bluuebunny/crossref_metadata_2025 huggingface dataset:
Fecal Microbiota Transfer for Clostridium difficile Infection and Its Effects on Recurrent Urinary Tract Infection
Authors: Wood Nicole , Propst Katie , Yao Meng , Ferrando Cecile A.
Published: September 2023

Importance

Recurrent urinary tract infection (rUTI) poses a significant management challenge, and fecal microbiota transfer (FMT) has been shown in a limited manner to positively effect rUTI.

Objectives

The objective of this study was to compare UTI rates after FMT for Clostridium difficile infection (CDI) in patients with previously diagnosed rUTI and patients without a previous diagnosis of rUTI.

Study Design

This was a retrospective cohort study of female patients who underwent FMT between 2015 and 2020 and were identified from a database at a tertiary care referral center. The electronic medical record was queried for demographic and UTI characteristics in the 3 years before and 5 years after FMT, which were compared between patients with or without a preexisting history of rUTI.

Results

One hundred thirty-five patients were included, 17 of whom had a preexisting history of rUTI. The median number of culture-proven UTIs was 1 in the rUTI group versus 0 in the non-rUTI group both in the 1 year (P = 0.003) and 3 years (P < 0.001) before FMT. Most UTIs before and after FMT were Escherichia coli UTIs (53.8%) and carried some antibiotic resistance (54.6%). Comparatively, in the year after FMT, there were no differences between groups in UTI frequency or antibiotic administration (0 [0–1] vs 0.5 [0–1], P = 0.28). A trend toward decreased frequency of UTI in the 1 year after FMT was seen in the rUTI group. On survival analysis, there was a nonsignificant decrease in the 3-year UTI-free rate for the rUTI group compared with the non-rUTI group (76.5% vs 90.1%, P = 0.07).

Conclusions

Patients with recurrent UTI undergoing FMT for recurrent CDI experienced a trend toward a decrease in frequency of UTI after FMT.
Recurrent Mild Acute Rejections and Donor-specific Antibodies as Risk Factors for Cardiac Allograft Vasculopathy in a National Pediatric Heart Transplant Cohort
Authors: Kaskinen Anu K. , Tainio Juuso , Pihkala Jaana I. , Peräsaari Juha P. , Lauronen Jouni , Raissadati Alireza , Merenmies Jussi M. , Jalanko Hannu J. , Jahnukainen Timo
Published: September 2023

Background.

Immune-mediated factors such as acute cellular rejections and donor-specific antibodies (DSAs) are risk factors for cardiac allograft vasculopathy (CAV). We studied a national cohort with a unified setting and thorough protocol endomyocardial biopsy (EMB) data for an association between cellular rejections, especially when mild and recurrent, and DSAs with CAV in pediatric heart transplant (HTx) patients.

Methods.

This is a retrospective, national cohort study of 94 pediatric HTxs performed between 1991 and 2019 and followed until December 31, 2020. Diagnosis of CAV was based on reevaluation of angiographies. Protocol and indication EMB findings with other patient data were collected from medical records. Associations between nonimmune and immune-mediated factors and CAV were analyzed with univariable and multivariable Cox regression analyses.

Results.

Angiographies performed on 76 patients revealed CAV in 23 patients (30%). Altogether 1138 EMBs (92% protocol biopsies) were performed on 78 patients (83%). During the first posttransplant year, grade 1 rejection (G1R) appeared in 45 patients (58%), and recurrent (≥2) G1R findings in 14 patients (18%). Pretransplant DSAs occurred in 13 patients (17%) and posttransplant DSAs in 37 patients (39%). In univariable analysis, pretransplant DSAs, appearance and recurrence of G1R findings, and total rejection score during the first posttransplant year, as well as recurrent G1R during follow-up, were all associated with CAV. In multivariable analysis, pretransplant DSAs and recurrent G1R during the first posttransplant year were found to be associated with CAV.

Conclusions.

Our results indicate that pretransplant DSA and recurrent G1R findings, especially during the first posttransplant year, are associated with CAV after pediatric HTx.
Reproducibility of Rejection Grading in Uterus Transplantation: A Multicenter Study
Authors: Broecker Verena , Brännström Mats , Bösmüller Hans , Sticová Eva , Malušková Jana , Chiesa-Vottero Andres , Mölne Johan
Published: September 2023

Background:

Diagnosis of rejection after uterus transplantation is based on histopathological examination of ectocervical biopsies. Inflammation at the stromal–epithelial interface is the backbone of the histopathological classification proposed by our group in 2017. However, the reproducibility of this grading scheme has not been tested, and it is unclear whether it covers the full morphological spectrum of rejection.

Methods:

We present a multicenter study in which 5 pathologists from 4 uterus transplantation centers performed 2 rounds of grading on 145 and 48 cervical biopsies, respectively. Three of the centers provided biopsies. Additionally, the presence of perivascular stromal inflammation was recorded. During discussions after the first round, further histological lesions (venous endothelial inflammation and apoptosis) were identified for closer evaluation and added to the panel of lesions to score in the second round. All participants completed a questionnaire to explore current practices in handling and reporting uterus transplant biopsies.

Results:

Cervical biopsies were commonly performed in all centers to monitor rejection. Intraobserver reproducibility of rejection grading (performed by 1 rater) was excellent, whereas interobserver reproducibility was moderate and did not improve in the second round. Reproducibility of perivascular stromal inflammation was moderate but unsatisfactory for venous endothelial inflammation and apoptosis. All lesions were more frequent in, but not restricted to, biopsies with rejection patterns.

