bluuebunny/crossref_metadata_2025 huggingface dataset:
Chest CT findings and outcomes of COVID-19 in second wave: A cross-sectional study in a tertiary care centre in Northern India
Authors: Cheema Taranjeet , Saroha Amit , Kumar Arjun , Panda Prasan Kumar , Saxena Sudhir
Published: March 2023

Introduction

The COVID-19 pandemic has posed a serious threat to global health, with developing nations like India being amongst the worst affected. Chest CT scans play a pivotal role in the diagnosis and evaluation of COVID-19, and certain CT features may aid in predicting the prognosis of COVID-19 illness.

Methods

This was a single-centre, hospital-based, cross-sectional study conducted at a tertiary care centre in Northern India during the second wave of the COVID-19 pandemic from May-June 2021. The study included 473 patients who tested positive for COVID-19. A high-resolution chest CT scan was performed within five days of hospitalization, and patient-related information was extracted retrospectively from medical records. Univariable and Multivariable analysis was done to study the predictors of poor outcome.

Results

A total of 473 patients were included in the study, with 75.5% being males. The mean total CT score was 29.89 ± 9.06. Fibrosis was present in 17.1% of patients, crazy paving in 3.6%, pneumomediastinum in 8.9%, and pneumothorax in 3.6%. Males had a significantly higher total score, while the patients who survived (30.00 ± 9.55 vs 35.00 v 6.21, p value - <.001), received Steroids at day 2 (28.04 ± 9.71 vs 31.66 ± 7.12, p value – 0.002) or Remdesivir had lower total scores (28.04 ± 9.71 vs 31.66 ± 7.12, p-value – 0.002). Total CT score (aHR 1.05, 95% CI 1.02 – 1.08, p – 0.001), pneumothorax (aHR 1.38, 95 % CI 0.67 – 2.87, p – 0.385), pneumomediastinum (aHR 1.20, 95% CI 0.71 - 2.03, p=0.298) and cardiovascular accident (CVA, aHR 4.75, 95% CI 0.84 – 26.72, p – 0.077) were associated with increased mortality, but the results were not significant after adjusting with other variables on multiple regression analysis.

Conclusion

This study identifies several radiological parameters, including fibrosis, crazy paving, pneumomediastinum, and pneumothorax, that are associated with poor prognosis in COVID-19. These findings highlight the role of CT thorax in COVID-19 illness and the importance of timely identification and interventions in severe and critical cases of COVID-19 to reduce mortality and morbidity.
Surgical and percutaneous coronary revascularization in patients with multivessel or left main disease; what happens beyond five years? A systematic review and study level meta-analysis of randomized trials
Authors: Formica Francesco , Hernandez-Vaquero Daniel , Tuttolomondo Domenico , Gallingani Alan , Singh Gurmeet , Pattuzzi Claudia , Niccoli Giampaolo , Lorusso Roberto , Nicolini Francesco
Published: March 2023

Meta-analysis exploring outcomes beyond 5-years of trials comparing coronary artery bypass graft (CABG) with percutaneous coronary intervention (PCI) utilizing drug-eluting stents in patients with coronary artery disease (CAD), are missing. We conducted a meta-analysis to compare very long-term outcomes, between the two interventions.

Using electronic databases, we retrieved 4 trials, between January, 2010 and January, 2023. The primary endpoint was all-cause mortality. Kaplan-Meier curves of endpoint was reconstructed. Comparisons were made by Cox-linear regression frailty model and by landmark analysis. A flexible parametric model for survival analysis was used to obtain the time-dependent hazard-ratio. A random-effect method was applied.

5180 patients were included and randomized to CABG (n=2586) or PCI with DES (n=2594). During 10-year follow-up, PCI showed an overall higher incidence of all-cause mortality [hazard ratio (HR) 1.19; 95% confidence interval (CI), 1.104-1.32; p=0.008)]. At landmark analysis, PCI showed higher risk of the endpoint within 5-years (HR 1.2; 95% CI, 1.06-1.53; p=0.008) while no difference was found at 5–10-year period (HR,1.03; 95%CI, 0.84-1.26; p=0.76). The time-varying HR analysis of PCI versus CABG was consistent with the results of the landmark analysis. There was no long-term difference between the two interventions for myocardial infarction (MI) (OR,1.42; 95%CI, 0.92-2.18; p=0.11), composite of all-cause mortality, stroke or MI (OR,1.07; 95%CI, 0.84-1.36; p=0.57), stroke (OR,0.97; 95%CI, 0.59-1.59; p=0.91) and cardiovascular death (OR,1.02; 95%CI, 0.75-1.40; p=0.90), while PCI was associated with an increased risk for repeat revascularization (OR,2.11; 95%CI, 1.58-2.81; p<0.001) and major adverse cardiac and cerebrovascular events (OR,1.41; 95%CI, 1.13-1.75; p<0.0001). In conclusion, in patients with CAD, there was a significantly overall higher incidence of all-cause mortality after PCI compared to CABG beyond 5-year follow-up. Specifically, CABG is still favorable beyond 5 years and maintains its gold standard role for the CAD treatment; PCI has an evident higher mortality during the first 5 years and a comparable outcome beyond 5 years.
Off-Label Dosing of Direct Oral Anticoagulants Among Inpatients with Atrial Fibrillation
Authors: Sandhu Amneet , Kaltenbach Lisa A. , Chiswell Karen , Shimoga Vijay , Ashur Carmel , Pribish Abby , Fonarow Gregg C. , Piccini Jonathan P. , Ho P. Michael , Varosy Paul D. , Hess Paul L.
Published: March 2023

Introduction

Among patients hospitalized for atrial fibrillation (AF), the frequency of off-label direct oral anticoagulant (DOAC) dosing, associated factors, hospital-level variation, and temporal trends in contemporary clinical practice are unknown.

