using a standardized questionnaire. Logistic regression method was applied to determine the factors associated with the use of mosquito nets.ResultsThe ownership (utilisation) of any mosquito nets, long-lasting insecticide treated nets (LLINs), and non-LLINs was 95.8% (82.3%), 71.6% (54.8%) and 42.7% (27.6%), respectively. The likelihood of the using of mosquito nets was significantly higher for adults in low malaria endemic settings (MES) than in high MES (adjusted odds ratio [AOR]: 10.1;95% CI, 6.17 to 16.5 for any mosquito nets, AOR: 11.1;95% CI, 7.32 to 16.7 for non-LLINs). The use of LLINs was significantly higher for adults living in Hills areas (AOR: 2.11;95%CI,1.37 to 3.25).ConclusionThe coverage of the ownership nets was not followed by the utilisation of the nets in this province. To progress to malaria elimination in ENTP, the coverage and the utilisation of any mosquito nets should be high. Public health promotion to improve the awareness of the using of these nets should be prioritized, particularly for those living in high MES.
The functional specificity of CDC42 isoforms is caused by their distinct subcellular localization
Authors: Ravichandran Yamini , Hänisch Jan , Murray Kerren , Roca Vanessa , Dingli Florent , Loew Damarys , Sabatet Valentin , Boëda Batiste , Stradal Theresia , Etienne-Manneville Sandrine 
Published: February 2023

AbstractThe small G-protein CDC42 is an evolutionary conserved polarity protein and a key regulator of numerous polarized cell functions, including directed cell migration. In vertebrates, alternative splicing gives rise to two CDC42 proteins: the ubiquitously expressed isoform (CDC42u) and the brain isoform (CDC42b), whose specific roles are not fully elucidated. The two isoforms only differ in their carboxy-terminal sequence, which includes the CAAX motif essential for CDC42 interaction with membrane. Here we show that these divergent sequences do not directly affect the range of CDC42’s potential binding partners, but indirectly influence CDC42-driven signaling by controlling the specific subcellular localization of the two isoforms. In astrocytes and neural precursors, which naturally express both variants, CDC42u is mainly cytosolic and associates with the leading-edge plasma membrane of migrating cells where it recruits the Par6-PKCζ complex to fulfill its polarity function. In contrast, CDC42b mainly localizes to intracellular membrane compartments, where it interacts with N-WASP. CDC42b does not participate in cell polarization but embodies the major isoform regulating endocytosis. Both CDC42 isoforms act in concert by contributing their specific functions to promote chemotaxis of neural precursors, demonstrating that the expression pattern of the two isoforms is decisive for the tissue-specific behavior of cells.
Uncovering the essential roles of human GCP 2 orthologs inCaenorhabditis elegans
Authors: Panska Lucie , Nedvedova Stepanka , Vacek Vojtech , Krivska Daniela , Konecny Lukas , Knop Filip , Kutil Zsofia , Skultetyova Lubica , Leontovyc Adrian , Ulrychova Lenka , Sakanari Judy , Asahina Masako , Barinka Cyril , Macurkova Marie , Dvorak Jan 
Published: February 2023

AbstractHuman glutamate carboxypeptidase 2 (GCP2) from the M28B metalloprotease group is an important target for therapy in neurological disorders and an established tumor marker. However, its physiological functions remain unclear. To better understand general roles, we used the model organismCaenorhabditis elegansgenetically manipulate its three existing orthologous genes and evaluate the impact on worm physiology. The results of gene knockout studies showed thatC. elegansGCP2 orthologs affect the pharyngeal physiology, reproduction, and structural integrity of the organism. Promoter-driven GFP expression revealed distinct localization for each of the three gene paralogs, withgcp-2.1being most abundant in muscles, intestine, and pharyngeal interneurons,gcp-2.2restricted to the phasmid neurons, andgcp-2.3located in the excretory cell. This study provides new insight into the unique phenotypic effects of GCP2 gene knockouts inC. elegans, and the specific tissue localizations. We believe that elucidation of particular roles in a non-mammalian organism can help to explain important questions linked to human GCP2 physiology and in extension to GCP2 involvement in pathophysiological processes.
Cautionary note on ribonuclease activity of recombinant PR-10 proteins
Authors: Longsaward Rawit , Sanguankiattichai Nattapong , Viboonjun Unchera , van der Hoorn Renier A.L. 
Published: February 2023

