bluuebunny/crossref_metadata_2025 huggingface dataset:
Single-cell RNA-sequencing of bronchoscopy specimens: development of a rapid, minimal-handling protocol
Authors: Gerayeli Firoozeh V , Milne Stephen , Yang Chen Xi , Li Xuan , Guinto Elizabeth , Yang Julia Shun-Wei , Cheung Chung Yan , Stach Tara R , Shaipanich Tawimas , Leung Janice M , Sin Don D
Published: March 2023

Single-cell RNA-sequencing (scRNA-seq) is an important tool for understanding disease pathophysiology, including airways diseases. Currently, the majority of scRNA-seq studies in airways diseases have used invasive methods (airway biopsy, surgical resection) which carry inherent risks and thus present a major limitation to scRNA-seq investigation of airway pathology. Bronchial brushing, where the airway mucosa is sampled using a cytological brush, is a viable, less invasive method of obtaining airway cells for scRNA-seq. Here we are describing the development of a rapid and minimal-handling protocol for preparing single cell suspensions from bronchial brush specimens for scRNA-seq. Our optimized protocol maximises cell recovery and cell quality, and may facilitate large-scale profiling of the airway transcriptome at single cell resolution.

Lay abstract

Single-cell RNA-sequencing (scRNA-seq) measures the gene expression of individual cells, and may be useful for understanding disease processes. scRNA-seq may be used to investigate lung diseases, but using invasive methods such as biopsy or surgery limits our ability to conduct large research studies. Bronchial brushing, where a soft brush is used to collect cells from inside the lungs, is a safer method but we need a better way to isolate individual cells from the brush specimens. We developed a method that is faster and involves less handling of the specimens compared to other published methods. Our method may therefore be useful for conducting large scRNA-seq studies in lung diseases.
The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder
Authors: Weibel Catherine , Wheeler Andrew L , James Jennifer E , Willis Sara , McShea Hanon , Masel Joanna
Published: March 2023

The nearly neutral theory of molecular evolution posits variation among species in the effectiveness of selection. In an idealized model, the census population size determines both this minimum magnitude of the selection coefficient required for deleterious variants to be reliably purged, and the amount of neutral diversity. Empirically, an effective population size is often estimated from the amount of putatively neutral genetic diversity and is assumed to also capture a species effectiveness of selection. A potentially more direct measure of the effectiveness of selection is the degree to which selection maintains preferred codons. However, past metrics that compare codon bias across species are confounded by among-species variation in %GC content and/or amino acid composition. Here we propose a new Codon Adaptation Index of Species (CAIS), based on Kullback-Leibler divergence, that corrects for both confounders. We demonstrate the use of CAIS correlations, as well as the Effective Number of Codons, to show that the protein domains of more highly adapted vertebrate species evolve higher intrinsic structural disorder
Host selection has stronger impact on leaf microbiome assembly compared to land-management practices
Authors: Singh Pankaj K. , Egidi Eleonora , Macdonald Catriona A. , Singh Brajesh K.
Published: March 2023

Plant microbiome contribute directly to plant health and productivity but mechanisms that underpin plant microbiome assembly in different compartments (e.g. root, leaf) are not fully understood. Identifying environmental and management factors that affect plant microbiome assembly is important to advance understanding of fundamental ecological processes and harnessing microbiome for improved primary productivity and environmental sustainability. Irrigation and fertilization are two common management practices in Australian tree plantations, but little is known about the effects of these treatments on soil, plant host, and their microbiome. Here, we investigated the impact of a decade long irrigation, fertilization, and their combined application, on soil, plant traits and microbiome of aEucalyptus salignaplantation at the Hawkesbury Forest Experiment, Western Sydney University, Richmond, NSW. Microbial profiling of bulk soil, rhizosphere, root, and leaves was performed using amplicon sequencing 16S rDNA and ITS markers for bacteria and fungi, respectively, along with measurements of soil properties and plant traits. The results indicated that both management practices affected soil properties and soil and root microbiome significantly. Irrigation increased but fertilizer treatment reduced microbial alpha diversity. However, neither irrigation nor fertilizer treatment significantly impacted the leaf microbiome. Our findings imply that management practices impact soil edaphic factors, which in turn influence the below ground microbiome (soil and root). In addition, the leaf microbiome was distinct from soil and root microbiome, and a source tracker analysis suggested root and bulk soils only contributed to 53% and 10% OTUs of the leaf bacterial community, suggesting strong and sequential host selection of the leaf microbiome. In addition, management practices had limited impact on leaf traits and, consequently, the leaf microbiome maintained its distinct composition. These findings provide mechanistic evidence for ecological processes that drive plant microbiome assembly and indicate that host selection plays a more important role than management practices on leaf microbiome assembly.
Excitatory: inhibitory imbalance in Alzheimer’s disease is exacerbated by seizures with attenuation after rapamycin treatment in 5XFAD mice
Authors: Barbour AJ , Gourmaud S , Lancaster E , Li X , Stewart D , Irwin DJ , Talos DM , Jensen FE
Published: March 2023