Conclusions:

Grading of rejection in cervical biopsies is reproducible and applicable to biopsies from different centers. Diagnosis of rejection may be improved by adding further histological lesions to the grading system; however, lesions require rigorous consensus definition.
Coincidence analysis of efflux pumps in the Escherichia coli pangenome
Authors: Shahabuddin Ammar A. , Clover Rosie , Gifford Danna R
Published: September 2023

Global rates of multi-drug resistance continue to rise, posing a significant challenge in the fight against antimicrobial resistance worldwide. Multi-drug efflux pumps are a significant contributor to this burden. Understanding connections between the diverse network of efflux pump genes, and their interactions with other genes, is important for understanding the landscape of multi-drug resistance and devising new interventions to mitigate it. To address this issue, we have investigated how efflux pumps and accessory genes covary across genomes. Using genomic data from 200 publicly available Escherichia coli isolates, we constructed a pangenome and performed coincidence analyses using the bioinformatic tool Coinfinder. On an aggregate level, efflux pumps formed more coincident gene pairs within the accessory genome than avoidant gene pairs. Genes with a functional annotation associated with ‘transport’ had the highest representation for both coincident and avoidant gene pairs. In contrast, when specifically considering gene pairs where both genes were related to efflux pumps, avoidant pairs were more frequent, though some coincident pairs were also found—primarily between subcomponents that make up tripartite pumps, as well as between subcomponents and single unit efflux pumps). Further exploration and understanding on the role the efflux pumps from the accessory genome play and how it expresses itself, would result in developing novel strategies to target increasingly resistant bacteria.
Ancient origin of the rod bipolar cell pathway in the vertebrate retina
Authors: Hellevik Ayana M , Mardoum Philip , Hahn Joshua , Kölsch Yvonne , D’Orazi Florence D , Suzuki Sachihiro C. , Godinho Leanne , Lawrence Owen , Rieke Fred , Shekhar Karthik , Sanes Joshua R , Baier Herwig , Baden Tom , Wong Rachel O , Yoshimatsu Takeshi
Published: September 2023

Vertebrates rely on rod photoreceptors for vision in low-light conditions1. Mammals have a specialized downstream circuit for rod signaling called the primary rod pathway, which comprises specific cell types and wiring patterns that are thought to be unique to this lineage2–6. Thus, it has been long assumed that the primary rod pathway evolved in mammals3, 5–7. Here, we challenge this view by demonstrating that the mammalian primary rod pathway is conserved in zebrafish, which diverged from extant mammals ∼400 million years ago. Using single-cell RNA-sequencing, we identified two bipolar cell (BC) types in zebrafish that are related to mammalian rod BCs (RBCs) of the primary rod pathway. By combining electrophysiology, histology, and ultrastructural reconstruction of the zebrafish RBCs, we found that, like mammalian RBCs8, both zebrafish RBC types connect with all rods and red-cones in their dendritic territory, and provide output largely onto amacrine cells. The wiring pattern of the amacrine cells post-synaptic to one RBC type is strikingly similar to that of mammalian RBCs. This suggests that the cell types and circuit design of the primary rod pathway may have emerged before the divergence of teleost fish and amniotes (mammals, bird, reptiles). The second RBC type in zebrafish, which forms separate pathways from the first RBC type, is either lost in mammals or emerged in fish to serve yet unknown roles.

Highlights

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Zebrafish have two rod bipolar cell types (RBC1/2).

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Synaptic connectivity of RBC1 resembles that of the mammalian RBCs.

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The primary rod pathway therefore probably evolved more than 400 million years ago.

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The second zebrafish RBC type, RBC2, forms a separate pathway from RBC1.
The intrinsically disordered region of the E3 ubiquitin ligase TRIP12 induces the formation of chromatin condensates and interferes with DNA damage response
Authors: Vargas Claire , Brunet Manon , Ricard Alban , Varry Damien , Larrieu Dorian , Muzzopappa Fernando , Erdel Fabian , Labrousse Guillaume , Hanoun Naïma , Ligat Laetitia , Farcé Manon , Stella Alexandre , Burlet-Schiltz Odile , Laurell Henrik , Bery Nicolas , Cordelier Pierre , Dufresne Marlène , Torrisani Jérôme
Published: September 2023

Chromatin compaction is crucial for the faithful expression and integrity of the genome. Although largely studied, proteins and mechanisms that control the chromatin compaction are not entirely discovered. We previously showed that the nuclear HECT-type E3 ubiquitin ligase Thyroid hormone Receptor Interacting Protein 12 (TRIP12) is tightly associated to chromatin. As TRIP12 is overexpressed in several types of cancers, we explored herein the consequences of a TRIP12 overexpression on chromatin homeostasis. First, we established the TRIP12 proxisome and unveiled its pleiotropic role in chromatin regulation. Second, we demonstrated that TRIP12 overexpression leads to the formation of chromatin condensates enriched in heterochromatin marks via its intrinsically disordered region (IDR). We further discovered that the formation of TRIP12-mediated chromatin condensates is highly dynamic and driven by a mechanism of phase separation. Chromatin condensate formation depends on the TRIP12 concentration, the length of the TRIP12-IDR and relies on electrostatic interactions. We found that the formation of TRIP12 mediated-condensates alters cell cycle progression, genome accessibility, transcription as well as DNA damage response by inhibiting the accumulation of Mediator of DNA Damage Checkpoint 1 (MDC1). Altogether, this study reveals a novel dynamic role for TRIP12 in chromatin compaction independently of its ubiquitin ligase activity with important consequences on cellular homeostasis.

