bluuebunny/crossref_metadata_2025 huggingface dataset:
Whole genome analyses reveal weak signatures of population structure and environmentally associated local adaptation in an important North American pollinator, the bumble beeBombus vosnesenskii
Authors: Heraghty Sam D. , Jackson Jason M. , Lozier Jeffrey D.
Published: March 2023

Studies of species that experience environmental heterogeneity across their distributions have become an important tool for understanding mechanisms of adaptation and predicting responses to climate change. We examine population structure, demographic history, and environmentally associated genomic variation inBombus vosnesenskii, a common bumble bee in the western U.S.A., using whole genome resequencing of populations distributed across a broad range of latitudes and elevations. We find thatB. vosnesenskiiexhibits minimal population structure and weak isolation by distance, confirming results from previous studies using other molecular marker types. Similarly, demographic analyses with Sequentially Markovian Coalescent (SMC) models suggest that minimal population structure may have persisted since the last interglacial period, with genomes from different parts of the species range showing similar historical effective population size (Ne) trajectories and relatively small fluctuations through time. Redundancy analysis revealed a small amount of genomic variation explained by bioclimatic variables, and environmental association analysis with latent factor mixed modeling (LFMM2) identified few outlier loci that were sparsely distributed throughout the genome. Some outlier loci were in genes with known regulatory relationships, suggesting the possibility of weak selection, although compared to other species examined with similar approaches, evidence for extensive local adaptation signatures in the genome was relatively weak. Overall, results indicateBombus vosnesenskiiis an example of a generalist with a high degree of flexibility in its environmental requirements that may ultimately benefit the species under periods of climate change.
QuaC: A Pipeline Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Data
Authors: Gajapathy Manavalan , Wilk Brandon M. , Worthey Elizabeth A.
Published: March 2023

Quality Control (QC) of human genome sequencing and exome sequencing data is necessary to ensure they are of sufficient quality for downstream analyses. While several QC tools are available to measure quality parameters at various levels post-sequencing, their output needs to be reviewed and interpreted in a very manual and time-consuming process. Such manual review is a major challenge towards standardization and consistency, as the process can be subjective depending on the reviewer. To address these difficulties, we have developed QuaC, which implements, integrates, and standardizes QC best practices at our Center. It performs three major steps: (1) runs several QC tools using data produced by the read alignment (BAM) and small variant calling (VCF) as input and optionally accepts QC output for raw sequencing reads (FASTQ); (2) executes QuaC-Watch to perform QC checkup based on the expected thresholds for quality metrics; and (3) aggregates QC metrics produced by all the QC tools as well as QuaC-Watch results into single, self-contained MultiQC report, both at the per-sample and across-project levels. This report provides aggregate summaries for all samples within a project/cohort for efficient comprehensive review while still allowing for granular review down to individual metrics for a single sample. Finally, we have developed a “Sample QC review system” schema to standardize QC reviewer’s logging of results and simplify downstream users’ interpretation of the reviewers finding.
Orthogonal coupling of a 3D cytoskeletal scaffold coordinates cell morphogenesis and maintains tissue organization in the Drosophila pupal retina
Authors: Sun Xiao , Decker Jacob , Sanchez-Luege Nicelio , Rebay Ilaria
Published: March 2023

How complex three-dimensional (3D) organs coordinate cellular morphogenetic events to achieve the correct final form is a central question in development. The question is uniquely tractable in the lateDrosophilapupal retina where cells maintain stereotyped contacts as they elaborate the specialized cytoskeletal structures that pattern the apical, basal and longitudinal planes of the epithelium. In this study, we combined cell type-specific genetic manipulation of the cytoskeletal regulator Abelson (Abl) with 3D imaging to explore how the distinct cellular morphogenetic programs of photoreceptors and interommatidial pigment cells coordinately organize tissue pattern to support retinal integrity. Our experiments revealed an unanticipated intercellular feedback mechanism whereby correct cellular differentiation of either cell type can non-autonomously induce cytoskeletal remodeling in the otherAblmutant cell type, restoring retinal pattern and integrity. We propose that genetic regulation of specialized cellular differentiation programs combined with inter-plane mechanical feedback confers spatial coordination to achieve robust 3D tissue morphogenesis.
Promoting diversity in ecological systems through toxin production
Authors: Lui Ga Ching , Goyal Sidhartha
Published: March 2023

Toxin production is generally thought as a mechanism to increase competitiveness of the toxin producers over other strains, thus driving down the diversity in the system. However, the production of toxin would also incur costs to the producer, and thus the overall effect may not be one-sided. In this work, we investigate the regime in which the presence of toxins is required to maintain high diversity, either at steady state or at persistence where the strain abundances shows oscillations or chaotic behaviors. Complementary to cross-feeding, which is one of several mechanisms previously proposed to resolve the paradox of plankton, we suggest the regulation of toxin production could play a role in increasing diversity above the upper bound given by the competitive exclusion principle.
Regulation of Traction Force through the Direct Binding of Basigin and Calpain 4
Authors: Hao Bingqing , Beningo Karen A.
Published: March 2023

