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Joseph, J.

Publications and source records attributed to Joseph, J..

At least 37 records · Page 2Linked to original sources

Towards a tracking of bird migratory behaviour through geological time: an isotopic and histological approach

O_LIBird seasonal migration is a remarkable biogeographic phenomenon, yet its deep-time origin(s) and evolutionary history remain poorly understood, with the bird fossil record largely overlooked. This study explores the predictability of bird migratory behaviour from the oxygen isotope composition of their bone apatite phosphate ({delta}18Op), a promising approach in this regard because: (i) sedentary and migratory birds tend to occupy distinct climatic niches year-round; (ii) their {delta}18Op values primarily reflect the climate-driven isotopic composition of their drinking water; and (iii) this isotopic signature can persist through fossilisation. C_LIO_LIBone tissues were categorised based on their potential to yield spatio-temporally distinct climatic records: Early Bone Tissues (EBT), deposited before somatic maturity, and Late Bone Tissues (LBT), formed through bone remodelling over the lifespan. The predictability of migratory behaviour was theoretically assessed by modelling tissue-specific {delta}18Op values for thousands of birds across 77 migratory and sedentary species, using tracking and observational data along with a revised phosphate-water fractionation equation. These theoretical results were confronted with data from 11 extant bird species, obtained using a new experimental framework combining histological and isotopic analyses. C_LIO_LIA significantly positive correlation between {delta}18Op and the proportion of LBT in bone samples was observed both theoretically and experimentally in migratory birds - particularly in long-distance migrants - and is predicted to be virtually absent in sedentary species at temperate latitudes. Migratory birds that died outside their natal sites can also be identified when their {delta}18Op,EBT values fall outside the range observed in local juvenile and sedentary birds. C_LIO_LIWe conclude that bird migratory behaviour can be inferred from the {delta}18Op values of their skeletal remains, provided the individuals migrated across sufficiently contrasting climatic zones. While this approach cannot detect all migratory behaviours - such as short-distance or longitudinal movements - it is unlikely to misclassify sedentary birds as migratory at temperate latitudes. We therefore argue that this approach can be extended to well-preserved fossil bones to infer past bird migratory behaviours, as long as the palaeoclimatic context is carefully considered. More broadly, this study establishes a framework for inferring migratory behaviour in any vertebrate from non-fully remodelled biomineralised remains. C_LI

evolutionary biology↗

A three-dimensional histological cell atlas of the developing human brain

The human brain is believed to contain a full complement of neurons by the time of birth together with a substantial amount of the connectivity architecture, even though a significant amount of growth occurs postnatally. The developmental process leading to this outcome is not well understood in humans in comparison with model organisms. Previous magnetic resonance imaging (MRI) studies give three-dimensional coverage but not cellular resolution. In contrast, sparsely sampled histological or spatial omics analyses have provided cellular resolution but not dense whole brain coverage. To address the unmet need to provide a quantitative spatiotemporal map of developing human brain at cellular resolution, we leveraged tape-transfer assisted serial section histology to obtain contiguous histological series and unbiased imaging with dense coverage. Interleaved 20 thick Nissl and H&E series and MRI volumes are co-registered into multimodal reference volumes with 60 isotropic resolution, together with atlas annotations and a stereotactic coordinate system based on skull landmarks. The histological atlas volumes have significantly more contrast and texture than the MRI volumes. We computationally detect cells brain-wide to obtain quantitative characterization of the cytoarchitecture of the developing brain at 13-14 and 20-21 gestational weeks, providing the first comprehensive regional cell counts and characterizing the differential growth of the different brain compartments. Morphological characteristics permit segmentation of cell types from histology. We detected and quantified brain-wide distribution of mitotic figures representing dividing cells, providing an unprecedented spatiotemporal atlas of proliferative dynamics in the developing human brain. Further, we characterized the abundance and distribution of Cajal-Retzius cells, a transient cell population that plays essential roles in organizing glutamatergic cortical neurons into layers. Together, our study provides an unprecedented quantitative window into the developing human brain and the reference volumes and coordinate space should be useful for integrating spatial omics data sets with dense histological context.