GRAPHICAL ABSTRACT
How persistent infection overcomes peripheral tolerance mechanisms to cause T cell-mediated autoimmune disease
Authors: Yin Rose , Melton Samuel , Huseby Eric , Kardar Mehran , Chakraborty Arup K.
Published: September 2023

T cells help orchestrate immune responses to pathogens, and their aberrant regulation can trigger autoimmunity. Recent studies highlight that a threshold number of T cells (a quorum) must be activated in a tissue to mount a functional immune response. These collective effects allow the T cell repertoire to respond to pathogens while suppressing autoimmunity due to circulating autoreactive T cells. Our computational studies show that increasing numbers of pathogenic peptides targeted by T cells during persistent or severe viral infections increase the probability of activating T cells that are weakly reactive to self-antigens (molecular mimicry). These T cells are easily re-activated by the self-antigens and contribute to exceeding the quorum threshold required to mount autoimmune responses. Rare peptides that activate many T cells are sampled more readily during severe/persistent infections than in acute infections, which amplifies these effects. Experiments in mice to test predictions from these mechanistic insights are suggested.
Deep learning predictions of TCR-epitope interactions reveal epitope-specific chains in dual alpha T cells
Authors: Croce Giancarlo , Bobisse Sara , Moreno Dana Léa , Schmidt Julien , Guillame Philippe , Harari Alexandre , Gfeller David
Published: September 2023

T cells have the ability to eliminate infected and cancer cells and play an essential role in cancer immunotherapy. T-cell activation is elicited by the binding of the T-cell receptor (TCR) to epitopes displayed on MHC molecules, and the TCR specificity is determined by the sequence of its α and β chains. Here, we collected and curated a dataset of 17,715 αβTCRs interacting with dozens of class I and class II epitopes. We used this curated data to develop MixTCRpred, a deep learning TCR-epitope interaction predictor. MixTCRpred accurately predicts TCRs recognizing several viral and cancer epitopes. MixTCRpred further provides a useful quality control tool for multiplexed single-cell TCR sequencing assays of epitope-specific T cells and pinpoints a substantial fraction of putative contaminants in public databases. Analysis of epitope-specific dual α T cells demonstrates that MixTCRpred can identify α chains mediating epitope recognition. Applying MixTCRpred to TCR repertoires from COVID-19 patients reveals enrichment of clonotypes predicted to bind an immunodominant SARS-CoV-2 epitope. Overall, MixTCRpred provides a robust tool to predict TCRs interacting with specific epitopes and interpret TCR-sequencing data from both bulk and epitope-specific T cells.
Integrative Spatial Analysis of H&E and IHC Images Identifies Prognostic Immune Subtypes Correlated with Progression-Free Survival in Human Papillomavirus (HPV)-Related Oropharyngeal Squamous Cell Carcinoma
Authors: Nakkireddy Sumanth Reddy , Jang Inyeop , Kim Minji , Yin Linda X. , Rivera Michael , Garcia Joaquin J. , Bartemes Kathleen R. , Routman David M. , Moore Eric. J. , Abdel-Halim Chadi N. , Ma Daniel J. , Van Abel Kathryn M. , Hwang Tae Hyun
Published: September 2023

Purpose

Deep learning techniques excel at identifying tumor-infiltrating lymphocytes (TILs) and immune phenotypes in hematoxylin and eosin (H&E)-stained slides. However, their ability to elucidate detailed functional characteristics of diverse cellular phenotypes within tumor immune microenvironment (TME) is limited. We aimed to enhance our understanding of cellular composition and functional characteristics across TME regions and improve patient stratification by integrating H&E with adjacent immunohistochemistry (IHC) images.

Methods

A retrospective study was conducted on patients with HPV(+) oropharyngeal squamous cell carcinoma (OPSCC). Using paired H&E and IHC slides for 11 proteins, a DL pipeline was used to quantify tumor, stroma, and TILs in the TME. Patients were classified into immune inflamed (IN), immune excluded (IE), or immune desert (ID) phenotypes. By registering the IHC and H&E slides, we integrated IHC data to capture protein expression in the corresponding tumor regions. We further stratified patients into specific immune subtypes, such as IN, with increased or reduced CD8+ cells, based on the abundance of these proteins. This characterization provided functional insight into the H&E-based subtypes.

Results

Analysis of 88 primary tumors and 70 involved lymph node tissue images revealed an improved prognosis in patients classified as IN in primary tumors with high CD8 and low CD163 expression (p = 0.007). Multivariate Cox regression analysis confirmed a significantly better prognosis for these subtypes.

Conclusions

Integrating H&E and IHC data enhances the functional characterization of immune phenotypes of the TME with biological interpretability, and improves patient stratification in HPV(+) OPSCC.
MocFormer: A Two-Stage Pre-training-Driven Transformer for Drug-Target Interactions Prediction
Authors: Zhang Yilun , Wang Wentao , Guan Jiahui , Jain Deepak Kumar , Wang Tianyang , Roy Swalpa Kumar
Published: September 2023

Drug-target interactions (DTIs) is essential for advancing pharmaceuticals. Traditional drug-target interaction studies rely on labor-intensive laboratory techniques. Still, recent advancements in computing power have elevated the importance of deep learning methods, offering faster, more precise, and cost-effective screening and prediction. Nonetheless, general deep learning methods often yield low-confidence results due to the complex nature of drugs and proteins, bias, limited labeled data, and feature extraction challenges. To address these challenges, a novel two-stage pre-trained framework is proposed for DTIs prediction. In the first stage, pre-trained molecule and protein models develop a comprehensive feature representation, enhancing the framework’s ability to handle drug and protein diversity. This also reduces bias, improving prediction accuracy. In the second stage, a transformer with bilinear pooling and a fully connected layer (FCN) enables predictions based on feature vectors. Comprehensive experiments were conducted using DrugBank dataset and Epigenetic-regulators dataset to evaluate the framework’s effectiveness. The results demonstrate that the proposed framework outperforms the state-of-the-art methods regarding accuracy, area under the ROC curve (AUC), recall, and the area under the precision-recall curve (AUPRC). The code will be available after being accepted:https://github.com/rickwang28574/MocFormer
The Discovery and Characterization of 1,4-Dihydroxy-2-naphthoic Acid Prenyltransferase Involved in the Biosynthesis of Anthraquinones inRubia cordifolia
Authors: Liu Changzheng , Wang Ruishan , Wang Sheng , Chen Tong , Lyu Chaogeng , Kang Chuanzhi , Wan Xiufu , Guo Juan , Huang Luqi , Guo Lanping
Published: September 2023

