bluuebunny/crossref_metadata_2025 huggingface dataset:
eXclusionarY: Ten years later, where are the sex chromosomes in GWAS?
Authors: Sun Lei , Wang Zhong , Lu Tianyuan , Manolio Teri A. , Paterson Andrew D.
Published: February 2023

Ten years ago, a detailed analysis of genome-wide association studies showed that only 33% of the studies included the X chromosome. Multiple recommendations were made to combat eXclusion. Here we re-surveyed the research landscape to determine if these earlier recommendations had been translated. Unfortunately, among the summary statistics reported in 2021 in the NHGRI-EBI GWAS catalog, only 25% provided results for the X chromosome and 3% for the Y chromosome, suggesting that the eXclusion phenomenon documented earlier not only persists but has also expanded into an eXclusionarY problem. Normalizing by physical length of the chromosome, the average number of studies published until 11/29/22 with genome-wide significant findings on the X chromosome is ~1 study/Mb. In contrast, it ranges from ~6 to ~16 studies/Mb for chromosomes 4 and 19, respectively. Compared with the autosomal growth rate of ~0.086 studies/Mb/year over the last decade, studies of the X chromosome grew at less than one-seventh that rate, only ~0.012 studies/Mb/year. Among the studies that reported significant association on the X chromosome, there were extreme heterogeneities in how they analyzed the data and documented the results, suggesting the need for guidelines. Not surprisingly, among the 430 scores sampled from the PolyGenic Score catalog, 0% contained weights for sex chromosomal SNPs. To overcome the dearth of sex chromosome analyses, we provide five sets of recommendations and future directions. Finally, until the sex chromosomes are included in a whole-genome study, instead of GWAS, we propose they be more properly referred to as “AWAS” for “autosome-wide scan”.
Naïve T lymphocytes chemotax to CCL21 but not to S1P-rich serum
Authors: Garcia-Seyda Nicolas , Song Solene , David-Broglio Luc , Matti Christoph , Artinger Marc , Biarnes-Pelicot Martine , Valignat Marie-Pierre , Legler Daniel F. , Bajénoff Marc , Theodoly Olivier
Published: February 2023

Naïve T lymphocytes traffic through the organism in their search for antigen, alternating between blood and secondary lymphoid organs. Lymphocyte homing to lymph nodes relies on the chemokine CCL21, while exit into efferent lymphatics relies on the sphingolipid S1P. Surprisingly, while both molecules are claimed chemotactic, a quantitative analysis of naïve T lymphocyte migration along defined gradients is missing. Here, we used a reductionistin vitroapproach to study the real-time, single-cell response of naïve T lymphocytes to CCL21 and S1P-rich serum. Using high-throughput microfluidic and optical micropatterning ad hoc tools, we show that CCL21 triggers long-range chemotaxis whereas S1P-rich serum does not. Instead, S1P-rich serum triggers a transient polarization that may represent a brief transmigration step through exit portals. Our data thus validate naïve T lymphocyte chemotaxis towards CCL21 but not S1P, which complementsin vivoobservations and is of interest for a better tailoring of immunosuppressive drugs.
Commensal bacteria can inhibit the growth ofP. aeruginosain cystic fibrosis airway infections through a released metabolite
Authors: Tony-Odigie Andrew , Dalpke Alexander H. , Boutin Sébastien , Yi Buqing
Published: February 2023

In cystic fibrosis (CF), infections withPseudomonas aeruginosaor other typical pathogens play a critical role in eliciting disease progression, leading to tissue damage and finally loss of lung function. Previous observations showed that the presence of various commensal bacteria and a higher airway microbiome diversity were associated with better lung function and less severe disease burden. Thus, the hypothesis was raised that commensal bacteria might be able to interfere with pathogenic bacteria. In this study, we aimed to identify airway commensal bacteria that inhibit the growth ofP. aeruginosa.

Through a screening experiment of co-culture withP. aeruginosaPAO1, we could identify more than 30 CF commensal strains from various species that inhibited the growth ofP. aeruginosa. With multiple selected strains, we further verified the results withP. aeruginosaCF isolates and several other pathogens isolated from CF patients, and most of the identified commensal strains showed consistent results strongly inhibiting the growth of diverse CF pathogens.

The underlying mechanisms of the growth-inhibition effects were first investigated through genomic analysis by comparing strains with and without growth-inhibition effects, which revealed that genes responsible for carbohydrate transport and metabolism were highly enriched in the inhibitory commensals. Metabolite analysis and functional analysis showed that commensals with inhibitory effects produce large amounts of acetate. Exogenous addition of acetate under a low pH inhibited the growth ofP. aeruginosa, indicating acetate produced and released by commensals may affect the growth ofP. aeruginosaliving in the same microenvironment.