ABSTRACTWe studied the biochemical properties of three splicing isoforms of PR-10 from rubber tree (Hevea brasiliensis) and found that purified recombinantHbPR10 can cause RNA degradationin vitro, a well-known activity described for many PR-10 proteins. This ribonuclease activity was observed for all threeHbPR10 splicing isoforms and is abolished by boiling. However, inclusion of a negative control proteins revealed that ribonuclease activity rather originates from RNases that are copurified fromE. coli, which are overlooked by traditionally used controls such as heat inactivation, RNase inhibitors and negative control proteins obtained with different procedures. The crucial control proteins are missing for at least nine reports on ribonuclease activity in PR-10 proteins published by different laboratories worldwide, indicating that proper controls are frequently overlooked in ribonuclease assays. The raised cautionary note applies to several PR-10 proteins with proclaimed ribonuclease activities and call for the use of different assays and mutant PR-10 proteins as control.
Distinct disease mutations in DNMT3A result in a spectrum of behavioral, epigenetic, and transcriptional deficits
Authors: Beard Diana C. , Zhang Xiyun , Wu Dennis Y. , Martin Jenna R. , Hamagami Nicole , Swift Raylynn G. , McCullough Katherine B. , Ge Xia , Bell-Hensley Austin , Zheng Hongjun , Lawrence Austin B. , Hill Cheryl A. , Papouin Thomas , McAlinden Audrey , Garbow Joel R. , Dougherty Joseph D. , Maloney Susan E. , Gabel Harrison W. 
Published: February 2023

AbstractPhenotypic heterogeneity is a common feature of monogenic neurodevelopmental disorders that can arise from differential severity of missense variants underlying disease, but how distinct alleles impact molecular mechanisms to drive variable disease presentation is not well understood. Here, we investigate missense mutations in the DNA methyltransferase DNMT3A associated with variable overgrowth, intellectual disability, and autism, to uncover molecular correlates of phenotypic heterogeneity in neurodevelopmental disease. We generate a DNMT3A P900L/+ mouse model mimicking a disease mutation with mild-to-moderate severity and compare phenotypic and epigenomic effects with a severe R878H mutation. We show that the P900L mutation leads to disease-relevant overgrowth, obesity, and social deficits shared across DNMT3A disorder models, while the R878H mutation causes more extensive epigenomic disruption leading to differential dysregulation of enhancers elements. We identify distinct gene sets disrupted in each mutant which may contribute to mild or severe disease, and detect shared transcriptomic disruption that likely drives common phenotypes across affected individuals. Finally, we demonstrate that core gene dysregulation detected in DNMT3A mutant mice overlaps effects in other developmental disorder models, highlighting the importance of DNMT3A-deposited methylation in neurodevelopment. Together, these findings define central drivers of DNMT3A disorders and illustrate how variable disruption of transcriptional mechanisms can drive the spectrum of phenotypes in neurodevelopmental disease.
Aging seeds of weedy broomrapes and witchweeds lose sensitivity to strigolactones as DNA demethylates
Authors: Brun Guillaume , Pöhl Jonathan , Wicke Susann 
Published: February 2023

ABSTRACTBroomrapes (PhelipancheandOrobanchespp.) and witchweeds (StrigaandAlectraspp.) are obligate root parasitic weeds responsible for major crop yield losses worldwide. Their success in agricultural landscapes is attributable to their ability to produce thousands of long-lived minute seeds that coordinate their germination with the presence of nearby hosts by perceiving host-derived strigolactones. Nevertheless, the processes underlying the alleged decade(s)-long persistence in the field are understudied. Using an accelerated seed aging method coupled to germination and ELISA bioassays, we report that the loss of seed viability and germinability along seed aging is accompanied by a decrease in both strigolactone sensitivity and global DNA methylation. Our results also suggest that seeds of broomrapes are longer-lived than those of witchweeds. Overall, this study deems to initiate further research into how epigenetic mechanisms contribute to alterations in seed viability in parasitic weeds, and how seed aging influence seed responses to their environment.
SIRT6 activation rescues the age-related decline in DNA damage repair in primary human chondrocytes
Authors: Copp Michaela E. , Shine Jacqueline , Brown Hannon L. , Nimmala Kirti R. , Chubinskaya Susan , Collins John A. , Loeser Richard F. , Diekman Brian O. 
Published: February 2023

