bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Chaperone NASP Contributes toDe NovoDeposition of the Centromeric Histone Variant CENH3 inArabidopsisEarly Embryogenesis
Authors: Takeuchi Hidenori , Nagahara Shiori , Higashiyama Tetsuya , Berger Frédéric 
Published: October 2023

AbstractThe centromere is an essential chromosome region where the kinetochore is formed to control equal chromosome distribution during cell division. The centromere-specific histone H3 variant CENH3 (also called CENP-A) is a prerequisite for the kinetochore formation. Since CENH3 evolves rapidly, associated factors, including histone chaperones mediating the deposition of CENH3 on the centromere, are thought to act through species-specific amino-acid sequences. The functions and interaction networks of CENH3 and histone chaperons have been well-characterized in animals and yeasts. However, molecular mechanisms involved in recognition and deposition of CENH3 are still unclear in plants. Here, we used a swapping strategy between domains of CENH3 ofArabidopsis thalianaand the liverwortMarchantia polymorphato identify specific regions of CENH3 involved in targeting the centromeres and interacting with the general histone H3 chaperone, NASP (nuclear autoantigenic sperm protein). CENH3’s LoopN-α1 region was necessary and sufficient for the centromere targeting in cooperation with the α2 region and was involved in interaction with NASP in cooperation with αN, suggesting a species-specific CENH3 recognition. In addition, by generating anArabidopsis naspknockout mutant in the background of a fully fertileGFP-CENH3/cenh3-1line, we found that NASP was implicated forde novoCENH3 deposition after fertilization and thus for early embryo development. Our results imply that the NASP mediates the supply of CENH3 in the context of the rapidly evolving centromere identity in land plants.
A supernumerary synthetic chromosome inKomagataella phaffiias a repository for extraneous genetic material
Authors: Abramczyk Dariusz , Sanchez Olmos Maria del Carmen , Ramirez Rojas Adan Andres , Schindler Daniel , Robertson Daniel , McColm Stephen , Marston Adele L. , Barlow Paul N. 
Published: October 2023

ABSTRACTBackgroundKomagataella phaffii (Pichia pastoris) is a methylotropic commercially important non-conventional species of yeast that grows in a fermentor to exceptionally high densities on simple media and secretes recombinant proteins efficiently. Genetic engineering strategies are being explored in this organism to facilitate cost-effective biomanufacturing. Small, stable artificial chromosomes inK. phaffiicould offer unique advantages by accommodating multiple integrations of extraneous genes and their promoters without accumulating perturbations of native chromosomes or exhausting the availability of selection markers.ResultsHere, we describe a linear “nano”chromosome (of 15-25 kb) that, according to whole-genome sequencing, persists inK. phaffiiover many generations with a copy number per cell of one, provided non-homologous end joining is compromised (byKU70-knockout). The nanochromosome includes a copy of the centromere fromK. phaffiichromosome 3, aK. phaffii-derived autonomously replicating sequence on either side of the centromere, and a pair ofK. phaffii-like telomeres. It contains, within its q arm, a landing zone in which genes of interest alternate with long (approx. 1-kb) non-coding DNA chosen to facilitate homologous recombination and serve as spacers. The landing zone can be extended along the nanochromosome, in an inch-worming mode of sequential gene integrations, accompanied by recycling of just two antibiotic-resistance markers. The nanochromosome was used to expressPDI, a gene encoding protein disulfide isomerase. Co-expression withPDIallowed the production, from a genomically integrated gene, of secreted murine complement factor H, a plasma protein containing 40 disulfide bonds. As further proof-of-principle, we co-expressed, from a nanochromosome, bothPDIand a gene for GFP-tagged human complement factor H under the control ofPAOX1and demonstrated that the secreted protein was active as a regulator of the complement system.ConclusionsWe have addedK. phaffiito the list of organisms that can produce human proteins from genes carried on a stable, linear, artificial chromosome. We envisage using nanochromosomes as repositories for numerous extraneous genes, allowing intensive engineering ofK. phaffiiwithout compromising its genome or weakening the resulting strain.
A comparative approach for selecting orthologous candidate genes in genome-wide association studies across multiple species
Authors: Whitt Lauren , Mahood Elizabeth H. , Ziegler Greg , Luebbert Collin , Gillman Jason D. , Norton Gareth J. , Price Adam H. , Salt David E. , Dilkes Brian P. , Baxter Ivan 
Published: October 2023