In summary, through co-culture ofP. aeruginosawith commensals, we could identify that a variety of airway commensal strains can inhibit the growth ofP. aeruginosaby producing acetate. The data provide insights into possible novel strategies for controlling infections in people with CF and also emphasize the importance of preserving airway commensals when designing infection treatment strategies.
Assembly and operation of a cooling stage to immobilizeC. eleganson their culture plates
Authors: Wang Yao L. , Grooms Noa William Franklin , Ma Claire , Chung Samuel H.
Published: February 2023

High-resolutionin vivomicroscopy approaches can reveal subtle information and fine details inside the model animalCaenorhabditis elegans(C. elegans) but requires strong animal immobilization. Unfortunately, most current immobilization techniques require substantial manual effort, rendering high-resolution imaging low-throughput. We greatly simplify theC. elegansimmobilization procedure by using a cooling approach that can easily immobilize entire populations ofC. elegansdirectly on their cultivation plates. The cooling stage can establish and maintain a wide range of temperatures on the cultivation plate and ensures even temperature distribution across the agarose surface. In this article, we document the whole process of building the cooling stage from scratch. We envision that a typical researcher can build an operational cooling stage in their lab following our protocol without difficulty. We show how to utilize the cooling stage under three protocols, which have advantages for different experiments. We also show an example cooling profile of the stage as it approaches its final temperature and include some helpful tips in using cooling immobilization.
Correspondence between functional scores from deep mutational scans and predicted effects on protein stability
Authors: Gerasimavicius Lukas , Livesey Benjamin J , Marsh Joseph A.
Published: February 2023

Many methodologically diverse computational methods have been applied to the growing challenge of predicting and interpreting the effects of protein variants. As many pathogenic mutations have a perturbing effect on protein stability or intermolecular interactions, one highly interpretable approach is to use protein structural information to model the physical impacts of variants and predict their likely effects on protein stability and interactions. Previous efforts have assessed the accuracy of stability predictors in reproducing thermodynamically accurate values and evaluated their ability to distinguish between known pathogenic and benign mutations. Here, we take an alternate approach, and explore how well stability predictor scores correlate with functional impacts derived from deep mutational scanning (DMS) experiments. In this work, we compare the predictions of 9 protein stability-based tools against mutant protein fitness values from 45 independent DMS datasets, covering 161,441 unique single amino acid variants. We find that FoldX and Rosetta show the strongest correlations with DMS-based functional scores, similar to their previous top performance in distinguishing between pathogenic and benign variants. For both methods, performance is considerably improved when considering intermolecular interactions from protein complex structures, when available. Finally, we also highlight that predicted stability effects show consistently higher correlations with certain DMS experimental phenotypes, particularly those based upon protein abundance, and, in certain cases, can be competitive with other sequence-based variant effect prediction methodologies for predicting functional scores from DMS experiments.
Sexual dimorphism and the multi-omic response to exercise training in rat subcutaneous white adipose tissue
Authors: Many Gina M. , Sanford James A. , Sagendorf Tyler J. , Hou Zhenxin , Nigro Pasquale , Whytock Katie , Amar David , Caputo Tiziana , Gay Nicole R. , Gaul David A. , Hirshman Michael , Jimenez-Morales David , Lindholm Malene E. , Muehlbauer Michael J. , Vamvini Maria , Bergman Bryan , Fernández Facundo M. , Goodyear Laurie J. , Ortlund Eric A. , Sparks Lauren M. , Xia Ashley , Adkins Joshua N. , Bodine Sue C. , Newgard Christopher B. , Schenk Simon ,   The MoTrPAC Study Group
Published: February 2023

Subcutaneous white adipose tissue (scWAT) is a dynamic storage and secretory organ that regulates systemic homeostasis, yet the impact of endurance exercise training and sex on its molecular landscape has not been fully established. Utilizing an integrative multi-omics approach with data generated by the Molecular Transducers of Physical Activity Consortium (MoTrPAC), we identified profound sexual dimorphism in the dynamic response of rat scWAT to endurance exercise training. Despite similar cardiorespiratory improvements, only male rats reduced whole-body adiposity, scWAT adipocyte size, and total scWAT triglyceride abundance with training. Multi-omic analyses of adipose tissue integrated with phenotypic measures identified sex-specific training responses including enrichment of mTOR signaling in females, while males displayed enhanced mitochondrial ribosome biogenesis and oxidative metabolism. Overall, this study reinforces our understanding that sex impacts scWAT biology and provides a rich resource to interrogate responses of scWAT to endurance training.
Recognizing the opponent: the consolidation of long-term social memory in zebrafish males
Authors: Cavallino Luciano , Scaia María Florencia , Pozzi Andrea Gabriela , Pedreira María Eugenia
Published: February 2023

Recognizing and remembering another individual in a social context could be beneficial for individual fitness. Especially in agonistic encounters, remembering an opponent and the previous fight could allow avoiding new conflicts. Considering this, we hypothesized that this type of social interaction forms a long-term recognition memory lasting several days. It has been shown that a second encounter 24 hours later between the same pair of zebrafish males is resolved with lower levels of aggression. Here, we evaluated if this behavioral change could last for longer intervals and a putative mechanism associated with memory storage: the recruitment of NMDA receptors. We found that if a pair of zebrafish males fight and 48 or 72 hours later fight again, they resolved the second encounter with lower levels of aggression. However, if immediately after the first encounter opponents were exposed to MK-801 (NMDA receptor antagonist), they resolve the second one with the same levels of aggression, that is, no reduction in aggressive behaviors was observed. These results suggest the formation of a long-term social memory related to recognizing a particular opponent and/or the outcome and features of a previous fight.
Visualizing and exploring patterns of large mutational events with SigProfilerMatrixGenerator
Authors: Khandekar Azhar , Vangara Raviteja , Barnes Mark , Díaz-Gay Marcos , Abbasi Ammal , Bergstrom Erik N. , Steele Christopher D. , Pillay Nischalan , Alexandrov Ludmil B.
Published: February 2023

