bluuebunny/crossref_metadata_2025 huggingface dataset:
Auditory Hair Cells and Spiral Ganglion Neurons Regenerate Synapses with Refined Release Properties In Vitro
Authors: Vincent Philippe F.Y. , Young Eric D. , Edge Albert S.B. , Glowatzki Elisabeth
Published: October 2023

Ribbon synapses between inner hair cells (IHCs) and type I spiral ganglion neurons (SGNs) in the inner ear are damaged by noise trauma and with aging, causing ‘synaptopathy’ and hearing loss. Co-cultures of neonatal denervated organs of Corti and newly introduced SGNs have been developed to find strategies for improving IHC synapse regeneration, but evidence of the physiological normality of regenerated synapses is missing. This study utilizes IHC optogenetic stimulation and SGN recordings, showing that newly formed IHC synapses are indeed functional, exhibiting glutamatergic excitatory postsynaptic currents. When older organs of Corti were plated, synaptic activity probed by deconvolution, showed more mature release properties, closer to the highly specialized mode of IHC synaptic transmission that is crucial for coding the sound signal. This newly developed functional assessment of regenerated IHC synapses provides a powerful tool for testing approaches to improve synapse regeneration.
Mimetic butterfly wings through mimetic butterfly eyes
Authors: Dang Andrew , Bernard Gary D. , Yuan Furong , Macias-Muñoz Aide , Hill Ryan I. , Lawrence J. P. , Rangel Olguin Aline G. , Luis-Martínez Armando , Mullen Sean P. , Llorente-Bousquets Jorge , Briscoe Adriana D.
Published: October 2023

Color vision is thought to play a key role in the evolution of animal coloration, while achromatic vision is rarely considered as a mechanism for species recognition. Here we test the hypothesis that brightness vision rather than color vision helpsAdelpha fessoniabutterflies identify potential mates while their co-mimetic wing coloration is indiscriminable to avian predators. We examine the trichromatic visual system ofA. fessoniaand characterize its photoreceptors using RNA-seq, eyeshine, epi- microspectrophotometry and optophysiology. We model the discriminability of its wing color patches in relation to those of its co-mimic,A. basiloides, throughA. fessoniaand avian eyes. Visual modeling suggests that neitherA. fessonianor avian predators can readily distinguish the co-mimics’ coloration using chromatic or achromatic vision under natural conditions. These results suggest that mimetic colors are well-matched to visual systems to maintain mimicry, and that mate avoidance between these two look-alike species relies on other cues.
An in vivo drug screen reveals that cyclooxygenase 2-derived prostaglandin D2promotes spinal cord neurogenesis
Authors: Laura González-Llera , Daniel Sobrido-Cameán , Ana Quelle-Regaldie , Laura Sánchez , Antón Barreiro-Iglesias
Published: October 2023

The study of neurogenesis is essential to understand fundamental developmental processes and for the development of cell replacement therapies for central nervous system disorders. Here, we designed an in vivo drug screening protocol in developing zebrafish to find new molecules and signalling pathways regulating neurogenesis in the ventral spinal cord. This unbiased drug screen revealed that 4 cyclooxygenase (COX) inhibitors reduce the generation of serotonergic interneurons in the developing spinal cord. These results fitted very nicely with available single cell RNAseq data revealing that the floor plate cells show differential expression of 1 of the 2 COX2 zebrafish genes (ptgs2a). Indeed, several selective COX2 inhibitors and 2 different morpholinos againstptgs2aalso caused a significant reduction in the number of serotonergic neurons in the ventral spinal cord and led to locomotor deficits. Single cell RNAseq data and different pharmacological manipulations further revealed that COX2-floor plate-derived prostaglandin D2promotes neurogenesis in the developing spinal cord by promoting mitotic activity in progenitor cells. Rescue experiments using a phosphodiesterase-4 inhibitor suggest that intracellular changes in cAMP levels underlie the effects of COX inhibitors on neurogenesis and locomotion. Our study provides compelling in vivo evidence showing that prostaglandin signalling promotes neurogenesis in the ventral spinal cord.
Understanding SARS-CoV-2 Spike glycoprotein clusters and their impact on immunity of the population from Rio Grande do Norte, Brazil
Authors: Teixeira Diego Gomes , Rodrigues-Neto João Firmino , Severiano da Cunha Dayse Caroline , Jeronimo Selma Maria Bezerra
Published: October 2023

SARS-CoV-2 genome underwent mutations since it started circulating intensively within the human populations. The aim of this study was to understand the fluctuation of the spike clusters concomitant to high rate of population immunity either due to natural infection and/or vaccination in a state of Brazil that had high rate of infection and vaccination coverage. A total of 1715 SARS-CoV-2 sequences from the state of Rio Grande do Norte, Brazil, were retrieved from GISAID and subjected to cluster analysis. Immunoinformatics were used to predict T- and B-cell epitopes, followed by simulation to estimate either pro- or anti-inflammatory responses and correlate with circulating variants. From March 2020 to June 2022, Rio Grande do Norte reported 579,931 COVID-19 cases with a 1.4% fatality rate across three major waves: May-Sept 2020, Feb-Aug 2021, and Jan-Mar 2022. Cluster 0 variants (wild type strain, Zeta) were prevalent in the first wave and Delta in the latter half of 2021, featuring fewer unique epitopes. Cluster 1 (Gamma [P1]) dominated the first half of 2021. Late 2021 had Clusters 2 (Omicron) and 3 (Omicron sublineages) with the most unique epitopes, while Cluster 4 (Delta sublineages) emerged in the second half of 2021 with fewer unique epitopes. Cluster 1 epitopes showed a high pro-inflammatory propensity, while others exhibited a balanced cytokine induction. The clustering method effectively identified Spike groups that may contribute to immune evasion and clinical presentation, and explain in part the clinical outcome.