Approximately 22% of Alzheimer’s disease (AD) patients suffer from seizures, and the co-occurrence of seizures and epileptiform activity exacerbate AD pathology and related cognitive deficits. Hence seizures may be a targetable component of AD progression. As epileptogenesis is associated with changes in neuronal excitatory: inhibitory (E:I) balance, we hypothesized that decreased markers of inhibition relative to those of excitation would be present in AD patients and exacerbated further when seizures were a comorbidity. We similarly hypothesized that an E:I imbalance would be present in five times familial AD (5XFAD) mice and augmented following pentylenetetrazol (PTZ) seizure kindling. AD temporal cortical tissue from patients with or without seizure history and brain tissue from 5XFAD mice were examined for changes in several markers of E:I balance, including the inhibitory GABAAreceptor, the chloride cotransporters, sodium potassium chloride cotransporter 1 (NKCC1) and potassium chloride cotransporter 2 (KCC2), and the excitatory NMDA and AMPA type glutamate receptors. We found that AD patients had decreased GABAAreceptor subunits and those with comorbid seizures had worsened cognitive and functional scores, and increased in NKCC1/KCC2 ratios, indicative of depolarizing GABA responses. The E:I imbalance appears to occur early in the disease course, as patch clamp recordings from CA1 neurons in hippocampal slices from prodromal 5XFAD mice showed decreased GABAergic inhibitory transmission and increased intrinsic excitability. In addition, seizure induction in prodromal 5XFAD mice further dysregulated NKCC1/KCC2, and altered the excitatory AMPA glutamate receptor protein expression, with a reduction in GluA2 subunit, indicative of calcium permeable-receptors. Finally, we found that chronic treatment with the mTORC1 inhibitor, rapamycin, at doses we have previously shown to attenuate seizure-induced α-amyloid pathology and cognitive deficits, could reverse aspects of E:I imbalance in these mice. Our data demonstrate novel mechanisms of interaction between AD and epilepsy and indicate that FDA-approved mTOR inhibitors hold therapeutic promise for AD patients with a seizure history.
A novel qPCR-based technique for identifying avian sex: an illustration within embryonic craniofacial bone
Authors: Houchen Claire J. , Bergman-Gonzalez Maria , Bumann Erin E.
Published: March 2023

Sex is a biological variable important to consider in all biomedical experiments. However, analyzing sex differences in avian models can be challenging as the sexes are morphologically indistinguishable in most avian embryos. Unlike humans, female birds are the heterogametic sex with a Z and W chromosome. The female-specific W chromosome has previously been identified using species-specific polymerase chain reaction (PCR) techniques. We developed a novel quantitative real-time PCR (RT-qPCR) technique which amplifies the W chromosome gene histidine triad nucleotide binding protein W (HINTW) in chick, quail, and duck. We confirmed the accuracy of the single set ofHINTWRT-qPCR primers in all three species using species-specific PCR. Bone development-related gene expression was then analyzed by sex in embryonic lower jaws of duck and quail, as duck beak size is known to be sexually dimorphic while quail beak size is not. Trends towards sexual dimorphism were found in duck gene expression but not in quail, as expected. Our novelHINTWRT-qPCR technique to identify the sex of avian embryos is a useful tool for including sex as a biological variable in analysis of a variety of tissues and cells used in developmental biology research.
Unveiling causal regulatory mechanisms through cell-state parallax
Authors: Wu Alexander Po-Yen , Singh Rohit , Walsh Christopher , Berger Bonnie
Published: March 2023

Genome-wide association studies (GWAS) identify numerous disease-linked genetic variants at noncoding genomic loci, yet therapeutic progress is hampered by the challenge of deciphering the regulatory roles of these loci in tissue-specific contexts. Single-cell multimodal assays that simultaneously profile chromatin accessibility and gene expression could predict tissue-specific causal links between noncoding loci and the genes they affect. However, current computational strategies either neglect the causal relationship between chromatin accessibility and transcription or lack variant-level precision, aggregating data across genomic ranges due to data sparsity. To address this, we introduce GrID-Net, a graph neural network approach that generalizes Granger causal inference to detect new causal locus–gene associations in graph-structured systems such as single-cell trajectories. Inspired by the principles of optical parallax, which reveals object depth from static snapshots, we hypothesized that causal mechanisms could be inferred from static single-cell snapshots by exploiting the time lag between epigenetic and transcriptional cell states, a concept we term “cell-state parallax.” Applying GrID-Net to schizophrenia (SCZ) genetic variants, we increased variant coverage by 36% and uncovered noncoding mechanisms that dysregulate 132 genes, including key potassium transporters such as KCNG2 and SLC12A6. Furthermore, we discovered evidence for the prominent role of neural transcription-factor binding disruptions in SCZ etiology. Our work not only provides a strategy for elucidating the tissue-specific impact of noncoding variants but also underscores the breakthrough potential of cell-state parallax in single-cell multiomics for discovering tissue-specific gene regulatory mechanisms.
The unique three-dimensional arrangement of Macrophage Galactose Lectin enablesE. coliLipoPolySaccharides recognition through two distinct interfaces
Authors: Abbas Massilia , Maalej Meriem , Nieto-Fabregat Ferran , Thépaut Michel , Kleman Jean-Philippe , Ayala Isabel , Molinaro Antonio , Simorre Jean-Pierre , Marchetti Roberta , Fieschi Franck , Laguri Cedric
Published: March 2023