AbstractAdvances in quantitative genetics have enabled researchers to identify genomic regions associated with changes in phenotype. However, genomic regions can contain hundreds to thousands of genes, and progressing from genomic regions to causative genes is still challenging. In genome-wide association studies (GWAS) measuring elemental accumulation (ionomic) traits, only 5% of loci overlap genes known to control the ionome - indicating that many causal genes are still unknown. To identify candidates for the remaining 95% loci, we developed a method that uses GWAS studies across multiple species to identify conserved causative genes. By Filtering the Results of Multi-species, Analogous, GWAS Experiments (FiREMAGE) we were able to take the GWAS of 19 ionomic traits in Arabidopsis, soybean, rice, maize, and sorghum, and identify alleles affecting trait variation at conserved genes. Permutation testing demonstrated that GWAS loci affecting the same trait contained homologs more often than expected by chance. Most of the top 10% most significant conserved candidate sets encoded alleles in all five species, highlighting the conservation of ionomic genetic regulators in flowering plants. The candidates include proteins with known biochemical functions that regulate the ionome, validating the approach. In addition to genes with known functions, this approach also identified many conserved genes underlying GWAS loci affecting the same trait in multiple species that have no previously identified function in regulating the ionome, providing a path to discover the as yet unknown mechanisms of element accumulation in plants. This method enables the identification of conserved genes of previously unknown function via GWAS.Author summaryQuantitative genetics identifies a genomic region of interest but not the causal gene. We developed an approach to narrow these gene lists using genetic loci affecting elemental (i.e., calcium, iron, zinc) accumulation. Comparative genomics and GWAS demonstrates that alleles at evolutionarily conserved genes alter the same phenotype in multiple species. This produced a list of conserved candidate genes including previously known elemental regulators and genes whose elemental accumulation mechanism has yet to be determined. Combining datasets across species boosted the signal at these loci. This approach accelerates the discovery of new functional roles of genes.
Identification and characterization of interactions between Influenza A Virus NS1 protein and the human ubiquitin proteasome system
Authors: Lamotte Laurie-Anne , Kindylides Samuel , Gaupin Chloé , Demeret Caroline , Tafforeau Lionel 
Published: October 2023

AbstractAs a key player involved in various cellular pathways, including innate immune response activation, the human ubiquitin-proteasome system (UPS) is particularly targeted by viral proteins upon infection. Indeed, most viruses have evolved to counteract and hijack this system, as it is the case for the influenza A virus (IAV). The non-structural protein 1 (NS1) is described as the main IAV virulence factor, which is known to interact with several cellular proteins, including some UPS factors that are important for the viral escape of the immune cell response. In this study, we profiled the overall interplay between the NS1 proteins of multiple IAV strains and the human UPS. We identified 98 UPS factors directly interacting with NS1 of all or a subset of the studied strains, and we functionally studied 18 of them. We highlighted the involvement of these UPS factors in the IAV life cycle by performing viral titrations, minigenome replicon assays and an ISRE-luc (IFN pathway) assays. Furthermore, we analyzed the expression and subcellular localizations of FZR1, MKRN3, RC3H2 and SHKBP1 upon IAV infection. This interactomics approach allows for an improved understanding of the interplay between NS1 and UPS pathway in the context of an IAV-mediated inhibition of cellular anti-viral responses.ImportanceInfluenza A viruses (IAV) are pathogens responsible for annual flu epidemics causing up to 650,000 deaths each year, resulting in a significant impact in public health and global economy. IAV are also responsible of occasionally pandemic outbreaks in human population, such as in 1918 that caused the death of 50-100 million people. Non-structural protein 1 (NS1) is the main IAV virulence factor; it acts by direct interactions with several cellular proteins, leading to the host shut-off and to the inhibition of the host cell innate immune response. Since the ubiquitin-proteasome system (UPS) plays a crucial role in the innate immune response activation, it is a designated target for NS1 upon infection. Our research thus focused on the identification of interactions between NS1 of 6 different IAV strains and the UPS, to better understand the interplay between this viral protein and the UPS upon viral infection.
Ectopic adipogenesis in response to injury and material implantation in an autoimmune mouse model
Authors: Ngo Tran B. , Josyula Aditya , DeStefano Sabrina , Fertil Daphna , Faust Mondreakest , Lokwani Ravi , Sadtler Kaitlyn 
Published: October 2023