Methods

Using the Get With The Guidelines®Atrial Fibrillation (GWTG-AF) registry, patients admitted from January 1st, 2014 to March 31st, 2020, and discharged on DOAC therapy were stratified according to receipt of underdosing, overdosing, or recommended dosing. Factors associated with off-label dosing were identified using logistic regression. Hospital-level variation and temporal trends were assessed.

Results

Of 22,470 patients prescribed a DOAC at discharge from hospitalization for AF (66% apixaban, 29% rivaroxaban, 5% dabigatran), underdosing occurred among 2006 (8.9%), overdosing among 511 (2.3%), and recommended dosing among 19953 (88.8%). Patient-related factors associated with off-label DOAC use included age (underdosing: OR 1.06 per 1-year increase [95% CI 1.06-1.07] and overdosing: OR 1.07 per 1-year increase [1.06-1.09]), dialysis dependence (underdosing: OR 5.50 [3.76-8.05] and overdosing: OR 5.47 [2.74-10.88]), female sex (overdosing: OR 0.79 [0.63-0.99]) and weight (overdosing: OR 0.96 per 1-Kg increase [0.95-1.00]). Across hospitals, the adjusted median odds ratio for off-label DOAC use was 1.45 [95% CI 1.34-1.65] (underdosing: 1.52 [1.39-1.76] and overdosing: 1.32 [1.20-1.84]), indicating significant hospital-level variation. Hospital characteristics associated with underdosing included West vs. Northeast location (OR: 1.55 [1.04-2.31]), rural vs. urban setting (OR: 0.48 [0.28-0.83]), and number of beds (<200 vs. 500+, OR: 1.95 [1.29-2.95]). Recommended dosing significantly increased over time (81.9% in 2014 to 90.9% in 2020, p<0.0001 for trend) with a corresponding decline in underdosing (14.4% in 2014 to 6.6% in 2020, p<0.0001 for trend) and overdosing (3.8% in 2014 to 2.5% in 2020, p=0.001 for trend).

Conclusion

One of 10 patients hospitalized for atrial fibrillation is discharged on off-label dosing of DOAC with significant variation across hospitals. While the proportion of patients receiving recommended dosing has significantly improved over time, opportunities to improve DOAC dosing persist.
Breathing pattern and pulmonary gas exchange in elderly patients with and without left ventricular dysfunction - modification with exercise-based cardiac rehabilitation and prognostic value
Authors: Eser Prisca , Marcin Thimo , Prescott Eva , Prins Leonie F. , Kolkman Evelien , Bruins Wendy , van der Velde Astrid E , Gil Carlos Peña , Iliou Marie-Christine , Ardissino Diego , Zeymer Uwe , Meindersma Esther P , Van’t Hof Arnoud W.J. , de Kluiver Ed P. , Wilhelm Matthias
Published: March 2023

Aims

In elderly patients with and without left ventricular dysfunction (LVD) we compared ventilatory parameters from before to after exercise-based cardiac rehabilitation (exCR) and assessed their prognostic value for major adverse cardiovascular events (MACE).

Methods and Results

Patients aged ≥65 years with acute or chronic coronary syndromes (ACS, CCS) without cardiac surgery who participated in a multicentre study on effectiveness of exCR from seven European countries were included. Cardiopulmonary exercise testing (CPET) was performed before, at termination of exCR and at 12 months follow-up. Ventilation (VE), breathing frequency (BF), tidal volume (VT) and end-expiratory carbon dioxide pressure (PETCO2) were measured at rest, at first ventilatory threshold and peak exercise.

In 818 patients, age was 72.5±5.4 years, 21.9% were women, 79.8% had ACS, and 151 (18%) had LVD. NYHA functional class was not different between LVD and noLVD (86% NYHA I in each group). Compared to noLVD, in LVD resting VE was increased 8%, resting BF 6%, peak VE, peak VT, and peak PETCO2reduced by 6%, 8%, and 5%, respectively, and VE/VVCO2slope increased by 11%. From before to after exCR, resting VE decreased and peak PETCO2increased significantly more in LVD compared to noLVD. In LVD, higher resting BF, higher nadir VE/VCO2, and lower peak PETCO2at baseline were associated with MACE

Conclusions

In elderly patients with ischemic LVD, exaggerated resting ventilation and impaired pulmonary gas exchange during exercise was related to worse outcomes. ExCR was associated with an improvement of abnormal breathing patterns and gas exchange parameters.
Medioapical contractile pulses coordinated between cells regulateDrosophilaeye morphogenesis
Authors: Birriel Christian Rosa , Malin Jacob , Hatini Victor
Published: March 2023

Lattice cells (LCs) in the developingDrosophilaretina constantly move and change shape before attaining final forms. Previously we showed that repeated contraction and expansion of apical cell contacts affect these dynamics. Here we describe a second contributing factor, the assembly of a medioapical actomyosin ring composed of nodes linked by filaments that attract each other, fuse, and contract the LCs’ apical area. This medioapical actomyosin network is dependent on Rho1 and its known effectors. Apical cell area contraction alternates with relaxation, generating pulsatile changes in apical cell area. Strikingly, cycles of contraction and relaxation of cell area are reciprocally synchronized between adjacent LCs. Further, in a genetic screen, we identified RhoGEF2 as an activator of these Rho1 functions and RhoGAP71E/C-GAP as an inhibitor. Thus, Rho1 signaling regulates pulsatile medioapical actomyosin contraction exerting force on neighboring cells, coordinating cell behavior across the epithelium. This ultimately serves to control cell shape and maintain tissue integrity during epithelial morphogenesis of the retina.