Anthraquinones constitute the largest group of natural quinones, which are used as safe natural dyes and have many pharmaceutical applications. In plants, anthraquinones are biosynthesized through two main routes: the polyketide pathway and the shikimate pathway. The shikimate pathway primarily forms alizarin-type anthraquinones, and the prenylation of 1,4-dihydroxy-2-naphthoic acid is the first pathway-specific step. However, the prenyltransferase responsible for this key step remains uncharacterized. In this study, the cell suspension culture ofRubia cordifolia, a plant rich in alizarin-type anthraquinones, was used in target prenyltransferase mining. The microsomal protein prepared from the cell suspension culture prenylated 1,4-dihydroxy-2-naphthoic acid to form 2-carboxyl-3-prenyl-1,4-naphthoquinone and 3-prenyl-1,4-naphthoquinone. Then a candidate gene belonging to UbiA superfamily,RcDT1, was discovered to account for the prenylation activity. Substrate specificity studies revealed that the recombinant RcDT1 recognized naphthoic acids primarily, followed by 4-hydroxyl benzoic acids. The prenylation activities ofR. cordifoliamicrosomes and the recombinant RcDT1 were both strongly inhibited by 1,2- and 1,4-dihydroxynaphthalene. The plastid localization and root-specific expression further confirmed the participation ofRcDT1in anthraquinone biosynthesis. The phylogenetic analyses ofRcDT1and its rubiaceous homologs indicated that DHNA-prenylation activity evolved convergently in Rubiaceae via recruitment from the ubiquinone biosynthetic pathway. The discovery and evolutionary studies ofRcDT1provide useful guidance for identifying additional and evolutionarily varied prenyltransferases which enable entry into quinones derived from shikimate pathway. Moreover, these findings will have profound implications for understanding the biosynthetic process of the anthraquinone/naphthoquinone ring derived from shikimate pathway.
Preclinical Synergistic Combination Therapy of Lurbinectedin with Irinotecan and 5-Fluorouracil in Pancreatic Cancer
Authors: Tummala Tej , Uruchurtu Ashley Sanchez Sevilla , De La Cruz Arielle , Huntington Kelsey E. , George Andrew , Liguori Nicholas R. , Zhang Leiqing , Zhou Lanlan , Abbas Abbas E. , Azzoli Christopher G. , El-Deiry Wafik S.
Published: September 2023

Pancreatic cancer is a devastating disease with a poor prognosis. Novel chemotherapeutics in pancreatic cancer have shown limited success, illustrating the urgent need for new treatments. Lurbinectedin (PM01183; LY-01017) received FDA approval in 2020 for metastatic small cell lung cancer on or after platinum-based chemotherapy and is currently undergoing clinical trials in a variety of tumor types. Lurbinectedin stalls and degrades RNA Polymerase II and introduces breaks in DNA, causing subsequent apoptosis. We now demonstrate lurbinectedin’s highly efficient killing of human-derived pancreatic tumor cell lines PANC-1, BxPC-3, and HPAF-II as a single agent. We further demonstrate that a combination of lurbinectedin and irinotecan, a topoisomerase I inhibitor with FDA approval for advanced pancreatic cancer, results in synergistic killing of pancreatic tumor cells. Western blot analysis of combination therapy indicates an upregulation of γH2AX, a DNA damage marker, and the Chk1/ATR pathway, involved in replicative stress and DNA damage response. We further demonstrate that the triple combination between lurbinectedin, irinotecan, and 5-fluorouracil (5-FU) results in highly efficient killing of tumor cells. Our results are developing insights regarding molecular mechanisms underlying therapeutic efficacy of a novel combination drug treatment for pancreatic cancer.
Picomolar-Level Sensing of Cannabidiol by Metal Nanoparticles Functionalized with Chemically Induced Dimerization Binders
Authors: Ikbal MD Ashif , Kang Shoukai , Chen Xiahui , Gu Liangcai , Wang Chao
Published: September 2023

