bluuebunny/crossref_metadata_2025 huggingface dataset:
Norcantharidin in cancer therapy – a new approach to overcoming therapeutic resistance: A review
Authors: Zeng Beilei , Chen Xulan , Zhang Lijuan , Gao Xi , Gui Yan
Published: March 2024

Therapeutic resistance in cancer remains a dilemma that scientists and oncologists are eager to solve. Despite several preclinical and clinical studies dedicated to overcoming therapeutic resistance, they often do not yield the expected outcomes. This is primarily due to the multifactorial phenomenon of therapeutic resistance. Norcantharidin (NCTD) is an artificial compound derived from cantharidin that has significant anticancer efficacy without incurring serious side effects. Intriguingly, extensive research suggests that NCTD is essential for boosting anticancer efficacy and reversing treatment resistance. This review article presents a full description of how NCTD can effectively overcome cancer resistance to standard treatments such as chemotherapy, radiation, hormone therapy, and targeted therapy. We also discuss the potential prospects and challenges associated with using NCTD as a therapeutic strategy for reversing resistance to cancer therapy. We anticipate that our review will serve as a valuable reference for researchers and clinicians.
Successful live birth of thin endometrium: A case report
Authors: Huang Baoyi , Lu Danying , Kong Yanxiang , Ma Lin
Published: March 2024

Rationale:

The success of pregnancy depends on various factors, with the endometrial receptivity being a crucial component. Endometrial thickness (EMT) serves as a direct indicator for assessing endometrial receptivity. Previous studies have suggested that a thin endometrium is associated with lower pregnancy rates, especially in patients with an EMT of less than 4 mm. Even in assisted reproductive technology cycles with high success rates, clinical pregnancy cases in patients with such thin endometrium are reported to be very few, let alone in natural conception cycles. Therefore, a thin endometrium poses significant challenges for infertility patients. In this study, patients with an extremely thin endometrium were able to achieve clinical pregnancy and successful live births through natural conception, highlighting the possibility of success even in challenging cases.

Patient concerns:

The patient presented with polycystic ovary syndrome and ovulation disorders. She underwent a natural cycle of letrozole-induced ovulation. On the day of the human chorionic gonadotropin trigger, she had an EMT of 3.8 mm.

Diagnoses:

Polycystic ovary syndrome, ovulation disorders, thin endometrium.

Interventions:

The patient received medications including Progynova, Aspirin, and Dydrogesterone.

Outcomes:

The patient achieved spontaneous conception and subsequently had a live birth.

Lessons:

This case report underscores the significance of managing a thin endometrium during letrozole-induced ovulation. While EMT is traditionally pivotal for predicting embryo implantation success, our findings indicate that endometrial receptivity extends beyond thickness alone. Factors such as endometrial morphology, type, and blood supply play crucial roles. Successful pregnancies with a 3.8 mm EMT are rare, making this case a beacon of hope for such patients. It highlights that, with appropriate interventions, successful pregnancies remain attainable. For those with a thin endometrium, emphasis should extend beyond thickness, addressing ways to enhance both endometrial blood supply and morphology for improved pregnancy rates.
When Equality Is Not Equity
Authors: Strong Bethany L. , Cosey-Gay Franklin , Wilson Kenneth L. , Rogers Selwyn O.
Published: March 2024

Objective:

The purpose of this surgical perspective is to describe the trauma care needs of the South Side of Chicago and the creation of an adult trauma center at the University of Chicago Medicine and associated hospital-based violence intervention program.

Summary Background Data:

Traumatic injury is a leading cause of death and disability in the US. Disparities across the continuum of trauma care exist, which are often rooted in the social determinants of health. Trauma center distribution is critical to timely treatment and should be based on the trauma needs of the area. The previous trauma ecosystem of Chicago was incongruent with the concentration of violent injuries on the south and west sides of the city leading to a fallacy of distributive justice.

Methods:

A descriptive analysis of community partners, trauma program leadership, trauma surgeons and the violence intervention program director was performed.

Results:

The UCM trauma center opened in May 2018 and has since been one of the busiest trauma centers in the country with a 40% penetrating trauma rate. There have been significant reductions in patient transport time on the South Side up to 8.9 minutes (P<0.001). The violence intervention program employs credible messengers with lived experience representing the community and has engaged over 8000 patients since 2018 developing both community-based and medical legal partnerships.

Conclusions:

The persistent efforts of the community and key stakeholders led to a system change improving trauma care for the South Side of Chicago.
Structural basis for nuclear import of bat adeno-associated virus capsid protein
Authors: Hoad Mikayla , Roby Justin A. , Forwood Jade K.
Published: March 2024