Short summary

Rosa et. al. describe a Rho1-dependent pulsatile medioapical actomyosin network that couples neighboring retina lattice cells biomechanically, creating an adaptive supracellular actomyosin network that coordinates the mechanical behavior of neighboring cells and regulates cell shape and tissue integrity.
Helicobacter pylorimodulates heptose metabolite biosynthesis and heptose-dependent innate immune host cell activation by multiple mechanisms
Authors: Hauke Martina , Metz Felix , Rapp Johanna , Faass Larissa , Bats Simon , Radziej Sandra , Link Hannes , Eisenreich Wolfgang , Josenhans Christine
Published: March 2023

Heptose metabolites including ADP-heptose are involved in bacterial lipopolysaccharide and cell envelope biosynthesis. Recently, heptoses were also identified to have potent pro-inflammatory activity on human cells as novel microbe-associated molecular patterns. The gastric pathogenic bacteriumHelicobacter pyloriproduces heptose metabolites which it transports into human cells through its Cag type 4 secretion system. UsingH. pylorias a model, we have addressed the question, how pro-inflammatory ADP-heptose biosynthesis can be regulated by the bacteria. We have characterized the inter-strain variability and regulation of heptose biosynthesis genes and the modulation of heptose metabolite production byH. pylori, which impact cell-autonomous pro-inflammatory human cell activation. HldE, a central enzyme of heptose metabolite biosynthesis, showed strong sequence variability between strains, and was also strain-variably expressed. Transcript amounts of genes in thehldEgene cluster displayed intra-strain and inter-strain differences, were modulated by host cell contact and the presence of thecagpathogenicity island, and were affected by carbon starvation regulator A (CsrA). We reconstituted four steps of theH. pyloriLPS heptose biosynthetic pathwayin vitrousing recombinant purified GmhA, HldE and GmhB proteins. On the basis of one- and two-dimensional NMR spectroscopy and mass spectrometry, the structures of major reaction products were identified as β-D-ADP-heptose and β-heptose-1-monophosphate. A pro-inflammatory heptose-monophosphate variant was also identified for the first time as a novel cell-active product inH. pyloribacteria. Separate purified HldE subdomains and variant HldE allowed to uncover additional strain variation in generating heptose metabolites.
Perirhinal Cortex Learns A Predictive Map of The Task Environment
Authors: Lee David G. , McLachlan Caroline A. , Nogueira Ramon , Kwon Osung , Carey Alanna E. , House Garrett , Lagani Gavin D. , LaMay Danielle , Fusi Stefano , Chen Jerry L.
Published: March 2023

Goal-directed tasks involve acquiring an internal model, known as a predictive map, of relevant stimuli and associated outcomes to guide behavior. Here, we identified neural signatures of a predictive map of task behavior in perirhinal cortex (Prh). Mice learned to perform a tactile working memory task by classifying sequential whisker stimuli over multiple training stages. Chemogenetic inactivation demonstrated that Prh is involved in task learning. Chronic two-photon calcium imaging, population analysis, and computational modeling revealed that Prh encodes stimulus features as sensory prediction errors. Prh forms stable stimulus-outcome associations that expand in a retrospective manner and generalize as animals learn new contingencies. Stimulus-outcome associations are linked to prospective network activity encoding possible expected outcomes. This link is mediated by cholinergic signaling to guide task performance, demonstrated by acetylcholine imaging and perturbation. We propose that Prh combines error-driven and map-like properties to acquire a predictive map of learned task behavior.
Phenotypic and spatial heterogeneity of brain myeloid cells after stroke is associated with cell ontogeny, tissue damage, and brain connectivity
Authors: Patir Anirudh , Barrington Jack , Szymkowiak Stefan , Straus Dana , Alfieri Alessio , Lefevre Lucas , Henderson Neil C , Horsburgh Karen , Ramachandran Prakash , McColl Barry W
Published: March 2023

Acute stroke causes substantial mortality and morbidity and provokes extensive changes to myeloid immune cell populations in the brain that may be targets for limiting brain damage and enhancing brain repair. The most effective immunomodulatory approaches will require precise manipulation of discrete myeloid cell phenotypes in time and space to avoid harmful effects of indiscriminate neuroimmune perturbation. We sought to define how stroke alters the composition and phenotypes of mononuclear myeloid cells with particular attention to how cell ontogeny and spatial organisation combine to expand myeloid cell diversity across the brain after stroke. Multiple reactive microglial states and dual monocyte-derived populations contributed to an extensive repertoire of myeloid cells in post-stroke brain. We identified important overlap and distinctions among different cell types and states that involved ontogeny- and spatial-related properties. Notably, brain connectivity with infarcted tissue underpinned the pattern of local and remote altered cell accumulation and reactivity. Our discoveries suggest a global but anatomically-governed brain myeloid cell response to stroke that comprises diverse phenotypes arising through intrinsic cell ontogeny factors interacting with exposure to spatially-organised brain damage and neuroaxonal cues.
Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria
Authors: Hegelmeyer Nuri K. , Previti Mary L. , Andrade Joshua , Utama Raditya , Sejour Richard J. , Gardin Justin , Muller Stephanie , Ketchum Steven , Yurovsky Alisa , Futcher Bruce , Goodwin Sara , Ueberheide Beatrix , Seeliger Jessica C.
Published: March 2023