neuroscience↗

XRN1 supplies free nucleotides to feed alphavirus replication

Several RNA viruses induce widespread degradation of cellular mRNAs upon infection; however, the biological significance and mechanistic details of this phenomenon remain unknown. Here, we make use of a model alphavirus, Sindbis virus (SINV), to fill this knowledge gap. We found that SINV triggers cellular RNA decay through the exonuclease XRN1 and the 5-to-3 degradation machinery (5-3DM). These proteins accumulate at viral replication organelles (VROs) and interact with the non-structural protein 1 (nsP1), bringing mRNA degradation into proximity with vRNA synthesis. Our data suggest that monophosphate nucleotides released by cellular RNA decay are recycled through the salvage pathway to feed viral replications. Our work thus reveals a fundamental connection between cellular mRNA degradation and viral replication via nucleotides repurposing. Research highlightsO_LI5-3 RNA decay is essential for the replication of a wide range of viruses. C_LIO_LIXRN1 directly interacts with transcripts which are degraded during infection. C_LIO_LIRNA decay factors and salvage pathway members localise to viral factories. C_LIO_LISupplying nucleosides to several 5-3DM deficient cells facilitates SINV infection. C_LI

biochemistry↗

Description of Bacterial RNA Transcripts Detected in Mycobacterium tuberculosis Infected Cells from Peripheral Human Granulomas using Single Cell RNA Sequencing

Mycobacterium tuberculosis (Mtb) remains a global human health threat and a significant cause of human morbidity and mortality. We document here the capture of Mtb transcripts in libraries designed to amplify eukaryotic mRNA. These reads are often considered spurious or nuisance and are rarely investigated. Because of early literature suggesting the possible presence of polyadenylated transcripts in Mtb RNA, we included the H37Rv Mtb reference genome when assembling scRNA seq libraries from fine needle aspirate samples from patients presenting at the TB clinic, Port Moresby General Hospital, Papua New Guinea. We used 10X Genomics single-cell RNA sequencing transcriptomics pipeline, which initiates mRNA amplification with poly-T primers on [~]30-micron beads designed to capture, in this case, human mRNA associated with individual cells in the clinical samples. Utilizing the 10X Genomics Cell Ranger tool to align sequencing reads, we consistently detected bacterial small and large ribosomal subunit RNA sequences (rrs and rrl, respectively) and other bacterial gene transcripts in the cell culture and patient samples. We interpret Mtb reads associated with the host cells unique molecular identifier (UMI) and transcriptome to indicate infection of that individual host cell. The Mtb transcripts detected showed frequent sequence variation from the reference genome, with greater than 90% of the rrs or rrl reads from many clinical samples having at least 1 sequence difference compared to the H37Rv reference genome. The data presented includes only bacterial sequences from patients with TB infections that were confirmed by the hospital pathology lab using acid-fast microscopy and/or GeneXpert analysis. The repeated, non-random nature of the sequence variations detected in Mtb rrs and rrl transcripts from multiple patients, suggests that, even though this appears to be a stochastic process, there is possibly some selective pressure that limits the types and locations of sequence variation allowed. The variation does not appear to be entirely artefactual, and it is hypothesized that it could represent an additional mechanism of adaptation to enhance bacterial fitness against host defenses or chemotherapy.

microbiology↗

The evolution of GC-biased gene conversion by means of natural selection

GC-biased gene conversion (gBGC) is a recombination-associated evolutionary process that biases the segregation ratio of AT:GC polymorphisms in the gametes of heterozygotes, in favour of GC alleles. This process is the major determinant of variation in base composition across the human genome and can be the cause of a substantial burden of GC deleterious alleles. While the importance of GC-biased gene conversion in molecular evolution is increasingly recognised, the reasons for its existence and its variation between species remain largely unknown. Using simulations and semi-analytical approximations, we investigated the evolution of gBGC as a quantitative trait evolving by mutation, drift and natural selection. We show that in a finite population where most mutations are deleterious, gBGC is under weak stabilising selection around a positive value that mainly depends on the intensity of the mutation bias and on the intensity of selective constraints exerted on the genome. Importantly, the levels of gBGC that evolve by natural selection do not minimize the load in the population, and even increase it substantially in regions of high recombination rate. Therefore, despite reducing the populations fitness, levels of gBGC that are currently observed in humans could in fact have been (weakly) positively selected.