ABSTRACTDue to the limited capacity of mammals to regenerate complex tissues, researchers have worked to understand the mechanisms of tissue regeneration in organisms that maintain that capacity. One example is the MRL/MpJ mouse strain with unique regenerative capacity in ear pinnae that is absent from other strains, such as the common C57BL/6 strain. The MRL/MpJ mouse has also been associated with an autoimmune phenotype even in the absence of the mutantFasgene described in its parent strain MRL/lpr. Due to these findings, we evaluated the differences between the responses of MRL/MpJ versus C57BL/6 strain in traumatic muscle injury and subsequent material implantation. One salient feature of the MRL/MpJ response to injury was a robust adipogenesis within the muscle. This was associated with a decrease in M2-like polarization in response to biologically derived extracellular matrix scaffolds. In pro-fibrotic materials, such as polyethylene, there were fewer foreign body giant cells in the MRL/MpJ mice. As there are reports of both positive and negative influences of adipose tissue and adipogenesis on wound healing, this model could provide an important lens to investigate the interplay between stem cells, adipose tissue, and immune responses in trauma and materials implantation.
Cadherin-dependent adhesion is required for muscle stem cell niche anchorage and maintenance
Authors: Hung Margaret , Lo Hsiao-Fan , Beckmann Aviva G. , Demircioglu Deniz , Damle Gargi , Hasson Dan , Radice Glenn L. , Krauss Robert S. 
Published: October 2023

ABSTRACTAdhesion between stem cells and their niche provides stable anchorage and signaling cues to sustain properties such as quiescence. Skeletal muscle stem cells (MuSCs) directly adhere to an adjacent myofiber via cadherin-catenin complexes. Previous studies on N- and M-cadherin function in MuSCs revealed that while N-cadherin is required for quiescence, they are collectively dispensable for MuSC niche localization and regenerative activity. While additional cadherins are expressed at low levels, these findings raise the possibility that cadherins are unnecessary for MuSC anchorage to the niche. To address this question, we conditionally removed from MuSCs β- and γ-catenin and, separately, αE- and αT-catenin, factors essential for cadherin-dependent adhesion. Catenin-deficient MuSCs break quiescence similarly to N-/M-cadherin-deficient MuSCs, but exit the niche, and are depleted. A combination of in vivo, ex vivo, and single cell RNA sequencing approaches reveal that MuSC attrition occurs via a single fate: precocious differentiation, reentry to the niche, and fusion to myofibers. These findings indicate that cadherin-catenin–dependent adhesion is required for anchorage of MuSCs to their niche and preservation of the stem cell compartment. Furthermore, separable, cadherin-regulated functions govern niche localization, quiescence, and stem cell maintenance in MuSCs.SUMMARY STATEMENTGenetic ablation of cadherin-based adhesion in skeletal muscle stem cells triggers activation, niche exit, precocious differentiation, and subsequent depletion of the stem cell pool.
Neural signatures of competition between voluntary and involuntary influences over the focus of attention in visual working memory
Authors: Ding Yun , Postle Bradley R. , van Ede Freek 
Published: October 2023