AbstractWhile advanced age has long been recognized as the greatest risk factor for osteoarthritis (OA), the biological mechanisms behind this connection remain unclear. Previous work has demonstrated that chondrocytes from older cadaveric donors have elevated levels of DNA damage as compared to chondrocytes from younger donors. The purpose of this study was to determine whether a decline in DNA repair efficiency is one explanation for the accumulation of DNA damage with age, and to quantify the improvement in repair with activation of Sirtuin 6 (SIRT6). Using an acute irradiation model to bring the baseline level of all donors to the same starting point, this study demonstrates a decline in repair efficiency during aging when comparing chondrocytes from young (≤45 years old), middle-aged (50-65 years old), or older (>70 years old) cadaveric donors with no known history of OA or macroscopic cartilage degradation at isolation. Activation of SIRT6 in middle-aged chondrocytes with MDL-800 (20 μM) improved the repair efficiency, while inhibition with EX-527 (10 μM) inhibited the rate of repair and the increased the percentage of cells that retained high levels of damage. Treating chondrocytes from older donors with MDL-800 for 48 hours significantly reduced the amount of DNA damage, despite this damage having accumulated over decades. Lastly, chondrocytes isolated from the proximal femurs of mice between 4 months and 22 months of age revealed both an increase in DNA damage with aging, and a decrease in DNA damage following MDL-800 treatment.
In vitroreconstitution of chromatin domains
Authors: Quililan Kimberly , Oberbeckmann Elisa , Cramer Patrick , Oudelaar A. Marieke 
Published: February 2023

ABSTRACTThe spatial organization of the genome modulates nuclear processes, including transcription, replication, and DNA repair1,2. Eukaryotic genomes are organized into distinct 3D chromatin domains3. However, the molecular mechanisms that drive the formation of these domains are difficult to dissectin vivoand remain poorly understood. Here, we reconstituteS. cerevisiaechromatinin vitroand determine its 3D organization at sub-nucleosome resolution by MNase-based chromosome conformation capture and molecular dynamics simulations. We show that regularly spaced and phased nucleosome arrays form chromatin domainsin vitrothat resemble domainsin vivo. This demonstrates that neither loop extrusion nor transcription are required for domain formation. In addition, we find that the boundaries of reconstituted domains correspond to nucleosome-free regions and that insulation strength scales with their width. Finally, we show that domain compaction depends on nucleosome linker length, with longer linkers forming more compact structures. Together, our results demonstrate that nucleosome positioning is sufficient to reconstitute chromatin domains and provide a proof-of-principle for bottom-up 3D genome studies.
Requirements for establishment and epigenetic stability of mammalian heterochromatin
Authors: Tatarakis Antonis , Saini Harleen , Moazed Danesh 
Published: February 2023