Traction force and mechanosensing (the ability to sense mechanical attributes of the environment) are two important factors used by a cell to modify behavior during migration. Previously it was determined that the calpain small subunit, calpain 4, regulates the production of traction force independent of its proteolytic holoenzyme. A proteolytic enzyme is formed by calpain4 binding to either of its catalytic partners, calpain 1 and 2. To further understand how calpain 4 regulates traction force, we used two-hybrid analysis to identify more components of the traction pathway. We discovered that basigin, an integral membrane protein and a documented matrix-metalloprotease (MMP) inducer binds to calpain 4 in two-hybrid and pull-down assays. Traction force was deficient when basigin was silenced in MEF cells, and defective in substrate adhesion strength. Consistent with Capn4-/-MEF cells, the cells deficient in basigin responded to localized stimuli. Together these results implicate basigin in the pathway in which calpain 4 regulates traction force independent of the catalytic large subunits.
The fingering patterns in the epithelial layer control the gap closure rate via curvature-mediated force
Authors: Jeong Hyuntae , Yeo Jinwook , Ryu Seunghwa , Shin Jennifer Hyunjong
Published: March 2023

Closing gaps in cellular monolayers is a fundamental aspect of both morphogenesis and wound healing. This closure can be achieved through leader cell crawling or actomyosin-based contraction, depending on the size of the gap. Here, we focus on wounds whose closure is driven by interfacial instabilities, featuring both leader cell-driven fingers and actin-mediated contraction. Our proposed model predicts a positive correlation between the frequency of fingering and the overall speed of boundary closure. This fingering frequency is precisely regulated through the orchestration of cell density-driven pressure, cell-cell repulsions, and the initial curvature of the wound boundary. Our findings demonstrate an inverse correlation between fingering frequency and boundary curvatures, indicating a “self-control” mechanism for closure rates independent of the initial curvatures of the wound periphery. Notably, changes in curvature caused by fingering formation generate force that aids in the healing process.
A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology
Authors: Zhang Yingying , Leung Alden K. , Kang Jin Joo , Sun Yu , Wu Guanxi , Li Le , Sun Jiayang , Cheng Lily , Qiu Tian , Zhang Junke , Wierbowski Shayne , Gupta Shagun , Booth James , Yu Haiyuan
Published: March 2023

A major goal of cancer biology is to understand the mechanisms underlying tumorigenesis driven by somatically acquired mutations. Two distinct types of computational methodologies have emerged: one focuses on analyzing clustering of mutations within protein sequences and 3D structures, while the other characterizes mutations by leveraging the topology of protein-protein interaction network. Their insights are largely non-overlapping, offering complementary strengths. Here, we established a unified, end-to-end 3D structurally-informed protein interaction network propagation framework, NetFlow3D, that systematically maps the multiscale mechanistic effects of somatic mutations in cancer. The establishment of NetFlow3D hinges upon the Human Protein Structurome, a comprehensive repository we compiled that incorporates the 3D structures of every single protein as well as the binding interfaces of all known protein interactions in humans. NetFlow3D leverages the Structurome to integrate information across atomic, residue, protein and network levels: It conducts 3D clustering of mutations across atomic and residue levels on protein structures to identify potential driver mutations. It then anisotropically propagates their impacts across the protein interaction network, with propagation guided by the specific 3D structural interfaces involved, to identify significantly interconnected network “modules”, thereby uncovering key biological processes underlying disease etiology. Applied to 1,038,899 somatic protein-altering mutations in 9,946 TCGA tumors across 33 cancer types, NetFlow3D identified 1,4444 significant 3D clusters throughout the Human Protein Structurome, of which ~55% would not have been found if using only experimentally-determined structures. It then identified 26 significantly interconnected modules that encompass ~8-fold more proteins than applying standard network analyses. NetFlow3D and our pan-cancer results can be accessed fromhttp://netflow3d.yulab.org.
Computational investigation of Scutellarein derivatives as an inhibitor against triple-negative breast cancer by Quantum calculation, and drug-designed approaches
Authors: Akash Shopnil , Aovi Farjana Islam , Azad Md. A.K , Kumer Ajoy , Chakma Unesco , Islam Md Rezaul , Mukerjee Nobendu , Rahman Md. Mominur , Bayıl Imren , Rashid Summya , Sharma Rohit
Published: March 2023