AbstractAdaptive behaviour relies on the selection and prioritisation of relevant sensory inputs from the external environment as well as from among internal sensory representations held in working memory. Recent behavioural evidence suggests that the classic distinction between voluntary (goal-driven) and involuntary (stimulus-driven) influences over attentional allocation also applies to the selection of internal representations held in working memory. In the current EEG study, we set out to investigate the neural dynamics associated with the competition between voluntary and involuntary control over the focus of attention in visual working memory. We show that when voluntary and involuntary factors compete for the internal focus of attention, prioritisation of the appropriate item is delayed – as reflected both in delayed gaze biases that track internal selection and in delayed neural beta (15-25 Hz) dynamics that track the planning for the upcoming memory-guided manual action. We further show how this competition is paralleled – possibly resolved – by an increase in frontal midline theta (4-8 Hz) activity that, moreover, predicts the speed of ensuing memory-guided behaviour. Finally, because theta increased following retrocues that effectively reduced working-memory load, our data unveil how frontal theta activity during internal attentional focusing tracks demands on cognitive control over and above working-memory load. Together, these data yield new insight into the neural dynamics that govern the focus of attention in visual working memory, and disentangles the contributions of frontal midline theta activity to the processes of control versus retention in working memory.
Natural is divine: Religious leaders’ nuanced views on birth spacing and contraceptives in Sierra Leone - qualitative insights
Authors: Yillah Regina , Bull Florence , Sawneh Alhaji , Reindorf Beryl , Turay Hamid , Wurie Haja , Hodges Mary 
Published: October 2023

AbstractThis research explored the viewpoints of 116 religious leaders in Sierra Leone including 32 Muslims and 84 Christians from nine different denominations. The study’s primary objectives were to understand their perspectives on family planning, modern contraceptives, sexual reproductive health education, and the religious doctrines influencing these beliefs. The study also aimed to gauge their knowledge of family planning and modern contraceptive methods.In September 2021, data was collected from religious figures purposefully selected from 11 districts and the Western Area Urban through 16 focus group discussions. The discussions, initially conducted in local languages, were translated and transcribed into English. The data was then subjected to a thematic analysis using NVIVO 12 software.The analysis revealed diverse opinions, both across different religions and within specific denominations. A common thread was the general support from both Christian and Muslim leaders for natural birth spacing methods, with some reservations about artificial techniques. There were clear distinctions in beliefs among denominations: Catholics largely considered artificial contraceptives to be against the divine will, while Pentecostals and some Muslims found them permissible under certain conditions.The findings underscore the potential of religious leaders in Sierra Leone to act as influential advocates for family planning, given their support for natural birth spacing. To maximize the impact of advocacy efforts, the study suggests a focus on engaging Pentecostals and Muslim leaders rather than Catholics. Additionally, religious leaders with professional backgrounds in health or education appear more receptive to modern contraceptive methods and could be particularly valuable allies in these endeavours.
Population-specific responses to developmental temperature in the arboviral vectorAedes albopictus: implications for climate change
Authors: Carlassara Martina , Khorramnejad Ayda , Oker Helen , Bahrami Romina , Lozada-Chávez Alejandro Nabor , Mancini Maria Vittoria , Body Mélanie J.A. , Lahondère Chloé , Bonizzoni Mariangela 
Published: October 2023

ABSTRACTThe increase of environmental temperature due to current global warming is not only favoring the expansion of the distribution range of many insect species, but it is also changing their phenology. Insect phenology is tightly linked to developmental timing, which is regulated by environmental temperatures. However, the degree to which effects of developmental temperatures extend across developmental stages and their inter-stage relationships have not been thoroughly quantified in mosquitoes. Here, we used the mosquitoAedes albopictus, which is an aggressive invasive species and an arboviral vector to study how developmental temperature influences fitness across developmental stages, thermal traits, energy reserves, transcriptome, andWolbachiaprevalence in populations from either temperate or tropical regions. We show that hatchability, larval and pupal viability, and developmental speed are strongly influenced by temperature and these effects extend to wing length, body mass, longevity, content of water, protein and lipids in adults, in a population-specific manner. On the contrary, neither adult thermal preference nor heat resistance significantly change with temperature. Development at 18°C revealed to be a limiting factor for the proliferation ofWolbachiain adults and transcriptome analysis showed enrichment for functions linked to stress responses (i.e. cuticle proteins and chitin, cytochrome p450, and heat shock proteins) in mosquitoes reared at both 18°C and 32°C. Our data showed an overall reduced vector fitness performance when mosquitoes were reared at 32°C, and the absence of isomorphy in the relationship between developmental stages and temperature in the temperate population. Altogether these results have important implications for reliable model projections of the invasion potentials ofAe. albopictusand its epidemiological impact.
Revisiting genomes of non-model species with long reads yields new insights into their biology and evolution
Authors: Guiglielmoni Nadège , Villegas Laura I. , Kirangwa Joseph , Schiffer Philipp H. 
Published: October 2023