evolutionary biology↗

Single Cell Analysis of Peripheral TB-Associated Granulomatous Lymphadenitis

We successfully employed a single cell RNA sequencing (scRNA-seq) approach to describe the cells and the communication networks characterizing granulomatous lymph nodes of TB patients. When mapping cells from individual patient samples, clustered based on their transcriptome similarities, we uniformly identify several cell types that known to characterize human and non-human primate granulomas. Whether high or low Mtb burden, we find the T cell cluster to be one of the most abundant. Many cells expressing T cell markers are clearly quantifiable within this CD3 expressing cluster. Other cell clusters that are uniformly detected, but that vary dramatically in abundance amongst the individual patient samples, are the B cell, plasma cell and macrophage/dendrocyte and NK cell clusters. When we combine all our scRNA-seq data from our current 23 patients (in order to add power to cell cluster identification in patient samples with fewer cells), we distinguish T, macrophage, dendrocyte and plasma cell subclusters, each with distinct signaling activities. The sizes of these subclusters also varies dramatically amongst the individual patients. In comparing FNA composition we noted trends in which T cell populations and macrophage/dendrocyte populations were negatively correlated with NK cell populations. In addition, we also discovered that the scRNA-seq pipeline, designed for quantification of human cell mRNA, also detects Mtb RNA transcripts and associates them with their host cells transcriptome, thus identifying individual infected cells. We hypothesize that the number of detected bacterial transcript reads provides a measure of Mtb burden, as does the number of Mtb-infected cells. The number of infected cells also varies dramatically in abundance amongst the patient samples. CellChat analysis identified predominating signaling pathways amongst the cells comprising the various granulomas, including many interactions between stromal or endothelial cells and the other component cells, such as Collagen, FN1 and Laminin. In addition, other more selective communications pathways, including MIF, MHC-1, MHC-2, APP, CD 22, CD45, and others, are identified as originating or being received by individual immune cell components. Author SummaryThe research conducted describes the cellular composition and communication networks within granulomatous lymph nodes of tuberculosis (TB) patients, employing a single-cell RNA sequencing (scRNA-seq) approach. By analyzing individual patient samples and clustering cells based on their transcriptome similarities, the study reveals several consistent cell types described to be present in both human and non-human primate granulomas. Notably, T cell clusters emerge as abundant in most samples. Additionally, variations in the abundance of B cells, plasma cells, macrophages/dendrocytes, and NK cells among patient samples are observed. Pooling scRNA-seq data from 23 patients enabled the identification of T, macrophage, dendrocyte, and plasma cell subclusters, each displaying distinct signaling activities. Moreover, the study uncovers a surprising capability of the scRNA-seq pipeline to detect Mtb RNA transcripts within host cells, providing insights into individual infected cells and Mtb burden. CellChat analysis unveils predominant signaling pathways within granulomas, highlighting interactions between stromal/endothelial cells and other immune cell components. Moreover, selective communication pathways involving molecules such as Collagen, FN1, Laminin, CD99, MIF, MHC-1, APP and CD45 are identified, shedding light on the intricate interplay within granulomatous lymph nodes during TB infection.

pathology↗

Green Jackfruit Flour Prevents Metabolic Dysfunction-Associated Steatohepatitis and Progression to Hepatocellular Carcinoma via the AMPK and MAPK Signaling Pathways

Metabolic dysfunction-associated steatotic liver disease (MASLD), encompassing metabolic-dysfunction associated steatotic liver (MAFL) and steatohepatitis (MASH), which further progresses to hepatocellular carcinoma (HCC), is a serious public health concern. Given the paucity of approved therapeutic strategies for this lifestyle disorder, dietary interventions may prove effective. We evaluated how green jackfruit flour (JF) prevents MASH and progression to HCC and its underlying mechanisms. The study utilized two murine models that mimicked human MASLD disease: (i) a diet-induced MASH model; (ii) a MASH-HCC model induced by diet and a very low dose of CCl4. C57Bl/6 mice were fed with chow (CD) or western diet (WD) with normal (NW) or sugar water (SW) for 12 weeks, then randomized to receive either 5 kcal% green jackfruit flour (JF) or an equal volume of placebo flour (PB). The biochemical, histological, and molecular analyses were assessed. JF significantly reduced body weight, liver injury, insulin resistance, and alleviated obesity, steatosis, inflammation, fibrosis, and tumor development in WDSW or WDSW/CCl4 mice compared to placebo groups. Furthermore, JF activated AMPK (AMP-activated protein kinase) and inhibited MAPK (mitogen-activated protein kinase) signaling pathways in MASH and MASH-HCC experimental models, respectively. This was supported by sodium propionate treatment, the primary short-chain fatty acid entering the liver from JFs soluble fiber microbial fermentation, which also regulated AMPK and MAPK signaling in cellular models of MASH and HCC, respectively. Hence, our findings present strong evidence of JFs therapeutic potential in the prevention of MASH and MASH-HCC, warranting further investigation of JFs efficacy as a dietary intervention in clinical trials.