Background

All cancers harbor somatic mutations in their genomes. In principle, mutations affecting between one and fifty base pairs are generally classified as small mutational events. Conversely, large mutational events affect more than fifty base pairs, and, in most cases, they encompass copy-number and structural variants affecting many thousands of base pairs. Prior studies have demonstrated that examining patterns of somatic mutations can be leveraged to provide both biological and clinical insights, thus, resulting in an extensive repertoire of tools for evaluating small mutational events. Recently, classification schemas for examining large-scale mutational events have emerged and shown their utility across the spectrum of human cancers. However, there has been no standard bioinformatics tool that allows visualizing and exploring these large-scale mutational events

Results

Here, we present a new version of SigProfilerMatrixGenerator that now delivers integrated capabilities for examining large mutational events. The tool provides support for examining copy-number variants and structural variants under two previously developed classification schemas and it supports data from numerous algorithms and data modalities. SigProfilerMatrixGenerator is written in Python with an R wrapper package provided for users that prefer working in an R environment.

Conclusions

The new version of SigProfilerMatrixGenerator provides the first standardized bioinformatics tool for optimized exploration and visualization of two previously developed classification schemas for copy number and structural variants. The tool is freely available athttps://github.com/AlexandrovLab/SigProfilerMatrixGeneratorwith an extensive documentation athttps://osf.io/s93d5/wiki/home/.
Conflict during learning reconfigures the neural representation of positive valence and approach behaviour
Authors: Molina-García Laura , Colinas-Fischer Susana , Benavides-Laconcha Sergio , Lin Lucy , Clark Emma , Treloar Neythen J. , García-Minaur-Ortíz Blanca , Barnes Chris P. , Barrios Arantza
Published: February 2023

Punishing and rewarding experiences can change the valence of sensory stimuli and guide animal behaviour in opposite directions, resulting in avoidance or approach. Often, however, a stimulus is encountered with both positive and negative experiences. How is such conflicting information represented in the brain and resolved into a behavioural decision? We address this question by dissecting a circuit for sexual conditioning inC. elegans. In this learning paradigm, an odour is conditioned with both a punishment (starvation) and a reward (mates) resulting in odour approach. We find that negative and positive experiences are both encoded by the neuropeptide PDF-1 being released from and acting on different neurons. Each experience creates a separate, parallel memory in the circuit for odour processing. This results in the sensorimotor representation of odour being different in naïve and sexually conditioned animals despite both displaying approach. Our results reveal that the positive valence of a stimulus is not represented in the activity of any single neuron class but flexibly represented within the circuit according to the experiences and predictions associated with the stimulus.
A systematic review of the diversity and virulence correlates of metastrongyle lungworms in marine mammals
Authors: Fischbach Jared R. , Seguel Mauricio
Published: February 2023

Metastrongyle lungworms could be particularly detrimental for diving animals such as marine mammals, however little is known of the drivers of pathogenic host-parasite relationships in this group. This systematic review analyzed the diversity of metastrongyles in marine mammals and the host and parasite traits associated with virulence. There have been at least 40 species of metastrongyles described in 66 species of marine mammals. After penalization for study biases,Halocercus hyperoodoni,Otostrongylus circumlitus,Parafilaroides gymnurus,Halocercus brasiliensis, andStenurus minorwere the metastrongyles with the widest host range. Most studies (80.12%, n=133/166) reported that metastrongyles caused bronchopneumonia, while in the cardiovascular system metastrongyles caused vasculitis in nearly half of the studies (45.45%, n=5/11) that assessed these tissues. Metastrongyles were associated with otitis in 23.08% (n=6/26) of the studies. Metastrongyle infection was considered a potential contributory to mortality in 44.78% (n=90/201) of the studies while 10.45% (n=21/201) of these studies considered metastrongyles the main cause of death. Metastrongyle species with a wider host range were more likely to induce pathogenic effects. Metastrongyles can cause significant tissue damage and mortality in marine mammals although virulent host-parasite relationships are dominated by a few metastrongyle species with wider host ranges.
Long-term unsupervised recalibration of cursor BCIs
Authors: Wilson Guy H. , Willett Francis R. , Stein Elias A. , Kamdar Foram , Avansino Donald T. , Hochberg Leigh R. , Shenoy Krishna V. , Druckmann Shaul , Henderson Jaimie M.
Published: February 2023

