bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of tissue-specific expression of ancestral genes across vertebrates and insects
Authors: Mantica Federica , Iñiguez Luis P. , Marquez Yamile , Permanyer Jon , Torres-Mendez Antonio , Cruz Josefa , Franch-Marro Xavi , Tulenko Frank , Burguera Demian , Bertrand Stephanie , Doyle Toby , Nouzova Marcela , Currie Peter , Noriega Fernando G. , Escriva Hector , Arnone Maria Ina , Albertin Caroline B , Wotton Karl R , Almudi Isabel , Martin David , Irimia Manuel
Published: November 2022

Regulation of gene expression is arguably the main mechanism contributing to tissue phenotypic diversity within and between species. Here, we assembled an extensive transcriptomic dataset covering twenty bilaterian species and eight tissues, selecting a specular phylogeny that allowed both the combined and parallel investigation of gene expression evolution between vertebrates and insects. We specifically focused on widely conserved ancestral genes, identifying strong cores of pan-bilaterian tissue-specific genes and even larger groups that diverged to define vertebrate and insect tissues. Systematic inferences of tissue-specificity gains and losses show that nearly half of all ancestral genes have been recruited into tissue-specific transcriptomes. This occurred during both ancient and, especially, recent bilaterian evolution, with several gains being associated with the emergence of unique phenotypes. Such pervasive evolution of tissue-specificity was linked to gene duplication coupled with specialization, including an unappreciated prolonged effect of whole genome duplications during recent vertebrate evolution.
Highly accurate genome assembly of an improved high-yielding silkworm strain, Nichi01
Authors: Waizumi Ryusei , Tsubota Takuya , Jouraku Akiya , Kuwazaki Seigo , Yokoi Kakeru , Iizuka Tetsuya , Yamamoto Kimiko , Sezutsu Hideki
Published: November 2022

The silkworm (Bombyx mori) is an important lepidopteran model insect, and an industrial domestic animal traditionally used for silk production. Here, we report the genome assembly of an improved Japanese strain Nichi01, in which the cocoon yield is comparable to that of commercial silkworm strains. The integration of PacBio Sequel II long-read and ddRAD-seq-based high-density genetic linkage map achieved the highest quality genome assembly of silkworms to date; 22 of the 28 pseudomolecules contained telomeric repeats at both ends, and only four gaps were present in the assembly. A total of 452 Mbp of the assembly with an N50 of 16.614 Mbp covered 99.3% of the complete orthologs of the Arthropod core genes. Although the genome sequence of Nichi01 and that of the previously reported low-yielding tropical strain p50T assured their accuracy in most regions, we corrected several regions, misassembled in p50T, in our assembly. A total of 18,397 proteins were predicted using over 95 Gb of mRNA-seq derived from 10 different organs, covering 96.9% of the complete orthologs of the Arthropod core genes. The final assembly and annotation files are available in KAIKObase (https://kaikobase.dna.affrc.go.jp/index.html) along with a genome browser and BLAST searching service, which would facilitate further studies and the breeding of silkworms and other insects.
Tau polarizes an aging transcriptional signature to excitatory neurons and glia
Authors: Wu Timothy , Deger Jennifer M. , Ye Hui , Guo Caiwei , Dhindsa Justin , Pekarek Brandon T. , Al-Ouran Rami , Liu Zhandong , Al-Ramahi Ismael , Botas Juan , Shulman Joshua M.
Published: November 2022

Aging is a major risk factor for Alzheimer’s disease (AD), and cell-type vulnerability underlies its characteristic clinical manifestations. We have performed longitudinal, single-cell RNA-sequencing inDrosophilawith pan-neuronal expression of human tau, which forms AD neurofibrillary tangle pathology. Whereas tau- and aging-induced gene expression strongly overlap (93%), they differ in the affected cell types. In contrast to the broad impact of aging, tau-triggered changes are strongly polarized to excitatory neurons and glia. Further, tau can either activate or suppress innate immune gene expression signatures in a cell type-specific manner. Integration of cellular abundance and gene expression pinpoints Nuclear Factor Kappa B signaling as a potential marker for neuronal vulnerability. We also highlight the conservation of cell type-specific transcriptional patterns betweenDrosophilaand human postmortem brain tissue. Overall, our results create a resource for dissection of dynamic, age-dependent gene expression changes at cellular resolution in a genetically tractable model of tauopathy.
Analysis of Larval Fish Feeding Behavior under Naturalistic Conditions
Authors: Bar Shir , Levy Liraz , Avidan Shai , Holzman Roi
Published: November 2022

Modern research efforts concerned with animal behavior rely heavily on image and video analysis. While such data are now quick to obtain, extracting and analyzing complex behaviors under naturalistic conditions is still a major challenge, specifically when the behavior of interest is sporadic and rare. In this study, we present an end-to-end system for capturing, detecting and analyzing larval fish feeding behavior in unconstrained naturalistic environments. We first constructed a specialized system for imaging these tiny, fast-moving creatures and deployed it in large aquaculture rearing pools. We then designed an analysis pipeline using several action classification backbones, and compare their performance. A natural feature of the data was the extremely low prevalence of feeding events, leading to low sample sizes and highly imbalanced datasets despite extensive annotation efforts. Nevertheless, our pipeline successfully detected and classified the sparsely-occurring feeding behavior of fish larvae in a curated experimental setting from videos featuring multiple animals. We introduce three new annotated datasets of underwater videography, in a curated and an uncurated setting. As challenges related to data imbalance and expert’s annotation are common to the analysis of animal behavior under naturalistic conditions, we believe our findings can contribute to the growing field of computer vision for the study and understanding of animal behavior.
Dynamic involvement of premotor and supplementary motor areas in bimanual pinch force control
Authors: Karabanov Anke Ninija , Chillemi Gaetana , Madsen Kristoffer Hougaard , Siebner Hartwig Roman
Published: November 2022