cancer biology↗

A Mechanically Resilient Soft Hydrogel Improves Drug Delivery for Treating Post-Traumatic Osteoarthritis in Physically Active Joints

Intra-articular delivery of disease-modifying osteoarthritis drugs (DMOADs) is likely to be most effective in early post-traumatic osteoarthritis (PTOA) when symptoms are minimal and patients are physically active. DMOAD delivery systems therefore must withstand repeated mechanical loading without affecting the drug release kinetics. Although soft materials are preferred for DMOAD delivery, mechanical loading can compromise their structural integrity and disrupt drug release. Here, we report a mechanically resilient soft hydrogel that rapidly self-heals under conditions resembling human running while maintaining sustained release of the cathepsin-K inhibitor L-006235 used as a proof-of-concept DMOAD. Notably, this hydrogel outperformed a previously reported hydrogel designed for intra-articular drug delivery, used as a control in our study, which neither recovered nor maintained drug release under mechanical loading. Upon injection into mouse knee joints, the hydrogel showed consistent release kinetics of the encapsulated agent in both treadmill-running and non-running mice. In a mouse model of aggressive PTOA exacerbated by treadmill running, L-006235 hydrogel markedly reduced cartilage degeneration. To our knowledge, this is the first hydrogel proven to withstand human running conditions and enable sustained DMOAD delivery in physically active joints, and the first study demonstrating reduced disease progression in a severe PTOA model under rigorous physical activity, highlighting the hydrogels potential for PTOA treatment in active patients.

bioengineering↗

Palynological studies on selected members of Fabaceae

The investigation into pollen biology encompasses various stages such as pollen production, transfer to stigma, and the ensuing interactions leading to fertilization. Stigma plays a crucial role in providing an optimal environment for pollen germination and subsequent tube growth. However, conducting in vivo studies presents challenges due to the complexities of pistillate tissues, thus necessitating a reliance on in vitro cultures to comprehend pollen physiology. This study focuses on assessing pollen viability and germination in a selection of Fabaceae species, including Canavalia gladiata, Centrosoma pubescens, Clitoria ternatea, Crotalaria pallida, Glyricidia maculata, Pueraria phaseoloides, and Vigna unguiculata, utilizing tetrazolium testing and hanging drop culture methods. Results demonstrate a range of variability in pollen viability (from 19.38% to 80.78%) and germination (ranging from 23.90% to 79.81%), with Crotalaria pallida exhibiting the highest rates of viability and germination, whereas Clitoria ternatea and Pueraria phaseoloides displayed the lowest rates. This investigation contributes valuable insights into the pollen characteristics of Fabaceae species, hinting at possible connections between pollen viability/germination and seed/fruit set percentages.

plant biology↗

PRDM9 drives the location and rapid evolution of recombination hotspots in salmonids