LipoPolySaccharides are a hallmark of Gram-negative bacteria and their presence at the cell surface is key for bacterial integrity. As surface exposed components, they are recognized by immunity C-type lectin receptors present on Antigen Presenting Cells. Human Macrophage Galactose Lectin bindsE. colisurface that presents a specific glycan motif. Nevertheless, this high affinity interaction occurs regardless of the integrity of its canonical calcium-dependent glycan binding site. Nuclear Magnetic Resonance of MGL carbohydrate recognition domain and complete extracellular domain revealed a new glycan binding site opposite to the canonical site. A model of trimeric Macrophage Galactose Lectin was determined based on a combination of Small Angle X-ray scattering and Alphafold. A disulphide bond positions the Carbohydrate Recognition Domain perpendicular to the coiled-coil domain. This unique configuration for a C-type lectin orients the six glycan sites of MGL in an ideal position to bind LipoPolySaccharides at the bacterial surface with high avidity.
Systematic analyses of the resistance potential of drugs targeting SARS-CoV-2 main protease
Authors: Flynn Julia M. , Huang Qiu Yu J. , Zvornicanin Sarah N. , Schneider-Nachum Gily , Shaqra Ala M. , Yilmaz Nese Kurt , Moquin Stephanie A. , Dovala Dustin , Schiffer Celia A. , Bolon Daniel N.A.
Published: March 2023

Drugs that target the main protease (Mpro) of SARS-CoV-2 are effective therapeutics that have entered clinical use. Wide-scale use of these drugs will apply selection pressure for the evolution of resistance mutations. To understand resistance potential in Mpro, we performed comprehensive surveys of amino acid changes that can cause resistance in a yeast screen to nirmatrelvir (contained in the drug Paxlovid), and ensitrelvir (Xocova) that is currently in phase III trials. The most impactful resistance mutation (E166V) recently reported in multiple viral passaging studies with nirmatrelvir showed the strongest drug resistance score for nirmatrelvir, while P168R had the strongest resistance score for ensitrelvir. Using a systematic approach to assess potential drug resistance, we identified 142 resistance mutations for nirmatrelvir and 177 for ensitrelvir. Among these mutations, 99 caused apparent resistance to both inhibitors, suggesting a strong likelihood for the evolution of cross-resistance. Many mutations that exhibited inhibitor-specific resistance were consistent with distinct ways that each inhibitor protrudes beyond the substrate envelope. In addition, mutations with strong drug resistance scores tended to have reduced function. Our results indicate that strong pressure from nirmatrelvir or ensitrelvir will select for multiple distinct resistant lineages that will include both primary resistance mutations that weaken interactions with drug while decreasing enzyme function and secondary mutations that increase enzyme activity. The comprehensive identification of resistance mutations enables the design of inhibitors with reduced potential of developing resistance and aids in the surveillance of drug resistance in circulating viral populations.
Genome-resolved metagenomics reveals abundant nitrate reducers and partitioning of nitrite usage within global oxygen deficient zones
Authors: Zhang Irene H. , Sun Xin , Jayakumar Amal , Fortin Samantha G. , Ward Bess B. , Babbin Andrew R.
Published: March 2023

Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially-mediated pathway proceeding stepwise from NO3−to N2. This process may be performed entirely by complete denitrifiers capable of all four steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes are primarily carried by complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. From 56 metagenomes spanning all three major ODZs, we use genome-resolved metagenomics to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 metagenome-assembled genomes presents the largest collection of pelagic ODZ microbes and reveals a clearer picture of the nitrogen cycling community within this environment.
No isolate, no problem: Using a novel insertion sequence PCR to link rats to human shigellosis cases in an underserved urban community
Authors: Ritchie Gordon , Leung Victor , Himsworth Chelsea G. , Byers Kaylee A. , Lee Lisa K.F. , Chorlton Samuel D. , Stefanovic Aleksandra , Romney Marc G. , Matic Nancy , Lowe Christopher F.
Published: March 2023

Introduction

During an investigation into a cluster ofShigella flexneriserotype 2a cases in an underserved community, we assessed the relatedness of human and ratS. flexneriisolates utilizing a novel PCR targeting insertion sites (IS-PCR) of mobile elements in theShigellagenome characteristic of the cluster strain.

Methods

Whole genome sequences ofS. flexneri(n=50) associated with the cluster were analyzed.de novogenome assemblies were analyzed by a Geneious V10.2.6 motif search, and 2 unique IS were identified in all humanShigellasequences of the local cluster. Hydrolysis probe PCR assays were designed to detect these sequences consisting of forward and reverse primers to amplify across each insertion site, and a hydrolysis probe spanning the insertion site. IS-PCR was performed for threeShigellaPCR-positive culture-negative rat intestine specimens from this community.

Results

Both insertion sites were detected in thede novogenome assemblies of all clinicalS. flexneriisolates (n=50). Two of the three PCR-positive culture-negative rat samples were positive for both unique IS identified in the humanS. flexneriisolates, suggesting that the ratShigellaspp. strains were closely related to the human strains in the cluster. The cycle threshold (Ct) values were >35, indicating that the bacterial load was very low in the rat samples.