Many bimanual activities of daily living require quick shifts between symmetric and asymmetric motor output generated by the right and left hand. Bimanual motor control has been mostly studied during continuous repetitive tasks, while little research has been carried out in experimental settings requiring dynamic changes in motor output generated by both hands. Here, we performed functional magnetic resonance imaging (MRI) while healthy volunteers performed a visually guided, bimanual pinch force task. This enabled us to map functional activity and connectivity of premotor and motor areas during bimanual pinch force control in different task contexts, requiring mirror-symmetric or inverse-asymmetric changes in discrete pinch force exerted with the right and left hand. The bilateral dorsal premotor cortex showed increased activity and effective coupling to the ipsilateral supplementary motor area (SMA) in the inverse-asymmetric context compared to the mirror-symmetric context of bimanual pitch force control. Compared to unilateral pinches, all bimanual pinch force conditions were characterized by an increased level of activation in the bilateral primary motor hand area (M1-HAND) and stronger coupling from SMA to the ipsilateral M1-HAND. Task-related activity of a cluster in the left caudal SMA scaled positively with the degree of synchronous initiation of bilateral pinch force adjustments, irrespectively of the task context. The results suggest that the dorsal premotor cortex mediates increasing complexity of bimanual coordination by increasing coupling to the SMA-M1 network.
Somatic Loss of the Y Chromosome and Alzheimer’s Disease Risk
Authors: Palmer Ellen , Benchek Penelope , Wheeler Nicholas , Smeiszek Sandra , Naj Adam C. , Haines Jonathan L. , Pericak-Vance Margaret A. , Forsberg Lars A. , Cukier Holly N. , Song Yeunjoo , Bush William S.
Published: November 2022

Mosaic loss of the Y chromosome (LOY) is a somatic, age-related event that has been previously associated with a variety of diseases of aging. A prior study of European cohorts demonstrated an association between LOY and Alzheimer’s Disease and more recent molecular studies have shown that LOY can also occur within microglia, suggesting a potential functional role in AD pathogenesis. In this study, we further validate the association between LOY and AD via prospective analyses of 1,447 males, and perform Mendelian Randomization analysis on 10,013 males across 26 US cohorts. Significant results from these analyses provide further evidence for a role of LOY in the development of Alzheimer’s Disease.
scAbsolute: measuring single-cell ploidy and replication status
Authors: Schneider Michael P. , Cullen Amy , Pangonyte Justina , Skelton Jason , Major Harvey , Van Oudenhove Elke , Garcia Maria J. , Chaves-Urbano Blas , Piskorz Anna M. , Brenton James D. , Macintyre Geoff , Markowetz Florian
Published: November 2022

Cancer cells often exhibit DNA copy number aberrations and can vary widely in their ploidy. Correct estimation of the ploidy of single cell genomes is paramount for downstream analysis. Based only on single-cell DNA sequencing information,scAbsoluteachieves accurate and unbiased measurement of single-cell ploidy and replication status, including whole-genome duplications. We demonstratescAbsolute’scapabilities using experimental cell multiplets, a FUCCI cell cycle expression system, and a benchmark against state-of-the-art methods.scAbsoluteprovides a robust foundation for single-cell DNA sequencing analysis across different technologies and has the potential to enable improvements in a number of downstream analyses.
MOT: a Multi-Omics Transformer for multiclass classification tumour types predictions
Authors: Osseni Mazid Abiodoun , Tossou Prudencio , Laviolette Francois , Corbeil Jacques
Published: November 2022

Motivation

Breakthroughs in high-throughput technologies and machine learning methods have enabled the shift towards multi-omics modelling as the preferred means to understand the mechanisms underlying biological processes. Machine learning enables and improves complex disease prognosis in clinical settings. However, most multi-omic studies primarily use transcriptomics and epigenomics due to their over-representation in databases and their early technical maturity compared to others omics. For complex phenotypes and mechanisms, not leveraging all the omics despite their varying degree of availability can lead to a failure to understand the underlying biological mechanisms and leads to less robust classifications and predictions.

Results

We proposed MOT (Multi-Omic Transformer), a deep learning based model using the transformer architecture, that discriminates complex phenotypes (herein cancer types) based on five omics data types: transcriptomics (mRNA and miRNA), epigenomics (DNA methylation), copy number variations (CNVs), and proteomics. This model achieves an F1-score of 98.37% among 33 tumour types on a test set without missing omics views and an F1-score of 96.74% on a test set with missing omics views. It also identifies the required omic type for the best prediction for each phenotype and therefore could guide clinical decisionmaking when acquiring data to confirm a diagnostic. The newly introduced model can integrate and analyze five or more omics data types even with missing omics views and can also identify the essential omics data for the tumour multiclass classification tasks. It confirms the importance of each omic view. Combined, omics views allow a better differentiation rate between most cancer diseases. Our study emphasized the importance of multi-omic data to obtain a better multiclass cancer classification.