Triple-negative breast cancer accounts for 10-15% of all breast tumors (TNBC). Triple-negative breast cancer lacks either estrogen or progesterone receptors (ER or PR), producing either too little or too much HER2. (All three tests result in “negative” results for the cells.) These cancers are more common in women under 40 who are Black or have the BRCA1 mutation. TNBC differs from other types of invasive breast cancer in that it has fewer treatment options, a worse prognosis, and grows and spreads more quickly (outcome). So, first of all, the protein of triple-negative breast cancer was collected from the PDB database having the most stable configuration, and a natural bioactive molecule, Scutellarein, was selected. Scutellarein is well-known to possess anti-cancer properties, so its derivatives were chosen to design anticancer drugs through computational tools. In this case, the functional group has applied and modified structural activity relationship methods. Then, the pass prediction score was taken, which indicates the probability of active (Pa) and the probability of inactive (Pi). After that, otherin-silcoapproaches, such as the ADMET parameter, and quantum calculation by Density Functional Theory (DFT), have been conducted. Finally, molecular docking and dynamics have been evaluated against TNBC to determine the binding affinity and stability. Scutellarein derivatives (DM03 at -10.7 kcal/mol, DM04 at -11.0 kcal/mol) have been reported to have a maximum tendency for binding against TNBC. Besides, the molecular dynamic simulation was performed at 100ns and described by root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF), which are much more stable compounds. The pharmacokinetics specifications for a suitable therapeutic candidate were satisfied by these molecules, like as non-carcinogenic, minimal to aquatic and non-aquatic toxicity. Almost all the molecules are highly soluble in the aqueous system. These all-computational data suggested that they might be suitable as a medication for the inhibition of TNBC, and further experimental studies should be carried out.
Factors associated with vaccine coverage improvements in Senegal between 2005-2019: A quantitative retrospective analysis
Authors: Smalley Hannah K , Castillo-Zunino Francisco , Keskinocak Pinar , Nazzal Dima , Sakas Zoe , Sarr Moussa , Freeman Matthew C.
Published: March 2023

Objective

Senegal has demonstrated catalytic improvements in national coverage rates for early childhood vaccination, despite lower development assistance for childhood vaccines in Senegal compared to other low and lower-middle income countries. Understanding factors associated with historical changes in childhood vaccine coverage in Senegal, as well as heterogeneities across its 14 regions, can highlight effective practices that might be adapted to improve vaccine coverage elsewhere.

Design

Childhood vaccination coverage rates, demographic information, and health system characteristics were identified from Senegal’s Demographic and Health Surveys (DHS) and Senegal national reports for years 2005 to 2019. Multivariate logistic and linear regression analyses were performed to determine statistical associations of demographic and health system characteristics with respect to childhood vaccination coverage rates.

Setting

The 14 administrative regions of Senegal were chosen for analysis.

Participants

DHS women’s survey respondents with living children aged 12-23 months for survey years 2005-2019.

Outcome Measures

Immunization with the third dose of the diphtheria-tetanus-pertussis vaccine (DTP3), widely used as a proxy for estimating immunization coverage levels and the retention of children in the vaccine program.

Results

Factors associated with childhood vaccination coverage include urban residence (β=0·61, p=0·0157), female literacy (β=1·11, p=0·0007), skilled prenatal care (β=1·80, p<0·0001), and self-reported ease of access to care when sick, considering travel distance to a healthcare facility (β=-0·70, p=0·0009) and concerns over traveling alone (β=-1·08, p<0·0001). Higher coverage with less variability over time was reported in urban areas near the capital and the coast (p=0·076), with increased coverage in recent years in more rural and landlocked areas.

Conclusions

Childhood vaccination was more likely among children whose mothers had higher literacy, received skilled prenatal care, and had perceived ease of access to care when sick. Overall, vaccination coverage is high in Senegal and disparities in coverage between regions have decreased significantly in recent years.
Machine learning based time series forecasting of chemical levels from the East Palestine, Ohio train derailment site
Authors: Ramachandra Vikas , Sethi Mohit
Published: March 2023

The paper presents a time series analysis of the air, water and soil data from the East Palestine, Ohio, train derailment site. The goal of the analysis is to investigate the temporal pattern of chemical pollutant levels in air, water and soil and to build machine learning and statistical models for forecasting various chemical concentrations over time.
Implementation and prospective real-time evaluation of a generalized system for in-clinic deployment and validation of machine learning models in radiology
Authors: Hawkins James R , Olson Marram P. , Harouni Ahmed , Qin Ming Melvin , Hess Christopher P , Majumdar Sharmila , Crane Jason C
Published: March 2023

The medical imaging community has embraced Machine Learning (ML) as evidenced by the rapid increase in the number of ML models being developed, but validating and deploying these models in the clinic remains a challenge. The engineering involved in integrating and assessing the efficacy of ML models within the clinical workflow is complex. This paper presents a general-purpose, end-to-end, clinically integrated ML model deployment and validation system implemented at UCSF. Engineering and usability challenges and results from 3 use cases are presented.

A generalized validation system based on free, open-source software was implemented, connecting clinical imaging modalities, the Picture Archiving and Communication System (PACS), and an ML inference server. ML pipelines were implemented in NVIDIA’s Clara Deploy framework with results and clinician feedback stored in a customized XNAT instance, linked within PACS. Prospective clinical validation studies of 3 ML models were conducted, with data routed from multiple clinical imaging modalities and PACS. Completed validation studies provided expert clinical feedback on model performance and usability, plus system reliability and performance metrics.

Clinical validation of ML models entails assessing model performance, impact on clinical infrastructure, robustness, and usability. Study results must be easily accessible to participating clinicians but remain outside the clinical record. Building a system that generalizes and scales across multiple ML models takes the concerted effort of software engineers, clinicians, data scientists, and system administrators, and benefits from the use of modular open-source software. The present work provides a template for institutions looking to translate and clinically validate ML models in the clinic, together with required resources and expected challenges.