Conclusions

Two unique IS were identified in clinical isolates from a communityS. flexnericluster. Both IS targets were identified in PCR-positive (Shigellaspp.), culture-negative rat tissue and clinical isolates from humans, indicating relatedness.
3D Confinement-enabled Priming of Synaptic Activation Promotes Primary T Cell Expansion
Authors: Jiang Ruoyu , Chen Yu-Hsi , Parajuli Ritesh , Agrawal Anshu , Lee Abraham P.
Published: March 2023

The success of autologous cell therapy, which depends highly on T lymphocyte expansion efficiency, is often hindered by suboptimal interactions between T-cell receptors and peptide-MHC molecules. Here, we demonstrate 3D confinement-enabled priming of T cell–MHC immune synapse junctions based on cytoskeletal forces within minutes, which is 200-fold faster than conventional 24 h bulk shaking method. Using T cell–Dynabead binding skeletons in the starting culture, two- to six-fold greater T cell expansion was achieved over the conventional T cell expansion approach without inducing excessive cell exhaustion. Under 3D force-confinement, T-cell division (G1, S, and G2 phases) was increased to be twice as fast. Creating 3D T cell–Dynabead skeletons as the “booster” material enables highly efficient T cell expansion, without requiring complex surface modification of antigen-presenting cells. This method can be modularly adapted to existing T cell expansion processes for a wide range of applications including adoptive cell therapies.

Teaser

3D confinement-enabled priming of synaptic activation enables radically faster autologous cell production.
The Human Mitochondrial Genome Encodes for an Interferon-Responsive Host Defense Peptide
Authors: Rice MC , Imun M , Jung SW , Park CY , Kim JS , Lai RW , Barr CR , Son JM , Tor K , Kim E , Lu RJ , Cohen I , Benayoun BA , Lee C
Published: March 2023

The mitochondrial DNA (mtDNA) can trigger immune responses and directly entrap pathogens, but it is not known to encode for active immune factors. The immune system is traditionally thought to be exclusively nuclear-encoded. Here, we report the identification of a mitochondrial-encoded host defense peptide (HDP) that presumably derives from the primordial proto-mitochondrial bacteria. We demonstrate that MOTS-c (mitochondrial open reading frame from the twelve S rRNA type-c) is a mitochondrial-encoded amphipathic and cationic peptide with direct antibacterial and immunomodulatory functions, consistent with the peptide chemistry and functions of known HDPs. MOTS-c targetedE. coliand methicillin-resistantS. aureus(MRSA), in part, by targeting their membranes using its hydrophobic and cationic domains. In monocytes, IFNγ, LPS, and differentiation signals each induced the expression of endogenous MOTS-c. Notably, MOTS-c translocated to the nucleus to regulate gene expression during monocyte differentiation and programmed them into macrophages with unique transcriptomic signatures related to antigen presentation and IFN signaling. MOTS-c-programmed macrophages exhibited enhanced bacterial clearance and shifted metabolism. Our findings support MOTS-c as a first-in-class mitochondrial-encoded HDP and indicates that our immune system is not only encoded by the nuclear genome, but also by the co-evolved mitochondrial genome.
Identification of Biomarkers and Trajectories of Prostate Cancer Progression: A Bioinformatics Fusion of Weighted Correlation Network Analysis and Machine Learning
Authors: Sheibani-Tezerji Raheleh , Pérez Malla Carlos Uziel , Wasinger Gabriel , Misura Katarina , Haase Astrid , Malzer Anna , Kalla Jessica , Tran Loan , Egger Gerda
Published: March 2023

Background

Prostate cancer diagnosis and prognosis is currently limited by the availability of sensitive and specific biomarkers. There is an urgent need to develop molecular biomarkers that allow for the distinction of indolent from aggressive disease, the sensitive detection of heterogeneous tumors, or the evaluation of micro-metastases. The availability of multi-omics datasets in publicly accessible databases provides a valuable foundation to develop computational workflows for the identification of suitable biomarkers for clinical management of cancer patients.

Results

We combined transcriptomic data of primary localized and advanced prostate cancer from two cancer databases. Transcriptomic analysis of metastatic tumors unveiled a distinct overexpression pattern of genes encoding cell surface proteins intricately associated with cell-matrix components and chemokine signaling pathways. Utilizing an integrated approach combining machine learning and weighted gene correlation network modules, we identified the EZH2-TROAP axis as the main trajectory from initial tumor development to lethal metastatic disease. In addition, we identified and independently validated 58 promising biomarkers that were specifically upregulated in primary localized or metastatic disease. Among those biomarkers, 22 were highly significant for predicting biochemical recurrence. Notably, we confirmed TPX2 upregulation at the protein level in an independent cohort of primary prostate cancer and matched lymph node metastases.