Availability and implementation

MOT source code is available athttps://github.com/dizam92/multiomic_predictions.
Age and Sex-Dependent Differences in Human Cardiac Matrix-Bound Exosomes Modulate Fibrosis through Synergistic miRNA Effects
Authors: Ronan George , Bahcecioglu Gokhan , Yang Jun , Zorlutuna Pinar
Published: November 2022

Aging is a risk factor for cardiovascular disease, the leading cause of death worldwide. Cardiac fibrosis is a harmful result of repeated myocardial infarction that increases risk of morbidity and future injury. Interestingly, rates of cardiac fibrosis are different between young and aged individuals, as well as men and women. Here, for the first time, we identify and isolate matrix-bound extracellular vesicles from the left ventricles (LVs) of young or aged men and women. These LV vesicles (LVVs) show differences in morphology and content between these four cohorts. LVVs effects on fibrosis were also investigatedin vitro, and it was shown that aged male LVVs were pro-fibrotic, while other LVVs were anti-fibrotic. miRNAs identified from these LVVs could partially recapitulate these effects together, but not individually, and confer other benefits. These data suggest that synergistic effects of matrix-resident exosomal miRNAs may influence the differential clinical response to MI.
Ultra-fast protein structure prediction to capture effects of sequence variation in mutation movies
Authors: Weissenow Konstantin , Heinzinger Michael , Steinegger Martin , Rost Burkhard
Published: November 2022

Top protein three-dimensional (3D) structure predictions require evolutionary information from multiple-sequence alignments (MSAs) and deep, convolutional neural networks and appear insensitive to small sequence changes. Here, we describeEMBER3Dusing embeddings from the pre-trained protein language model (pLM) ProtT5 to predict 3D structure directly from single sequences. Orders of magnitude faster than others, EMBER3D predicts average-length structures in milliseconds on consumer-grade machines. Although not nearly as accurate asAlphaFold2, the speed of EMBER3D allows a glimpse at future applications such as the almost real-time rendering of deep mutational scanning (DMS) movies that visualize the effect of all point mutants on predicted structures. This also enables live-editing of sequence/structure pairs. EMBER3D is accurate enough for highly sensitive rapid remote homology detection byFoldseekidentifying structural similarities. Overall, our use cases suggest that speed can complement accuracy, in particular when accessible through consumer-grade machines. EMBER3D is free and publicly available:https://github.com/kWeissenow/EMBER3D.
Subset-specific mitochondrial and DNA damage shapes T cell responses to fever and inflammation
Authors: Heintzman Darren R. , Elasy Joel , Chi Channing , Ye Xiang , Krystoviak Evan S. , Khan Wasay , Olson Lana , Jones Angela , Voss Kelsey , Patterson Andrew R. , Sugiura Ayaka , Mason Frank M. , Hong Hanna S. , Bass Lindsay , Beier Katherine L. , Deng Wentao , Lyssiotis Costas A. , Bick Alexander G. , Rathmell W. Kimryn , Rathmell Jeffrey C.
Published: November 2022

Heat is a cardinal feature of inflammation. Despite temperature variability and dependence of enzymes and complexes, how heat and fever affect immune cells remains uncertain. We found that heat broadly increased inflammatory activity of CD4+T cell subsets and decreased Treg suppressive function. Th1 cells, however, also selectively developed mitochondrial dysfunction with high levels of ROS production and DNA damage. This led Th1 cells to undergoTp53-dependent death, which was required to minimize the accumulation of mutations in heat and inflammation. Th1 cells with similar DNA damage signatures were also detected in Crohn’s disease and rheumatoid arthritis. Fever and inflammation-associated heat thus selectively induce mitochondrial stress and DNA damage in activated Th1 cells that requires p53 to maintain genomic integrity of the T cell repertoire.

One Sentence Summary

Fever temperatures augment CD4+T cell-mediated inflammation but induce differential metabolic stress and DNA damage in T cell subsets, with Th1 cells selectively sensitive and dependent on p53 to induce apoptosis and maintain genomic integrity.
Controlled Hydrogen Sulfide Delivery to Enhance Cell Survival in Bone Tissue Engineering
Authors: Ghavimi Soheila Ali Akbari , Faulkner Trent J. , Tata Rama Rao , Lungren Ethan S. , Zhang Rui , Bumann Erin E. , Ulery Bret D.
Published: November 2022

The increased local concentration of calcium ions (Ca2+) and phosphate (Pi), a natural body process for bone healing and remodeling, as well as local delivery of these ions as signaling molecules by synthetic bone graft substitutes, may lead to cytotoxic ion levels that can result in Ca2+/ Pimitochondria overload, oxidative stress, and cell death. In this research, the effect of H2S as a cytoprotective signaling molecule to increase the tolerance of mesenchymal stem cells (MSCs) in the presence of cytotoxic level of Ca2+/Piwas evaluated. Different concentrations of sodium hydrogen sulfide (NaSH), a fast-releasing H2S donor, were exposed to cells in order to evaluate the influence of H2S on MSC proliferation. The results suggested that a range of NaSH (i.e., 0.25 - 4 mM NaSH) was non-cytotoxic and could improve cell proliferation and differentiation in the presence of cytotoxic levels of Ca2+(32 mM) and/or Pi(16 mM). To controllably deliver H2S over time, a novel donor molecule in thioglutamic acid (GluSH) was synthesized and evaluated for its H2S release profile. Excitingly, GluSH successfully maintained cytoprotective level of H2S over 7 days. Furthermore, MSCs exposed to cytotoxic Ca2+/Piconcentrations in the presence of GluSH were able to thrive and differentiate into osteoblasts. These findings suggest that the incorporation of a sustained H2S donor such as GluSH into CaP-based bone substitutes can facilitate considerable cytoprotection making it an attractive option for complex bone regenerative engineering applications.
Optimizing bioink composition for human chondrocyte expression of lubricin
Authors: Martyniak Kari , Kennedy Sean , Cruz Maria A. , Karimzadeh Makan , Jeon Oju , Alsberg Eben , Kean Thomas J.
Published: November 2022