Author summary

Academic medical centers gather and store vast quantities of digital data, and with the increase in accessibility of Machine Learning (ML) techniques, there has been an explosion of ML model development in the medical imaging community. Most of this work remains in research, though, and connecting ML models to the clinic for testing on live patient data and integration into the clinical workflow remains a challenge and impedes clinical impact. We present a general-purpose system, implemented and deployed at UCSF, for in-clinic validation of ML models and their incorporation into patient care. This work, based on free and open-source software packages, can serve as a template for other institutions looking to solve ML’s “last mile” problem and move their models out of research and into the clinic.
Rafting a waterfall: Artificial selection for collective composition can succeed or fail depending on the initial and target values
Authors: Lee Juhee , Shou Wenying , Park Hye Jin
Published: March 2023

Collectives, such as microbial communities, can perform functions beyond the capability of individual members. Enhancing these collective functions through artificial selection, however, presents significant challenges. Here, we explore the ‘rafting-a-waterfall’ phenomenon, a metaphor illustrating how the success in achieving a target population composition in microbial collectives depends on both the target characteristics and initial conditions. Specifically, collectives comprising fast-growing (F) and slow-growing (S) individuals were grown for a period of “maturation” time, and the collective with S-frequency closest to the target value is chosen to “reproduce” (inoculate) offspring collectives. Such collective selection is dictated by two opposing forces: during collective maturation, intra-collective selection acts like a waterfall, relentlessly driving the S-frequency to lower values, while during collective reproduction, inter-collective selection resembles a rafter striving to reach the target frequency. Due to this model structure, maintaining a target frequency requires the continued action of inter-collective selection. Using simulations and analytical calculations, we show that intermediate target S frequencies are the most challenging, akin to a target within the vertical drop of a waterfall, rather than above or below it. This arises because intra-collective selection is the strongest at intermediate S-frequencies, which can overpower inter-collective selection. While achieving low target S frequencies is consistently feasible, attaining high target S-frequencies requires an initially high S-frequency — much like a raft that can descend but not ascend a waterfall. The range of attainable target frequencies depends on the initial population size of the collectives: as the population size in Newborn collectives increases, the region of achievable target frequency is reduced until no frequency is achievable. In contrast, the number of collectives under selection plays a less critical role. In scenarios involving more than two populations, the evolutionary trajectory must navigate entirely away from the metaphorical ‘waterfall drop.’ Our findings illustrate that the strength of intra-collective evolution is frequency-dependent, with implications in experimental planning.
Replisome loading reduces chromatin motion independent of DNA synthesis
Authors: Pabba Maruthi K. , Ritter Christian , Chagin Vadim O. , Meyer Janis , Celikay Kerem , Stear Jeffrey H. , Loerke Dinah , Kolobynina Ksenia , Prorok Paulina , Schmid Alice Kristin , Leonhardt Heinrich , Rohr Karl , Cardoso M. Cristina
Published: March 2023

Chromatin has been shown to undergo diffusional motion, which is affected during gene transcription by RNA polymerase activity. However, the relationship between chromatin mobility and other genomic processes remains unclear. Hence, we set out to label the DNA directly in a sequence unbiased manner and followed labeled chromatin dynamics in interphase human cells expressing GFP-tagged PCNA, a cell cycle marker and core component of the DNA replication machinery. We detected decreased chromatin mobility during the S-phase compared to G1 and G2 phases in tumor as well as normal diploid cells using automated particle tracking. To gain insight into the dynamical organization of the genome during DNA replication, we determined labeled chromatin domain sizes and analyzed their motion in replicating cells. By correlating chromatin mobility proximal to the active sites of DNA synthesis, we showed that chromatin motion was locally constrained at the sites of DNA replication. Furthermore, inhibiting DNA synthesis led to increased loading of DNA polymerases. This was accompanied by accumulation of the single-stranded DNA binding protein on the chromatin and activation of DNA helicases further restricting local chromatin motion. We, therefore, propose that it is the loading of replisomes but not their catalytic activity that reduces the dynamics of replicating chromatin segments in the S-phase as well as their accessibility and probability of interactions with other genomic regions.