Conclusions

This study demonstrates the effectiveness of using advanced bioinformatics approaches to identify the biological factors that drive prostate cancer progression. Furthermore, the targets identified show promise as prognostic biomarkers in clinical settings. Thus, integrative bioinformatics methods provide both deeper understanding of disease dynamics and open the doors for future personalized interventions.
Adaptive dynamics of memory-1 strategies in the repeated donation game
Authors: LaPorte Philip , Hilbe Christian , Nowak Martin A.
Published: March 2023

Social interactions often take the form of a social dilemma: collectively, individuals fare best if everybody cooperates, yet each single individual is tempted to free ride. Social dilemmas can be resolved when individuals interact repeatedly. Repetition allows individuals to adopt reciprocal strategies which incentivize cooperation. The most basic model to study reciprocity is the repeated donation game, a variant of the repeated prisoner’s dilemma. Two players interact over many rounds, in which they repeatedly decide whether to cooperate or to defect. To make their decisions, they need a strategy that tells them what to do depending on the history of previous play. Memory-1 strategies depend on the previous round only. Even though memory-1 strategies are among the most elementary strategies of reciprocity, their evolutionary dynamics has been difficult to study analytically. As a result, most previous work relies on simulations. Here, we derive and analyze their adaptive dynamics. We show that the four-dimensional space of memory-1 strategies has an invariant three-dimensional subspace, generated by the memory-1 counting strategies. Counting strategies record how many players cooperated in the previous round, without considering who cooperated. We give a partial characterization of adaptive dynamics for memory-1 strategies and a full characterization for memory-1 counting strategies.

Author summary

Direct reciprocity is a mechanism for evolution of cooperation based on the repeated interaction of the same players. In the most basic setting, we consider a game between two players and in each round they choose between cooperation and defection. Hence, there are four possible outcomes: (i) both cooperate; (ii) I cooperate, you defect; (ii) I defect, you cooperate; (iv) both defect. A memory-1 strategy for playing this game is characterized by four quantities which specify the probabilities to cooperate in the next round depending on the outcome of the current round. We study evolutionary dynamics in the space of all memory-1 strategies. We assume that mutant strategies are generated in close proximity to the existing strategies, and therefore we can use the framework of adaptive dynamics, which is deterministic.
Antimicrobial peptides originating from expression libraries ofAurelia auritaandMnemiopsis leidyiprevent biofilm formation of opportunistic pathogens
Authors: Ladewig Lisa , Gloy Leon , Langfeldt Daniela , Pinnow Nicole , Weiland-Bräuer Nancy , Schmitz Ruth A.
Published: March 2023

The demand for novel antimicrobial compounds is rapidly growing due to the rising appearance of antibiotic resistance in bacteria; accordingly, alternative approaches are urgently needed. Antimicrobial peptides (AMPs) are promising since they are a naturally occurring part of the innate immune system and display remarkable broad-spectrum activity and high selectivity against various microbes. Marine invertebrates are a primary resource of natural AMPs. Consequently, cDNA expression (EST) libraries from the Cnidarian moon jellyfishAurelia auritaand the Ctenophore comb jellyMnemiopsis leidyiwere constructed inEscherichia coli. Cell-free size-fractionated cell extracts (< 3 kDa) of the two libraries (each with 29,952 clones) were consecutively screened for peptides preventing the biofilm formation of opportunistic pathogens using the crystal violet assay. The 3 kDa fraction of ten individual clones demonstrated promising biofilm-preventing activities againstKlebsiella oxytocaandStaphylococcus epidermidis. Sequencing the respective activity-conferring inserts allowed the identification of small ORFs encoding peptides (10 – 22 aa), which were subsequently chemically synthesized to validate their inhibitory potential. Biofilm-preventing effects againstK. oxytoca, Pseudomonas aeruginosa, S. epidermidis, andS. aureuswere verified for five synthetic peptides in a concentration-dependent manner, with peptide BiP_Aa_5 showing the strongest effects. The impact of BiP_Aa_2, BiP_Aa_5, and BiP_Aa_6 on dynamic biofilm formation ofK. oxytocawas further validated in microfluidic flow cells, demonstrating a significant reduction in biofilm thickness and volume by BiP_Aa_2 and BiP_Aa_5. Overall, the structural characteristics of the marine invertebrate-derived AMPs, their physicochemical properties, and promising anti-biofilm effects highlight them as attractive candidates for discovering new antimicrobials.
A network medicine approach to elucidate mechanisms underlying menopause-induced knee osteoarthritis
Authors: Gilmer Gabrielle , Iijima Hirotaka , Jackson Natalie , Hettinger Zachary , Bean Allison C. , Bergmann Juliana , Evans Christopher , Thurston Rebecca C. , Ambrosio Fabrisia
Published: March 2023

Post-menopausal women present with the highest incidence and morbidity of knee osteoarthritis (KOA), but no disease-modifying therapies are available. This treatment gap may be driven by the absence of menopause in preclinical studies, as rodents do not naturally maintain a menopausal phenotype. Here, we employed a chemically-induced menopause model to map the trajectory of KOA at the tissue and proteome levels and test therapeuticsin silico. Middle-aged female mice were randomized to sesame oil (non-menopause) or 4-vinycyclohexene diepoxide (menopause) injections. Following comprehensive validation of our model, knees were collected across perimenopause and menopause for histology, and cartilage samples were micro-dissected for mass spectrometry proteomics. Menopause mice displayed aggravated cartilage degeneration and synovitis relative to non-menopause mice. An unbiased pathway analysis revealed progesterone as a predominant driver of pathological signaling cascades within the cartilage proteome. Network medicine-based analyses suggested that menopause induction amplifies chondrocyte senescence, actin cytoskeleton-based stress, and extracellular matrix disassembly. We then usedin silicodrug testing to evaluate how restoration of sex hormones impacted the cartilage network. The greatest restoration was observed with combined estradiol/progesterone treatment (i.e., hormone therapy), althoughin silicotreatment with a senolytic drug also partially recovered the cartilage proteome. Taken together, our findings using a translatable female aging model demonstrate that menopausal aging induces progressive cartilage degeneration and amplifies age-related synovitis. These changes may be driven by a previously unappreciated role of progesterone loss and menopause-induced cellular senescence. Lastly,in silicotreatment suggests an estradiol/progesterone cocktail or senolytics may attenuate menopause-induced cartilage pathology.