Each genome encodes some codons more frequently than their synonyms (codon usage bias), but codons are also arranged more frequently into specific pairs (codon pair bias). Recoding viral genomes and yeast or bacterial genes with non-optimal codon pairs has been shown to decrease gene expression. Gene expression is thus importantly regulated not only by the use of particular codons but by their proper juxtaposition. We therefore hypothesized that non-optimal codon pairing could likewise attenuateMtbgenes. We explored the role of codon pair bias by recodingMtbgenes (rpoB, mmpL3, ndh) and assessing their expression in the closely related and tractable model organismM. smegmatis. To our surprise, recoding caused the expression of multiple smaller protein isoforms from all three genes. We confirmed that these smaller proteins were not due to protein degradation, but instead issued from new transcription initiation sites positioned within the open reading frame. New transcripts gave rise to intragenic translation initiation sites, which in turn led to the expression of smaller proteins. We next identified the nucleotide changes associated with these new sites of transcription and translation. Our results demonstrated that apparently benign, synonymous changes can drastically alter gene expression in mycobacteria. More generally, our work expands our understanding of the codon-level parameters that control translation and transcription initiation.

IMPORTANCE

Mycobacterium tuberculosis(Mtb) is the causative agent of tuberculosis, one of the deadliest infectious diseases worldwide. Previous studies have established that synonymous recoding to introduce rare codon pairings can attenuate viral pathogens. We hypothesized that non-optimal codon pairing could be an effective strategy for attenuating gene expression to create a live vaccine forMtb. We instead discovered that these synonymous changes enabled the transcription of functional mRNA that initiated in the middle of the open reading frame and from which many smaller protein products were expressed. To our knowledge, this is the first report that synonymous recoding of a gene in any organism can create or induce intragenic transcription start sites.
Tracking Early Mammalian Organogenesis – Prediction and Validation of Differentiation Trajectories at Whole Organism Scale
Authors: Imaz-Rosshandler Ivan , Rode Christina , Guibentif Carolina , Ton Mai-Linh N. , Dhapola Parashar , Keitley Daniel , Argelaguet Ricard , Calero-Nieto Fernando J. , Nichols Jennifer , Marioni John C. , de Bruijn Marella F.T.R. , Göttgens Berthold
Published: March 2023

Early organogenesis represents a key step in animal development, where pluripotent cells divide and diversify to initiate formation of all major organs. Here, we used scRNA-Seq to profile over 300,000 single cell transcriptomes sampled in 6 hour intervals from mouse embryos between E8.5 and E9.5. Combining this dataset with our previous E6.5 to E8.5 atlas resulted in a densely sampled time course of over 400,000 cells from early gastrulation to organogenesis. Computational lineage reconstruction at full organismal scale identified complex waves of blood and endothelial development, including a new molecular programme for somite-derived endothelium. To assess developmental fates across the primitive streak, we dissected the E7.5 primitive streak into four adjacent regions, performed scRNA- Seq and predicted cell fates computationally. We next defined early developmental state/fate relationships experimentally by a combination of orthotopic grafting, microscopic analysis of graft contribution as well as scRNA-Seq to transcriptionally determine cell fates of the grafted primitive streak regions after 24h ofin vitroembryo culture. Experimentally determined fate outcomes were in good agreement with the fates predicted computationally, thus demonstrating how classical grafting experiments can be revisited to establish high-resolution cell state/fate relationships. Such interdisciplinary approaches will benefit future studies in both developmental biology as well as guide thein vitroproduction of cells for organ regeneration and repair.
Identification of RNA-Binding Protein Targets with HyperTRIBE inSaccharomyces cerevisiae
Authors: Piao Weilan , Li Chong , Sun Pengkun , Yang Miaomiao , Ding Yansong , Song Wei , Jia Yunxiao , Yu Liqun , Jin Hua
Published: March 2023

As a mater regulator in cells, RNA-binding protein (RBP) plays critical roles in organismal development, metabolism and various diseases. It controls gene expression at multiple levels mostly by specific recognition of target RNA. The traditional CLIP-seq method to detect transcriptome-wide RNA targets of RBP is less efficient in yeasts due to their cell walls. Here, we established an efficient HyperTRIBE (Targets of RNA-binding proteins Identified By Editing) in yeast, by fusing a RBP to the hyper active catalytic domain of human RNA editing enzyme ADAR2 and expressing the fusion protein in yeast cells. The target transcripts of RBP were marked with new RNA editing events and identified by high-throughput sequencing. We successfully applied TRIBE to identifying the RNA targets of two yeast RBPs, KHD1 and BFR1. The antibody-free HyperTRIBE has competitive advantages including low background, high sensitivity and reproducibility, and a simple library preparation procedure, which provides a reliable strategy for RBP target identification inSaccharomyces cerevisiae.
Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments
Authors: Rasmussen Torben Sølbeck , Mao Xiaotian , Forster Sarah , Larsen Sabina Birgitte , Von Münchow Alexandra , Tranæs Kaare Dyekær , Brunse Anders , Larsen Frej , Castro Mejia Josue Leonardo , Adamberg Signe , Hansen Axel Kornerup , Adamberg Kaarel , Hansen Camilla Hartmann Friis , Nielsen Dennis Sandris
Published: March 2023

Background

Fecal microbiota transplantation (FMT) and fecal virome transplantation (FVT, sterile filtrated donor feces) have been effective in treating recurrentClostridioides difficileinfections, possibly through bacteriophage-mediated modulation of the gut microbiome. However, challenges like donor variability, costly screening, coupled with concerns over pathogen transfer (incl. eukaryotic viruses) with FMT or FVT hinders their wider clinical application in treating less acute diseases.