Adeno-associated viruses (AAV) are one of the world’s most promising gene therapy vectors and as a result, are one of the most intensively studied viral vectors. Despite a wealth of research into these vectors, the precise characterisation of AAVs to translocate into the host cell nucleus remains unclear. Recently we identified the nuclear localization signals of an AAV porcine strain and determined its mechanism of binding to host importin proteins. To expand our understanding of diverse AAV import mechanisms we sought to determine the mechanism in which the Cap protein from a bat-infecting AAV can interact with transport receptor importins for translocation into the nucleus. Using a high-resolution crystal structure and quantitative assays, we were able to not only determine the exact region and residues of the N-terminal domain of the Cap protein which constitute the functional NLS for binding with the importin alpha two protein, but also reveal the differences in binding affinity across the importin-alpha isoforms. Collectively our results allow for a detailed molecular view of the way AAV Cap proteins interact with host proteins for localization into the cell nucleus.
Fes-deficient macrophages enhance CD8+T cell priming and tumour control through increased pro-inflammatory cytokine production and localization
Authors: Laight Brian J. , Harper Danielle , Dmytryk Natasha , Zhang Shengnan , Garven Andrew , Shi Changnian , Nauman Richard , Kment Jacob , Alotaibi Faizah , Shapavalov Ivan , Gao Yan , Mewburn Jeff , Vlasschaert Caitlyn , LeBrun David , Tyryshkin Kathrin , Berman David , Simpson Amber , Graham Charles , Craig Andrew W. , Basta Sameh , Koti Madhuri , Greer Peter A.
Published: March 2024

Homeostatic immunoregulatory mechanisms that prevent adverse effects of immune overaction can serve as barriers to successful anti-cancer immunity, representing attractive targets to improve cancer immunotherapy. Here, we demonstrate a novel role of the Fes tyrosine kinase, abundantly expressed in immune cells, as an innate intracellular immune checkpoint. Host Fes-deficiency delays tumour onset in a gene dose-dependent manner and improves murine triple negative breast cancer and melanoma tumour control, survival, doxorubicin efficacy, and anti-PD-1 therapy sensitization. These effects were associated with a shift to an anti-tumourigenic tumour immune microenvironment.In vitro, we observed increased Toll-like receptor signaling, and proinflammatory cytokine production and presentation from antigen presenting cells, leading to increased T cell activation, cancer cell killing and tumour control. This study highlights Fes as a novel innate immune checkpoint with potential as a predictive biomarker for effective immune checkpoint blockade treatment, and a potential therapeutic target to improve anti-cancer immunotherapy.
Circulating low-molecular-weight (poly)phenol metabolites in the brain: unveiling in vitro and in vivo blood–brain barrier transport
Authors: Carecho Rafael , Marques Daniela , Carregosa Diogo , Masuero Domenico , Garcia-Aloy Mar , Tramer Federica , Passamonti Sabina , Vrhovsek Urska , Ventura M. Rita , Brito Maria Alexandra , Nunes dos Santos Cláudia , Figueira Inês
Published: March 2024

Circulating metabolites resulting from colonic metabolism of dietary (poly)phenols are highly abundant in the bloodstream, though still marginally explored, particularly concerning their brain accessibility. Our goal is to disclose (poly)phenol metabolites’ blood–brain barrier (BBB) transport, in vivo and in vitro, as well as their role at BBB level. For three selected metabolites, benzene-1,2-diol-3-sulfate/benzene-1,3-diol-2-sulfate (pyrogallol-sulfate – Pyr-sulf), benzene-1,3-diol-6-sulfate (phloroglucinol-sulfate – Phlosulf), and phenol-3-sulfate (resorcinol-sulfate – Res-sulf), BBB transport was assessed in human brain microvascular endothelial cells (HBMEC). Their potential in modulating in vitro BBB properties at circulating concentrations was also studied. Metabolites’ fate towards the brain, liver, kidney, urine, and blood was disclosed in Wistar rats upon injection. Transport kinetics in HBMEC highlighted different BBB permeability rates, where Pyr-sulf emerged as the most in vitro BBB permeable metabolite. Pyr-sulf was also the most potent regarding BBB properties improvement, namely increased beta(β)-catenin membrane expression and reduction of zonula occludens-1 membrane gaps. Whereas no differences were observed for transferrin, increased expression of caveolin-1 upon Pyr-sulf and Res-sulf treatments was found. Pyrsulf was also capable of modulating gene and protein expression of some solute carrier transporters. Notably, each of the injected metabolites exhibited a unique tissue distribution in vivo, with the remarkable ability to almost immediately reach the brain.
The Underground World of Plant Disease: How Does Rhizosphere Dysbiosis Affect Plant Health Above-ground?
Authors: Ketehouli Toi , Pasche Josephine , Buttrós Victor Hugo , Goss Erica M. , Martins Samuel J.
Published: March 2024

Similar to the human gut microbiome, diverse microbes colonize the plant rhizosphere, and an imbalance of this microbial community, known as dysbiosis, may negatively impact plant health. This study aimed to investigate the influence of rhizosphere dysbiosis on above-ground plant health using tomato plants (Solanum lycopersicumL.) and the foliar bacterial spot pathogenXanthomonas perforansas model organisms. Four-week-old tomato plant’s rhizospheres were treated with streptomycin (0.6 g × L-1), or water (negative control) and spray-inoculated withX. perforans(105cells × mL-1) after 24 h. Half of the plants treated with streptomycin andX. perforansreceived soil microbiome transplants (SMT) from uninfected plant donors 48 h after streptomycin application. Streptomycin-treated plants showed a 26% increase in disease severity compared to plants that received no antibiotic, while plants that received the SMT had an intermediate level of disease severity. Antibiotic-treated plants showed a reduced abundance of rhizobacterial taxa like Cyanobacteria from the genusCylindrospermumas well as down-regulation of genes related to plant primary and secondary metabolism and up-regulation of plant defense genes associated with induced systemic resistance (ISR). This study highlights the crucial role of beneficial rhizosphere microbes in disease resistance, even to foliar pathogens.
Acute kidney injury triggers hypoxemia by inducing intravascular neutrophil retention that reduces lung capillary blood flow
Authors: Komaru Yohei , Ning Liang , Lama Carine , Suresh Anusha , Kefaloyianni Eirini , Miller Mark J. , Kawana Shinichi , Shepherd Hailey M. , Li Wenjun , Kreisel Daniel , Herrlich Andreas
Published: March 2024