Simple and fast detection of small molecules is critical to health and environmental monitoring. Methods for chemical detection often use mass spectrometers or enzymes; the former relies on expensive equipment and the latter is limited to those that can act as enzyme substrates. Affinity reagents like antibodies can target a variety of small-molecule analytes, but the detection requires successful design of chemically conjugated targets or analogs for competitive binding assays. Here, we developed a generalizable method for highly sensitive and specific in-solution detection of small molecules, using cannabidiol (CBD) as an example. Our sensing platform uses gold nanoparticles (AuNPs) functionalized with a pair of chemically induced dimerization (CID) nanobody binders (nano-binders), where CID triggers AuNPs aggregation and sedimentation in the presence of CBD. Despite moderate binding affinities of the two nano-binders to CBD (KDs of ∼6 and ∼56 µM), a scheme consisting of CBD-AuNP pre-analytical incubation, centrifugation, and electronic detection (ICED) was devised to demonstrate a high sensitivity (limit of detection of ∼100 picomolar) in urine and saliva, a relatively short assay time (∼2 hours), a large dynamic range (5 logs), and a sufficiently high specificity to differentiate CBD from its analog, tetrahydrocannabinol. The high sensing performance was achieved with the multivalency of AuNP sensing, the ICED scheme that increases analyte concentrations in a small assay volume, and a portable electronic detector. This sensing system is readily coupled to other binders for wide molecular diagnostic applications.
Automatic vocalisation detection delivers reliable, multi-faceted, and global avian biodiversity monitoring
Authors: Sethi Sarab S. , Bick Avery , Chen Ming-Yuan , Crouzeilles Renato , Hillier Ben V. , Lawson Jenna , Lee Chia-Yun , Liu Shih-Hao , Freitas Parruco Celso Henrique de , Rosten Carolyn , Somveille Marius , Tuanmu Mao-Ning , Banks-Leite Cristina
Published: September 2023

Tracking biodiversity and its dynamics at scale is essential if we are to solve global environmental challenges. Detecting animal vocalisations in passively recorded audio data offers a highly automatable, inexpensive, and taxonomically broad way to monitor biodiversity. However, uptake is slow due to the expertise and labour required to label new data and fine-tune algorithms for each deployment. In this study, we applied an off-the-shelf bird vocalisation detection model, BirdNET, to 152,376 hours of audio comprising of datasets from Norway, Taiwan, Costa Rica, and Brazil. We manually listened to a subset of detections for each species in each dataset and found precisions of over 80% for 89 of the 139 species (100% for 57 species). Whilst some species were reliably detected across multiple datasets, the performance of others was dataset specific. By filtering out unreliable detections, we could extract species and community level insight on diel (Brazil) and seasonal (Taiwan) temporal scales, as well as landscape (Costa Rica) and national (Norway) spatial scales. Our findings demonstrate that, with a relatively fast validation step, a single vocalisation detection model can deliver multi-faceted community and species level insight across highly diverse datasets; unlocking the scale at which acoustic monitoring can deliver immediate applied impact.
A latent cardiomyocyte regeneration potential in human heart disease
Authors: Derks Wouter , Rode Julian , Collin Sofia , Rost Fabian , Heinke Paula , Hariharan Anjana , Pickel Lauren , Simonova Irina , Lázár Enikő , Graham Evan , Jashari Ramadan , Andrä Michaela , Jeppsson Anders , Salehpour Mehran , Alkass Kanar , Druid Henrik , Kyriakopoulos Christos P. , Taleb Iosif , Shankar Thirupura S. , Selzman Craig H. , Sadek Hesham , Jovinge Stefan , Brusch Lutz , Frisén Jonas , Drakos Stavros , Bergmann Olaf
Published: September 2023

Cardiomyocytes in the adult human heart show a regenerative capacity, with an annual renewal rate around 0.5%. Whether this regenerative capacity of human cardiomyocytes is employed in heart failure has been controversial. Using retrospective14C birth dating we analyzed cardiomyocyte renewal in patients with end-stage heart failure. We show that cardiomyocyte generation is minimal in end-stage heart failure patients at rates 18-50 times lower compared to the healthy heart. However, patients receiving left ventricle support device therapy, who showed significant functional and structural cardiac improvement, had a >6-fold increase in cardiomyocyte renewal relative to the healthy heart. Our findings reveal a substantial cardiomyocyte regeneration potential in human heart disease, which could be exploited therapeutically.
Blimp-1 and c-Maf regulate common and unique gene networks to protect against distinct pathways of pathobiont-induced colitis
Authors: Alvarez-Martinez Marisol , Cox Luke S. , Pearson Claire F. , Branchett William J. , Chakravarty Probir , Wu Xuemei , Slawinski Hubert , Al-Dibouni Alaa , Samelis Vasileios A. , Gabryšová Leona , Priestnall Simon L. , Suárez-Bonnet Alejandro , Mikolajczak Anna , Briscoe James , Powrie Fiona , O’Garra Anne
Published: September 2023

Intestinal immune responses to commensals and pathogens are controlled by IL-10 to avoid intestinal immune pathology. We show that the transcription factors Blimp-1(Prdm-1)and c-Maf are co-dominant regulators ofIl10in Foxp3+regulatory T cells, but also negatively regulate proinflammatory cytokines in effector T cells. Mice with T cell-specific deletion ofPrdm-1, Mafor the combination of both transcription factors did not develop inflammatory intestinal pathologies at the steady state. Double deficientPrdm1fl/flMaffl/flCd4Cremice infected withHelicobacter hepaticusdeveloped severe colitis with a major increase in TH1/NK/ILC1 effector genes in lamina propria leucocytes (LPLs), whilePrdm1fl/flCd4CreandMaffl/flCd4Cremice showed mild/moderate pathology and a less-marked Type I effector response. LPLs from infectedMaffl/flCd4Cremice showed increasedIl17aexpression and an accompanying increase in granulocytes and myeloid cells, which was less marked inPrdm1fl/flMaffl/flCd4Cremice, with increased T cell-myeloid-neutrophil interactions inferred from scRNA-seq analysis and confirmed by immunofluorescent analysis of colon sections. Genes over-expressed in human IBD showed differential expression in the LPL from infected mice in the absence ofPrdm1orMaf,revealing potential pathobiologic mechanisms of human disease.
Keras/TensorFlow in Drug Design for Immunity Disorders
Authors: Dragan Paulina , Joshi Kavita , Atzei Alessandro , Latek Dorota
Published: September 2023