Methods

To overcome these challenges, we developed methods to broaden FVT’s clinical application while maintaining efficacy and increasing safety. Specifically, we employed the following approaches: 1) Chemostat-fermentation to reproduce the bacteriophage FVT donor component and remove eukaryotic viruses (FVT-ChP), 2) solvent-detergent treatment to inactivate enveloped viruses (FVT-SDT), and 3) pyronin-Y treatment to inhibit RNA-virus replication (FVT-PyT). We assessed the efficacy of these processed FVTs in aC. difficileinfection mouse model and compared them with untreated FVT (FVT-UnT), FMT, and saline.

Results

FVT-SDT, FVT-UnT, and FVT-ChP reduced the incidence of mice reaching the humane endpoint (0/8, 2/7, and 3/8, respectively) compared to the FMT, FVT-PyT, and saline control (5/8, 7/8, and 5/7, respectively) and significantly reduced the load of colonizingC. difficilecells and toxin A/B levels. There was a potential elimination ofC. difficilecolonization, with 7 out of 8 mice treated with FVT-SDT testing negative with qPCR. In contrast, all other treatments exhibited the continued presence ofC. difficile. Moreover, the results were supported by changes in the gut microbiome profiles, cecal cytokine levels and histopathological findings. Assessment of viral engraftment following FMT/FVT treatment and host-phage correlations analysis suggested that transfer of phages likely were an important contributing factor associated with treatment efficacy.

Conclusions

This proof-of-concept study show that specific modifications to FVT hold promise in addressing challenges related to donor variability and infection risks. Two strategies lead to treatments significantly limitingC. difficilecolonization in mice, with solvent/detergent treatment and chemostat-propagation emerging as promising approaches.
Combining cancer chemotherapeutics with bacterial DNA repair inhibitors to develop novel antimicrobials
Authors: Bernacchia Lorenzo , Gupta Arya , Paris Antoine , Moores Alexandra A. , Kad Neil M
Published: March 2023

Cancer chemotherapeutics kill rapidly dividing cells, which includes cells of the immune system. The resulting neutropenia predisposes patients to infection, which delays treatment and is a major cause of morbidity and mortality. Here we have exploited the cytotoxicity of the anti-cancer compound cisplatin to screen for FDA-approved drugs that impair bacterial nucleotide excision DNA repair (NER), the primary mechanism bacteria use to repair cisplatin lesions. Five compounds have emerged of which three possess ideal antimicrobial properties including cell penetrance, specific activity for NER, and the ability to kill a multi-drug resistant clinically relevantE. colistrain. Targeting NER offers a new therapeutic approach for infections in cancer patients by combining antimicrobial activity with cancer chemotherapy.
A CUG-initiated CATSPERθ functions in the CatSper channel assembly and serves as a checkpoint for flagellar trafficking
Authors: Huang Xiaofang , Miyata Haruhiko , Wang Huafeng , Mori Giulia , Iida-Norita Rie , Ikawa Masahito , Percudani Riccardo , Chung Jean-Ju
Published: March 2023

Calcium signaling is critical for successful fertilization. In spermatozoa, calcium influx into the sperm flagella mediated by the sperm specific CatSper calcium channel is necessary for hyperactivated motility and male fertility. CatSper is a macromolecular complex and is repeatedly arranged in zigzag rows within four linear nanodomains along the sperm flagella. Here, we report that theTmem249-encoded transmembrane domain containing protein, CATSPERθ, is essential for the CatSper channel assembly during sperm tail formation. CATSPERθ facilitates the channel assembly by serving as a scaffold for a pore forming subunit CATSPER4. CATSPERθ is specifically localized at the interface of a CatSper dimer and can self-interact, suggesting its potential role in CatSper dimer formation. Male mice lacking CATSPERθ are infertile because the sperm lack the entire CatSper channel from sperm flagella, rendering sperm unable to hyperactivate, regardless of their normal expression in the testis. In contrast, genetic abrogation of any of the other CatSper transmembrane subunits results in loss of CATSPERθ protein in the spermatid cells during spermatogenesis. CATSPERθ might acts as a checkpoint for the properly assembled CatSper channel complex to traffic to sperm flagella. This study provides insights into the CatSper channel assembly and elucidates the physiological role of CATSPERθ in sperm motility and male fertility.
THE RIBOREGULATION MECHANISM OF HUMAN SERINE HYDROXYMETHYLTRANSFERASE IS ROOTED IN AN ALLOSTERIC SWITCH
Authors: Spizzichino Sharon , Di Fonzo Federica , Marabelli Chiara , Tramonti Angela , Chaves-Sanjuan Antonio , Parroni Alessia , Boumis Giovanna , Liberati Francesca Romana , Paone Alessio , Montemiglio Linda Celeste , Ardini Matteo , Jakobi Arjen J. , Bharadwaj Alok , Swuec Paolo , Tartaglia Gian Gaetano , Paiardini Alessandro , Contestabile Roberto , Rinaldo Serena , Bolognesi Martino , Giardina Giorgio , Cutruzzolà Francesca
Published: March 2023