Highlights

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Direct and sequence unbiased labeling of DNA genome-wide

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DNA labeled chromatin is more mobile in G1/G2 relative to the S-phase

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Restriction of chromatin motion occurs proximal to sites of DNA replication

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Loading of replisomes, even in the absence of processive DNA synthesis, restricts chromatin motion
Global identification of direct SWI/SNF targets reveals compensation by EP400
Authors: Martin Benjamin J.E. , Ablondi Eileen F. , Goglia Christine , Adelman Karen
Published: March 2023

Mammalian SWI/SNF chromatin remodeling complexes move and evict nucleosomes at gene promoters and enhancers to modulate DNA access. Although SWI/SNF subunits are commonly mutated in disease, therapeutic options are limited by our inability to predict SWI/SNF gene targets and conflicting studies on functional significance. Here, we leverage a fast-acting inhibitor of SWI/SNF remodeling to elucidate direct targets and effects of SWI/SNF. Blocking SWI/SNF activity causes a rapid and global loss of chromatin accessibility and transcription. Whereas repression persists at most enhancers, we uncover a compensatory role for the EP400/TIP60 remodeler, which reestablishes accessibility at most promoters during prolonged loss of SWI/SNF. Indeed, we observe synthetic lethality between EP400 and SWI/SNF in lung cancer cell lines and human cancer patient data. Our data define a set of molecular genomic features that accurately predict gene sensitivity to SWI/SNF inhibition in diverse cancer cell lines, thereby improving the therapeutic potential of SWI/SNF inhibitors.

Highlights

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Genes repressed by long-term SWI/SNF loss do not accurately reflect direct targets

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Promoters that fail to reestablish activity are those lacking a compensatory remodeler

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Accessibility and activity recovery requires EP400, synthetically lethal with SWI/SNF

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SWI/SNF dependence in cancer cells can be predicted from the promoter chromatin state
Structurally divergent and recurrently mutated regions of primate genomes
Authors: Mao Yafei , Harvey William T. , Porubsky David , Munson Katherine M. , Hoekzema Kendra , Lewis Alexandra P. , Audano Peter A. , Rozanski Allison , Yang Xiangyu , Zhang Shilong , Gordon David S. , Wei Xiaoxi , Logsdon Glennis A. , Haukness Marina , Dishuck Philip C. , Jeong Hyeonsoo , del Rosario Ricardo , Bauer Vanessa L. , Fattor Will T. , Wilkerson Gregory K. , Lu Qing , Paten Benedict , Feng Guoping , Sawyer Sara L. , Warren Wesley C. , Carbone Lucia , Eichler Evan E.
Published: March 2023

To better understand the pattern of primate genome structural variation, we sequenced and assembled using multiple long-read sequencing technologies the genomes of eight nonhuman primate species, including New World monkeys (owl monkey and marmoset), Old World monkey (macaque), Asian apes (orangutan and gibbon), and African ape lineages (gorilla, bonobo, and chimpanzee). Compared to the human genome, we identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. Across 50 million years of primate evolution, we estimate that 819.47 Mbp or ~27% of the genome has been affected by SVs based on analysis of these primate lineages. We identify 1,607 structurally divergent regions (SDRs) wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (CARDs,ABCD7,OLAH) and new lineage-specific genes are generated (e.g.,CKAP2,NEK5) and have become targets of rapid chromosomal diversification and positive selection (e.g.,RGPDs). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species for the first time.
Prediction of protein assemblies by structure sampling followed by interface-focused scoring
Authors: Olechnovič Kliment , Valančauskas Lukas , Dapkūnas Justas , Venclovas Česlovas
Published: March 2023

Proteins often function as part of permanent or transient multimeric complexes, and understanding function of these assemblies requires knowledge of their three-dimensional structures. While the ability of AlphaFold to predict structures of individual proteins with unprecedented accuracy has revolutionized structural biology, modeling structures of protein assemblies remains challenging. To address this challenge, we developed a protocol for predicting structures of protein complexes involving model sampling followed by scoring focused on the subunit-subunit interaction interface. In this protocol, we diversified AlphaFold models by varying construction and pairing of multiple sequence alignments as well as increasing the number of recycles. In cases when AlphaFold failed to assemble a full protein complex or produced unreliable results, additional diverse models were constructed by docking of monomers or subcomplexes. All the models were then scored using a newly developed method, VoroIF-jury, which relies only on structural information. Notably, VoroIF-jury is independent of AlphaFold self-assessment scores and therefore can be used to rank models originating from different structure prediction methods. We tested our protocol in CASP15 and obtained top results, significantly outperforming the standard AlphaFold-Multimer pipeline. Analysis of our results showed that the accuracy of our assembly models was capped mainly by structure sampling rather than model scoring. This observation suggests that better sampling, especially for the antibody-antigen complexes, may lead to further improvement. Our protocol is expected to be useful for modeling and/or scoring protein assemblies.
From maternal glucocorticoid and thyroid hormones to epigenetic regulation of gene expression: an experimental study in a wild bird species
Authors: Hukkanen Mikaela , Hsu Bin-Yan , Cossin-Sevrin Nina , Crombecque Mélanie , Delaunay Axelle , Hollmen Lotta , Kaukonen Riina , Konki Mikko , Lund Riikka , Marciau Coline , Stier Antoine , Ruuskanen Suvi
Published: March 2023