Sterile acute kidney injury (AKI) is common in the clinic and frequently associated with hypoxemia that does not improve with dialysis and remains incompletely understood. AKI induces remote lung inflammation with neutrophil recruitment in mice and humans, but which cellular cues establish neutrophilic inflammation and how it contributes to hypoxemia is not known. Here we report that AKI induces rapid intravascular neutrophil retention in lung alveolar capillaries without any significant extravasation into tissue or alveoli, causing hypoxemia by reducing lung capillary blood flow in the absence of any significant lung interstitial or alveolar edema. In contrast to direct ischemic lung injury, lung neutrophil recruitment during remote lung inflammation did not require cues from intravascular non-classical monocytes or tissue-resident alveolar macrophages. Instead, lung neutrophil retention depended on neutrophil chemoattractant CXCL2 released by activated intravascular classical monocytes. Comparative single-cell RNA-sequencing analysis of direct and remote lung inflammation revealed that alveolar macrophages are highly activated and produce the neutrophil chemoattractant CXCL2 only in direct lung inflammation. Establishing a CXCL2 gradient into the alveolus by intratracheal administration of CXCL2 during AKI-induced remote lung inflammation enabled neutrophils to extravasate. We thus discovered important differences in lung neutrophil recruitment in direct versus remote lung inflammation and identified lung capillary neutrophil retention that negatively affects oxygenation by causing a ventilation-perfusion mismatch as a novel driver of AKI-induced hypoxemia.
Online psychometric performance of the Athens Insomnia Scale among Colombian people
Authors: Campo-Arias Adalberto , Caballero-Domínguez Carmen Cecilia , Pedrozo-Pupo John Carlos
Published: March 2024

Objective

The study aimed to perform confirmatory factor, internal consistency, and differential item functioning analyses of AIS in two Colombian online samples.

Methods

Two samples were recruited online at different times. A secondary validation study was conducted with the participation of adults. The first sample was adults from the general population (n = 700, between 18 and 76 years, M = 37.05, SD = 12.70, and 68% were female adults). The second sample included patients with asthma or chronic obstructive pulmonary disease (n = 292, between 18 and 96 years (M = 60.44, SD = 17.57, and 64.73% were female). Separated confirmatory factor analyses and Cronbach’s alpha and McDonald’s omega were computed for each factor. Moreover, gender DIF was calculated using Kendall’s tau.

Results

The data adjusted better for the AIS two-dimensional model in the general population sample (chi-squared of 111.25 [df of 19, p < .001], RMSEA of .08, CFI of .96, TLI of .95, and SRMR of .04) and the clinical sample (chi-squared of 96.83 [df of 19, p < .001], RMSEA of .12, CFI of .94, TLI of .91, and SRMR of .05). The internal consistency was high, both Cronbach alpha and McDonald’s omega of .88 in the general population sample, and Cronbach’s alpha of .85 and McDonald’s omega of .88 in the clinical sample. Gender non-differential item functioning was not found among any sample.

Conclusions

AIS shows a two-dimensional structure, high internal consistency, and gender non-differential item functioning in two online samples in Colombia. It is necessary to corroborate these findings in other samples.
The antioxidants esculetin and quercetin modulate differently redox balance in human NB4 leukemia cells
Authors: Rubio Virginia , García-Pérez Ana Isabel , Herráez Angel , Puebla Lilian , Diez José C.
Published: March 2024

The aim is to study the involvement of reactive oxygen species on redox homeostasis of acute promyelocytic leukemia cells using two antioxidants as models for tentative leukemia therapies. The NB4 leukemia cell line has increased reactive oxygen species (ROS) levels. Esculetin and quercetin are antioxidants that alter redox equilibrium, diminishing cell viability and inducing cell death in some cancer cells. The analysis of the role of reactive oxygen species on redox balance and apoptosis in NB4 leukemia cells was addressed by modulating redox balance with oxidants hydrogen peroxide (H2O2) andtert-butylhydroperoxide (t-BHP) and antioxidant compounds (esculetin and quercetin). Cell viability of NB4 cells was measured by flow cytometry using propidium iodide (PI). Colorimetric MTT (3-(4, 5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) gave an index of cell metabolism. Apoptosis was measured using Annexin V-FITC (fluorescein isothiocyanate coupled to annexin V). Intracellular ROS levels were detected using the fluorescent probes H2DCFDA (2’, 7’-dichloro-dihydrofluorescein diacetate) and DHE (dihydro-ethidine). Pre-treatment with quercetin prevented early loss of cell viability induced by either H2O2ort-BHP. It reduced apoptosis produced by H2O2and prevented that induced byt-BHP. Pre-treatment with esculetin, in contrast, increased apoptosis induced by H2O2but reduced that produced byt-BHP. The superoxide anion content increased after incubation with either H2O2ort-BHP, mainly in esculetin pretreatment. Esculetin, but not quercetin, prevented peroxide production by either H2O2ort-BHP. Therefore, esculetin and quercetin regulate differentially redox balance in human NB4 human leukemia cells, presumably via different redox mechanisms, which opens up potential applications in antileukemia therapy.
A differential requirement for ciliary transition zone proteins in human and mouse neural progenitor fate specification
Authors: Wiegering Antonia , Anselme Isabelle , Brunetti Ludovica , Metayer-Derout Laura , Calderon Damelys , Thomas Sophie , Nedelec Stéphane , Eschstruth Alexis , Serpieri Valentina , Catala Martin , Antoniewski Christophe , Schneider-Maunoury Sylvie , Stedman Aline
Published: March 2024