Homeostasis of the host immune system is regulated by white blood cells with a variety of cell surface receptors for cytokines. Chemotactic cytokines (chemokines) activate their receptors to evoke the chemotaxis of immune cells in homeostatic migrations or inflammatory conditions towards inflamed tissue or pathogens. Dysregulation of the immune system leading to disorders such as allergies, autoimmune diseases, or cancer requires efficient, fast-acting drugs to minimize the long-term effects of chronic inflammation. Here, we performed structure-based virtual screening (SBVS) assisted by the Keras/TensorFlow neural network (NN) to find novel compound scaffolds acting on three chemokine receptors: CCR2, CCR3 and one CXC receptor CXCR3. Keras/TensorFlow NN was used here not as a typically used binary classifier, but as an efficient multi-class classifier that can discard not only inactive compounds but also low or medium-activity compounds. Several compounds proposed by SBVS and NN were tested in 100 ns all-atom molecular dynamics simulations to confirm their binding affinity. To improve the basic binding affinity of the compounds, new chemical modifications were proposed. The modified compounds were compared with known antagonists of these three chemokine receptors. Known CXCR3 were among the top predicted compounds and thus benefits of using Keras/TensorFlow in drug discovery have been shown in addition to structure-based approaches. Furthermore, we showed that Keras/TensorFlow NN can accurately predict the receptor subtype selectivity of compounds, for which SBVS often fails. We cross-tested chemokine receptor datasets retrieved from ChEMBL and curated datasets for cannabinoid receptors available at:http://db-gpcr-chem.uw.edu.pl. The NN model trained on the cannabinoid receptor datasets retrieved from ChEMBL was the most accurate in the receptor subtype selectivity prediction. Among NN models trained on the chemokine receptor datasets, the CXCR3 model showed the highest accuracy in differentiating the receptor subtype for a given compound dataset.
Effects of age and noise on tympanal displacement in the Desert Locust
Authors: Austin Thomas T , Woodrow Charlie , Montealegre-Z Fernando , Warren Ben
Published: September 2023

Insect cuticle is an evolutionary-malleable exoskeleton that has specialised for various functions. Insects that detect the pressure component of sound bear specialised sound-capturing tympani evolved from cuticular thinning. Whilst the outer layer of insect cuticle is composed of non-living chitin, its mechanical properties change during development and aging. Here, we measured the displacements of the tympanum of the desert Locust,Schistocerca gregaria, to understand biomechanical changes as a function of age and noise-exposure. We found that the stiffness of the tympanum decreases within 12 hours of noise-exposure and increases as a function of age, independent of noise-exposure. Noise-induced changes were dynamic with an increased tympanum displacement to sound within 12 hours post noise-exposure. Within 24 hours, however, the tone-evoked displacement of the tympanum decreased below that of control Locusts. After 48 hours, the tone-evoked displacement of the tympanum was not significantly different to Locusts not exposed to noise. Tympanal displacements reduced predictably with age and repeatably noise-exposed Locusts (every three days) did not differ from their non-noise-exposed counterparts. Changes in the biomechanics of the tympanum may explain an age-dependent decrease in auditory detection in tympanal insects.
Global analysis of Poales diversification – parallel evolution in space and time into open and closed habitats
Authors: Elliott Tammy L , Spalink Daniel , Larridon Isabel , Zuntini Alexandre Rizzo , Escudero Marcial , Hackel Jan , Barrett Russell L , Martín-Bravo Santiago , Márquez-Corro José Ignacio , Mendoza Carolina Granados , Mashau Aluoneswi C. , Romero-Soler Katya J , Zhigila Daniel A. , Gehrke Berit , Andrino Caroline Oliveira , Crayn Darren M , Vorontsova Maria S , Forest Félix , Baker William J , Wilson Karen L , Simpson David A , Muasya A Muthama
Published: September 2023

Poales are one of the most species-rich, ecologically and economically important orders of plants and often characterise open habitats, enabled by unique suites of traits. We test the hypotheses that Poales species are assembled into distinct phyloregions, with centres of high phylogenetic diversity and endemism clustered in tropical regions, and that cosmopolitan families show parallel transitions into open and closed habitats at different times.

We sampled 42% of Poales species and obtained taxonomic and biogeographic data from the World Checklist of Vascular Plants database, which was combined with open/closed habitat data scored by taxonomic experts. A dated supertree of Poales was constructed. We integrated spatial phylogenetics with regionalization analyses, historical biogeography, ancestral state estimations, and models of contingent evolution.

Diversification in Poales and assembly of open and closed habitats result from dynamic evolutionary processes that vary across lineages, time, space, and traits, most prominently in tropical and southern latitudes. Our results reveal parallel and recurrent patterns of habitat and trait transitions in the species-rich families Poaceae and Cyperaceae, yet other smaller families display unique evolutionary trajectories.

The Poales have achieved global dominance via parallel evolution in open habitats, with notable, spatially and phylogenetically restricted divergences into strictly closed habitats.
Reversions mask the contribution of adaptive evolution in microbiomes
Authors: Torrillo Paul A. , Lieberman Tami D.
Published: September 2023