Offspring phenotype at birth is determined by its genotype and the prenatal environment including exposure to maternal hormones. Variation in both maternal glucocorticoids and thyroid hormones can affect offspring phenotype. However, the underlying molecular mechanisms shaping the offspring phenotype, especially those contributing to long-lasting effects, remain unclear. Epigenetic changes (such as DNA methylation) have been postulated as mediators of long-lasting effects of early-life environment. In this study, we determined the effects of elevated prenatal glucocorticoid and thyroid hormones on handling stress response (breath rate), DNA methylation and gene expression of glucocorticoid receptor (GCR) and thyroid hormone receptor (THR) in great tit (Parus major). Eggs were injected before incubation onset with corticosterone (main avian glucocorticoid) and/or thyroid hormones (thyroxine and triiodothyronine) to simulate variation in maternal hormone deposition. Breath rate during handling and gene expression of GCR and THR were evaluated 14 days after hatching. Methylation status of GCR and THR genes were analyzed from the longitudinal blood samples taken 7 and 14 days after hatching, as well as in the following autumn. Elevated prenatal corticosterone level significantly increased the breath rate during handling, indicating enhanced stress response and/or metabolism. Prenatal corticosterone manipulation had CpG-site-specific effects on DNA methylation at the GCR putative promoter region, while it did not significantly affect GCR gene expression. GCR expression was negatively associated with earlier hatching date and chick size. THR methylation or expression did not exhibit any significant relationship with the hormonal treatments or the examined covariates, suggesting that TH signaling may be more robust due to its crucial role in development. This study supports the view that maternal corticosterone may influence offspring metabolism and stress response via epigenetic alterations, yet their possible adaptive role in optimizing offspring phenotype to the prevailing conditions, context-dependency, and the underlying molecular interplay needs further research.
Lineage Commitment of Dermal Fibroblast Progenitors is Mediated by Chromatin De-repression
Authors: Phan Quan M , Salz Lucia , Kindl Sam S , Lopez Jayden S , Thompson Sean M , Makkar Jasson , Driskell Iwona M , Driskell Ryan R
Published: March 2023

Dermal Fibroblast Progenitors (DFPs) differentiate into distinct fibroblast lineages during skin development. However, the mechanisms that regulate lineage commitment of naive dermal progenitors to form niches around the hair follicle, dermis, and hypodermis, are unknown. In our study, we used multimodal single-cell approaches, epigenetic assays, and allografting techniques to define a DFP state and the mechanisms that govern its differentiation potential. Our results indicate that the overall chromatin profile of DFPs is repressed by H3K27me3 and has inaccessible chromatin at lineage specific genes. Surprisingly, the repressed chromatin profile of DFPs renders them unable to reform skin in allograft assays despite their multipotent potential. Distinct fibroblast lineages, such as the dermal papilla and adipocytes contained specific chromatin profiles that were de-repressed during late embryogenesis by the H3K27-me3 demethylase, Kdm6b/Jmjd3. Tissue-specific deletion of Kdm6b/Jmjd3 resulted in ablating the adipocyte compartment and inhibiting mature dermal papilla functions in single-cell-RNA-seq, ChIPseq, and allografting assays. Altogether our studies reveal a mechanistic multimodal understanding of how DFPs differentiate into distinct fibroblast lineages, and we provide a novel multiomic search-tool within skinregeneration.org.
Novel axonemal protein ZMYND12 interacts with TTC29 and DNAH1, and is required for male fertility and flagellum function
Authors: Dacheux Denis , Martinez Guillaume , Broster Reix Christine E. , Beurois Julie , Lorès Patrick , Tounkara Magamba , Dupuy Jean-William , Robinson Derrick R. , Loeuillet Corinne , Lambert Emeline , Wehbe Zeina , Amiri-Yekta Amir , Daneshipour Abbas , Hosseini Seyedeh-Hanieh , Zouari Raoudha , Ben Mustapha Sélima Fourati , Halouani Lazhar , Jiang Xiaohui , Shen Ying , Liu Chunyu , Thierry-Mieg Nicolas , Septier Amandine , Bidart Marie , Satre Véronique , Cazin Caroline , Kherraf Zine-Eddine , Arnoult Christophe , Ray Pierre F. , Touré Aminata , Bonhivers Mélanie , Coutton Charles
Published: March 2023

Male infertility is common and complex, presenting a wide range of heterogeneous phenotypes. Although about 50% of cases are estimated to have a genetic component, the underlying cause often remains undetermined. Here, from whole-exome sequencing on samples from 168 infertile men with asthenoteratozoospermia due to severe sperm flagellum, we identified homozygousZMYND12variants in four unrelated patients. In sperm cells from these individuals, immunofluorescence revealed altered localization of DNAH1, DNALI1, WDR66 and TTC29. Axonemal localization of ZMYND12 ortholog TbTAX-1 was confirmed using theTrypanosoma bruceimodel. RNAi knock-down of TbTAX-1 dramatically affected flagellar motility, with a phenotype similar to the sperm from men bearing homozygousZMYND12variants. Co-immunoprecipitation and ultrastructure expansion microscopy inT. bruceirevealed TbTAX-1 to form a complex with TTC29. Comparative proteomics with samples fromTrypanosomaandTtc29KO mice identified a third member of this complex: DNAH1. The data presented revealed that ZMYND12 is part of the same axonemal complex as TTC29 and DNAH1, which is critical for flagellum function and assembly in humans, and Trypanosoma. ZMYND12 is thus a new asthenoteratozoospermia-associated gene, bi-allelic variants of which cause severe flagellum malformations and primary male infertility.
Discovery of long non-coding RNAs in the liver fluke,Fasciola hepatica
Authors: McVeigh Paul , McCammick Erin , Robb Emily , Brophy Peter , Morphew Russell M , Marks Nikki J , Maule Aaron G
Published: March 2023