IMPORTANCE

Identification of epitopes of emerging or endemic pathogens is of importance to estimate population responses and predict clinical outcomes and contribute to vaccine improvement. In the case of SARS-CoV-2, the virus within 6 months of circulation transitioned from the wild-type to novel variants leading to distinct clinical outcomes. Immunoinformatics analysis of viral epitopes of isolates from the Brazilian state of Rio Grande do Norte was performed using a clustering method. This analysis aimed to clarify how the introduction of novel variants in a population characterized by high infection and/or vaccination rates resulted in immune evasion and distinct clinical disease. Our analysis showed that the epitope profiles of each variant explained the respective potential for cytokine production, including the variants that were more likely to cause cytokine storms. Finally, it serves as a mean to explain the multi-wave patterns observed during SARS-CoV-2 pandemics.
SmartEM: machine-learning guided electron microscopy
Authors: Meirovitch Yaron , Park Core Francisco , Mi Lu , Potocek Pavel , Sawmya Shashata , Li Yicong , Chandok Ishaan Singh , Athey Thomas L. , Karlupia Neha , Wu Yuelong , Berger Daniel R. , Schalek Richard , Pfister Hanspeter , Schoenmakers Remco , Peemen Maurice , Lichtman Jeff W. , Samuel Aravinthan D.T. , Shavit Nir
Published: October 2023

Connectomics provides essential nanometer-resolution, synapse-level maps of neural circuits to understand brain activity and behavior. However, few researchers have access to the high-throughput electron microscopes necessary to generate enough data for whole circuit or brain reconstruction. To date, machine-learning methods have been used after the collection of images by electron microscopy (EM) to accelerate and improve neuronal segmentation, synapse reconstruction and other data analysis. With the computational improvements in processing EM images, acquiring EM images has now become the rate-limiting step. Here, in order to speed up EM imaging, we integrate machine-learning into real-time image acquisition in a single-beam scanning electron microscope. This SmartEM approach allows an electron microscope to perform intelligent, data-aware imaging of specimens. SmartEM allocates the proper imaging time for each region of interest – scanning all pixels equally rapidly, then re-scanning small subareas more slowly where a higher quality signal is required to achieve accurate segmentability, in significantly less time. We demonstrate that this pipeline achieves a 7-fold acceleration of image acquisition time for connectomics using a commercial single-beam SEM. We apply SmartEM to reconstruct a portion of mouse cortex with the same accuracy as traditional microscopy but in less time.
Competition between stacking and divalent cation mediated electrostatic interactions determines the conformations of short DNA sequences
Authors: Mondal Balaka , Chakraborty Debayan , Hori Naoto , Nguyen Hung T. , Thirumalai D.
Published: October 2023

Interactions between divalent cations (Mg2+and Ca2+) and highly charged single stranded DNA (ssDNA) and double stranded DNA (dsDNA), as well as stacking interactions, are important in a variety of problems, including nucleosome stability and phase separation in nucleic acids. Quantitative techniques accounting for ion-DNA interactions are needed to obtain insights into these and related problems. Towards this end, we created a computational model that explicitly takes into account monovalent and divalent ions, within the framework of the sequence-dependent coarse-grained Three Interaction Site (TIS) model for DNA. Molecular simulations of the rigid 24 base-pair (bp) dsDNA and flexible ssDNA sequences, dT30and dA30, in a buffer containing Na+and Cl−, with varying amounts of the divalent cations, are used to show that the calculated excess number of ions around the dsDNA and ssDNAagree quantitatively with ion-counting experiments. Using an ensemble of all-atom structures generated from coarse-grained simulations, we calculated the Small Angle X-ray Scattering (SAXS) profiles, which are also in excellent agreement with experiments. Strikingly, recapitulation of all the experimental findings was achieved without adjusting any of the parameters in the energy function to fit the data. At a molecular level, we find that Mg2+and Ca2+sense the differences between the major and minor grooves in dsDNA even though they are masked in ion-counting and SAXS experiments. The smaller Mg2+binds predominantly to the minor grooves and phosphate groups whereas Ca2+binds specifically only to the minor groove. The dA30conformations are dominated by stacking interactions, resulting in structures with considerable helical order. In contrast, the near cancellation of the favorable stacking and unfavorable electrostatic interactions leads to dT30populating an ensemble of heterogeneous conformations.
The maizestriate leaves2(sr2) gene encodes a conserved DUF3732 domain homologous to the riceyss1gene
Authors: Brady Meghan J. , Cheam Maya , Gent Jonathan I. , Dawe R. Kelly
Published: October 2023

Maize striate leaves2(sr2) is a mutant that causes white stripes on leaves that has been used in mapping studies for decades, though the underlying gene has not been identified. Thesr2locus has been previously mapped to small regions of the normal chromosome 10 (N10) and a rearranged variant called Abnormal Chromosome 10 (Ab10). A comparison of assembled genomes carrying N10 and Ab10 revealed only five candidatesr2genes. Analysis of a stock carrying thesr2reference allele (sr2-ref) showed that one of the five genes has a transposon insertion that disrupts its protein sequence and has a severe reduction in mRNA. An independent Mutator transposon insertion in the gene (sr2-Mu) failed to complement thesr2-refmutation, and plants homozygous forsr2-Mushowed white striped leaf margins. Thesr2gene encodes a DUF3732 protein with strong homology to a rice gene with a similar mutant phenotype calledyoung seedling stripe1(yss1). These and other published data suggest thatsr2may have a function in plastid gene expression.
The commonTMEM173 HAQ, AQalleles rescue CD4 T cellpenia, restore T-regs, and preventSAVI (N153S)inflammatory disease in mice
Authors: Aybar-Torres Alexandra , Saldarriaga Lennon A , Pham Ann T. , Emtiazjoo Amir M. , Sharma Ashish K , Bryant Andrew J. , Jin Lei
Published: October 2023