The surface zone of articular cartilage is the first area impacted by cartilage defects, commonly resulting in osteoarthritis. Chondrocytes in the surface zone of articular cartilage synthesize and secrete lubricin, a proteoglycan that functions as a lubricant protecting the deeper layers from shear stress. 3D bioprinting is a tissue engineering technique that uses cells encapsulated in biomaterials to fabricate 3D constructs. Gelatin methacrylate (GelMA) is a frequently used biomaterial for 3D bioprinting cartilage. Oxidized methacrylated alginate (OMA) is a chemically modified alginate designed for its tunable degradation rate and mechanical properties. To determine an optimal combination of GelMA and OMA for lubricin expression, we used our novel high-throughput human articular chondrocyte reporter system. Primary human chondrocytes were transduced withPRG4(lubricin) promoter-drivenGaussialuciferase, allowing for temporal assessment of lubricin expression. A lubricin expression driven Design of Experiment screen and subsequent validation identified 14% GelMA/2% OMA for further study. Therefore, 14% GelMA/2% OMA, 14% GelMA and 16% GelMA were 3D bioprinted. The combination of lubricin protein expression and shape retention over the 22 days in culture, determined the 14% GelMA/2%OMA to be the optimal formulation for lubricin secretion.
Standards needed? An Exploration of Qualifying Exams from a Literature Review and Website Analysis of University-Wide Policies
Authors: McLaughlin Jacqueline E. , Morbitzer Kathryn , Meilhac Margaux , Poupart Natalie , Layton Rebekah L. , Jarstfer Michael B.
Published: November 2022

Purpose

While known by many names, qualifying exams function as gatekeepers to graduate student advancement to PhD Candidacy, yet there has been little formal study on best qualifying exam practices particularly in biomedical and related STEM PhD programs. The purpose of this study was to examine the current state of qualifying exams through an examination of the literation and exploration of university policies.

Design/methodology/approach

We conducted a literature review of studies on qualifying exams and completed an external evaluation of peer institutions’ and internal institutional qualifying exam requirements to inform our discussion of common practices of qualifying exams in doctoral training at a research-intensive institutions.

Findings

Our research identified the need for more evidence-based research on qualifying exams, which are nearly universal as a major doctoral training milestone across US institutions of higher education. Our findings indicate a wide variety of qualifying exam formats, often lacking the establishment of explicit expectations and evidence for specific formats. This lack of understanding of best practices coupled with insufficient clarity has a real potential to disadvantage doctoral students, particularly first generation, underrepresented minority, international, and/or other trainees who are not privileged or socialized to navigate training environments with vague landmarks such as the qualifying exams.

Originality

There are very few studies that evaluate qualifying exams in US doctoral education, particularly in STEM fields, and to our knowledge, there has been no analysis of campus wide policies on qualifying exams reported. The lack of evidence for best practices and the need for to evaluate the implementation and effectiveness of qualifying exams are discussed.
Investigations into hydrogen sulfide-induced suppression of neuronal activity in vivo and calcium dysregulation in vitro
Authors: Kim Dong-Suk , Pessah Isaac N. , Santana Cristina M , Purnell Benton , Li Rui , Buchanan Gordon F , Rumbeiha Wilson K.
Published: November 2022

Acute exposure to high concentrations of hydrogen sulfide (H2S) leads to sudden death and, if survived, lingering neurological disorders. Clinical signs include seizures, loss of consciousness, and dyspnea. The proximate mechanisms underlying H2S-induced acute toxicity and death have not been clearly elucidated. We investigated electrocerebral, cardiac and respiratory activity during H2S exposure using EEG, EKG and plethysmography. H2S suppressed electrocerebral activity and disrupted breathing. Cardiac activity was comparatively less affected. To test whether Ca2+dysregulation contributes to H2S-induced EEG suppression, we developed an in vitro real-time rapid throughput assay measuring patterns of spontaneous synchronized Ca2+oscillations in cultured primary cortical neuronal (PCN) networks loaded with the indicator Fluo-4 using the fluorescent imaging plate reader (FLIPR-Tetra®). Sulfide >5 ppm dysregulated SCO patterns in a dose-dependent manner. Inhibitors of NMDA and AMPA receptors magnified H2S-induced SCO suppression. Inhibitors of L-type voltage gated Ca2+channels (VGCC) and transient receptor potential (TRP) channels prevented H2S-induced SCO suppression. Inhibitors of T-type VGCC, ryanodine receptors, and sodium channels had no measurable influence on H2S-induced SCO suppression. Exposures to >5 ppm sulfide also suppressed neuronal electrical activity in PCN measured by multi-electrode array (MEA), an effect alleviated by pretreatment with the nonselective TRP inhibitor 2-APB. The TRP inhibitor also reduced PCN cell death from sulfide exposure. These results improve our understanding of the role of different Ca2+channels in acute H2S-induced neurotoxicity and identify TRP channel modulators as novel structures with potential therapeutic benefits.
Misaligned plastic and evolutionary responses of lifespan to novel carbohydrate diets
Authors: Narayan Vikram P. , Wasana Nidarshani , Wilson Alastair J. , Chenoweth Stephen F.
Published: November 2022