Studying developmental processes in the context of the human central nervous system is essential to understand neurodevelopmental diseases. In this paper we perform a comparative functional study of the ciliopathy geneRPGRIP1Lin human and mouse spinal development usingin vitro3D differentiation of pluripotent stem cells.RPGRIP1L, a causal gene of severe neurodevelopmental ciliopathies such as Joubert and Meckel syndromes, encodes a scaffolding protein of the ciliary transition zone involved in ciliary gating. Previous work has identified a major role forRpgrip1lin mouse brain and spinal cord development, via controlling the Sonic Hedgehog (SHH)/GLI pathway. We show that spinal organoids derived fromRpgrip1lmutant mouse embryonic stem cells faithfully recapitulate the loss of motoneurons and the strong reduction of SHH signaling observed in the mutant mice. In contrast, human induced pluripotent stem cells mutant forRPGRIP1Lproduce motoneurons and activate the SHH pathway at levels similar to wild types, a property shared by human iPSCs mutant for another ciliopathy geneTMEM67. Moreover, we show that, in humanRPGRIP1Lmutant organoids, motoneurons acquire a more anterior identity, expressingHOXgenes and other proteins normally present in the hindbrain and cervical spinal cord while motoneurons from wild type organoids strictly display a caudal brachial identity. By performing a temporal transcriptome analysis throughout the differentiation process, we find that the antero-posterior specification defect arises in early axial progenitors and correlates with the loss of cilia in these cells. Thus, this study uncovers distinct functions in humans and mice for ciliopathy proteins and a novel role for RPGRIP1L in human spinal antero-posterior patterning. These findings have important implications for understanding the role of cilia in human spinal cord development and the pathogenic mechanisms of neurodevelopmental ciliopathies.
Disordered proteins interact with the chemical environment to tune their protective function during drying
Authors: KC Shraddha , Nguyen Kenny , Nicholson Vincent , Walgren Annie , Trent Tony , Gollub Edith , Romero Sofia , Holehouse Alex S. , Sukenik Shahar , Boothby Thomas C.
Published: March 2024

The conformational ensemble and function of intrinsically disordered proteins (IDPs) are sensitive to their solution environment. The inherent malleability of disordered proteins combined with the exposure of their residues accounts for this sensitivity. One context in which IDPs play important roles that is concomitant with massive changes to the intracellular environment is during desiccation (extreme drying). The ability of organisms to survive desiccation has long been linked to the accumulation of high levels of cosolutes such as trehalose or sucrose as well as the enrichment of IDPs, such as late embryogenesis abundant (LEA) proteins or cytoplasmic abundant heat soluble (CAHS) proteins. Despite knowing that IDPs play important roles and are co-enriched alongside endogenous, species-specific cosolutes during desiccation, little is known mechanistically about how IDP-cosolute interactions influence desiccation tolerance. Here, we test the notion that the protective function of desiccation-related IDPs is enhanced through conformational changes induced by endogenous cosolutes. We find that desiccation-related IDPs derived from four different organisms spanning two LEA protein families and the CAHS protein family, synergize best with endogenous cosolutes during drying to promote desiccation protection. Yet the structural parameters of protective IDPs do not correlate with synergy for either CAHS or LEA proteins. We further demonstrate that for CAHS, but not LEA proteins, synergy is related to self-assembly and the formation of a gel. Our results suggest that functional synergy between IDPs and endogenous cosolutes is a convergent desiccation protection strategy seen among different IDP families and organisms, yet, the mechanisms underlying this synergy differ between IDP families.
PIKfyve controls dendritic cell function and tumor immunity
Authors: Choi Jae Eun , Qiao Yuanyuan , Kryczek Ilona , Yu Jiali , Gurkan Jonathan , Bao Yi , Gondal Mahnoor , Tien Jean Ching-Yi , Maj Tomasz , Yazdani Sahr , Parolia Abhijit , Xia Houjun , Zhou JiaJia , Wei Shuang , Grove Sara , Vatan Linda , Lin Heng , Li Gaopeng , Zheng Yang , Zhang Yuping , Cao Xuhong , Su Fengyun , Wang Rui , He Tongchen , Cieslik Marcin , Green Michael D. , Zou Weiping , Chinnaiyan Arul M.
Published: March 2024

The modern armamentarium for cancer treatment includes immunotherapy and targeted therapy, such as protein kinase inhibitors. However, the mechanisms that allow cancer-targeting drugs to effectively mobilize dendritic cells (DCs) and affect immunotherapy are poorly understood. Here, we report that among shared gene targets of clinically relevant protein kinase inhibitors, highPIKFYVEexpression was least predictive of complete response in patients who received immune checkpoint blockade (ICB). In immune cells, highPIKFYVEexpression in DCs was associated with worse response to ICB. Genetic and pharmacological studies demonstrated that PIKfyve ablation enhanced DC function via selectively altering the alternate/non-canonical NF-κB pathway. Both loss ofPikfyvein DCs and treatment with apilimod, a potent and specific PIKfyve inhibitor, restrained tumor growth, enhanced DC-dependent T cell immunity, and potentiated ICB efficacy in tumor-bearing mouse models. Furthermore, the combination of a vaccine adjuvant and apilimod reduced tumor progressionin vivo. Thus, PIKfyve negatively controls DCs, and PIKfyve inhibition has promise for cancer immunotherapy and vaccine treatment strategies.
Designed fluorescent protein cages as fiducial markers for targeted cell imaging
Authors: Gee Morgan , Atai Kaiser , Coller Hilary A. , Yeates Todd O. , Castells-Graells Roger
Published: March 2024