The significance of STING (encoded by theTMEM173gene) in tissue inflammation and cancer immunotherapy has been increasingly recognized. Intriguingly, common humanTMEM173alleles R71H-G230A-R293Q (HAQ)and G230A-R293Q (AQ) are carried by ∼60% of East Asians and ∼40% of Africans, respectively. Here, we examine the modulatory effects ofHAQ, AQalleles on STING-associated vasculopathy with onset in infancy (SAVI), an autosomal dominant, fatal inflammatory disease caused by gain-of-function humanSTINGmutations. CD4 T cellpenia is evident in SAVI patients and mouse models. Using STING knock-in mice expressing common humanTMEM173allelesHAQ,AQ, andQ293, we found thatHAQ, AQ, andQ293splenocytes resist STING-mediated cell deathex vivo,establishing a critical role of STING residue 293 in cell death. TheHAQ/SAVI(N153S)andAQ/SAVI(N153S)mice did not have CD4 T cellpenia. TheHAQ/SAVI(N153S), AQ/SAVI(N153S)mice have more (∼10-fold, ∼20-fold, respectively) T-regs thanWT/SAVI(N153S)mice. Remarkably, while they have comparable TBK1, IRF3, and NFκB activation as theWT/SAVI, theAQ/SAVImice have no tissue inflammation, regular body weight, and normal lifespan. We propose that STING activation promotes tissue inflammation by depleting T-regs cellsin vivo. Billions of modern humans have the dominantHAQ, AQalleles. STING research and STING-targeting immunotherapy should considerTMEM173heterogeneity in humans.

Teaser

Common humanHAQ, AQ TMEM173alleles dominate the gain-of-functionSAVI(N154S) TMEM173mutant in mice.
Photosynthesis is led by stomatal circadian rhythm and not by starch depletion after a long period of darkness
Authors: Dresch Cédric , Vidal Véronique , Suchail Séverine , Sallanon Huguette , Charles Florence , Truffault Vincent
Published: October 2023

The circadian rhythm is an endogenous rhythm, defined by repeated metabolic oscillations every 24 hours under constant parameters. In plants, the circadian rhythm regulates the growth through photosynthesis and the management of carbohydrates. In indoor farming, the photoperiod is independent from the sunlight and is of interest to increase energy savings. In this work, we studied the effects of modifications of photoperiods on indoor-grown lettuces (L. sativa), which were then not tuned with the circadian rhythm. The pattern of photoperiods applied was: 16/12-16/8-16/8. A mutant-free study was carried out to avoid genes shutdown unintended side effects and to evaluate the impact of the circadian rhythm under marketable production conditions. We observed that the circadian regulation of the stomatal conductance was the main limiting factor of net photosynthesis when the photoperiod is exceptionally not tuned with the circadian rhythm. In our experiment, the disruption of the circadian rhythm decreased the photosynthetic activity by 6.2% throughout the light period, with no alteration of the yield, morphology or light and water use efficiencies. Furthermore, starch depletion induced by the changes in the photoperiod could not explain variations of the net photosynthetic activity during the following light period. Interestingly, disrupting the circadian rhythm saved 5% of lighting time compared to the control, which can be converted into energy savings. Consequently, the circadian rhythm can be defined as a limiting factor for reducing energy consumption in indoor farming. Further characterization of the links between the photosynthesis-carbohydrates-growth continuum and the circadian rhythm is thus required.
Human GM-CSF/IL-3 enhance tumor immune infiltration in humanized HCC patient-derived xenografts
Authors: Weinfurtner Kelley , Tischfield David , McClung George , Crainic Jennifer , Gordan John , Jiao Jing , Furth Emma E. , Li Wuyan , Tuzneen Supan Erena , Nadolski Gregory J. , Hunt Stephen J. , Kaplan David E. , Gade Terence P.F.
Published: October 2023

Background & Aims

Responses to immunotherapies in hepatocellular carcinoma (HCC) are suboptimal with no biomarkers to guide patient selection. “Humanized” mice represent promising models to address this deficiency but are limited by variable chimerism and underdeveloped myeloid compartments. We hypothesized that expression of human GM-CSF and IL-3 increases tumor immune cell infiltration, especially myeloid-derived cells, in humanized HCC patient-derived xenografts (PDXs).

Material and Methods

NOG (NOD/Shi-scid/IL-2Rnull) and NOG-EXL (huGM-CSF/huIL-3 NOG) mice conditioned with Busulfan underwent i.v. injection of human CD34+ cells. HCC PDX tumors were then implanted subcutaneously (SQ) or orthotopically (OT). Following serial blood sampling, mice were euthanized at defined tumor sizes. Tumor, blood, liver, and spleen were analyzed by flow cytometry and immunohistochemistry.