AbstractHeterochromatic domains of DNA account for a large fraction of mammalian genomes and play critical roles in silencing transposons and genes, but the mechanisms that establish and maintain these domains are not fully understood. Here we use an inducible heterochromatin formation system combined with a CRISPR-based genetic screen to investigate the requirements for the establishment and maintenance of heterochromatin in mouse embryonic stem cells (mESCs). We show that DNA sequence-independent and histone H3 lysine 9 methylation (H3K9me)-dependent heterochromatin can be inherited for a limited number of cell divisions in mESCs but becomes stable upon differentiation. We provide evidence that the increased stability of heterochromatin in differentiated cells results from the downregulation of one or more enzymes that erase H3K9me and DNA methylation. Moreover, we show that in addition to components of the H3K9 and DNA methylation pathways, heterochromatin maintenance requires DHX9 and other RNA processing proteins. DHX9 is an RNA/DNA helicase with previously described roles in preventing genomic instability resulting from transcription-associated replication stress. We found that deletion of DHX9 results in defective heterochromatin inheritance and is associated with increased transcription of major satellite repeats, accumulation of R-loops, and loss of H3K9me. Our findings define the requirements for the establishment and epigenetic inheritance of mammalian heterochromatin and suggest that R-loops and replication stress lead to epigenetic instability.
Detecting the effect of genetic diversity on brain composition in an Alzheimer’s disease mouse model
Authors: Gurdon Brianna , Yates Sharon C. , Csucs Gergely , Groeneboom Nicolaas E. , Hadad Niran , Telpoukhovskaia Maria , Ouellette Andrew , Ouellette Tionna , O’Connell Kristen , Singh Surjeet , Murdy Tom , Merchant Erin , Bjerke Ingvild , Kleven Heidi , Schlegel Ulrike , Leergaard Trygve B. , Puchades Maja A. , Bjaalie Jan G. , Kaczorowski Catherine C. 
Published: February 2023

AbstractAlzheimer’s disease (AD) is characterized by neurodegeneration, pathology accumulation, and progressive cognitive decline. There is significant variation in age at onset and severity of symptoms highlighting the importance of genetic diversity in the study of AD. To address this, we analyzed cell and pathology composition of 6- and 14-month-old AD-BXD mouse brains using the semi-automated workflow (QUINT); which we expanded to allow for nonlinear refinement of brain atlas-registration, and quality control assessment of atlas-registration and brain section integrity. Near global age-related increases in microglia, astrocyte, and amyloid-beta accumulation were measured, while regional variation in neuron load existed among strains. Furthermore, hippocampal immunohistochemistry analyses were combined with bulk RNA- sequencing results to demonstrate the relationship between cell composition and gene expression. Overall, the additional functionality of the QUINT workflow delivers a highly effective method for registering and quantifying cell and pathology changes in diverse disease models.
Sterically enhanced control of enzyme-assisted DNA assembly
Authors: Irving Oliver J , Matthews Lauren , Coulthard Steven , Neely Robert K , Grant Mellissa M. , Albrecht Tim 
Published: February 2023

AbstractTraditional methods for the assembly of functionalised DNA structures, involving enzyme restriction and modification, present difficulties when working with small DNA fragments (<100bp), in part due to a lack of control over enzymatic action during the DNA modification process. This limits the design flexibility and range of accessible DNA structures. Here, we show that these limitations can be overcome by introducing chemical modifications into the DNA, which spatially restrict enzymatic activity. This approach, Sterically Controlled Nuclease Enhanced (SCoNE) DNA assembly, thereby circumvents the size limitations of conventional Gibson assembly (GA) and allows for the preparation of well-defined, functionalised DNA structures with multiple probes for specific analytes, such as IL-6, procalcitonin (PCT), and a biotin reporter group. Notably, using the same starting materials conventional GA under typical conditions fails. We demonstrate successful analyte capture based on standard and modified sandwich ELISA and also show how the inclusion of biotin probes provides additional functionality for product isolation.
RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life
Authors: Meyer McCauley O. , Yamagami Ryota , Choi Saehyun , Keating Christine D. , Bevilacqua Philip C. 
Published: February 2023

AbstractCompartmentalization of RNA in biopolymer-rich membraneless organelles is now understood to be pervasive and critical for the function of extant biology and has been proposed as a prebiotically-plausible way to accumulate RNA. However, compartment-RNA interactions that drive encapsulation have the potential to influence RNA structure and function in compartment- and RNA sequence-dependent ways. Herein, we detail Next-Generation Sequencing (NGS) experiments performed for the first time in membraneless compartments called complex coacervates to characterize the fold of many different transfer RNAs (tRNAs) simultaneously under the potentially denaturing conditions of these compartments. Strikingly, we find that natural modifications favor the native fold of tRNAs in these compartments. This suggests that covalent RNA modifications could have played a critical role in metabolic processes at the origin of life.One Sentence SummaryWe demonstrate that RNA folds into native secondary and tertiary structures in protocell models and that this is favored by covalent modifications, which is critical for the origins of life.