RNA can directly control protein activity in a process called riboregulation; only a few mechanisms of riboregulation have been described in detail, none of these being characterized on structural grounds. Here we present a comprehensive structural, functional, and phylogenetic analysis of riboregulation of cytosolic serine hydroxymethyltransferase (SHMT1), the enzyme interconverting serine and glycine in one-carbon metabolism. We show that the RNA modulator competes with polyglutamylated folates and acts as an allosteric switch, selectively altering the enzyme’s reactivity vs. serine. In addition, we identify the tetrameric assembly and a flap structural motif as key structural elements necessary for binding of RNA to eukaryotic SHMT1. The results presented here suggest that riboregulation may have played a role in the evolution of eukaryotic SHMT1 and the compartmentalization of one-carbon metabolism. The findings also provide insights for RNA-based therapeutic strategies targeting this cancer-linked metabolic pathway.
BCL7 proteins, metazoan-specific subunits of the mammalian SWI/SNF complex, bind the nucleosome core particle
Authors: Diaz Dana , Kazrani Asgar Abbas , Martin Franck , Lafouge Julie , Siebert Stéphanie , Birck Catherine , Blais Alexandre , Bergamin Elisa
Published: March 2023

BCL7 proteins are among the most recently identified subunits of the mammalian SWI/SNF (mSWI/SNF) chromatin remodeling complex and are absent from the unicellular version of the complex. Mutations in BCL7 proteins are associated with different kind of cancers including blood malignancies. The information on the molecular function and on the structure of BCL7 proteins is to date very limited. Here we report that BCL7 proteins directly bind the nucleosome core particle (NCP) and free DNA with high affinity. We demonstrate that BCL7 proteins form defined complexes with the NCP and we identify the conserved N-terminal part of BCL7 proteins as sufficient to nucleosome binding. We further characterize the impact of BCL7 protein mutations reported in cancer patients on NCP binding and show that the R11S driver mutation reduces the affinity for the nucleosome. Our findings clarify the molecular function of BCL7 proteins and help rationalize the impact of cancer-associated mutations.
ZIP4is required for normal progression of synapsis and for over 95% of crossovers in wheat meiosis
Authors: Draeger Tracie N. , Rey María-Dolores , Hayta Sadiye , Smedley Mark , Alabdullah Abdul Kader , Moore Graham , Martín Azahara C.
Published: March 2023

Tetraploid and hexaploid wheat have multiple genomes, with successful meiosis and preservation of fertility relying on synapsis and crossover only taking place between homologous chromosomes. In hexaploid wheat, the major meiotic geneTaZIP4-B2(Ph1) on chromosome 5B, promotes crossover between homologous chromosomes, whilst suppressing crossover between homeologous (related) chromosomes. Tetraploid wheat has threeZIP4copies:TtZIP4-A1on chromosome 3A,TtZIP4-B1on 3B andTtZIP4-B2on 5B. Previous studies showed thatZIP4mutations eliminate approximately 85% of crossovers, consistent with loss of the class I crossover pathway. Here, we show that disruption of twoZIP4gene copies inTtzip4-A1B1double mutants, results in a 76-78% reduction in crossovers when compared to wild-type plants. Moreover, when all three copies are disrupted inTtzip4-A1B1B2triple mutants, crossover is reduced by over 95%, suggesting that theTtZIP4-B2copy is also affecting class II crossovers. This implies that, in wheat, the class I and class II crossover pathways may be interlinked. WhenZIP4duplicated and diverged from chromosome 3B on wheat polyploidization, the new 5B copy,TaZIP4-B2, may have acquired an additional function to stabilize both crossover pathways. In plants deficient in all threeZIP4copies, synapsis is delayed and does not complete, consistent with our previous studies in hexaploid wheat, when a similar delay in synapsis was observed in a 59.3Mb deletion mutant,ph1b, encompassing theTaZIP4-B2gene on chromosome 5B. These findings confirm the requirement ofZIP4-B2for efficient synapsis, and suggest thatTtZIP4genes have a stronger effect on synapsis than previously described in Arabidopsis and rice. Thus,ZIP4-B2accounts for the two major phenotypes reported forPh1, promotion of homologous synapsis and suppression of homeologous crossover.

Key message

In tetraploid wheat,ZIP4is required for efficient chromosome synapsis and for over 95% of crossovers, involving both the class I and class II crossover pathways.

Author contribution statement

TD grew and maintained the plants, made the crosses, carried out the KASP genotyping and sequencing, carried out the meiotic metaphase I studies and produced the corresponding figure, and wrote the manuscript. M-DR scored chromosome crossover, performed the statistical analysis and produced the graphs. AM selected the TILLING mutant, carried out the immunolocalization and FISH experiments and produced the immunolocalization figure; SH and MS developed theTtzip4-B2CRISPR mutant in Kronos using RNA-guided Cas9 and produced the CRISPRTtzip4-B2sequence figure; AKA designed the KASP primers; AM and GM provided the concept, provided thoughts and guidance, and revised and edited the manuscript.

Conflict of interest

The authors declare that they have no conflict of interest.
Reduction of Spermine Synthase Suppresses Tau Accumulation Through Autophagy Modulation in Tauopathy
Authors: Tao Xianzun , Liu Jiaqi , Diaz-Perez Zoraida , Foley Jackson R , Stewart Tracy Murray , Casero Robert A , Zhai R. Grace
Published: March 2023