When examining bacterial genomes for evidence of past selection, the results obtained depend heavily on the mutational distance between chosen genomes. Even within a bacterial species, genomes separated by larger mutational distances exhibit stronger evidence of purifying selection as assessed by dN/dS, the normalized ratio of nonsynonymous to synonymous mutations. Here, we show that the classical interpretation of this scale-dependence, weak purifying selection, leads to problematic mutation accumulation when applied to available gut microbiome data. We propose an alternative, adaptive reversion model with exactly opposite implications for dynamical intuition and applications of dN/dS. Reversions that occur and sweep within-host populations are nearly guaranteed in microbiomes due to large population sizes, short generation times, and variable environments. Using analytical and simulation approaches, we show that adaptive reversion can explain the dN/dSdecay given only dozens of locally-fluctuating selective pressures, which is realistic in the context ofBacteroidesgenomes. The success of the adaptive reversion model argues for interpreting low values of dN/dSobtained from long-time scales with caution, as they may emerge even when adaptive sweeps are frequent. Our work thus inverts the interpretation of an old observation in bacterial evolution, illustrates the potential of mutational reversions to shape genomic landscapes over time, and highlights the importance of studying bacterial genomic evolution on short time scales.
Unique territorial and compartmental organization of chromosomes in the holocentric silkmoth
Authors: Gil J. , Navarrete E. , Rosin L.F. , Chowdhury N. , Abraham S. , Cornilleau G. , Lei E.P. , Mozziconacci J. , Mirny L.A. , Muller H. , Drinnenberg I.A.
Published: September 2023

The hallmarks of chromosome organization in multicellular eukaryotes are chromosome territories (CT), chromatin compartments, and insulated domains, including topologically associated domains (TADs). Yet, most of these elements of chromosome organization are derived from analyses of a limited set of model organisms, while large eukaryotic groups, including insects, remain mostly unexplored. Here we combine Hi-C, biophysical modeling, and microscopy to characterize the 3D genome architecture of the silkworm,Bombyx mori. In contrast to other eukaryotes,B. morichromosomes form highly separated territories. Similar to other eukaryotes,B. morichromosomes segregate into active A and inactive B compartments, yet unlike in vertebrate systems, contacts between euchromatic A regions appear to be a strong driver of compartmentalization. Remarkably, we also identify a third compartment, called secluded “S,” with a unique contact pattern. Each S region shows prominent short-range self-contacts and is remarkably devoid of contacts with the rest of the chromosome, including other S regions. Compartment S hosts a unique combination of genetic and epigenetic features, localizes towards the periphery of CTs, and shows developmental plasticity. Biophysical modeling reveals that the formation of such secluded domains requires highly localized loop extrusion within them, along with a low level of extrusion in A and B. Our Hi-C data supports predicted genome-wide and localized extrusion. Such a broad, non-uniform distribution of extruders has not been seen in other organisms. Overall, our analyses support loop extrusion in insects and highlight the evolutionary plasticity of 3D genome organization, driven by a new combination of known processes.
Tim4 enables large peritoneal macrophages to cross-present tumor antigens at early stages of tumorigenesis
Authors: Joshi Sonal , Rodríguez Lucía López , Morosi Luciano Gastón , Amadio Roberto , Pachauri Manendra , Giacca Mauro , Piperno Giulia Maria , Benvenuti Federica
Published: September 2023

Cross-presentation of tumor antigens by subsets of macrophages at different stages along tumor progression may have divergent impacts on anti-tumoral immune responses. Here we show that TIM4+large peritoneal macrophages (LPM) avidly capture tumor cells and cross-present tumor-associated antigens at early stages of peritoneal infiltration by ovarian cancer cells. The phosphatidylserine (PS) receptor TIM4 promotes maximal uptake and triggers inflammatory and metabolic gene programs in combination with cytoskeletal remodeling and upregulation of transcriptional signatures related to antigen processing. At the cellular levels, TIM4 is recruited with F-actin at the phagocytic cup and translocates in nascent phagosomes, controlling the kinetic of phagosomal acidification and cargo degradation. TIM4 deletion abrogates cross-presentation of tumor-associated antigens and blunts expansion of effector CD8 T cells at tumor inception. In addition, targeting tumor antigens to LPM by PS liposomes can trigger CD8 T cell activation. Together these results suggest that TIM4 enables LPMs to scan the antigenic content of incoming tumor cells to promote immune surveillance by CD8 T cells and, at defined temporal windows, may be exploited for therapeutic purposes.
Gene Deletion of the PACAP/VIP Receptor, VPAC2R, Alters Glycemic Responses During Metabolic and Psychogenic Stress in Adult Female Mice
Authors: Kozlova Elena V. , Bishay Anthony E. , Denys Maximillian E. , Chinthirla Bhuvaneswari D. , Valdez Matthew C. , Spurgin Kurt A. , Krum Julia M. , Basappa Karthik R. , Curras-Collazo Margarita C.
Published: September 2023

Pituitary adenylate cyclase-activating polypeptide (PACAP) and the homologous peptide, vasoactive intestinal peptide (VIP), participate in glucose homeostasis using insulinotropic and counterregulatory processes. These opposing actions need further characterization, as does the role of VIP receptor 2 (VPAC2R) in the regulation of glucose metabolism. In this study, we examined the participation of VPAC2R on basal glycemia, fasted glucoregulatory hormones and on glycemia responses during metabolic and psychogenic stress using gene-deleted (Vipr2-/-) female mice. The mean basal glycemia was significantly greater inVipr2-/-in the fed state and after an 8h overnight fast as compared to wildtype (WT) mice. Insulin tolerance testing following a 5h fast (morning fast, 0.38 U/kg) indicated no effect of genotype. However, during a more intense metabolic challenge (8 h, ON fast, 0.25 U/kg),Vipr2-/-females displayed significantly impaired insulin hypoglycemia. During immobilization stress, the hyperglycemic response and plasma epinephrine levels were significantly elevated above basal inVipr2-/-, but not WT mice, in spite of similar stress levels of plasma corticosterone. Together, these results implicate the action of upregulated counterregulatory processes influenced by enhanced sympathoexcitation. Moreover, the suppression of plasma GLP-1 levels inVipr2-/-mice may have removed the inhibition on hepatic glucose production and the promotion of glucose disposal by GLP-1. qPCR analysis indicated deregulation of central gene markers of PACAP/VIP signaling inVipr2-/-: upregulated medullary tyrosine hydroxylase (Th) and downregulated hypothalamicVip. These results demonstrate a physiological role for VPAC2R in glucose metabolism, especially during insulin challenge and psychogenic stress, likely involving the participation of sympathoadrenal activity and/or metabolic hormones.
Diverse Plant-Parasitic Nematodes are Selectively Killed by Oxadiazole Thioether Pro-Nematicides
Authors: Knox Jessica , Burns Andrew R. , Cooke Brittany , Cammalleri Savina R. , Kitner Megan , Ching Justin , Castelli Jack M.P. , Puumala Emily , Snider Jamie , Koury Emily , Collins J.B. , Andersen Erik C. , Stagljar Igor , Cowen Leah E. , Lautens Mark , Zasada Inga , Roy Peter J.
Published: September 2023