Diet elicits varied effects on longevity across a wide range of animal species. For example, diets low in protein and high in carbohydrate typically extend lifespan while diets high in protein tend to reduce it. Although studies have also shown that diet-induced lifespan changes can persist through transgenerational plasticity, whether such changes lead to evolutionary shifts in lifespan remains unclear. In this study we combine experimental evolution and phenotypic plasticity assays to address this gap. UsingDrosophila serrata, we investigated the evolutionary potential of lifespan in response to four novel diets spanning a carbohydrate-protein gradient. We also examined developmental plasticity effects using a set of control populations that were raised on the four novel environments. Our results show that although lifespan evolved in response to changes in dietary carbohydrate concentration, the plastic responses for lifespan differed from the evolved responses. The direction of the evolved response (increased lifespan) observed on low carbohydrate diets was in the opposite direction to the plastic response (decreased lifespan). Our results imply that plastic responses to low carbohydrates can be maladaptive for lifespan and misaligned with the evolved responses, laying the groundwork for future investigations of carbohydrate contributions to evolved and plastic effects on lifespan.
Brain energy metabolism is optimized to minimize the cost of enzyme synthesis and transport
Authors: Gustafsson Johan , Robinson Jonathan L. , Zetterberg Henrik , Nielsen Jens
Published: November 2022

Energy metabolism of the brain is poorly understood partly due to the complex morphology of neurons. Here we used metabolic models that estimate costs of enzyme usage per pathway, enzyme utilization over time, and enzyme transport to evaluate a paradigm that suggests that brain energy metabolism is optimized to minimize enzyme synthesis and transportation costs. Our models recapitulate known metabolic behaviors and provide explanation for the astrocyte-neuron lactate shuttle theory.
A complex evolutionary history of genetic barriers to gene flow in hybridizing warblers
Authors: Wang Silu , Coop Graham
Published: November 2022

TheSetophagawarbler sister species in western North America,Setophaga occidentalisandS. townsendiprovide a rare opportunity to explore how the accumulation of genetic barriers to gene flow contributes to speciation. These sister species are at the very early stages of speciation, as their genome-wide divergence is limited, and they hybridize extensively upon secondary contact. However, there are several well-characterized loci involved in speciation. There is a plumage difference between the species controlled by mutations close to the agouti signaling protein (ASIP), which generates underdominance due to compromised hybrid territorial signaling. A second large region (~2Mb) on chromosome 5 encodes many mitochondrial-interacting genes and coevolves with the mitochondrial genome. Here we reconstructed the ancestral recombination graphs of these genomic regions relative to the genome-wide background to learn about the evolutionary history of these barriers. We find signatures of long-lasting barrier effects that lasted for ~190 K generations, and recent selective sweeps in chr5 mitonuclear genetic block in both species within the past 60 K generations ago. We further observed heterogeneity within the long-lasting mitonuclear barrier with localized signals of much more recent selective sweeps unique one of the species. The divergence of ASIP is elevated by a species-specific selective sweep withinS. occidentalisthat occurred 21 K generations ago. However, the signature of long-lasting barrier effect is much weaker at ASIP suggesting that it may have arisen later than the mitonuclear system. Associating the evolutionary history of these genetic barriers with Pleistocene climate change history sheds light on the intrinsic and extrinsic reciprocity underlying the origin of species.
A dynamic Campylobacterales epibiont community associated with the bone eating wormOsedax
Authors: Goffredi Shana , Panossian Balig , Brzechffa Camille , Field Naomi , King Chad , Moggioli Giacomo , Rouse Greg W. , Martín-Durán José M. , Henry Lee
Published: November 2022

Osedax, the deep-sea annelid found at sunken whalefalls, is known to host Oceanospirillales bacterial endosymbionts intracellularly in specialized roots, that help it feed exclusively on vertebrate bones. Past studies, however, have also made mention of external bacteria on their trunks. During a 14-year study, we reveal a dynamic, yet persistent, succession of Campylobacterales integrated into the epidermis ofOsedax, that change over time as the whale carcass degrades on the sea floor. The Campylobacterales associated with seven species ofOsedax, which comprise 67% of the bacterial community on the trunk, are initially dominated by the genusArcobacter(at early time points < 24 months), theSulfurospirillumat intermediate stages (~ 50 months), and theSulfurimonasat later stages (>140 months) of whale carcass decomposition. Metagenome analysis of the epibiont metabolic capabilities suggests a transition from heterotrophy to autotrophy along the successional gradient, and differences in their capacity to metabolize oxygen, carbon, nitrogen, and sulfur. Compared to free living relatives, theOsedaxepibionts were highly enriched in transposable elements, implicating genetic exchange on the host surface, and contained numerous secretions systems with eukaryotic-like protein domains, suggesting a long evolutionary history with these enigmatic, yet widely distributed deep-sea worms
Interleukin-2 immunotherapy reveals human regulatory T cell subsets with distinct functional and gatekeeper features
Authors: Raeber Miro E. , Caspar Dominic , Zurbuchen Yves , Guo Nannan , Schmid Jonas , Michler Jan , Steiner Urs C. , Moor Andreas E. , Koning Frits , Boyman Onur
Published: November 2022