One Sentence Summary

Menopause induces cartilage degradation, senescence, and extracellular matrix disassembly, while hormone therapy restores the cartilage proteome.
Seasonal gene-expression signatures of delayed fertilization in Fagaceae
Authors: Satake Akiko , Ohta Kayoko , Takeda-Kamiya Noriko , Toyooka Kiminori , Kusumi Junko
Published: March 2023

In the family Fagaceae, fertilization is delayed by several weeks to one year after pollination, leading to one- or two-year fruiting species depending on whether fruiting occurs in the same or the next year after flowering. To investigate physiological responses underlying the regulation of delayed fertilization, we monitored seasonal changes in genome-wide gene expression in tissues including leaves and buds over two years under natural conditions in one- (Quercus glauca) and two-year fruiting species (Lithocarpus edulis). Genes associated with the responses to cold stress, photosynthesis, and cell proliferation, which are essential for survival and growth, showed highly conserved seasonal expression profiles regardless of species. However, seasonal expression profiles diverged between the one- and two-year fruiting species in genes associated with pollination, an important process contributing to the origin and maintenance of the reproductive barrier between plant species. By comparing seasonal progression of ovule development and gene expression in pistillate flowers, we revealed that ovules started developing after winter in the two-year fruiting species, which could be linked to the activation of genes involved in fertilization and female gametophyte development after winter. These findings suggest that the two-year fruiting species may have evolved a requirement of winter cold to prevent fertilization before winter and facilitate fertilization and embryo development in the following spring when temperature rises. This study offers new possibilities to explore the evolution of reproductive strategies in Fagaceae.
Differentiating shame- and guilt-proneness with heart rate variability in Chinese young adults
Authors: Ip Isaac N. , Ching Fiona N. Y. , Chiu Hey Tou , Keung Ariel H. Y. , Wong Savio W. H.
Published: March 2023

A high proneness to experience shame and guilt has been associated with psychopathology. Despite their similarity, shame- and guilt-proneness have different psychological and neurobiological correlates. The present study aims to compare the physiological correlates between shame- and guilt-proneness. Resting heart rate variability (HRV), a peripheral biomarker of emotion dysregulation and psychopathology, was measured in a sample of 60 Chinese young adults with two sessions of electrocardiogram recording. Proneness to shame and guilt were measured by the Test of Self-Conscious Affect 3. Hierarchical linear modeling indicated that guilt-proneness was positively associated with HRV while shame-proneness was not. Our findings implied that shame- and guilt-proneness have different relations with HRV. The distinct physiological relations are discussed with respect to the adaptive/maladaptive nature of shame- and guilt-proneness.
The claustrum drives large-scale interactions of cortical circuits relevant to long-term memory
Authors: Mutel S. , Renfer JR. , Rodriguez I. , Carleton A. , Salazar RF.
Published: March 2023

The consolidation and recall of episodic memories rely on distributed cortical activity. The claustrum, a subcortical structure reciprocally connected to most of the cortex, may facilitate inter-areal communication necessary for these processes. We report here that the functional inhibition of claustral projection neurons affects directional interactions and the coordination of oscillatory neuronal patterns in the fronto-parietal network. Moreover, the inhibition of these neurons has a detrimental effect on concurrent oscillatory events relevant to the consolidation of contextual fear memory. Last, we demonstrate that biasing the directional flow of information between the latter two cortical areas enhances the retrieval of a remote contextual memory. We propose that the claustrum orchestrates inter-areal cortical interactions relevant to contextual memory processes by affecting the latency of neuronal responses.

One-Sentence Summary

The claustrum coordinates inter-areal cortical activity.
Response of adult carrion beetlesNecrodes littoralis(L.) (Staphylinidae: Silphinae) to selected cadaveric volatile organic compounds: laboratory and field tests
Authors: Mądra-Bielewicz Anna , Gruszka Joanna , Matuszewski Szymon
Published: March 2023