Results

Humanized NOG-EXL mice demonstrated earlier and increased human chimerism compared to humanized NOG mice (82.1% vs 43.8%, p<0.0001) with increased proportion of human monocytes (3.2% vs 1.1%, p=0.001) and neutrophils (0.8% vs 0.3%, p=0.02) in circulation. HCC tumors in humanized NOG-EXL mice had increased human immune cell infiltration (57.6% vs 30.2%, p=0.04), noting increased regulatory T cells (14.6% vs 6.8%, p=0.04), CD4+ PD-1 expression (84.7% vs 32.0%, p<0.01), macrophages (1.2% vs 0.6%, p=0.02), and neutrophils (0.5% vs 0.1%, p<0.0001). No differences were observed in tumor engraftment or growth latency in SQ tumors, but OT tumors required implantation at two rather than four weeks post-humanization for successful engraftment. Finally, utilizing adult bone marrow instead of fetal livers enabled partial HLA-matching to HCC tumors but required more CD34+ cells.

Conclusions

Human GM-CSF and IL-3 expression in humanized mice resulted in features more closely approximating the immune microenvironment of human disease, providing a promising model for investigating critical questions in immunotherapy for HCC.

Impact and Implications

This study introduces a unique mouse model at a critical point in the evolution of treatment paradigms for patients with hepatocellular carcinoma (HCC). Immunotherapies have become first line treatment for advanced HCC; however, response rates remain low with no clear predictors of response to guide patient selection. In this context, animal models that recapitulate human disease are greatly needed. Leveraging xenograft tumors derived from patients with advanced HCCs and a commercially available immunodeficient mouse strain that expresses human GM-CSF and IL-3, we demonstrate a novel but accessible approach for modeling the HCC tumor microenvironment.
Methanotroph phenotypic heterogeneity in a methane-oxygen counter gradient
Authors: Beals Delaney G. , Puri Aaron W.
Published: October 2023

Connecting genes to phenotypic traits in bacteria is often challenging because of a lack of environmental context in laboratory settings. Laboratory-based model ecosystems offer a means to better account for environmental conditions compared to standard planktonic cultures, and can help link genotypes and phenotypes. Here, we present a simple, cost-effective, laboratory-based model ecosystem to study aerobic methane-oxidizing bacteria (methanotrophs) within the methane-oxygen counter gradient typically found in the natural environment of these organisms. Culturing the methanotrophMethylomonassp. strain LW13 in this system resulted in formation of a distinct horizontal band at the intersection of the counter gradient, which we discovered was not due to increased numbers of viable bacteria at this location but instead to an increased amount of polysaccharides. We also discovered that different methanotrophic taxa form polysaccharide bands with distinct locations and morphologies when grown in the methane-oxygen counter gradient. By comparing transcriptomic data from LW13 growing within and surrounding this band, we identified genes upregulated within the band and validated their involvement in growth and band formation within the model ecosystem using knockout strains. Notably, deletion of these genes did not negatively affect growth using standard laboratory conditions. This work highlights the use of a laboratory-based model ecosystem that more closely mimics the natural environment to uncover methanotroph phenotypes missing from standard planktonic cultures, and to link these phenotypes with their genetic determinants.
Differential encoding of odor and place in mouse piriform and entorhinal cortex
Authors: Mena Wilson , Baker Keeley , Rubin Alon , Kohli Shaun , Yoo Yun , Bathellier Brice , Ziv Yaniv , Rezaei-Mazinani Shahab , Fleischmann Alexander
Published: October 2023

The integration of olfactory and spatial information is critical for guiding animal behavior. The lateral entorhinal cortex (LEC) is reciprocally interconnected with cortical areas for olfaction and the hippocampus and thus ideally positioned to encode odor-place associations. Here, we used mini-endoscopes to record neural activity in the mouse piriform cortex (PCx) and LEC. We show that in head-fixed mice, odor identity could be decoded from LEC ensembles, but less accurately than from PCx. In mice freely navigating a linear track, LEC ensemble activity at the odor ports was dominated by spatial information. Spatial position along the linear track could be decoded from LEC and PCx activity, however, PCx but not LEC exhibited strong behavior-driven modulation of positional information. Together, our data reveal that information about odor cues and spatial context is differentially encoded along the PCx-LEC axis.

Significance statement

For most animals, the sense of smell is essential for successfully navigating the environment to find food, shelter, and mates. However, how olfactory and spatial information is integrated in the brain to support olfactory-guided behaviors remains poorly understood. In mammals, candidate brain regions thought to support odor-place associations include the olfactory (piriform, PCx) cortex, entorhinal cortex, and hippocampus. We here characterize the activity of cells in the PCx and lateral entorhinal cortex (LEC) of freely moving mice in response to odor cues presented in a linear track. Using mini-endoscope microscopy and population coding analyses, we find that information about odors, spatial location, and behavior is differentially encoded along the PCx-LEC axis.
Large-scale imputation models for multi-ancestry proteome-wide association analysis
Authors: Wu Chong , Zhang Zichen , Yang Xiaochen , Zhao Bingxin
Published: October 2023

Proteome-wide association studies (PWAS) decode the intricate proteomic landscape of biological mechanisms for complex diseases. Traditional PWAS model training relies heavily on individual-level reference proteomes, thereby restricting its capacity to harness the emerging summary-level protein quantitative trait loci (pQTL) data in the public domain. Here we introduced a novel framework to train PWAS models directly from pQTL summary statistics. By leveraging extensive pQTL data from the UK Biobank, deCODE, and ARIC studies, we applied our approach to train large-scale European PWAS models (totaln= 88,838 subjects). Furthermore, we developed PWAS models tailored for Asian and African ancestries by integrating multi-ancestry summary and individual-level data resources (totaln= 914 for Asian and 3,042 for African ancestries). We validated the performance of our PWAS models through a systematic multi-ancestry analysis of over 700 phenotypes across five major genetic data resources. Our results bridge the gap between genomics and proteomics for drug discovery, highlighting novel protein-phenotype links and their transferability across diverse ancestries. The developed PWAS models and data resources are freely available atwww.gcbhub.org.
Modelling termites’ tunnelling and decision-making behaviors
Authors: Mandal Sajib , Oberst Sebastian , Lai Joseph C. S.
Published: October 2023