Intracortical brain-computer interfaces (iBCIs) require frequent recalibration to maintain robust performance due to changes in neural activity that accumulate over time. Compensating for this nonstationarity would enable consistently high performance without the need for supervised recalibration periods, where users cannot engage in free use of their device. Here we introduce a hidden Markov model (HMM) to infer what targets users are moving toward during iBCI use. We then retrain the system using these inferred targets, enabling unsupervised adaptation to changing neural activity. Our approach outperforms the state of the art in large-scale, closed-loop simulations over two months and in closed-loop with a human iBCI user over one month. Leveraging an offline dataset spanning five years of iBCI recordings, we further show how recently proposed data distribution-matching approaches to recalibration fail over long time scales; only target-inference methods appear capable of enabling long-term unsupervised recalibration. Our results demonstrate how task structure can be used to bootstrap a noisy decoder into a highly-performant one, thereby overcoming one of the major barriers to clinically translating BCIs.
Elevator Mechanism of Alternating Access in theEscherichia coliConcentrative Nucleoside Transporter NupC
Authors: Sun Lijie , Patching Simon G.
Published: February 2023

Members of the concentrative nucleoside transporter (CNT) family of proteins mediate uptake of nucleosides into cells driven by a cation gradient, which then enter salvage pathways for nucleic acid synthesis. In humans, they also transport hydrophilic anticancer and antiviral nucleoside analogue drugs into cells and tissues where they exert their pharmacological effects.Escherichia coliCNT NupC (400 residues) is pyrimidine-specific and driven by a proton gradient. We have used computational, biochemical, and biophysical methods to characterize evolutionary relationships, conservation of residues, structural domains, transmembrane helices, and residues involved in nucleoside binding and/or transport activity in NupC compared with those of sodium-drivenVibrio cholerae CNT (vcCNT) and human CNTs (hCNT1−3). As in the crystal structure of vcCNT, NupC appears to contain eight transmembrane-spanning α-helices. Wild-type NupC and single-cysteine-containing mutants were tested for transport activity in energizedE. coliwhole cells and for binding of nucleosides in non-energized native inner membranes using novel cross-polarization magic-angle spinning solid-state nuclear magnetic resonance methods. Wild-type NupC had an apparent affinity of initial rate transport (Kmapp) for [14C]uridine of 22.2 ± 3.7μM and an apparent binding affinity (Kdapp) for [1′-13C]uridine of 1.8−2.6 mM. Mutant S142C retained transport and binding affinities similar to those of the wild type. Mutants G146C and E149C had no transport activity but retained varying degrees of partial binding activity with affinities decreasing in the following order: wild type > S142C > G146C > E149C. Results were explained with respect to a homology model of NupC based on the structure of vcCNT and a hypothetical elevator-type mechanism of alternating access membrane transport in NupC.
Comparison of TRIBE and STAMP for identifying targets of RNA binding proteins in human andDrosophilacells
Authors: Abruzzi Katharine C. , Ratner Corrie , Rosbash Michael
Published: February 2023

RNA binding proteins (RBPs) perform a myriad of functions and are implicated in numerous neurological diseases. To identify the targets of RBPs in small numbers of cells, we developed TRIBE, in which the catalytic domain of the RNA editing enzyme ADAR (ADARcd) is fused to a RBP. When the RBP binds to a mRNA, ADAR catalyzes A to G modifications in the target mRNA that can be easily identified in standard RNA-sequencing. In STAMP, the concept is the same except the ADARcd is replaced by the RNA editing enzyme APOBEC. Here we compared the two enzymes fused to the RBP TDP-43 in human cells. Although they both identified TDP-43 target mRNAs, combining the two methods more successfully identified high confidence targets. We also assayed the two enzymes inDrosophilacells: RBP-APOBEC fusions generated only low numbers of editing sites, comparable to the level of control editing. This was true for two different RBPs, Hrp48 and Thor (DrosophilaEIF4E-BP), indicating that TRIBE performed better inDrosophila.
The self-renewal procedures of mesenchymal stem cells in the blood
Authors: Kong Wuyi , Wang Hong , Zhu XiaoPing , Han XiuJuan
Published: February 2023

Background

Although mesenchymal stem cells (MSCs) are most commonly used in cell therapy and stem cell research, the mechanism and the locations of their self-renewal are still unknown.

Method

Mouse blood was collected, and examined under microscopy. The results were compared with the data of human umbilical cord blood (hUCB) collected 10 years ago.

Results

We found that the procedure of self-renewal for the mesenchymal stem cells in mouse blood and hUCB needs at least 5 steps. First, tube-shaped stem cell niches release long segmented materials composed of sand-like particles and semitransparent granules. Second, the sand-like particles and semitransparent granules separate from the segmented materials. Third, each of the individual semitransparent granules releases groups of fusiform-shaped structures that do not stain to H&E. The sizes of the fusiform-shaped structures range from 1 to 100 μm in length in mouse blood, but can be 200 μm in hUCB. Fourth, the large-sized fusiform structures can directly transform into lineage-restricted cellular structures; the medium-sized fusiform structures fuse or engulf each other to form cellular structures. The cellular structures further acquire membranes from the adjacent nucleated cells. Fifth, the nucleolus appears in the new cellular structures before the nucleus. During all the procedures, the adjacent nucleated mesenchymal cells are must needed. Thus, these newly formed cellular structures will further differentiate into nucleated mesenchymal stem cells.