In many eukaryotes, meiotic recombination occurs preferentially at discrete sites, called recombination hotspots. In various lineages, recombination hotspots are located in regions with promoter-like features and are evolutionarily stable. Conversely, in some mammals, hotspots are driven by PRDM9 that targets recombination away from promoters. Paradoxically, PRDM9 induces the self-destruction of its targets and this triggers an ultra-fast evolution of mammalian hotspots. PRDM9 is ancestral to all animals, suggesting a critical importance for the meiotic program, but has been lost in many lineages with surprisingly little effect on meiosis success. However, it is unclear whether the function of PRDM9 described in mammals is shared by other species. To investigate this, we analyzed the recombination landscape of several salmonids, the genome of which harbors one full-length PRDM9 and several truncated paralogs. We identified recombination initiation sites in Oncorhynchus mykiss by mapping meiotic DNA double-strand breaks (DSBs). We found that DNA DSBs clustered at hotspots positioned away from promoters, enriched for the H3K4me3 and H3K4me36 marks and the location of which depended on the genotype of full-length Prdm9. We observed a high level of polymorphism in the zinc finger domain of full-length Prdm9, but not of the truncated paralogs. Moreover, population-scaled recombination maps in O. mykiss, Oncorhynchus kisutch and Salmo salar revealed a rapid turnover of recombination hotspots caused by PRDM9 target motif erosion. Our results imply that PRDM9 function is conserved across vertebrates and that the peculiar evolutionary runaway caused by PRDM9 has been active for several hundred million years.

evolutionary biology↗

Increased positive selection in highly recombining genes is not an evidence for an evolutionary advantage of recombination

It is commonly thought that the long-term advantage of meiotic recombination is to dissipate genetic linkage, allowing natural selection to act independently on different loci. It is thus theoretically expected that genes with higher recombination rates evolve under more effective selection. On the other hand, recombination is often associated with GC-biased gene conversion (gBGC), which theoretically interferes with selection by promoting the fixation of deleterious GC alleles. To test these predictions, several studies assessed whether selection was more effective in highly recombining genes (due to dissipation of genetic linkage) or less effective (due to gBGC), assuming a fixed distribution of fitness effects (DFE) for all genes. In this study, I directly derive the DFE from a genes evolutionary history (shaped by mutation, selection, drift and gBGC) under empirical fitness landscapes. I show that genes that have experienced high levels of gBGC are less fit and thus have more opportunities for beneficial mutations. Only a small decrease in the genome-wide intensity of gBGC leads to the fixation of these beneficial mutations, particularly in highly recombining genes. This results in increased positive selection in highly recombining genes that is not caused by more effective selection. Additionally, I show that the death of a recombination hotspot can lead to a higher dN/dS than its birth, but with substitution patterns biased towards AT, and only at selected positions. This shows that controlling for a substitution bias towards GC is therefore not sufficient to rule out the contribution of gBGC to signatures of accelerated evolution. Finally, although gBGC does not affect the fixation probability of GC-conservative mutations, I show that by altering the DFE, gBGC can also significantly affect non-synonymous GC-conservative substitution patterns.

evolutionary biology↗

Comprehensive Codon Usage Analysis Across Diverse Plant Lineages

The variation of codon usage patterns in response to the evolution of organisms is an intriguing question to answer. The purpose of this study was to investigate the relevance of the evolutionary events of vascularization and seed production with the codon usage patterns in different plant lineages. We found that the optimal codons of non-vascular lineages generally end with GC, whereas those of the vascular lineages end with AU. Correspondence analysis and model-based clustering showed that the evolution of the codon usage pattern follows the evolutionary event of the vascularization more precisely than that of the seed production. The dinucleotides CpG and TpA were under-represented in all the lineages, whereas the dinucleotide TpG was found over-represented in all the lineages, except algae. Evolutionary-related lineages showed similar codon pair bias (CPB). The dinucleotide CpA showed a similar representation as those of its parent codon pairs. Although natural selection predominates over mutational pressure in determining the codon usage bias (CUB), the relative influence of mutational pressure is higher in the non-vascular lineages than in the vascular lineages.