Understanding how proteins function within their cellular environments is essential for cellular biology and biomedical research. However, current imaging techniques exhibit limitations, particularly in the study of small complexes and individual proteins within cells. Previously, protein cages have been employed as imaging scaffolds to study purified small proteins using cryo-electron microscopy (cryo-EM). Here we demonstrate an approach to deliver designed protein cages – endowed with fluorescence and targeted binding properties – into cells, thereby serving as fiducial markers for cellular imaging. We used protein cages with anti-GFP DARPin domains to target a mitochondrial protein (MFN1) expressed in mammalian cells, which was genetically fused to GFP. We demonstrate that the protein cages can penetrate cells, are directed to specific subcellular locations, and are detectable with confocal microscopy. This innovation represents a milestone in developing tools for in-depth cellular exploration, especially in conjunction with methods such as cryo-correlative light and electron microscopy (cryo-CLEM).
Autism-associated PTCHD1 missense variants bind to the SNARE-associated protein, SNAPIN, but exhibit impaired subcellular trafficking
Authors: Pastore Stephen F. , Xie Connie T.Y. , RoyaDerwish  , Muhammad Tahir , Blahova Tereza , El-masri Sierra C. , Frankland Paul W. , Hamel Paul A. , Vincent John B.
Published: March 2024

Background

Patched domain-containing 1 (PTCHD1) is a susceptibility gene for autism spectrum disorder and intellectual disability. Its function in brain development and neurotransmission remains elusive. Studies have sought to characterize PTCHD1 function by elucidating its neural network of interacting proteins. However, given the current paucity of functional information, many PTCHD1 missense variants in clinical databases are classified as variants of uncertain significance (VUSs), severely limiting the healthcare resources available to patients and families.

Methods

A yeast two-hybrid assay was used to identify synaptic PTCHD1-interacting proteins. Candidate binding partners were validated by cloning; transient over-expression in HEK293T cells, followed by co-immunoprecipitation and immunoblotting; and immunocytochemistry in differentiated P19 cells. To evaluate the pathogenicity of clinical missense variants, site-directed mutagenesis was employed, followed by transient over-expression and immunocytochemistry in non-neuronal (HEK293T) and neuronal (Neuro-2A cells) systems.

Results

A novel interaction was identified between the first lumenal loop of PTCHD1 and the SNARE-associated protein SNAPIN, which is implicated in synaptic vesicle exocytosis. Clinically associated missense variants within this region did not disrupt SNAPIN binding, indicating that the pathoetiology of these variants is unrelated to this interaction. However, six of the 12 missense variants tested exhibited pronounced retention within the endoplasmic reticulum, and impaired neuronal and non-neuronal trafficking to the plasma membrane.

Conclusions

These data yield insights regarding the role of PTCHD1 in neurodevelopment and neurotransmission, and suggest a neuropathological mechanism for missense variants. These findings provide a platform for diagnostic assay and VUS interpretation, allowing for clinical re-classification of these variants.
Deciphering mixed infections by plant RNA virus and reconstructing complete genomes simultaneously present within-host
Authors: BANGRATZ Martine , COMTE Aurore , BILLARD Estelle , GUIGMA Abdoul Kader , GANDOLFI Guillaume , KASSANKOGNO Abalo Itolou , SEREME Drissa , POULICARD Nils , TOLLENAERE Charlotte
Published: March 2024

The local co-circulation of multiple phylogenetic lineages is particularly likely for rapidly evolving pathogens in the current globalization context. When various phylogenetic lineages co-occur in the same fields, they may simultaneously be present in the same host plant (i.e. mixed infection), with potential important consequences for disease outcome. This is the case in Burkina Faso for the rice yellow mottle virus (RYMV), endemic to Africa, where it constitutes a major constraint to rice production. We aimed at deciphering the distinct RYMV isolates simultaneously infecting a single rice plant and sequencing their genomes. To this purpose, we tested various sequencing strategies, and we finally combined direct cDNA ONT (Oxford Nanopore Technology) sequencing with the bioinformatics tool RVhaplo. This methodology was validated though the successful reconstruction of two viral genomes distant from as less as a hundred nucleotides (out of 4450nt length genome, i.e. 2-3%), and present within artificial mixes at up to a 99/1 ratio. Then, we used this method to subsequently analyze mixed infections from field samples, revealing up to three RYMV isolates within one single rice plant sample from Burkina Faso. In most cases, the complete genome sequences were obtained, which is particularly important to better estimate the viral diversity and permits to detect recombination events. The described methodology consequently allows to identify various haplotypes of RYMV simultaneously infecting a single rice plant, obtain their full-length sequences, as well as a rough estimate of relative frequencies within the sample. It is efficient, cost-effective, as well as portable, so that it could further be implemented where RYMV is endemic. Perspectives include to decipher mixed infections involving other RNA viruses threatening crop production worldwide.
Hominin brain size increase has emerged from within-species encephalization
Authors: Püschel Thomas A. , Nicholson Samuel L. , Baker Joanna , Barton Robert A. , Venditti Chris
Published: March 2024