Conclusion

Our findings again provide new evidence that, in physiological conditions, mesenchymal stem cell self-renewal needs several steps to complete, which, however, does not occur by mitotic division. The tube-shaped structures are the niches of the stem cells.
Advancing Glycan Analysis: A New Platform Integrating SERS, Boronic Acids, and Machine Learning Algorithms
Authors: Hu Qiang , Kuai Dacheng , Park Hyundo , Clark Haley , Balbuena Perla B. , Kwon Joseph Sang-Il , Wu Hung-Jen
Published: February 2023

Glycans are the most abundant and diverse fundamental biomolecules. Profiling glycans is essential to elucidate biomolecular mechanisms and to predict biological consequences; however, the analysis of glycans remains challenging due to their structural complexity. A novel glycan detection platform is established through the integration of surface-enhanced Raman spectroscopy (SERS), boronic acid receptors, and machine learning tools. SERS is able to distinguish isomeric structures and provide fingerprint information of molecules. Boronic acid receptors can selectively bind with glycans, and the reaction influences molecular vibrations, leading to unique Raman spectral patterns. For proof-of-concept, two boronic acids, 4-mercaptophenylboronic acid (4MBA) and 1-thianthrenylboronic acid (1TBA) were used for glycan detection. The spectra were analyzed by the machine learning algorithm. The sensing platform successfully recognized the stereoisomers (glucose, mannose, and galactose), the structural isomers with α-1,4 and α-1,6 glycosidic linkages, and the β-1,4 glycosidic linkage within lactose molecules. The collective spectra that combine the spectra from both boronic acid receptors could improve the performance of the support vector machine model due to the enrichment of the structural information of glycans. In addition to qualitative analysis, this new sensor could quantify the mole fraction of sialic acid in lactose background using the machine learning regression technique. The quantification accuracy reached a coefficient of determination (R2) value of 0.998 and a normalized mean square error (NMSE) of 0.00195. This low-cost, rapid, and highly accessible sensor will provide the scientific community with another option for frequent glycan screening in standard biological laboratories.
GardnerellaDiversity and Ecology in Pregnancy and Preterm Birth
Authors: Berman Hanna L. , Aliaga Goltsman Daniela S. , Anderson Megan , Relman David A. , Callahan Benjamin J.
Published: February 2023

The vaginal microbiome has been linked to numerous negative health outcomes including preterm birth. Specific taxa, includingGardnerellaspp., have been identified as risk factors for these conditions. Historically, microbiome analysis methods have treated allGardnerellaspp. as one species, but the broad diversity ofGardnerellahas recently become more apparent. In the present study, we explore the diversity ofGardnerellaclades and genomic species in the vaginal microbiome of pregnant women and their impacts on microbiome composition and associations with preterm birth.

Shotgun metagenomic sequencing data collected longitudinally from three distinct cohorts of pregnant women were assessed. Relative abundance ofGardnerellaclades and genomic species and other taxa was quantified, and associations betweenGardnerellaclades and signatures of the vaginal microbiome were measured. We also assessed the diversity and abundance ofGardnerellavariants in 16S rRNA gene amplicon sequencing data from seven previously conducted studies in differing populations on the vaginal microbiome and preterm birth.

Individual microbiomes often contained multipleGardnerellavariants, and the number of clades was associated with increased microbial load. The genusGardnerellawas also associated with increased microbial load, or the ratio of non-human reads to human reads. Taxon co-occurrence patterns matched previously described community structures, and were largely consistent acrossGardnerellaclades and among cohorts. Some variants previously described as rare were prevalent in other cohorts, highlighting the importance of surveying a diverse set of populations to fully capture the diversity ofGardnerella.

The diversity ofGardnerellaboth across populations and within individual vaginal microbiomes has long been unappreciated, as has been the intra-species diversity of many other members of the vaginal microbiome.1The broad genomic diversity ofGardnerellahas led to its reclassification as multiple species; here we demonstrate the diversity ofGardnerellafound within and between vaginal microbiomes. Further studies should investigate the phenotypes ofGardnerellavariants that may underlie the mechanisms by whichGardnerellaspecies may differentially shape the vaginal microbiome.
OSCAR: an open-source controller for animal research
Authors: Dastin-van Rijn Evan M. , Sachse Elizabeth , Iacobucci Francesca , Mensinger Megan , Widge Alik S.
Published: February 2023

Operant animal behavior training and monitoring is fundamental to scientific inquiry across fields necessitating evaluation via controlled laboratory tasks. However, current commercial and open-source systems enforce particular hardware and software, limiting reproducibility and technique and data sharing across sites. To address this issue, we developed OSCAR: an open-source controller for animal research that enables flexible control of a variety of industry standard hardware with platform-independent software. OSCAR offers millisecond latency with a flexible array of inputs and outputs at a fraction of the cost of commercial options. These features position OSCAR as a valuable option for improving consistency of behavioral experiments across studies.
Single-cell genomics reveals the divergent mitochondrial genomes of Retaria (Foraminifera and Radiolaria)
Authors: Macher Jan-Niklas , Coots Nicole L. , Poh Yu-Ping , Girard Elsa B. , Langerak Anouk , Muñoz-Gómez Sergio A. , Sinha Savar D. , Jirsová Dagmar , Vos Rutger , Wissels Richard , Gile Gillian H. , Renema Willem , Wideman Jeremy G.
Published: February 2023