Termites’ digging and construction behavior plays an important role in understanding termites’ foraging and nesting strategies. Termites build galleries when they tunnel that building behavior is different from ants. Therefore, termite tunnelling behavior such as tunnelling networks (tunnel growth and branching), and direction-changing when generating new branches and encountering obstacles require more research. Measurement of termites’ tunnel growth in the experimental arena is often conducted manually by comparing photo sequences. Here, we observe the tunnelling behaviors of the small-sized desert subterranean termite (Heterotermes aureus) and the larger arid land subterranean termite (Reticulitermes tibialis) and develop a mathematical model to describe termites’ tunnelling behavior in the arena. The model can estimate the possible tunnel length with respect to termite body length over a certain time based on three data inputs. Another advantage of this model is that it takes only a few seconds to show results. The results of the model are verified numerically. A behavioral model based on a decision tree is also developed to investigate termites’ direction-changing mechanisms in tunnelling when generating branches and encountering obstacles. Thus, this study demonstrates methods to characterize and model termites’ tunnelling mechanism and direction-changing behavior, which might be applicable to other insects’ behavior and algorithm mimicking digging and tunneling behavior of ants.
Profiling Chromatin Accessibility in Humans Using Adenine Methylation and Long-Read Sequencing
Authors: Akbari Vahid , Leelakumari Sreeja , Jones Steven J.M.
Published: October 2023

Chromatin accessibility demonstrates accessible DNA regions that usually have regulatory function. Several studies have demonstrated DNA accessibility profiling using nanopore sequencing and GpC or adenine modification. However, the GpC dinucleotide is not evenly distributed across the genome and there are regions sparse in GpC. 6mA studies have demonstrated chromatin accessibility in yeast using nanopore based sequencing, although a high-false positive in 6mA detection rate and low coverage have previously precluded the effective use in mammalian sized genomes. Here, we have developed accurate 6mA base calling and demonstrated high-resolution profiling of accessible regions and simultaneous CpG methylation detection in humans using long read sequencing.
The role of family and environment in determining the skin microbiome of captive aquatic frogs,Xenopus laevis
Authors: Chapman Phoebe A. , Hudson Daniel , Morgan Xochitl C. , Beck Caroline W.
Published: October 2023

Background

The amphibian skin microbiome has drawn interest due to the ecological threat posed by chytridiomycosis, which drives changes in symbiotic microbial communities and may be inhibited by certain bacterial taxa. However, skin microbes also play a role in amphibian tissue regeneration.Xenopusspp. are well-established model organisms used to study development, regeneration, genetics and disease. Husbandry protocols, including use of antibiotics and other sterilising agents, may affect experimental outcomes by altering microbiomes. It is therefore essential to improve our understanding ofXenopusmicrobiome characteristics and inheritance. We undertook bacterial 16S rRNA based sampling of a captive, closedXenopus laeviscolony. A total of 16 female frogs, their eggs, and tadpoles were sampled, covering multiple aquarium systems and tanks, along with testes from males used for in vitro fertilisation and a range of environmental samples.

Results

Tank environments supported the most complex microbial communities. Mother frogs harboured the most diverse microbial communities of the frog life stages, with tadpole skin microbiomes being relatively simple. Frog samples were dominated by Proteobacteria and Bacteroidota.RhizobiumandChryseobacteriumwere dominant in tadpoles, whereas mothers supported high proportions ofVogesellaandAcinetobacteras well asChryseobacterium. While the mothers’ habitats contained low levels of these taxa, the tadpole’s environmental microbes were very similar to those on tadpole skin. A total of 34 genera were found to be differentially abundant between the mothers and tadpoles. Analysis of Bray-Curtis distances indicated that mother and tadpole microbiomes varied according to the mothers’ aquarium system, the tanks within them, and the individual mother. Source tracking analyses showed that egg jelly and tadpoles received a mean of approximately two thirds of their microbiomes via vertical transmission, although a sizeable proportion came from unknown sources at all life stages.

Conclusions

The skin of mother frogs appears to select for certain taxa that are otherwise present at low abundances in the environment. While tadpoles inherit a proportion of their microbiomes from their mothers via the egg, they support a distinct and less diverse microbial community than adult frogs. The microbiome varies between individual mothers, and is also affected by the aquarium system and individual tank within that the mother occupies.
Immune response and resistance of clear cell renal cell carcinoma patients following immune checkpoint blockade
Authors: Mestrallet Guillaume
Published: October 2023