Carrion insects need to quickly and accurately locate a suitable carcass to maximize their reproductive success. They are attracted by cadaveric volatile organic compounds (VOCs). However, very little is known about VOCs that attract insects at later stages of carrion decomposition. Here, we tested the response ofNecrodes littoralis(Linnaeus, 1758). (Staphylinidae: Silphinae), a Palearctic beetle that colonizes large carrion late in decomposition, to selected VOCs. First, in the laboratory choice tests we demonstrated that the beetles reveal no preference for meat with larval blow flies over meat alone. This finding indicates that both, the fly larvae and the feeding matrix they form on meat are not the source of specific attractants for the adult beetles ofNecrodesLeach, 1815. Therefore, we focused on VOCs that are related to carrion putrefaction. We tested the response of the beetles to benzyl butyrate, butan-1-ol, butyric acid, cadaverine, dimethyl disulfide (DMDS), dimethyl trisulfide, indole, phenol, putrescine and skatole in laboratory choice assays and field trapping tests. None of the compounds elicited the positive and significant response of the beetles under laboratory or field conditions, indicating that these VOCs are probably not the attractants ofN. littoralis. Moreover, in the field tests we found a significant attraction ofLucilia sericata(Meigen, 1826) (Diptera: Calliphoridae) to traps with DMDS. DMDS revealed also a positive (however insignificant) response ofSaprinusspp. (Coleoptera: Histeridae) andSarcophagaspp. (Diptera: Sarcophagidae).Sarcophagaflies were also attracted to traps with butyric acid. These findings expand the knowledge on chemoecology of carrion insects, highlighting the need to further search for VOCs that attract late-colonizers of carrion.
The proton-activated receptor TDAG8 is upregulated in oligodendrocytes during maturation and under acidic conditions
Authors: Opiełka Mikołaj , Caratis Fionä , Hausmann Martin , Velasco-Estevez Maria , de Vallière Cheryl , Seuwen Klaus , Rogler Gerhard , Karaszewski Bartosz , Rutkowska Aleksandra
Published: March 2023

Acidosis is one of the hallmarks of demyelinating central nervous system (CNS) lesions in multiple sclerosis (MS). Response to acidic pH is primarily mediated by a family of G protein-coupled proton-sensing receptors: OGR1, GPR4, and TDAG8. These receptors are inactive at alkaline pH, while at acidic pH they are maximally activated. Genome-wide association studies identified a locus within the TDAG8 gene to be associated with several autoimmune diseases including MS. Notably, we here found that TDAG8 expression is upregulated in MS plaques which prompted us to explore the expression and function of TDAG8 in the CNS in human MO3.13 oligodendrocytesin vitroandin vivoin the lipopolysaccharide-induced neuroinflammation model. We found that TDAG8 is upregulated in maturing oligodendrocytes and temporarily under acidic conditions. Acidic pH also induces oligodendrocyte branching, inhibits chemotaxis and affects the expression of oligodendrocyte maturation markers, PDGFRα and MBPin vitro. Even though myelination was not affected in the adult TDAG8-deficient mice, the expression of human and murine TDAG8 was strongly regulated upon inflammationin vivoin the brain andin vitroin lipopolysaccharide and pro-inflammatory cytokine-treated oligodendrocytes. Together these findings point toward a potential role of TDAG8 in oligodendrocyte biology, neuroinflammation and pathophysiology of MS and provide new directions for further scientific enquiry.
Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth
Authors: Shoemaker William R. , Grilli Jacopo
Published: March 2023

The structure and diversity of microbial communities is intrinsically hierarchical due to the shared evolutionary history of their constituents. This history is typically captured through taxonomic assignment and phylogenetic reconstruction, sources of information that are frequently used to group microbes into higher levels of organization in experimental and natural communities. Connecting community diversity to the joint ecological dynamics of the abundances of these groups is a central problem of community ecology. However, how microbial diversity depends on the scale of observation at which groups are defined has never been systematically examined. Here, we used a macroecological approach to quantitatively characterize the structure and diversity of microbial communities among disparate environments across taxonomic and phylogenetic scales. We found that measures of biodiversity at a given scale can be consistently predicted using a minimal model of ecology, the Stochastic Logistic Model of growth (SLM). This result suggests that the SLM is a more appropriate null-model for microbial biodiversity than alternatives such as the Unified Neutral Theory of Biodiversity. Extending these within-scale results, we examined the relationship between measures of biodiversity calculated at different scales (e.g., genus vs. family), an empirical pattern predicted by the Diversity Begets Diversity (DBD) hypothesis. We found that the relationship between richness estimates at different scales can be quantitatively predicted assuming independence among community members.Contrastingly, only by including correlations between the abundances of community members (e.g., as the consequence of interactions) can we predict the relationship between estimates of diversity at different scales. The results of this study characterize novel microbial patterns across scales of organization and establish a sharp demarcation between recently proposed macroecological patterns that are not and are affected by ecological interactions.
Feedback control of organ size precision is mediated by BMP2-regulated apoptosis in theDrosophilaeye
Authors: Navarro T. , Iannini A. , Neto M. , Campoy-Lopez A. , Muñoz-Garcia J. , Pereira P.S. , Ares S. , Casares F.
Published: March 2023

Biological processes are intrinsically noisy and yet, the result of development –like the species-specific size and shape of organs– is usually remarkably precise. This precision suggests the existence of mechanisms of feedback control that ensure that deviations from a target size are minimized. Still, we have very limited understanding of how these mechanisms operate. Here, we investigate the problem of organ size precision using theDrosophilaeye. The size of the adult eye depends on the rates at which eye progenitor cells grow and differentiate. We first find that the progenitor net growth rate results from the balance between their proliferation and apoptosis, with this latter contributing to determining both final eye size and its variability. In turn, apoptosis of progenitor cells is hampered by Dpp, a BMP2/4 signaling molecule transiently produced by early differentiating retinal cells. Our genetic and computational experiments show how the status of retinal differentiation is communicated to progenitors through the differentiation-dependent production of Dpp which, by adjusting the rate of apoptosis, exerts a feedback control over the net growth of progenitors to reduce final eye size variability.
Done in 65 ms: Express visuomotor responses in upper limb muscles in Rhesus Macaques
Authors: Cecala Aaron L. , Kozak Rebecca A. , Pruszynski J. Andrew , Corneil Brian D.
Published: March 2023