Tauopathy, including Alzheimer Disease (AD), is characterized by Tau protein accumulation and autophagy dysregulation. Emerging evidence connects polyamine metabolism with the autophagy pathway, however the role of polyamines in Tauopathy remains unclear. In the present study we investigated the role of spermine synthase (SMS) in autophagy regulation and tau protein processing inDrosophilaand human cellular models of Tauopathy. Our previous study showed thatDrosophila spermine synthase(dSms) deficiency impairs lysosomal function and blocks autophagy flux. Interestingly, partial loss-of-function of SMS in heterozygousdSmsflies extends lifespan and improves the climbing performance of flies with human Tau (hTau) overexpression. Mechanistic analysis showed that heterozygous loss-of-function mutation ofdSmsreduces hTau protein accumulation through enhancing autophagic flux. Measurement of polyamine levels detected a mild elevation of spermidine in flies with heterozygous loss ofdSms. SMS knock-down in human neuronal or glial cells also upregulates autophagic flux and reduces Tau protein accumulation. Proteomics analysis of postmortem brain tissue from AD patients showed a significant albeit modest elevation of SMS protein level in AD-relevant brain regions compared to that of control brains consistently across several datasets. Taken together, our study uncovers a correlation between SMS protein level and AD pathogenesis and reveals that SMS reduction upregulates autophagy, promotes Tau clearance, and reduces Tau protein accumulation. These findings provide a new potential therapeutic target of Tauopathy.
Pten, Pi3K and PtdIns(3,4,5)P3dynamics modulate pulsatile actin branching inDrosophilaretina morphogenesis
Authors: Malin Jacob , Birriel Christian Rosa , Hatini Victor
Published: March 2023

Epithelial remodeling of theDrosophilaretina depends on the pulsatile contraction and expansion of apical contacts between the cells that form its hexagonal lattice. Phosphoinositide PI(3,4,5)P3(PIP3) accumulates around tricellular adherens junctions (tAJs) during contact expansion and dissipates during contraction, but with unknown function. Here we found that manipulations of Pten or Pi3K that either decreased or increased PIP3resulted in shortened contacts and a disordered lattice, indicating a requirement for PIP3dynamics and turnover. These phenotypes are caused by a loss of protrusive branched actin, resulting from impaired activity of the Rac1 Rho GTPase and the WAVE regulatory complex (WRC). We additionally found that during contact expansion, Pi3K moves into tAJs to promote the cyclical increase of PIP3in a spatially and temporally precise manner. Thus, dynamic regulation of PIP3by Pten and Pi3K controls the protrusive phase of junctional remodeling, which is essential for planar epithelial morphogenesis.

Graphical Abstract: Control of contact length by Pi3K, Pten and PIP3.

Pi3K regulates the transition from contraction to expansion through its tension-dependent localization to tAJs and modulation of its lipid phosphatase activity. Pten localizes uniformly to regulate PIP3turnover and attenuate PIP3production. (A) Tension shortens contacts, concentrates Pi3K at four spots at a distance from tAJs, and inhibits Pi3K’s lipid phosphatase function. (B) High tension ultimately disassembles contractile networks allowing Pi3K to flow toward tAJs, produce PIP3and activate the WRC to promote actin branching and contact expansion. (C) High protrusion in expanded contacts disperses the WRC and disassembles the branched actin network. (D) Branched actin disassembly allows the assembly and contraction of an actomyosin network, which increases tension and contracts the contact leading to the flow of Pi3K away from tAJs and inhibition of its lipid phosphatase function, thus completing the cycle.
Sensory cortical ensembles exhibit differential coupling to ripples in distinct hippocampal subregions
Authors: Jeong Huijeong , Namboodiri Vijay Mohan K , Jung Min Whan , Andermann Mark L.
Published: March 2023

Cortical neurons activated during recent experiences often reactivate with dorsal hippocampal CA1 sharp-wave ripples (SWRs) during subsequent rest. Less is known about cortical interactions with intermediate hippocampal CA1, whose connectivity, functions, and SWRs differ from those of dorsal CA1. We identified three clusters of visual cortical excitatory neurons that are excited together with either dorsal or intermediate CA1 SWRs, or suppressed before both SWRs. Neurons in each cluster were distributed across primary and higher visual cortices and co-active even in the absence of SWRs. These ensembles exhibited similar visual responses but different coupling to thalamus and pupil-indexed arousal. We observed a consistent activity sequence: (i) suppression of SWR-suppressed cortical neurons, (ii) thalamic silence, and (iii) activation of the cortical ensemble preceding and predicting intermediate CA1 SWRs. We propose that the coordinated dynamics of these ensembles relay visual experiences to distinct hippocampal subregions for incorporation into different cognitive maps.
Targeted DNA integration in human cells without double-strand breaks using CRISPR RNA-guided transposases
Authors: Lampe George D. , King Rebeca T. , Halpin-Healy Tyler S. , Klompe Sanne E. , Hogan Marcus I. , Vo Phuc Leo H. , Tang Stephen , Chavez Alejandro , Sternberg Samuel H.
Published: March 2023

Traditional genome-editing reagents such as CRISPR-Cas9 achieve targeted DNA modification by introducing double-strand breaks (DSBs), thereby stimulating localized DNA repair by endogenous cellular repair factors. While highly effective at generating heterogenous knockout mutations, this approach suffers from undesirable byproducts and an inability to control product purity. Here we develop a system in human cells for programmable, DSB-free DNA integration using Type I CRISPR-associated transposons (CASTs). To adapt our previously described CAST systems, we optimized DNA targeting by the QCascade complex through a comprehensive assessment of protein design, and we developed potent transcriptional activators by exploiting the multi-valent recruitment of the AAA+ ATPase, TnsC, to genomic sites targeted by QCascade. After initial detection of plasmid-based transposition, we screened 15 homologous CAST systems from a wide range of bacterial hosts, identified a CAST homolog fromPseudoalteromonasthat exhibited improved activity, and increased integration efficiencies through parameter optimization. We further discovered that bacterial ClpX enhances genomic integration by multiple orders of magnitude, and we propose that this critical accessory factor functions to drive active disassembly of the post-transposition CAST complex, akin to its demonstrated role in Mu transposition. Our work highlights the ability to functionally reconstitute complex, multi-component machineries in human cells, and establishes a strong foundation to realize the full potential of CRISPR-associated transposons for human genome engineering.
Scaling models of visual working memory to natural images
Authors: Bates Christopher J. , Alvarez George A. , Gershman Samuel J.
Published: March 2023