Left unchecked, plant-parasitic nematodes have the potential to devastate crops globally. Highly effective but non-selective nematicides are justifiably being phased-out, leaving farmers with limited options for managing nematode infestation. Here, we report our discovery of a 1,3,4-oxadiazole thioether scaffold called Cyprocide that selectively kills diverse plant-parasitic nematodes. Cyprocide is bioactivated into a lethal reactive electrophilic metabolite by specific nematode cytochrome P450 enzymes. Because Cyprocide fails to kill non-target organisms, we infer that the targeted lethality of this pro-nematicide derives from P450 substrate selectivity. Our findings demonstrate that Cyprocide is a selective nematicidal scaffold with broad-spectrum activity that holds the potential to help safeguard our global food supply.
The origin of secondary structure transitions and peptide self-assembly propensity in trifluoroethanol-water mixtures
Authors: Prasad Anup Kumar , Samajdar Rajarshi , Panwar Ajay Singh , Martin Lisandra L.
Published: September 2023

The formation of transient helical intermediates, implicated in the early-stages of amyloid formation in amyloidogenic peptides, is thought to be enhanced by membrane-peptide interactions. Uperin 3.5 is a seventeen-residue antimicrobial, amyloidogenic peptide that forms amyloid in phosphate buffered saline (PBS). The role of 2,2,2-trifluoroethanol (TFE) concentration, a known α-helical stabiliser, in modulating aggregation of Uperin 3.5 peptide in membrane-mimetic TFE:water mixtures was investigated. Thioflavin T (ThT) fluorescence assays showed complete inhibition of aggregation at higher concentrations of TFE (≥ 20% TFE:water v/v). However, a five-to-seven-fold increase in fibrillation kinetics was observed at 10% TFE:water mixtures in comparison to aggregation in a buffer. Further, aggregation in TFE:water mixtures was only observed upon addition of buffer. Interestingly, circular dichroism (CD) spectra showed the appearance of partial helical structures in 10% TFE:water, which transitioned to β-sheet rich structures only after addition of buffer. Microsecond time-scale molecular dynamics (MD) simulations of multiple U3.5 peptides in both salt-free and salt-containing TFE:water mixtures showed that changes in the local environment of peptide residues determined the structural transition and aggregation trajectories for U3.5. Consistent with experiments, the greatest extent of aggregation was observed for low TFE concentration (10% TFE:water simulations), characterised by faster formation of helical intermediates (oligomers). While the presence of 10% TFE efficiently induced partial helical structure in individual U3.5 peptides, it did not impede peptide-peptide interactions, thus enabling peptide aggregation. Addition of salt, screened like-charge repulsion between positively charged residues of different peptides, leading to stronger inter-peptide interactions. Significantly, the presence of salt determined subsequent structural transitions in the helical intermediates; either forming a predominantly α-helical oligomer in salt-free solutions or a β-sheet-rich oligomer in salt-containing solutions.
CDK6-mediated endothelial cell cycle acceleration drives arteriovenous malformations in hereditary hemorrhagic telangiectasia
Authors: Dinakaran Sajeth , Zhao Haitian , Tang Yuefeng , Wang Zhimin , Ruiz Santiago , Nomura-Kitabayashi Aya , Blanc Lionel , Faughnan Marie E. , Marambaud Philippe
Published: September 2023

Increased endothelial cell (EC) proliferation is a hallmark of arteriovenous malformations (AVMs) in hereditary hemorrhagic telangiectasia (HHT). The underlying mechanism and disease relevance of this abnormal cell proliferative state of the ECs remain unknown. Here, we report the identification of a CDK6-driven mechanism of cell cycle progression deregulation directly involved in EC proliferation and HHT vascular pathology. Specifically, HHT mouse liver ECs exhibited defects in their cell cycle control characterized by a G1/S checkpoint bypass and acceleration of cell cycle speed. Phosphorylated retinoblastoma (p-RB1)—a marker of G1/S transition through the restriction point—significantly accumulated in ECs of HHT mouse retinal AVMs and HHT patient skin telangiectasias. Mechanistically, ALK1 loss of function increased the expression of key restriction point mediators, and treatment with palbociclib or ribociclib, two CDK4/6 inhibitors, blocked p-RB1 increase and retinal AVMs in HHT mice. Palbociclib also improved vascular pathology in the brain and slowed down endothelial cell cycle speed and EC proliferation. Specific deletion ofCdk6in ECs was sufficient to protect HHT mice from AVM pathology. Thus, CDK6-mediated endothelial cell cycle acceleration controls EC proliferation in AVMs and is a central determinant of HHT pathogenesis. We propose that clinically approved CDK4/6 inhibitors have repurposing potential in HHT.