175,000 patients die because of renal cell carcinoma (RCC) each year. Clear cell renal cell carcinoma (ccRCC or KIRC) is the most frequent subtype of RCC. Current therapies include immune checkpoint inhibitors (ICB) or VEGFR tyrosine kinase inhibitors (TKIs). However, many patients did not respond to ICB and immune resistance still occurred. Immune resistance may be explained by expression of various immune checkpoints and immunosuppressive pathways in KIRC patients. Thus, it is important to identify mechanisms driving immune response and resistance following ICB. To address this question, we performed an analysis of 3 KIRC cohorts treated with 3 different ICB. Overall, 20-30% of KIRC patients respond to ICB. Responders with metastasized stage IV cancer with tumorectomy prior to anti-PD-L1 are characterized by an increase in CD4+ and CD8+ T cell infiltration, and by better antigen presentation and T cell responses (BTN3A1, PRF1andCD27genes). However, the expression of CTLA4, TIGIT and BTLA in Th1, Th17 and M2 subsets may limit complete response in responders. Importantly, non-responders patients are characterized by higher infiltration by macrophages, and by overexpression of regulatory gene (ADORA2A) in Th2, CD8+ T cell, M1 and M2 clusters. Targeting these pathways may help to develop combination therapies to improve KIRC patient outcomes.
A customizable multiplex protein microarray for antibody testing and its application for tick-borne and other infectious diseases
Authors: Krishnamurthy Hari Krishnan , Jayaraman Vasanth , Krishna Karthik , Wang Tianhao , Bei Kang , Suresh Chithra , Matilda Shiny , Rai Alex J , Welc-Falęciak Renata , Pawełczyk Agnieszka , Blanton Lucas S. , Chrdle Aleš , Fořtová Andrea , Růžek Daniel , Nasrallah Gheyath K. , Abu-Raddadi Laith J. , Al-Sadeq Duaa W. , Abdallah Marah Abed Alhakim , Lilleri Daniele , Fornara Chiara , D’Angelo Piera , Furione Milena , Venermo Maria Söderlund- , Hedman Klaus , Chochlakis Dimosthenis , Psaroulaki Anna , Makridaki Eirini , Ntoula Artemis , Rajasekaran John J.
Published: October 2023

Tick-borne infections are the most common vector-borne diseases in the USA. Ticks harbor and spread several infections with Lyme disease being the most common tickborne infection in the US and Europe. Lack of awareness about tick populations, specific diagnostic tests, and overlapping symptoms of tick-borne infections can often lead to misdiagnosis affecting treatment and the prevalence data reported especially for non-Lyme tick-borne infections. The diagnostic tests currently available for tick-borne diseases are severely limited in their ability to provide accurate results and cannot detect multiple pathogens in a single run. The multiplex protein microarray developed at Vibrant was designed to detect multiple serological antibodies thereby detecting exposure to multiple pathogens simultaneously. Our microarray in its present form can accommodate 400 antigens and can multiplex across antigen types, whole cell sonicates, recombinant proteins, and peptides. A designed array containing multiple antigens of several microbes includingBorrelia burgdorferi,the Lyme disease spirochete, was manufactured and evaluated. The immunoglobulin M (IgM) and G (IgG) responses against several tick-borne microbes and other infectious agents were analyzed for analytical and clinical performance. The microarray improved IgM and IgG sensitivities and specificities of individual microbes when compared with the respective gold standards. The testing was also performed in a single run in comparison to multiple runs needed for comparable testing standards. In summary, our study presents a flexible multiplex microarray platform that can provide quick results with high sensitivity and specificity for evaluating exposure to varied infectious agents especially tick-borne infections.
Bone canonical Wnt signaling is downregulated in type 2 diabetes and associates with higher Advanced Glycation End-products (AGEs) content and reduced bone strength
Authors: Leanza Giulia , Cannata Francesca , Faraj Malak , Pedone Claudio , Viola Viola , Tramontana Flavia , Pellegrini Niccolò , Vadalà Gianluca , Piccoli Alessandra , Strollo Rocky , Zalfa Francesca , Beeve Alec , Scheller Erica L , Tang Simon , Civitelli Roberto , Maccarrone Mauro , Papalia Rocco , Napoli Nicola
Published: October 2023

Type 2 diabetes (T2D) is associated with higher fracture risk, despite normal or high bone mineral density. We reported that bone formation genes (SOSTandRUNX2) and Advanced Glycation End-products (AGEs) were impaired in T2D. We investigated Wnt signaling regulation and its association with AGEs accumulation and bone strength in T2D from bone tissue of 15 T2D and 21 non-diabetic postmenopausal women undergoing hip arthroplasty. Bone histomorphometry revealed a trend of low mineralized volume in T2D [(T2D 0.249% (0.156-0.366) vs non-diabetic subjects 0.352% (0.269-0.454); p=0.053)], as well as reduced bone strength [T2D 21.60 MPa (13.46-30.10) vs non-diabetic subjects 76.24 MPa (26.81-132.9); p=0.002]. We also showed that gene expression of Wnt agonistsLEF-1(p=0.0136) andWNT10B(p=0.0302) were lower in T2D. Conversely, gene expression ofWNT5A(p=0.0232),SOST(p<0.0001) andGSK3B(p=0.0456) were higher, while collagen (COL1A1) was lower in T2D (p=0.0482). AGEs content was associated withSOSTandWNT5A(r=0.9231, p<0.0001; r=0.6751, p=0.0322), but inversely correlated withLEF-1andCOL1A1(r= -0,7500, p=0.0255; r= -0,9762, p=0.0004).SOSTwas associated with glycemic control and disease duration (r=0.4846, p=0.0043; r=0.7107, p=0.00174), whereasWNT5AandGSK3Bwere only correlated with glycemic control (r=0.5589, p=0.0037; r=0.4901, p=0.0051). Finally, Young’s Modulus was negatively correlated withSOST(r=-0.5675, p=0.0011),AXIN2(r=-0.5523, p=0.0042) andSFRP5(r=-0.4442, p=0.0437), while positively correlated withLEF -1(r=0.4116, p=0.0295) andWNT10B(r=0.6697, p=0.0001). These findings suggest that Wnt signaling, and AGEs could be the main determinants of bone fragility in T2D.