Due to its stimulatory potential for immunomodulatory CD4+regulatory T (Treg) cells, low-dose interleukin-2 (IL-2) immunotherapy has recently gained considerable attention for treatment of various autoimmune diseases. Although early-stage clinical trials have correlated expansion of circulating Treg cells with clinical response to IL-2 treatment, detailed mechanistic data on responding Treg cell subsets are lacking. In this investigator-initiated phase-2 clinical trial of low-dose IL-2 immunotherapy in systemic lupus erythematosus (SLE) patients, we performed an in-depth study of circulating and cutaneous Treg cell subsets by imaging mass cytometry, high-parameter spectral flow cytometry, bulk and single-cell RNA sequencing with cellular indexing, and targeted serum proteomics. Low-dose IL-2 stimulated circulating Treg cells with skin-homing properties that appeared in the skin of SLE patients in close interaction with endothelial cells, suggestive of a gatekeeper function. Analysis of surface proteins and transcriptomes detected different IL-2-driven Treg cell programs, including highly proliferative CD38+HLA-DR+, activated gut-homing CD38+, and skin-homing HLA-DR+Treg cells. These data identify distinct and functionally characteristic Treg cell subsets in human blood and skin, including the Treg cell subsets most responsive to IL-2 immunotherapy, thus providing unprecedented insight into Treg cell biology during IL-2 treatment.
Latent tuberculosis and depressive symptoms in household contacts of persons with active TB: A cohort study
Authors: Galea Jerome , Chu Alexander L. , Sweetland Annika , Jimenez Judith , Yataco Rosa , Calderón Roger , Zhang Zibiao , Huang Chuan-Chin , Lecca Leonid , Murray Megan
Published: November 2022

Background

Depression is common among persons with TB and associated with poor clinical outcomes. However, little is known about the relationship between latent TB infection (LTBI) and depression. Here, we assessed the association between LTBI and depressive symptoms among household contacts (HHCs) of patients receiving TB treatment.

Methods

We enrolled 1,009 HHCs of 307 patients receiving TB treatment in Lima, Peru, 2016-2018. We assessed HHC LTBI status at enrollment using interferon gamma release assay (IGRA). Depressive symptoms were assessed at baseline and 12 months later using the Patient Health Questionnaire-9 (PHQ-9) using a cutoff of ≥5. We used logistic regression to estimate the odds ratio for PHQ-9 ≥5 comparing HHCs with and without baseline LTBI.

Results

Among 921 HHCs, 378 (41.0%) had LTBI at baseline, and 70 (12.4%) of 563 HHCs had PHQ-9 ≥5. Compared to HHCs without LTBI at enrollment, those with LTBI had almost two times the odds of PHQ-9 ≥5 at follow-up after controlling for potential confounders (adjusted OR, 1.93, 95% CI, 1.09-3.39); this association was driven by greater severities of depressive symptoms.

Conclusion

HHCs with LTBI had increased odds of depressive symptoms one year later. This at-risk population may benefit from mental health screening and interventions integrated within TB programs.
Longitudinal analysis of retinal ganglion cell damage at individual axon bundle level in mice using visible-light optical coherence tomography fibergraphy
Authors: Grannonico Marta , Miller David A. , Gao Jingyi , McHaney Kara M. , Liu Mingna , Krause Michael , Netland Peter A. , Zhang Hao F. , Liu Xiaorong
Published: November 2022

We developed a new analytic tool based on visible-light optical coherence tomography fibergraphy (vis-OCTF) to longitudinally track individual axon bundle transformation following acute optic nerve crush injury (ONC) in mice. We analyzed four parameters: lateral bundle width, axial bundle height, cross-sectional area, and the shape of individual bundles. We showed that axon bundles became wider and thicker at 3-days post ONC. The bundle swelling at 3-days post-ONC has correlated with about 15% retinal ganglion cell (RGC) soma loss. At 6-days post-ONC, axon bundles showed a significant reduction in lateral width and cross-sectional area, followed by a reduction in bundle height at 9-days post-ONC. Bundle shrinking at 9-days post-ONC has correlated with about 68% RGC soma loss. Both experimental and simulated results suggested that the cross-sectional area of individual RGC axon bundles is more sensitive than the bundle width and height to indicate RGC soma loss. This study is the first to track and quantify individual RGC axon bundlesin vivofollowing ONC injury and establish the correlation between the morphological changes of RGC axon bundles and RGC soma loss.
Inflammation durably imprints memory CD4+ T cells
Authors: Gray-Gaillard Sophie L. , Solis Sabrina , Chen Han M. , Monteiro Clarice , Ciabattoni Grace , Samanovic Marie I. , Cornelius Amber R. , Williams Tijaana , Geesey Emilie , Rodriguez Miguel , Ortigoza Mila Brum , Ivanova Ellie N. , Koralov Sergei B. , Mulligan Mark J. , Herati Ramin Sedaghat
Published: November 2022

Adaptive immune responses are induced by vaccination and infection, yet little is known about how CD4+ T cell memory differs when primed in these two contexts. Notably, viral infection is generally associated with higher levels of systemic inflammation than is vaccination. To assess whether the inflammatory milieu at the time of CD4+ T cell priming has long-term effects on memory, we compared Spike-specific memory CD4+ T cells in 22 individuals around the time of the participants’ third SARS-CoV-2 mRNA vaccination, with stratification by whether the participants’ first exposure to Spike was via virus or mRNA vaccine. Multimodal single-cell profiling of Spike-specific CD4+ T cells revealed 755 differentially expressed genes that distinguished infection- and vaccine-primed memory CD4+ T cells. Spike-specific CD4+ T cells from infection-primed individuals had strong enrichment for cytotoxicity and interferon signaling genes, whereas Spike-specific CD4+ T cells from vaccine-primed individuals were enriched for proliferative pathways by gene set enrichment analysis. Moreover, Spike-specific memory CD4+ T cells established by infection had distinct epigenetic landscapes driven by enrichment of IRF-family transcription factors, relative to T cells established by mRNA vaccination. This transcriptional imprint was minimally altered following subsequent mRNA vaccination or breakthrough infection, reflecting the strong bias induced by the inflammatory environment during initial memory differentiation. Together, these data suggest that the inflammatory context during CD4+ T cell priming is durably imprinted in the memory state at transcriptional and epigenetic levels, which has implications for personalization of vaccination based on prior infection history.