The fact that rapid brain size increase was clearly a key aspect of human evolution has prompted many studies focussing on this phenomenon1–4, and many suggestions as to the underlying evolutionary patterns and processes5–10. No study to date has however separated out the contributions of change through time within-vs. between-hominin species whilst simultaneously incorporating effects of body size. Using a phylogenetic approach never applied before to palaeoanthropological data, we show that brain size increase across ~ 7 million years of hominin evolution arose from increases within individual species which account for an observed overall increase in relative brain size. Variation among species in brain size after accounting for this effect is associated with body mass differences but not time. In addition, our analysis also reveals that the within-species trend escalated in more recent lineages, implying an overall pattern of accelerating brain size increase through time.
The diversity of clinicalMycobacterium abscessusisolates in morphology, glycopeptidolipids and infection rates in a macrophage model
Authors: Pichler Virginia , Dalkilic Lara , Shoaib Ghazaleh , Shapira Tirosh , Rankine-Wilson Leah , Boudehen Yves-Marie , Chao Joseph , Sexton Danielle , Prieto Miguel , Quon Bradley , Tocheva Elitza , Kremer Laurent , Hsiao William , Av-Gay Yossef
Published: March 2024

Mycobacterium abscessus(Mab) colonies adopt smooth (S) or rough (R) morphotypes, which are linked to the presence or absence of glycopeptidolipids (GPL), respectively. Though clinically relevant, the association between GPL levels, morphotype and pathogenesis are poorly understood. To investigate the degree of correlation between Mab morphology, GPL levels, and infectivity, we generated isolates from Mab-positive sputum samples from cystic fibrosis patients. Isolated strains were categorised based on their morphology, GPL profile, and replication rate in macrophages. Our findings revealed that around 50% of isolates displayed mixed morphologies and GPL analysis confirmed a consistent relationship between GPL content and morphotype was only found in smooth isolates. Across morphotype groups, no differences were observedin vitro, yet using a high-content THP-1 cellex vivoinfection model, clinical R strains were observed to replicate at higher levels. Moreover, the proportion of infected macrophages was notably higher among clinical R strains compared to their S counterparts at 72 hours post-infection. Clinical variants also infected at significantly higher rates compared to laboratory strains, highlighting the limited translatability of lab strain infection data to clinical contexts. Our study confirmed the general correlation between morphotype and GPL levels in smooth strains yet unveiled more variability within morphotype groups than previously recognised, particularly during intracellular infection. As the rough morphotype is of highest clinical concern, these findings contribute to the expanding knowledge base surrounding Mab infections, offering insights that can steer diagnostic methodologies, and treatment approaches.
Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria
Authors: Sastre-Dominguez Jorge , DelaFuente Javier , Toribio-Celestino Laura , Herencias Cristina , Herrador-Gomez Pedro , Costas Coloma , Hernandez-Garcia Marta , Canton Rafael , Rodriguez-Beltran Jeronimo , Santos-Lopez Alfonso , San Millan Alvaro
Published: March 2024

Plasmids are extrachromosomal genetic elements commonly found in bacteria. Plasmids are known to fuel bacterial evolution through horizontal gene transfer (HGT), but recent analyses indicate that they can also promote intragenomic adaptations. However, the role of plasmids as catalysts of bacterial evolution beyond HGT remains poorly explored. In this study, we investigate the impact of a widespread conjugative plasmid, pOXA-48, on the evolution of various multidrug-resistant clinical enterobacteria. Combining experimental and within-patient evolution analyses, we unveil that plasmid pOXA-48 promotes bacterial evolution through the transposition of plasmid-encoded insertion sequence 1 (IS1) elements. Specifically, IS1-mediated gene inactivations expedite the adaptation rate of clinical strains in vitro and foster within-patient adaptation in the gut microbiota. We decipher the mechanism underlying the plasmid-mediated surge in IS1 transposition, revealing a negative feedback loop regulated by the genomic copy number of IS1. Given the overrepresentation of IS elements in bacterial plasmids, our findings propose that plasmid-mediated IS transposition represents a crucial mechanism for swift bacterial adaptation.
A gnotobiotic mouse model with divergent equol-producing phenotype: potential for determining microbial-driven health impacts of soy isoflavone daidzein
Authors: Leonard Lindsay M. , Simpson Abigayle M. R. , Li Shiyu , Reddivari Lavanya , Cross Tzu-Wen L.
Published: March 2024

The implications of soy consumption on human health have been a subject of debate, largely due to the mixed evidence regarding its benefits and potential risks. The variability in responses to soy has been partly attributed to differences in the metabolism of soy isoflavones, compounds with structural similarities to estrogen. Approximately one-third of humans possess gut bacteria capable of converting soy isoflavone daidzein into equol, a metabolite produced exclusively by gut microbiota with significant estrogenic potency. In contrast, lab-raised rodents are efficient equol producers, except for those raised germ-free. This discrepancy raises concerns about the applicability of traditional rodent models to humans. Herein, we designed a gnotobiotic mouse model to differentiate between equol producers and non-producers by introducing synthetic bacterial communities with and without the capacity into female and male germ-free mice. These gnotobiotic mice display equol-producing phenotypes consistent with the capacity of the gut microbiota received. Our findings confirm the model’s efficacy in mimicking human equol production capacity, offering a promising tool for future studies to explore the relationship between endogenous equol production and health outcomes like cardiometabolic and fertility. This approach aims to refine dietary guidelines by considering individual microbiome differences.
Orderly specification and precise laminar deployment of cortical glutamatergic projection neuron types through intermediate progenitors
Authors: Huilgol Dhananjay , Levine Jesse M , Galbavy William , Wang Bor-Shuen , Josh Huang Z.
Published: March 2024