Long non-coding (lnc)RNAs are a class of eukaryotic RNA that do not code for protein and are linked with transcriptional regulation, amongst a myriad of other functions. Using a customin silicopipeline we have identified 6,436 putative lncRNA transcripts in the liver fluke parasite,Fasciola hepatica; none of which are conserved with those previously described fromSchistosoma mansoni. F. hepaticalncRNAs were distinct fromF. hepaticamRNAs in transcript length, coding probability, exon/intron composition, expression patterns, and genome distribution. RNA-Seq and digital droplet PCR measurements demonstrated developmentally regulated expression of lncRNAs between intra-mammalian life stages; a similar proportion of lncRNAs (14.2 %) and mRNAs (12.8 %) were differentially expressed (p<0.001), supporting a functional role for lncRNAs inF. hepaticalife stages. While most lncRNAs (81%) were intergenic, we identified some that overlapped protein coding loci in antisense (13%) or intronic (6%) configurations. We found no unequivocal evidence for correlated developmental expression within positionally correlated lncRNA:mRNA pairs, but global co-expression analysis identified five lncRNA that were inversely co-regulated with 89 mRNAs, including a large number of functionally essential proteases. The presence of micro (mi)RNA binding sites in 3135 lncRNAs indicates the potential for miRNA-based post-transcriptional regulation of lncRNA, and/or their function as competing endogenous (ce)RNAs. This first description of lncRNAs inF. hepaticaprovides an avenue to future functional and comparative genomics studies that will provide a new perspective on a poorly understood aspect of parasite biology.
Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
Authors: Eme Laura , Tamarit Daniel , Caceres Eva F. , Stairs Courtney W. , Anda Valerie De , Schön Max E. , Seitz Kiley W. , Dombrowski Nina , Lewis William H. , Homa Felix , Saw Jimmy H. , Lombard Jonathan , Nunoura Takuro , Li Wen-Jun , Hua Zheng-Shuang , Chen Lin-Xing , Banfield Jillian F. , John Emily St , Reysenbach Anna-Louise , Stott Matthew B. , Schramm Andreas , Kjeldsen Kasper U. , Teske Andreas P. , Baker Brett J. , Ettema Thijs J. G.
Published: March 2023

In the ongoing debates about eukaryogenesis, the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors, members of the Asgard archaea play a key role as the closest archaeal relatives of eukaryotes. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved. Here, we analyze distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea, as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree/species tree reconciliation approaches, we show that, in analogy to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared to other archaea. Finally, we infer that the last common ancestor of Asgard archaea likely was a thermophilic chemolithotroph, and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and the platform for the emergence of cellular complexity in eukaryotic cells.
CaudalFgfr1disruption produces localised spinal mis-patterning and a terminal myelocystocele-like phenotype in mice
Authors: Maniou Eirini , Farah Faduma , Crane-Smith Zoe , Krstevski Andrea , Stathopoulou Athanasia , Greene Nicholas D.E. , Copp Andrew J. , Galea Gabriel L.
Published: March 2023

Closed spinal dysraphisms are poorly understood neurodevelopmental malformations commonly classed as neural tube defects. Several, including terminal myelocystocele, selectively affect the distal lumbosacral spine. We previously identified a neural tube closure-initiating point, Closure 5, involved in forming the distal spine of mice. Here we document equivalent morphology of the caudal-most end of the closing posterior neuropore (PNP) in mice and humans, suggesting Closure 5 is conserved in humans. It forms in a region of active fibroblast growth factor (FGF) signalling and pharmacological blockade of FGF receptors (Fgfr) impairs Closure 5 formation in cultured mouse embryos. Conditional genetic deletion ofFgfr1in caudal embryonic tissues withCdx2Cresimilarly impairs Closure 5 formation and leads to morphologically abnormal PNPs, which nonetheless achieve delayed closure although delayed. After PNP closure, a localised region of the distal neural tube ofFgfr1-disrupted embryos re-opens into a trumpet-like flared central canal between the presumptive hindlimbs, progressing to form a distal fluid-filled sac overlying ventrally flattened spinal cord. This phenotype resembles terminal myelocystocele. Histological analysis of spinal progenitor domains reveals regional and progressive loss of ventral spinal cord progenitor domains preceding cystic dilation of the central canal. Initially, the Shh and FoxA2-positive ventral domains are lost, resulting in Olig2-labelling of the ventral-most neural tube. The Olig2-domain is also subsequently lost, eventually producing a neural tube entirely positive for the dorsal marker Pax3. Thus, a terminal myelocystocele-like phenotype can arise after completion of neural tube closure due to localised spinal mis-patterning caused by disruption of Fgfr1 signalling.
The role of glutathione in periplasmic redox homeostasis and oxidative protein folding inEscherichia coli
Authors: Knoke Lisa R. , Zimmermann Jannik , Lupilov Natalie , Schneider Jannis F. , Celebi Beyzanur , Morgan Bruce , Leichert Lars I.
Published: March 2023