How rapidly can the brain transform vision into action? Work in humans has established that the transformation for visually-guided reaching can be remarkably rapid, with the first phase of upper limb muscle recruitment, theexpress visuomotor response, beginning within less than 100 ms of visual target presentation. Such short-latency responses limit the opportunities for extensive cortical processing, leading to the hypothesis that they are generated via the subcortical tectoreticulospinal pathway. Here, we examine if non-human primates (NHPs) exhibit express visuomotor responses. Two male macaques made visually-guided reaches in a behavioral paradigm known to elicit express visuomotor responses in humans, while we acquired intramuscular recordings from the deltoid muscle. Across several variants of this paradigm, express visuomotor responses began within 65 ms (range 48–91 ms) of target presentation. Although the timing of the express visuomotor response did not co-vary with reaction time, larger express visuomotor responses tended to precede shorter latency reaches. Finally, the magnitude of the express visuomotor response was muted on trials where NHPs withheld a reach to one stimulus in order to move to a stimulus appearing 34 ms later in the opposite direction. Overall, the response properties and contextual control of express visuomotor responses in NHPs resemble those in humans. Our results establish a new benchmark for visuomotor transformations underlying visually-guided reaches, setting the stage for experiments that can directly compare the role of cortical and subcortical areas in reaching when time is of the essence.

Significance statement

Express visuomotor responses in upper limb muscles are brief periods of recruitment preceding visually-guided reaches. Such responses begin ∼90 ms after visual target presentation in humans, and potentially arise from signaling along the tecto-reticulo-spinal pathway. Here, we show that express visuomotor responses in macaques upper limb muscles resemble those in humans, excepting that they evolve ∼65 ms after target onset, consistent with shorter responses latencies in macaques versus humans. Our results clock the completion of the visuomotor transformation for rapid reaching, and set the stage for experiments to directly test the underlying substrates.
FFPE DNA shows two major error profiles derived from deamination of cytosine and methylcytosine that can be mitigated using distinct repair strategies
Authors: Chen Lixin , Chen Minyong , Heiter Dan , Samuelson Jim , Evans Tom , Ettwiller Laurence
Published: March 2023

Avoiding damage-induced sequencing errors is a critical step for the accurate identification of medium to rare frequency mutations in DNA samples. In the case of FFPE samples, deamination of cytosine moieties represents a major damage resulting in the loss of DNA material and sequencing errors. In this study, we demonstrated that, while damage from deamination of both cytosine and methylated cytosine moieties results in elevated C to T transition, the error profiles and mediation strategies are different and easily distinguishable. While damage-induced sequencing errors from cytosine deamination is driven by the end-repair step commonly used in NGS workflow, DNA damage resulting from deamination of methylated cytosine is another major contributor to sequencing errors at CpG sites. Uracil DNA glycosylase and human thymine DNA glycosylase can respectively eliminate and mitigate both damages in FFPE DNA samples, therefore increasing sequencing accuracy notably for the identification of moderate allelic frequency variants.
LINC00261expression reduces mutation accumulation while conferring resistance to cisplatin and altering the tumor-immune microenvironment in lung adenocarcinoma
Authors: Castillo Jonathan , Xue Tianchun , Joseph Samantha , Norwood Mayela , Mullen Daniel J. , Berrellez Stephanie , James Sophia , Epstein Alan L. , McEachron Troy , Marconett Crystal N.
Published: March 2023

Immunotherapy has emerged as a major breakthrough that has the ability to improve survival outcomes for multiple solid tumor types, however effective response requires the combination of blocking inhibitory signals on the tumor surface and antigen presentation to the tumor surface for proper immune recognition. Several commercially available and robust methods exist for identification of tumors displaying immune-inhibitory surface receptors, including PD-L1 and CTLA-4, however it is currently difficult to predict effectiveness of antigen presentation on the cell surface. To address this, we utilized clinical and next-generation sequencing data generated by The Cancer Genome Atlas (TCGA) to identify gene signatures that are correlated to tumor mutational burden (TMB) within cancers of epithelial origins as a surrogate for neoantigen signatures. We identifiedLINC00261as a top gene correlated to mutational burden (TMB), whose expression activates DNA damage response pathwaysin vitroalong with resistance to cisplatin.LINC00261expression was also significantly correlated to MHC Class II genes involved in endogenous neoantigen presentation expression within the TCGA-LUAD cohort. This relationship was confirmedin vitrothrough ectopic reintroduction ofLINC00261for key MHC Class II presentation genes. Interferon gamma-induced MHC gene activationin vitrowas also able to induce endogenous expression ofLINC00261. Our results suggest there is a mechanistic relationship betweenLINC00261expression and functional MHC Class II neoantigen presentation in LUAD. The silencing ofLINC00261in LUAD results in compromised DNA repair, accumulation of mutations, and reduced antitumor immune response.