One Sentence Summary

SARS-CoV-2 infection versus SARS-CoV-2 mRNA vaccination prime durable transcriptionally and epigenetically distinct Spike-specific CD4+ T cell memory landscapes.
Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq
Authors: Schwarzl Thomas , Sahadevan Sudeep , Lang Benjamin , Miladi Milad , Backofen Rolf , Huber Wolfgang , Hentze Matthias W , Tartaglia Gian G
Published: November 2022

Enhanced crosslinking and immunoprecipitation (eCLIP) sequencing is a powerful method for transcriptome-wide detection of binding sites of RNA-binding proteins (RBPs). However, identified crosslink sites can profoundly deviate from experimentally established functional elements of even well-studied RBPs. Current peak-calling strategies result in low replication and high false-positive rates. Here, we present the R/Bioconductor packageDEWSeqthat makes full use of replicate information and size-matched input controls. We benchmarkedDEWSeqon 107 RBPs for which both eCLIP data and RNA sequence motifs are available and were able to more than double the number of motif-containing binding regions relative to standard eCLIP processing (2.3-fold median). The improvement not only relates to the number of binding sites (e.g., 3.1-fold of known motifs for RBFOX2), but also their subcellular localisation (e.g., 1.9-fold of mitochondrial genes for FASTKD2) and structural targets (e.g., 2.2-fold increase of stem-loop regions for SLBP). DEWSeq therefore shows promise as an improved processing method for eCLIP protein–RNA interaction data.
Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning
Authors: Maasch Jacqueline R. M. A. , Torres Marcelo D. T. , Melo Marcelo C. R. , de la Fuente-Nunez Cesar
Published: November 2022

Molecular de-extinction could offer new avenues for drug discovery by reintroducing bioactive molecules that are no longer encoded by extant organisms. To prospect for antimicrobial peptides encrypted as subsequences of extinct and extant human proteins, we introduce the panCleave random forest model for proteome-wide cleavage site prediction. Our model outperformed multiple protease-specific cleavage site classifiers for three modern human caspases, despite its pan-protease design. Antimicrobial activity was observedin vitrofor modern and archaic protein fragments identified with panCleave. Lead peptides were tested for mechanism of action, resistance to proteolysis, and anti-infective efficacy in two pre-clinical mouse models. These results suggest that machine learning-based encrypted peptide prospection can identify stable, nontoxic antimicrobial peptides. Moreover, we establish molecular de-extinction through paleoproteome mining as a framework for antibacterial drug discovery.

Highlights

Machine learning guides bioinspired prospection for encrypted antimicrobial peptides.

Modern and extinct human proteins harbor antimicrobial subsequences.

Ancient encrypted peptides displayin vitroandin vivoactivity with low host toxicity.

Paleoproteome mining offers a new framework for antibiotic discovery.
Genome-wide single-molecule analysis of long-read DNA methylation reveals heterogeneous patterns at heterochromatin
Authors: Kerr Lyndsay , Kafetzopoulos Ioannis , Grima Ramon , Sproul Duncan
Published: November 2022

High-throughput sequencing technology is central to our current understanding of the human methylome. The vast majority of studies use chemical conversion to analyse bulk-level patterns of DNA methylation across the genome from a population of cells. While this technology has been used to probe single-molecule methylation patterns, such analyses are limited to short reads of a few hundred basepairs. DNA methylation can also be directly detected using Nanopore sequencing which can generate reads measuring megabases in length. However, thus far these analyses have largely focused on bulk-level assessment of DNA methylation. Here, we analyse DNA methylation in single Nanopore reads with a mean length of 24.6kb, to show that bulk-level metrics underestimate large-scale heterogeneity in the methylome. We use the correlation in methylation state between neighbouring sites to quantify single-molecule heterogeneity and find that heterogeneity varies significantly across the human genome, with some regions having heterogeneous methylation patterns at the single-molecule level and others possessing more homogeneous methylation patterns. By comparing the genomic distribution of the correlation to epigenomic annotations, we find that the greatest heterogeneity in single-molecule patterns is observed within heterochromatic partially methylated domains (PMDs). In contrast, reads originating from euchromatic regions and gene bodies have more ordered DNA methylation patterns. By analysing the patterns of single molecules in more detail, we show the existence of a 185bp periodicity in DNA methylation that accounts for some of the heterogeneity we uncover in long single-molecule DNA methylation patterns. We find that this periodic structure is partially masked in bulk data in a manner that is consistent with imperfect phasing of nucleosomes between molecules. Our findings demonstrate the power of single-molecule analysis of long-read data to understand the structure of the human methylome.
Nonhomologous tails direct heteroduplex rejection and mismatch correction during single-strand annealing inSaccharomyces cerevisisae
Authors: Sapède Elena , Sugawara Neal , Tyers Randall G. , Nakajima Yuko , Afreen Mosammat Faria , Escobar Jesselin Romero , Haber James E.
Published: November 2022