Mitochondria originated from an ancient bacterial endosymbiont that underwent reductive evolution by gene loss and endosymbiont gene transfer to the nuclear genome. The diversity of mitochondrial genomes published to date has revealed that gene loss and transfer processes are ongoing in many lineages. Most well-studied eukaryotic lineages are represented in mitochondrial genome databases, except for the superphylum Retaria—the lineage comprising Foraminifera and Radiolaria. Using single-cell approaches, we present two complete mitochondrial genomes of Foraminifera and two near-complete mitochondrial genomes of radiolarians. We report the complete coding content of an additional 14 foram species. We show that foraminiferan and radiolarian mitochondrial genomes encode a nearly fully overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. In contrast to animals and fungi, many protists encode a diverse set of proteins on their mitochondrial genomes, including several ribosomal genes; however, some aerobic eukaryotic lineages (euglenids, myzozoans, and chlamydomonas-like algae) have reduced mitochondrial gene content and lack all ribosomal genes. Similar to these reduced outliers, we show that retarian mitochondrial genomes lack ribosomal protein and tRNA genes, contain truncated and divergent small and large rRNA genes, and encode only 14-15 protein-coding genes, including nad1, 3, 4, 4L, 5, 7, cob, cox1, 2, 3, atp1, 6, and 9, with forams and radiolarians additionally encoding nad2 and nad6, respectively. In radiolarian mitogenomes, a non-canonical genetic code was identified in which all three stop codons encode amino acids. Collectively, these results add to our understanding of mitochondrial genome evolution and fill in one of the last major gaps in mitochondrial sequence databases.
Ligament injury in adult zebrafish triggers ECM remodeling and cell dedifferentiation for scar-free regeneration
Authors: Anderson Troy , Mo Julia , Gagarin Ernesto , Sherwood Desmarie , Blumenkrantz Maria , Mao Eric , Leon Gianna , Chen Hung-Jhen , Tseng Kuo-Chang , Fabian Peter , Crump J. Gage , Smeeton Joanna
Published: February 2023

After traumatic injury, healing of mammalian ligaments is typically associated with fibrotic scarring as opposed to scar-free regeneration. In contrast, here we show that the ligament supporting the jaw joint of adult zebrafish is capable of rapid and complete scar-free healing. Following surgical transection of the jaw joint ligament, we observe breakdown of ligament tissue adjacent to the cut sites, expansion of mesenchymal tissue within the wound site, and then remodeling of extracellular matrix (ECM) to a normal ligament morphology. Lineage tracing of mature ligamentocytes following transection shows that they dedifferentiate, undergo cell cycle re-entry, and contribute to the regenerated ligament. Single-cell RNA sequencing of the regenerating ligament reveals dynamic expression of ECM genes in neural-crest-derived mesenchymal cells, as well as diverse immune cells expressing the endopeptidase-encoding genelegumain. Analysis oflegumainmutant zebrafish shows a requirement for early ECM remodeling and efficient ligament regeneration. Our study establishes a new model of adult scar-free ligament regeneration and highlights roles of immune-mesenchyme cross-talk in ECM remodeling that initiates regeneration.

Highlights

Rapid regeneration of the jaw joint ligament in adult zebrafish

Dedifferentiation of mature ligamentocytes contributes to regeneration

scRNAseq reveals dynamic ECM remodeling and immune activation during regeneration

Requirement of Legumain for ECM remodeling and ligament healing
Metabolomic Phenotypes Reflect Patient Sex and Injury Status: A Cross-Sectional Analysis of Human Synovial Fluid
Authors: Welhaven Hope D. , Welfley Avery H. , Pershad Prayag , Satalich James , O’Connell Robert , Bothner Brian , Vap Alexander R. , June Ronald K.
Published: February 2023

1.

Background

Post-traumatic osteoarthritis (PTOA) is caused by knee injuries like anterior cruciate ligament (ACL) injuries. Often, ACL injuries are accompanied by damage to other tissues and structures within the knee including the meniscus. Both are known to cause PTOA but underlying cellular mechanisms driving disease remain unknown. Aside from injury, patient sex is a prevalent risk factor associated with PTOA.

Hypothesis

Metabolic phenotypes of synovial fluid that differ by knee injury pathology and participant sex will be distinct from each other.

Study Design

A cross-sectional study.

Methods

Synovial fluid from n=33 knee arthroscopy patients between 18 and 70 years with no prior knee injuries was obtained pre-procedure and injury pathology assigned post-procedure. Synovial fluid was extracted and analyzed via liquid chromatography mass spectrometry metabolomic profiling to examine differences in metabolism between injury pathologies and participant sex. Additionally, samples were pooled and underwent fragmentation to identify metabolites.

Results

Metabolite profiles revealed that injury pathology phenotypes were distinct from each other where differences in endogenous repair pathways that are triggered post-injury were detected. Specifically, acute differences in metabolism mapped to amino acid metabolism, lipid-related oxidative metabolism, and inflammatory-associated pathways. Lastly, sexual dimorphic metabolic phenotypes were examined between male and female participants, and within injury pathology. Specifically, Cervonyl Carnitine and other identified metabolites differed in concentration between sexes.