Graphical abstract
Rethinking Blood Eosinophils for Assessing ICS Response in COPD: A Post-Hoc Analysis from FLAME
Authors: Mathioudakis Alexander G. , Bate Sebastian , Sivapalan Pradeesh , Jensen Jens-Ulrik , Singh Dave , Vestbo Jørgen
Published: October 2023

Background

The varied treatment response to inhaled corticosteroids (ICS) in COPD, and the increased risk of pneumonia necessitate a personalised ICS approach. This is informed by blood eosinophil count (BEC), which predicts ICS treatment response. This post-hoc analysis evaluates the ability of different BEC measurements to predict ICS treatment response. BEC measured either on or off ICS treatment, and BEC change during ICS treatment were investigated.

Methods

FLAME, a 52-week, double-blind RCT compared LABA/LAMA versus LABA/ICS. Corticosteroids were prohibited during a 4-week run-in period. We chose patients previously on ICS, thereby allowing pre and post run-in period BEC to represent BEC on and off ICS, respectively. In this post-hoc analysis, we revisited outcome data, exploring how the three BEC biomarkers interacted with treatment response to the ICS containing regimen.

Results

Our study confirms that LABA/LAMA combination is superior, or at least non-inferior, to LABA/ICS in curbing exacerbations for most FLAME participants. Lower BEC off and BEC on ICS and lack of significant BEC suppression during ICS treatment corresponded to superior response to LABA/LAMA in terms of exacerbation rate, time-to-first exacerbation, and time-to-first pneumonia. In a subgroup, including 9% of participants, BEC changed significantly during ICS treatment, and higher BEC on ICS did not predict ICS treatment response. For these patients BEC off ICS and BEC change proved more predictive.

Conclusion

This exploratory analysis advocates preferentially using BEC off ICS or BEC change during ICS treatment for guiding ICS treatment decisions. BEC measured on ICS is less predictive of treatment response.

What is already known on this topic

Blood eosinophil count (BEC) is used to guide the administration of inhaled corticosteroids (ICS) for COPD, but they may be suppressed in response to systemic or inhaled corticosteroids.

What this study adds

This post-hoc analysis suggests that BEC change during treatment with ICS and this change is associated with treatment response to ICS containing regimens. More specifically, BEC suppression is associated with favourable response to ICS, while unchanged or increased BEC is associated with inferior ICS treatment effect and increased risk of pneumonia. In 9% of participants, BEC changes significantly (≥200 cells/μL) during ICS treatment, and in these patients, BEC on ICS is not reliable in predicting treatment response to ICS, as it appears that some ICS responders may actually have low BEC on ICS and vice versa.

How this study might affect research, practice or policy

These findings highlight the potential utility of BEC change during ICS treatment as a predictive biomarker of treatment response to ICS and question the use of BEC on ICS to guide withdrawal of ICS, but need prospective validation.
Optimal targeting of interventions uses estimated risk of infectiousness to control a pandemic with minimal collateral damage
Authors: Petrie James , Masel Joanna
Published: October 2023

1

In this paper, we present a simple model that shows how to optimally target interventions based on the estimated risk of infectiousness of individuals. Our model can help policymakers decide when to use different types of interventions during a pandemic, depending on their precision, which is the fraction of positive predictions that are true positives. We show that targeted interventions, even with very low precision, can impose a much smaller overall burden on the population than non-targeted alternatives, such as lockdowns or mass testing. To illustrate this, we use data from the NHS contact tracing system in the UK to construct a risk function based on second degree contact tracing, which is similar to the strategy used by Vietnam in 2020. We find that with moderate precision (greater than 1/1000) and sufficient sensitivity (greater than 1 − 1/R0), countries can cope with a large number of imported cases without resorting to social distancing measures, while keeping the per-person probabilities of both infection and quarantine very low. We also show that targeted strategies are often orders of magnitude better than default strategies, making them robustly beneficial even under significant uncertainty about most parameters.
Facilitators and barriers to community pharmacy PrEP delivery: A scoping review
Authors: Harrison China , Family Hannah , Kesten Joanna , Denford Sarah , Scott Anne , Dawson Sarah , Scott Jenny , Sabin Caroline , Copping Joanna , Harryman Lindsey , Cochrane Sarah , Horwood Jeremy
Published: October 2023

Introduction

Pre-exposure prophylaxis (PrEP) is an effective medication to reduce the risk of acquiring HIV. PrEP is available free of charge in the United Kingdom from sexual health clinics. Expanding PrEP delivery to community pharmacies holds promise and aligns with UK government goals to eliminate new cases of HIV by 2030. The aim of this scoping review was to describe the existing evidence about the barriers to and facilitators of community pharmacy PrEP delivery, for pharmacists and pharmacy clients, as aligned with the Capacity Opportunity, Motivation Behaviour (COM-B) Model.

Methods

Five bibliographic and five review databases were searched from inception to August 2023. Literature of any study design was included if it discussed barriers and facilitators of community pharmacy PrEP delivery. Trial registrations, protocols and news articles were excluded.