Single-strand annealing (SSA) is initiated when a double strand break (DSB) occurs between two flanking repeated sequences, resulting in a deletion that leaves a single copy of the repeat. We studied budding yeast strains carrying two 200-bpURA3sequences separated by 2.3-kb of phage lambda DNA in which a site-specific DSB can be created by HO or Cas9 endonucleases. Repeat-mediated deletion requires removal of long 3’-ended single-stranded tails (flaps) by Rad1-Rad10 with the assistance of Msh2-Msh3 and Slx4. A natural 3% divergence between repeats (designated F and A) causes a significant reduction in the frequency of SSA repair. This decrease is caused by heteroduplex rejection in which mismatches (MMs) in the annealed intermediate are recognized by the MutSα (Msh2 and Msh6) components of the MM repair (MMR) pathway coupled to unwinding of the duplex by the Sgs1-Rmi1-Top3 helicase. MutL homologs, Mlh1-Pms1 (MutLα) are not required for rejection but play their expected role in mismatch correction. Remarkably, heteroduplex rejection is very low in strains where the identical repeats were immediately adjacent (Tailless strains) and the DSB was induced by Cas9. These results suggest that the presence of nonhomologous tails strongly stimulates heteroduplex rejection in SSA. DNA sequencing analysis of SSA products from the FA Tailed strain, where the F variant carries six single-base mutations and one +1(T) insertion within a run of 10 Ts showed a gradient of correction favoring the sequence opposite each 3’ end of the annealed strand. Mismatches (MMs) located in the center of the repair intermediate were corrected by Msh2-Msh6 mediated mismatch correction, while correction of MMs at the extremity of the SSA intermediate often appears to use a different mechanism, using either 3’ nonhomologous tail removal or 3’ to 5’ “proofreading” resection by DNA polymerase δ followed by synthesis to fill in the gap. In contrast, in FA Tailless strains there was a uniform repair of the MMs across the repeat, with a bias in favor of the “left” copy. A distinctive pattern of correction was found in the absence ofMSH2, in both Tailed and Tailless strains, while the deletion ofMSH6resulted in unrepaired MMs.
The UBP5 histone H2A deubiquitinase counteracts PRC2-mediated repression to regulate Arabidopsis development and stress responses
Authors: Godwin James , March Eduardo , Govindasamy Mohan , Bourbousse Clara , Wolff Léa , Fort Antoine , Krzyszton Michal , López Jesús , Swiezewski Szymon , Barneche Fredy , Schubert Daniel , Farrona Sara
Published: November 2022

Polycomb Repressive Complexes (PRCs) control gene expression through the incorporation of H2Aub and H3K27me3. However, there is limited knowledge about PRCs’ interacting proteins and their interplay with PRCs in epigenome reshaping, which is fundamental to understand gene regulatory mechanisms. Here, we identified UBIQUITIN SPECIFIC PROTEASE 5 (UBP5) as a novel interactor of the PRC2 subunit SWINGER and its associated factor PWO1 inArabidopsis thaliana. As inferred from the functional analyses ofubp5CRISPR-Cas9 mutant plants, UBP5 regulates plant development and stress responses, notably by promoting H2A monoubiquitination erasure, leading to transcriptional de-repression. Preferential association of UBP5 at PRC2 recruiting motifs and local H3K27me3 gaining inubp5mutant plants further suggest the existence of functional interplays between UBP5 and PRC2 in regulating epigenome dynamics. In summary, UBP5 provides novel insights to disentangle the complex PRC2 interaction network and is a crucial regulator of the pivotal epigenetic repressive marks H2Aub and H3K27me3.
Nitrogen cycling activities during decreased stratification in the coastal oxygen minimum zone off Namibia
Authors: Vuillemin Aurèle
Published: November 2022

Productive oxygen minimum zones are regions dominated by heterotrophic denitrification fueled by sinking organic matter. Microbial redox-sensitive transformations therein result in the loss and overall geochemical deficit in inorganic fixed nitrogen in the water column, thereby impacting global climate in terms of nutrient equilibrium and greenhouse gases.

Here, geochemical data are combined with metagenomes, metatranscriptomes and stable-isotope probing incubations from the water column and subseafloor of the Benguela Upwelling System. Taxonomic assemblages and relative expression of functional marker genes are used to explore metabolic activities by nitrifiers and denitrifiers under decreased stratification and increased lateral ventilation in Namibian coastal waters. Active planktonic nitrifiers were affiliated withCandidatusNitrosopumilus andCandidatusNitrosopelagicus among Archaea, andNitrospina, Nitrosomonas, Nitrosococcus, andNitrospiraamong Bacteria. Concurrent evidence from taxonomic and functional marker genes shows that populations of Nitrososphaeria and Nitrospinota were highly active under dysoxic conditions, coupling ammonia and nitrite oxidation with respiratory nitrite reduction, but minor metabolic activity towards mixotrophic use of simple nitrogen compounds. Although active reduction of nitric oxide to nitrous oxide by Nitrospirota, Gammaproteobacteria and Desulfobacterota was tractable in bottom waters, the produced nitrous oxide was apparently scavenged at the ocean surface by Bacteroidota. Planctomycetota involved in anaerobic ammonia oxidation were identified in dysoxic waters and their underlying sediments, but were not found to be metabolically active due to limited availability of nitrite. Consistent with water column geochemical profiles, metatranscriptomic data demonstrate that nitrifier denitrification prevails over canonical denitrification when Namibian coastal waters are ventilated during austral winter.