Conclusions

The results of this study suggest that different injuries (e.g., ligament vs. meniscus), as well as sex are associated with distinct metabolic phenotypes. Considering these phenotypic associations, a greater understanding of metabolic mechanisms associated with specific injuries and PTOA development may yield data regarding how endogenous repair pathways differ between injury types. Furthermore, ongoing metabolomic analysis of synovial fluid in injured male and female patients can be performed to monitor PTOA development and progression.

Clinical Relevance

Extension of this work may potentially lead to the identification of biomarkers as well as drug targets that slow, stop, or reverse PTOA progression based on injury type and patient sex.
A novel enhancer-AAV approach selectively targeting dentate granule cells
Authors: Banks Emmie , Gutekunst Claire-Anne , Vargish Geoffrey A. , Eaton Anna , Pelkey Kenneth A. , McBain Chris J. , Zheng James Q. , Oláh Viktor Janos , Rowan Matthew JM
Published: February 2023

The mammalian brain contains the most diverse array of cell types of any organ, including dozens of neuronal subtypes with distinct anatomical and functional characteristics. The brain leverages these neuron-type-specializations to perform diverse circuit operations and thus execute different behaviors properly. Through the use of Cre lines, access to specific neuron types has steadily improved over past decades. Despite their extraordinary utility, development and cross-breeding of Cre lines is time-consuming and expensive, presenting a significant barrier to entry for many investigators. Furthermore, cell-based therapeutics developed in Cre mice are not clinically translatable. Recently, several AAV vectors utilizing neuron-type-specific regulatory transcriptional sequences (enhancer-AAVs) were developed which overcome these limitations. Using a publicly available RNAseq dataset, we evaluated the potential of several candidate enhancers for neuron-type-specific targeting in the hippocampus. Here we identified a promising enhancer-AAV for targeting dentate granule cells and validated its selectivity in wild-type adult mice.
Data-driven identification of major axes of functional variation in bacteria
Authors: Lajoie Geneviève , Kembel Steven W.
Published: February 2023

The discovery of major axes of correlated functional variation among species and habitats has revealed the fundamental trade-offs structuring both functional and taxonomic diversity in eukaryotes such as plants. Whether such functional axes exist in the bacterial realm and whether they could explain bacterial taxonomic turnover among ecosystems remains unknown. Here we use a data-driven approach to leverage global genomic and metagenomic datasets to reveal the existence of major axes of functional variation explaining both evolutionary differentiation within Bacteria and their ecological sorting across diverse habitats. We show that metagenomic variation among bacterial communities from various ecosystems is structured along a few axes of correlated functional pathways. Similar clusters of traits explained phylogenetic trait variation among >16,000 bacterial genomes, suggesting that functional turnover among bacterial communities from distinct habitats does not only result from the differential filtering of similar functions among communities, but also from phylogenetic correlations among these functions. Concordantly, functional pathways associated with trait clusters that were most important for defining functional turnover among bacterial communities were also those that had the highest phylogenetic signal in the bacterial genomic phylogeny. This study overall underlines the important role of evolutionary history in shaping contemporary distributions of bacteria across ecosystems.

Originality-Significance Statement

In this article, we use a trait screening approach based on genomic and metagenomic data to identify the key functional strategies of bacteria across ecosystems but also across the bacterial tree of life. This novel approach allows us to quantify the role of evolutionary processes in structuring microbial ecological differences among ecosystems. By reducing the high-dimensionality of trait variation observed among microorganisms around a small number of fundamental axes of trait covariation, we make a significant step towards generalization of the drivers of biological diversity in microbes but also across study systems. This research provide a major advance in our understanding of the origin and maintenance of bacterial biological diversity, expanding on related findings for plants and animals.
A role for the Gram-negative outer membrane in bacterial shape determination
Authors: Fivenson Elayne M. , Rohs Patricia D.A. , Vettiger Andrea , Sardis Marios F. , Torres Grasiela , Forchoh Alison , Bernhardt Thomas G.
Published: February 2023

The cell envelope of Gram-negative bacteria consists of three distinct layers: the cytoplasmic membrane, a cell wall made of peptidoglycan (PG), and an asymmetric outer membrane (OM) composed of phospholipid in the inner leaflet and lipopolysaccharide (LPS) glycolipid in the outer leaflet. The PG layer has long been thought to be the major structural component of the envelope protecting cells from osmotic lysis and providing them with their characteristic shape. In recent years, the OM has also been shown to be a load-bearing layer of the cell surface that fortifies cells against internal turgor pressure. However, whether the OM also plays a role in morphogenesis has remained unclear. Here, we report that changes in LPS synthesis or modification predicted to strengthen the OM can suppress the growth and shape defects ofEscherichia colimutants with reduced activity in a conserved PG synthesis machine called the Rod system (elongasome) that is responsible for cell elongation and shape determination. Evidence is presented that OM fortification in the shape mutants restores the ability of MreB cytoskeletal filaments to properly orient the synthesis of new cell wall material by the Rod system. Our results are therefore consistent with a role for the OM in the propagation of rod shape during growth in addition to its well-known function as a diffusion barrier promoting the intrinsic antibiotic resistance of Gram-negative bacteria.