The cerebral cortex comprises diverse types of glutamatergic projection neurons (PNs) generated from radial glial progenitors (RGs) through either direct neurogenesis or indirect neurogenesis (iNG) via intermediate progenitors (IPs). A foundational concept in corticogenesis is the “inside-out” model whereby successive generations of PNs sequentially migrate to deep then progressively more superficial layers, but its biological significance remains unclear; and the role of iNG in this process is unknown. Using genetic strategies linking PN birth-dating to projection mapping in mice, we found that the laminar deployment of IP-derived PNs substantially deviate from an inside-out rule: PNs destined to non-consecutive layers are generated at the same time, and different PN types of the same layer are generated at non-contiguous times. The overarching scheme of iNG is the sequential specification and precise laminar deployment of projection-defined PN types, which may contribute to the orderly assembly of cortical output channels and processing streams.

HIGHLIGHTS

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Each IP is fate-restricted to generate a pair of near-identical PNs

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Corticogenesis involves the orderly generation of fate-restricted IP temporal cohorts

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IP temporal cohorts sequentially as well as concurrently specify multiple PN types

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The deployment of PN types to specific layers does not follow an inside-out order
Release of P-TEFb from the Super Elongation Complex promotes HIV-1 latency reversal
Authors: Cisneros William J. , Walter Miriam , Soliman Shimaa H.A. , Simons Lacy M. , Cornish Daphne , Halle Ariel W. , Kim Eun-Young , Wolinsky Steven M. , Shilatifard Ali , Hultquist Judd F.
Published: March 2024

The persistence of HIV-1 in long-lived latent reservoirs during suppressive antiretroviral therapy (ART) remains one of the principal barriers to a functional cure. Blocks to transcriptional elongation play a central role in maintaining the latent state, and several latency reversal strategies focus on the release of positive transcription elongation factor b (P-TEFb) from sequestration by negative regulatory complexes, such as the 7SK complex and BRD4. Another major cellular reservoir of P-TEFb is in Super Elongation Complexes (SECs), which play broad regulatory roles in host gene expression. Still, it is unknown if the release of P-TEFb from SECs is a viable latency reversal strategy. Here, we demonstrate that the SEC is not required for HIV-1 replication in primary CD4+ T cells and that a small molecular inhibitor of the P-TEFb/SEC interaction (termed KL-2) increases viral transcription. KL-2 acts synergistically with other latency reversing agents (LRAs) to reactivate viral transcription in several cell line models of latency in a manner that is, at least in part, dependent on the viral Tat protein. Finally, we demonstrate that KL-2 enhances viral reactivation in peripheral blood mononuclear cells (PBMCs) from people living with HIV on suppressive ART, most notably in combination with inhibitor of apoptosis protein antagonists (IAPi). Taken together, these results suggest that the release of P-TEFb from cellular SECs may be a novel route for HIV-1 latency reactivation.

AUTHOR SUMMARY

Since the start of the HIV pandemic, it is estimated that nearly 86 million people have been infected with the virus, and about 40 million people have died. Modern antiretroviral therapies potently restrict viral replication and prevent the onset of AIDS, saving millions of lives. However, these therapies are not curative due to the persistence of the virus in a silenced or ‘latent’ state in long-lived cells of the body. One proposed strategy to clear this latent reservoir, termed “shock and kill”, is to activate these silenced viruses such that the infected cells can be cleared from the body by the immune system. While several drugs have been developed that can activate latent viruses, none have proven effective at reducing the size of the latent reservoir in patients in clinical trials. Here, we describe a new method for latency reactivation using a small molecule inhibitor of a human protein complex called the Super Elongation Complex (SEC). Inhibiting the SEC enhances viral transcription during active infection and triggers the reactivation of latent viruses, especially when in combination with other latency reversing agents. These results pave the way for developing more effective strategies to reactivate latent viruses towards a functional cure.
A platform for the recombinant production of Group A Streptococcus glycoconjugate vaccines
Authors: Castro Sowmya Ajay , Passmore Ian J. , Ndeh Didier , Shaw Helen Alexandra , Ruda Alessandro , Burns Keira , Thomson Sarah , Nagar Rupa , Alagesan Kathirvel , Lucas Kieron , Abouelhadid Sherif , Reglinski Mark , Schwarz-Linek Ulrich , Mawas Fatme , Widmalm Göran , Wren Brendan W. , Dorfmueller Helge C.
Published: March 2024