Results

A total of 649 records were identified, 73 full texts were reviewed, and 56 met the inclusion criteria. Most of the included literature was original research (55%), from the United States of America (77%) conducted during or after the year 2020 (63%). Barriers to PrEP delivery for pharmacists included lack of knowledge, training and skills (capability), not having the necessary facilities (opportunity), concern about the costs of PrEP and believing that PrEP use could lead to risk behaviour’s and STIs (motivation). Facilitators included staff training (capability), time, the right facilities (opportunity), believing PrEP could be a source of profit and could reduce new HIV infections (motivation). For clients, barriers included lack of PrEP awareness (capability), pharmacy facilities (opportunity) and not considering pharmacists as healthcare providers (motivation). Facilitators included awareness of PrEP and pharmacist’s training to deliver it (capability), the accessibility of pharmacies (opportunity) and having an interest in PrEP (motivation).

Conclusion

To effectively enhance PrEP delivery in UK community pharmacies, the identified barriers and facilitators should be explored for relevance in the UK and subsequently addressed and leveraged at the pharmacy team, client and care pathway level. By comprehensively considering all aspects of the COM-B framework, community pharmacies could become crucial providers in expanding PrEP accessibility, contributing significantly to HIV prevention efforts.
Virtual Primary Care for People with Opioid Use Disorder: A Scoping Review of Current Strategies, Benefits, and Challenges
Authors: Narayan Shawna , Gooderham Ellie , Spencer Sarah , McCracken Rita , Hedden Lindsay
Published: October 2023

Background

There is a pressing need to understand the implications of the rapid adoption of virtual primary care for people with opioid use disorder. Potential impacts, including disruptions to opiate agonist therapies, and the prospect of improved service accessibility remain underexplored. This scoping review synthesizes current literature on virtual primary care for people with opioid use disorder, with a specific focus on benefits, challenges, and strategies.

Methods

We followed the Joanna Briggs Institute methodological approach for scoping reviews and reported our findings consistent with the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews. We conducted searches on MEDLINE, Web of Science, CINAHL Complete, and Embase using our developed search strategy with no date restrictions. We incorporated all study types that included the three concepts (i.e., virtual care; primary care; people with opioid use disorder). We excluded research on minors, asynchronous virtual modalities, and care not provided in a primary care setting. We used Covidence to screen and extract data, pulling information on study characteristics, health system features, patient outcomes, and challenges and benefits of virtual primary care. We conducted inductive content analysis and calculated descriptive statistics. We appraised the quality of studies using the Quality Assessment with Diverse Studies tool and categorized findings using the Consolidated Framework for Implementation Science.

Results

Our search identified 1474 studies. We removed 536 duplicates, leaving 936 studies for title and abstract screening. After a double review process, we retained 28 studies for extraction. Most studies described virtual primary care delivered via phone (n=18, 64.3%) rather than video. While increased healthcare accessibility was a significant benefit (n=13, 46.4%) to the adoption of virtual visits, issues around access to technology and digital literacy stood out as the main challenge (n=12, 42.9%).

Conclusions

The available studies highlight the potential for enhancing accessibility and continuous access care for people with opioid use disorder using virtual modalities. Future research and policies must focus on bridging gaps to ensure virtual primary care does not exacerbate or entrench health inequities.
Stroke Incidence According to Cardiorespiratory Fitness: A Cohort Study of 483,379 Hypertensive Patients
Authors: Kokkinos Peter , Faselis Charles , Pittaras Andreas , Samuel Immanuel Babu Henry , Lavie Carl J. , Ross Robert , Lamonte Michael , Franklin Barry A. , Sui Xuemei , Myers Jonathan
Published: October 2023

Objectives

We assessed stroke incidence in hypertensive patients according to cardiorespiratory fitness (CRF) and changes in CRF.

Methods

A prospective cohort study of 483,379 US Veterans. Participants completed a maximal standardized Exercise Treadmill test (ETT) performed within the Veterans Affairs medical centers across the United States between 1999 and 2020. None exhibited evidence of unstable cardiovascular disease during the ETT. Participants were stratified into 5 age-and-gender specific CRF categories based on the peak metabolic equivalents (METs) achieved. A subgroup of participants with two ETT evaluations (n=110, 576) were also assigned to 4 categories based on MET changes from the initial ETT to the final ETT. Multivariable Cox models, adjusted for age, and co-morbidities were used to estimate HRs and 95% CIs for stroke risk.

Results

The mean age ± standard deviation (SD) was 59.4±9.0 years. During the median follow-up time of 10.6 years (5,182,179 person-years), there were 15,925 stroke events with an average annual rate of 3.1 events per 1,000 person-years. In a final adjusted model, relatively poor CRF was the strongest predictor of stroke risk than any other comorbidity (HR: 2.24; 95% CI: 2.10-2.40; P< 0.001). For each 1-MET higher exercise capacity, the risk was 10% lower (0.90, 95% CI 0.90-0.91, p<0.001). Compared to the Least-fit, stroke risk was 23% lower for Low-fit individuals (HR 0.77; 95% CI, 0.73-0.80; p<0.001); and declined progressively to 55% for those in the highest CRF category (HR 0.45; 95% CI 0.42-0.48; p<0.001). We also assessed stroke incidence according to change in CRF. Compared to fit individuals during both evaluations, the risk was 27% higher for those who became unfit (HR 1.27, 95% CI 1.15-1.41, p<0.001), and not significantly different for unfit who became fit (HR 1.10, 95% CI 0.97-1.25, p=0.13).

Conclusions

Poor CRF was the strongest predictor of stroke incidence in hypertensive patients, regardless of age race, or gender. The association was independent, inverse, and graded for all stroke types. Changes in CRF over time reflected inverse changes in stroke risk, suggesting that risk of stroke can be modulated by improved CRF.