SIGNIFICANCE

The cell wall has traditionally been thought to be the main structural determinant of the bacterial cell envelope that resists internal turgor and determines cell shape. However, the outer membrane (OM) has recently been shown to contribute to the mechanical strength of Gram-negative bacterial envelopes. Here, we demonstrate that changes to OM composition predicted to increase its load bearing capacity rescue the growth and shape defects ofEscherichia colimutants defective in the major cell wall synthesis machinery that determines rod shape. Our results therefore reveal a previously unappreciated role for the OM in bacterial shape determination in addition to its well-known function as a diffusion barrier that protects Gram-negative bacteria from external insults like antibiotics.
Automated Agnostic Designation of Pathogen Lineages
Authors: McBroome Jakob , de Bernardi Schneider Adriano , Roemer Cornelius , Wolfinger Michael T. , Hinrichs Angie S. , O’Toole Aine Niamh , Ruis Christopher , Turakhia Yatish , Rambaut Andrew , Corbett-Detig Russell
Published: February 2023

Pathogen nomenclature systems are a key component of effective communication and collaboration for researchers and public health workers. Since February 2021, the Pango nomenclature for SARS-CoV-2 has been sustained by crowdsourced lineage proposals as new isolates were added to a growing global dataset. This approach to dynamic lineage designation is dependent on a large and active epidemiological community identifying and curating each new lineage. This is vulnerable to time-critical delays as well as regional and personal bias. To address these issues, we developed a simple heuristic approach that divides a phylogenetic tree into lineages based on shared ancestral genotypes. We additionally provide a framework that automatically prioritizes the lineages by growth rate and association with key mutations or locations, extensible to any pathogen. Our implementation is efficient on extremely large phylogenetic trees and produces similar results to existing Pango lineage designations when applied to SARS-CoV-2. This method offers a simple, automated and consistent approach to pathogen nomenclature that can assist researchers in developing and maintaining phylogeny-based classifications in the face of ever increasing genomic datasets.
Gene panel selection for targeted spatial transcriptomics
Authors: Zhang Yida , Petukhov Viktor , Biederstedt Evan , Que Richard , Zhang Kun , Kharchenko Peter V.
Published: February 2023

Targeted spatial transcriptomics hold particular promise in analysis of complex tissues. Most such methods, however, measure only a limited panel of transcripts, which need to be selected in advance to inform on the cell types or processes being studied. A limitation of existing gene selection methods is that they rely on scRNA-seq data, ignoring platform effects between technologies. Here we describe gpsFISH, a computational method to perform gene selection through optimizing detection of known cell types. By modeling and adjusting for platform effects, gpsFISH outperforms other methods. Furthermore, gpsFISH can incorporate cell type hierarchies and custom gene preferences to accommodate diverse design requirements.
Behavioral measurements of motor readiness in mice
Authors: Mangin Elise N. , Chen Jian , Lin Jing , Li Nuo
Published: February 2023

Motor planning facilitates rapid and precise execution of volitional movements. Although motor planning has been classically studied in humans and monkeys, the mouse has become an increasingly popular model system to study neural mechanisms of motor planning. It remains yet untested whether mice and primates share common behavioral features of motor planning. We combined videography and a delayed response task paradigm in an autonomous behavioral system to measure motor planning in non-body- restrained mice. Motor planning resulted in both reaction time savings and increased movement accuracy, replicating classic effects in primates. We found that motor planning was reflected in task-relevant body features. Both the specific actions prepared and the degree of motor readiness could be read out online during motor planning. The online readout further revealed behavioral evidence of simultaneous preparation for multiple actions under uncertain conditions. These results validate the mouse as a model to study motor planning, demonstrate body feature movements as a powerful real-time readout of motor readiness, and offer behavioral evidence that motor planning can be a parallel process that permits rapid selection of multiple prepared actions.
Lung microenvironments harborMycobacterium tuberculosisphenotypes with distinct treatment responses
Authors: Walter Nicholas D. , Ernest Jackie P. , Dide-Agossou Christian , Bauman Allison A. , Ramey Michelle E. , Rossmassler Karen , Massoudi Lisa M. , Pauly Samantha , Al Mubarak Reem , Voskuil Martin I. , Kaya Firat , Sarathy Jansy P. , Zimmerman Matthew D. , Dartois Véronique , Podell Brendan K. , Savic Radojka M. , Robertson Gregory T.
Published: February 2023

Tuberculosis lung lesions are complex and harbor heterogeneous microenvironments that influence antibiotic effectiveness. Major strides have been made recently in understanding drug pharmacokinetics in pulmonary lesions, but the bacterial phenotypes that arise under these conditions and their contribution to drug tolerance is poorly understood. A pharmacodynamic marker called the RS ratio quantifies ongoing rRNA synthesis based on the abundance of newly-synthesized precursor rRNA relative to mature structural rRNA. Application of the RS ratio in the C3HeB/FeJ mouse model demonstrated thatMycobacterium tuberculosispopulations residing in different tissue microenvironments are phenotypically distinct and respond differently to drug treatment with rifampin, isoniazid or bedaquiline. This work provides a foundational basis required to address how anatomic and pathologic microenvironmental niches may contribute to the long treatment duration and drug tolerance during treatment of human tuberculosis.