AbstractHigh-quality genomes obtained using long-read data allow not only for a better understanding of heterozygosity levels, repeat content, and more accurate gene annotation, and prediction when compared to those obtained with short-read technologies, but also allow to understand haplotype divergence. Advances in long-read sequencing technologies in the last years have made it possible to produce such high-quality assemblies for non-model organisms. This allows us to revisit genomes, which have been problematic to scaffold to chromosome-scale with previous generations of data, and assembly software. Nematoda, one of the most diverse, and speciose animal phyla within metazoans, remains poorly studied, and many previously assembled genomes are fragmented. Using long reads obtained with Nanopore R10.4.1 and PacBio HiFi, we generated highly contiguous assemblies of a diploid nematode of the Mermithidae family, for which no closely related genomes are available to date, as well as a collapsed assembly and a phased assembly for a triploid nematode from the Panagrolaimidae family. Both genomes had been analysed before, but the fragmented assemblies had scaffold sizes comparable to the length of long reads prior to assembly. Our new assemblies illustrate how long-read technologies allow for a much better representation of species genomes. We are now able to conduct more accurate downstream assays based on more complete gene and transposable element predictions.
Deep indel mutagenesis reveals the impact of amino acid insertions and deletions on protein stability and function
Authors: Topolska Magdalena , Beltran Antoni , Lehner Ben 
Published: October 2023

AbstractAmino acid insertions and deletions (indels) are an abundant class of genetic variants. However, compared to substitutions, the effects of indels on protein stability are not well understood and are poorly predicted. To better understand indels here we analyze new and existing large-scale deep indel mutagenesis (DIM) of structurally diverse proteins. The effects of indels on protein stability vary extensively among and within proteins and are not well predicted by existing computational methods. To address this shortcoming we present INDELi, a series of models that combine experimental or predicted substitution effects and secondary structure information to provide good prediction of the effects of indels on both protein stability and pathogenicity. Moreover, quantifying the effects of indels on protein-protein interactions suggests that insertions can be an important class of gain-of-function variants. Our results provide an overview of the impact of indels on proteins and a method to predict their effects genome-wide.
A primordial TFEB-TGFβ signaling axis systemically regulates diapause and stem cell longevity
Authors: Nonninger Tim J. , Mak Jennifer , Gerisch Birgit , Ramponi Valentina , Kawamura Kazuto , Schilling Klara , Latza Christian , Kölschbach Jonathan , Ripa Roberto , Serrano Manuel , Antebi Adam 
Published: October 2023

ABSTRACTFasting/refeeding enhances animal health and lifespan across taxa.C. eleganscan endure months of fasting in adult reproductive diapause (ARD) and upon refeeding, regenerate and reproduce.hlh-30/TFEBis an ARD master regulator whose mutants live mere days in ARD and don’t recover with refeeding. Here we find that downregulation of TGFβ signaling bypasseshlh-30collapse, and restores recovery, germline stem cell proliferation and reproductive competence. Upon fasting, HLH-30/TFEB(+) downregulates TGFβ in sensory neurons, to inhibit Notch and promote reproductive quiescence in the germline. Upon refeeding, these pathways are upregulated to activate stem cells and promote reproduction.hlh-30loss induces a senescent-like DNA damage, immune and growth metabolic signature reversed by inhibiting TGFβ signaling. TFEB’s role is conserved in mammalian diapause models, including mouse embryonic and human cancer diapause. Thus, TFEB-TGFβ axis relays systemic signals matching nutrient supply with growth signaling, to regulate stem cell longevity, senescence and regeneration across species.