Strep A is a human-exclusive bacterial pathogen killing annually more than 500,000 patients, and no current licensed vaccine exists. Strep A bacteria are highly diverse, but all produce an essential, abundant, and conserved surface carbohydrate, the Group A Carbohydrate, which contains a rhamnose polysaccharide (RhaPS) backbone. RhaPS is a validated universal vaccine candidate in a glycoconjugate prepared by chemical conjugation of the native carbohydrate to a carrier protein. We engineered the Group A Carbohydratte biosynthesis pathway to enable recombinant production using the industry standard route to couple RhaPS to selected carrier proteins withinE. colicells. The structural integrity of the produced recombinant glycoconjugate vaccines was confirmed by NMR spectroscopy and mass spectrometry. Purified RhaPS glycoconjugates elicited carbohydrate-specific antibodies in mice and rabbits and bound to the surface of multiple Strep A strains of diverse M-types, confirming the recombinantly produced RhaPS glycoconjugates as valuable vaccine candidates.
Tick-borne pathogens identified inHyalomma marginatum(Acari: Ixodidae) collected from various vertebrate hosts in the South of France
Authors: Célia Bernard , Thomas Pollet , Clémence Galon , Charlotte Joly Kukla , Vincent Cicculli , Alessandra Falchi , Sebastien Grech-Angelini , Paul-Eric Poli , Matthieu Bastien , Benoit Combes , Sara Moutailler , Philippe Holzmuller , Laurence Vial
Published: March 2024

Hyalomma marginatumis a common ectoparasitic tick of ungulates, lagomorphs, insectivores, ground-foraging birds, observed in Corsica for decades, but whose permanent establishment in mainland France is very recent. This species is known to be one of the main vectors of the Crimean-Congo Hemorrhagic Fever virus, but also of various parasitic, bacterial or viral pathogens. In this study, we investigated the molecular infection rates of numerous tick-borne pathogens inH. marginatumticks mainly sampled on horses, and occasionally on other animal species, from the French Mediterranean rim and Corsica between 2016 and 2020. In total, 1, 195 DNA and RNA purified from individual ticks or pools of ticks were screened for 26 microbial genera or species (viruses, bacteria and parasites), using a high-throughput microfluidic real-time PCR system (BioMark™ dynamic array system, Standard Biotools). For individual ticks and pooled ones, respectively, the most prevalent tick-borne microorganisms wereFrancisella-like endosymbionts at 97.0% and 96.8%, followed byRickettsia aeschlimannii(76.4% and 96.4%),Theileriaspp. andTheileria equi(3,5% and 0%; 1,9% and 5,8%),Anaplasma phagocytophilum(3.7% and 6.7%), and West Nile virus (0.1% and 0.4%).Babesia occultans(0.9%),Ehrlichia minasensis(0.3%), andCoxiella-like endosymbionts (0.1%) were only detected in individual ticks. Our study provides an overview of the diversity of microorganisms and tick-borne pathogens detected in the invasive tickH. marginatumin Corsica and the continental departments of the Mediterranean rim. Our study opens up new research perspectives on the epidemiology of tick-borne pathogens carried byH. marginatumand on the associated public and veterinary health risks.
Cellulose fermentation by the gut microbiota is likely not essential for the nutrition of millipedes
Authors: Nweze Julius Eyiuche , Gupta Shruti , Salcher Michaela M. , Šustr Vladimír , Horváthová Terézia , Angel Roey
Published: March 2024

Millipedes are thought to depend on their gut microbiome for processing plant-litter-cellulose through fermentation, similar to many other arthropods. However, this hypothesis lacks sufficient evidence. To investigate this, we disrupted the gut microbiota of juvenileEpibolus pulchripes(tropical, CH4-emitting) andGlomeris connexa(temperate, non-CH4-emitting) using chemical inhibitors and isotopic labelling. Feeding the millipedes sterile or antibiotics-treated litter notably reduced faecal production and microbial load without major impacts on survival or weight. Bacterial diversity remained similar, withBacteroidotadominant inE. pulchripesandPseudomonadotainG. connexa. Sodium-2-bromoethanesulfonate treatment halted CH4emissions and reduced the faecalmcrAcopies inE. pulchripesafter 14 days, but emissions resumed after returning to normal feeding. Methanogens in the orderMethanobacterialesandMethanomasscilliicoccalesassociated with protists were detected using Catalysed Reporter Deposition FluorescenceIn situHybridization (CARD-FISH) on day 21, despite suppressed CH4-emission. Employing13C-labeled leaf litter and RNA-SIP revealed a slow and gradual prokaryote labelling, indicating a significant density shift only by day 21. In addition to labelling of taxa from orders well-recognized for their role in (ligno)cellulose fermentation (e.g.,Bacteroidales,Burkholderiales, andEnterobacterales), others, such as members ofDesulfovibrionaleswere also labelled. Surprisingly, labelling of the fungal biomass was somewhat quicker. Our findings suggest that fermentation by the gut microbiota is likely not essential for the millipede’s nutrition.

Importance

Millipedes (Diplopoda) constitute the third most significant group of detritivores after termites and earthworms, yet they have been comparatively understudied. Traditionally, it was believed that millipedes gain energy from fermenting cellulose using their gut microbiota, similar to wood-feeding termites, but this belief lacks evidence. This study used two model millipede species,Epibolus pulchripes(large, tropical, and methane emitter) andGlomeris connexa(small, temperate, and non-methane emitter) to test this belief. We used chemical manipulation experiments, stable isotope labelling, and DNA sequencing to comprehend the microbiota’s role in the millipede’s nutrition. The findings suggest that cellulose fermentation by the gut microbiota may not be essential for millipede nutrition; instead, bacteriovory and fungivory might be the dominant feeding strategies of millipedes.