Over the last few decades, psychologists have developed precise quantitative models of human recall performance in visual working memory (VWM) tasks. However, these models are tailored to a particular class of artificial stimulus displays and simple feature reports from participants (e.g., the color or orientation of a simple object). Our work has two aims. The first is to build models that explain people’s memory errors in continuous report tasks with natural images. Here, we use image generation algorithms to generate continuously varying response alternatives that differ from the stimulus image in natural and complex ways, in order to capture the richness of people’s stored representations. The second aim is to determine whether models that do a good job of explaining memory errors with natural images also explain errors in the more heavily studied domain of artificial displays with simple items. We find that: (i) features taken from state-of-the-art deep encoders predict trial-level difficulty in natural images better than several reasonable baselines; and (ii) the same visual encoders can reproduce set-size effects and response bias curves in the artificial stimulus domains of orientation and color. Moving forward, our approach offers a scalable way to build a more generalized understanding of VWM representations by combining recent advances in both AI and cognitive modeling.
The power and limitations of species tree-aware phylogenetics
Authors: Williams Tom A. , Davin Adrian A. , Morel Benoit , Szánthó Lénárd L. , Spang Anja , Stamatakis Alexandros , Hugenholtz Philip , Szöllősi Gergely J.
Published: March 2023

Species tree-aware phylogenetic methods model how gene trees are generated along the species tree by a series of evolutionary events, including the duplication, transfer and loss of genes. Over the past ten years these methods have emerged as a powerful tool for inferring and rooting gene and species trees, inferring ancestral gene repertoires, and studying the processes of gene and genome evolution. However, these methods are complex and can be more difficult to use than traditional phylogenetic approaches. Method development is rapid, and it can be difficult to decide between approaches and interpret results. Here, we review ALE and GeneRax, two popular packages for reconciling gene and species trees, explaining how they work, how results can be interpreted, and providing a tutorial for practical analysis. It was recently suggested that reconciliation-based estimates of duplication and transfer frequencies are unreliable. We evaluate this criticism and find that, provided parameters are estimated from the data rather than being fixed based on prior assumptions, reconciliation-based inferences are in good agreement with the literature, recovering variation in gene duplication and transfer frequencies across lineages consistent with the known biology of studied clades. For example, published datasets support the view that transfers greatly outnumber duplications in most prokaryotic lineages. We conclude by discussing some limitations of current models and prospects for future progress.

Significance statement

Evolutionary trees provide a framework for understanding the history of life and organising biodiversity. In this review, we discuss some recent progress on statistical methods that allow us to combine information from many different genes within the framework of an overarching phylogenetic species tree. We review the advantages and uses of these methods and discuss case studies where they have been used to resolve deep branches within the tree of life. We conclude with the limitations of current methods and suggest how they might be overcome in the future.
Whose energy cost would birds like to save? a revisit of the migratory formation flight
Authors: Shi Mingming , Ransquin Ignace , Chatelain Philippe , Hendrickx Julien M.
Published: March 2023

Line formation of migrating birds is well-accepted to be caused by birds exploiting wake benefits to save energy expenditure. A flying bird generates wingtip trailing vortices that stir the surrounding air upward and downward, and the following bird can get a free supportive lift when positioned at the upward airflow region. However, little to no attention has been paid to clarifying birds’ interests in energy saving, namely, do birds intend to reduce their individual energy consumption or the total energy of the flock? Here, by explicitly considering birds’ interests, we employ a modified fixed-wing wake model that includes the wake dissipation to numerically reexamine the energy saving mechanism in line formation. Surprisingly, our computations show that line formation cannot be explained simply by energy optimization. This remains true whether birds are selfish or cooperative. However, line formations may be explained by strategies optimizing energy cost and either avoiding collision or maintaining vision comfort. We also find that the total wake benefit of the formation attained by selfish birds does not differ much from that got by cooperative birds, the maximum that birds can attain. This implies that selfish birds are still able to fly in formation with very high efficiency of energy saving. In addition, we explore the hypothesis that birds are empathetic and would like to optimize their own energy cost and the neighbors’. Our analysis shows that if birds are more empathetic, the resulting line formation shape deviates more from a straight line, and the flock enjoys higher total wake benefit.

Author summary

Migratory birds can achieve remarkable performance and efficiency in energy exploitation during annual round-trip migration flight. Theoretical and experimental results have shown that this might be achieved because birds fly together in formation with specific shapes, e.g. the noticeable V formation, to utilize the aerodynamic benefits generated by their flock mates. However, it is still unclear whether energy-guided behavior indeed can lead to these formations. We show that the special formation adopted by migratory birds cannot be explained purely by the energy exploitation mechanism, and that birds’ vision performance and collision avoidance very likely also play important roles in the formation emergence. Our results imply that birds fly together in formation because of energy saving, but the specific shape of the formation depends on non-aerodynamic reasons. The research provides further understandings of the emergence of migratory formation and the energy saving mechanism of animal groups. It may also indicate that wing flapping, currently not considered, has an important effect on the way birds exploit aerodynamic benefits from others during the formation flight.