The thiol redox balance in the periplasm ofE. colidepends on the DsbA/B pair for oxidative power and the DsbC/D system as its complement for isomerization of non-native disulfides. While the standard redox potentials of those systems are known, thein vivoredox potential imposed onto protein thiol disulfide pairs in the periplasm remains unknown. Here, we used genetically encoded redox probes (roGFP2 and roGFP-iL), targeted to the periplasm, to directly probe the thiol redox homeostasis in this compartment. These probes contain two cysteine residues, that are virtually completely reduced in the cytoplasm, but once exported into the periplasm, can form a disulfide bond, a process that can be monitored by fluorescence spectroscopy. Even in the absence of DsbA, roGFP2, exported to the periplasm, was fully oxidized, suggesting the presence of an alternative system for the introduction of disulfide bonds into exported proteins. However, the absence of DsbA shifted the periplasmic thiol-redox potential from -228 mV to a more reducing -243 mV and the capacity to re-oxidize periplasmic roGFP2 after a reductive pulse was significantly decreased. Re-oxidation in a DsbA strain could be fully restored by exogenous oxidized glutathione (GSSG), while reduced GSH accelerated re-oxidation of roGFP2 in the WT. In line, a strain devoid of endogenous glutathione showed a more reducing periplasm, and was significantly worse in oxidatively folding PhoA, a native periplasmic protein and substrate of the oxidative folding machinery. PhoA oxidative folding could be enhanced by the addition of exogenous GSSG in the WT and fully restored in a ΔdsbAmutant. Taken together this suggests the presence of an auxiliary, glutathione-dependent thiol-oxidation system in the bacterial periplasm.
ORC1 binds tocis-transcribed RNAs for efficient activation of replication origins
Authors: Mas Aina Maria , Goñi Enrique , de los Mozos Igor Ruiz , Arcas Aida , Statello Luisa , Gonzalez Jovanna , Blázquez Lorea , Chelsea Lee Wei Ting , Gupta Dipika , Sejas Álvaro , Hoshina Shoko , Armaos Alexandros , Tartaglia Gian Gaetano , Waga Shou , Ule Jernej , Rothenberg Eli , Gómez María , Huarte Maite
Published: March 2023

Cells must coordinate the activation of thousands of replication origins dispersed throughout their genome. Active transcription is known to favor the formation of mammalian origins, although the role that RNA plays in this process remains unclear. We show that the ORC1 subunit of the human Origin Recognition Complex interacts with RNAs transcribed from genes with origins in their transcription start sites (TSSs), displaying a positive correlation between RNA binding and origin activity. RNA depletion, or the use of ORC1 RNA-binding mutant, result in inefficient activation of proximal origins, linked to impaired ORC1 chromatin release. ORC1 RNA binding activity resides in its intrinsically disordered region, involved in intra- and inter-molecular interactions, regulation by phosphorylation, and phase-separation. We show that RNA binding favors ORC1 chromatin release, by regulating its phosphorylation and subsequent degradation. We propose that fluctuating concentrations of RNA during the cell cycle may play a sequential role in controlling origins through interaction with this flexible region of ORC1. Our results unveil a novel non-coding function of RNA as a dynamic component of the chromatin, orchestrating the activation of replication origins.

One sentence summary

The human origin recognition complex subunit 1 ORC1, binds to RNAs transcribed from genes with origins of replication at the TSS, which is required for optimal origin activation.
Smart Lattice Light Sheet Microscopy for imaging rare and complex cellular events
Authors: Shi Yu , Tabet Jimmy S. , Milkie Daniel E. , Daugird Timothy A. , Yang Chelsea Q. , Giovannucci Andrea , Legant Wesley R.
Published: March 2023

Light sheet microscopes enable rapid, high-resolution imaging of biological specimens; however, biological processes span a variety of spatiotemporal scales. Moreover, long-term phenotypes are often instigated by rare or fleeting biological events that are difficult to capture with a single imaging modality and constant imaging parameters. To overcome this limitation, we present smartLLSM, a microscope that incorporates AI-based instrument control to autonomously switch between epifluorescent inverted imaging and lattice light sheet microscopy. We apply this technology to two major scenarios. First, we demonstrate that the instrument provides population-level statistics of cell cycle states across thousands of cells on a coverslip. Second, we show that by using real-time image feedback to switch between imaging modes, the instrument autonomously captures multicolor 3D datasets or 4D time-lapse movies of dividing cells at rates that dramatically exceed human capabilities. Quantitative image analysis on high-content + high-throughput datasets reveal kinetochore and chromosome dynamics in dividing cells and determine the effects of drug perturbation on cells in specific mitotic stages. This new methodology enables efficient detection of rare events within a heterogeneous cell population and records these processes with high spatiotemporal 4D imaging over statistically significant replicates.