evolutionary biology↗

High prevalence of Prdm9-independentrecombination hotspots in placental mammals

In many mammals, recombination events are concentrated into hotspots directed by a sequence specific DNA-binding protein named Prdm9. This protein facilitates chromosome pairing and its inactivation has been shown to induce fertility losses in mice and rats. Intriguingly, Prdm9 has been lost several times in vertebrates, and notably among mammals, it has been pseudogenized in the ancestor of canids (dogs, wolves foxes). When this gene is inactive, either naturally in dogs, or through knock-out experiments in mice, recombination hotspots still exist, but they tend to occur in promoter-like features such as CpG islands. It has thus been proposed that one role of Prdm9 could be to direct recombination away from those Prdm9-independent hotspots. However, the ability of Prdm9 to direct recombination hotspots has been assessed only in a handful of species, and a clear picture of how much recombination occurs outside of Prdm9-directed hotspots in mammals is still lacking. In this study, we derived an estimator of past recombination activity based on signatures of GC-biased gene conversion in substitution patterns. We applied it to quantify recombination activity in Prdm9-independent hotspots in 52 species of boreoeutherian mammals. We observed a wide range of recombination rate at these loci: several species (such as mice, humans, some felids or cetaceans) show a deficit of recombination, while a majority of mammals display a clear peak of recombination. Our results demonstrate that Prdm9-directed and Prdm9-independent hotspots can co-exist in mammals, and that their co-existence seem to be the rule rather than an exception.

genetics↗

An injectable in situ crosslinkable platform for ultra-long-acting delivery of hydrophilic therapeutics

Achieving ultra-long-term release of hydrophilic drugs over several months remains a significant challenge for existing long-acting injectables (LAIs). Existing platforms, such as in situ forming implants (ISFI), exhibit high burst release due to solvent efflux and microsphere-based approaches lead to rapid drug diffusion due to significant water exchange and large pores. Addressing these challenges, we have developed an injectable platform that, for the first time, achieves ultra-long-term release of hydrophilic drugs for over six months. This system employs a methacrylated ultra-low molecular weight pre-polymer (polycaprolactone) to create in situ cross-linked depots (ISCD). The ISCDs solvent-free design and dense mesh network, both attributed to the ultra-low molecular weight of the pre-polymer, effectively minimizes burst release and water influx/efflux. In vivo studies in rats demonstrate that ISCD outperforms ISFI by achieving lower burst release and prolonged drug release. We demonstrated the versatility of ISCD by showcasing ultra-long-term delivery of several hydrophilic drugs, including antiretrovirals (tenofovir alafenamide, emtricitabine, abacavir, and lamivudine), antibiotics (vancomycin and amoxicillin) and an opioid antagonist naltrexone. Additionally, ISCD achieved ultra-long-term release of the hydrophobic drug tacrolimus and enabled co-delivery of hydrophilic drug combinations encapsulated in a single depot. We also identified design parameters to tailor the polymer network, tuning drug release kinetics and ISCD degradation. Pharmacokinetic modeling predicted over six months of drug release in humans, significantly surpassing the one-month standard achievable for hydrophilic drugs with existing LAIs. The platforms biodegradability, retrievability, and biocompatibility further underscore its potential for improving treatment adherence in chronic conditions.

bioengineering↗

Identification of the KIF18A alpha-4 helix as a therapeutic target for chromosomally unstable tumor cells

The mitotic kinesin, KIF18A, is required for proliferation of cancer cells that exhibit chromosome instability (CIN), implicating it as a promising target for treatment of a subset of aggressive tumor types. Determining regions of the KIF18A protein to target for inhibition will be important for the design and optimization of effective small molecule inhibitors. In this study, we investigated the effects of mutating S284 within the alpha-4 helix of KIF18A, which was previously identified as a phosphorylated residue. Mutations in S284 cause relocalization of KIF18A from the plus-ends of spindle microtubules to the spindle poles. Furthermore, KIF18A S284 mutants display loss of KIF18A function and fail to support proliferation in CIN tumor cells. Interestingly, similar effects on KIF18A localization and function were seen after treatment of CIN cells with KIF18A inhibitory compounds that are predicted to interact with residues within the alpha-4 helix. These data implicate the KIF18A alpha-4 helix as an effective target for inhibition and demonstrate that small molecules targeting KIF18A selectively limit CIN tumor cell proliferation and result in phenotypically similar effects on mitosis at the single cell level compared to genetic perturbations.

cancer biology↗

A Drug-Free Pathogen Capture and Neutralizing Nasal Spray to Prevent Emerging Respiratory Infections

Respiratory infections pose a global health crisis. Vaccines are pathogen specific, and new vaccines are needed for mutants and emerging pathogens. Here, we report a "drug free" prophylactic platform - a "Pathogen Capture and Neutralizing Spray" (PCANS) that acts via a multi-pronged approach to prevent a broad spectrum of respiratory infections. PCANS forms a protective coating in the nasal cavity that enhances the capture of large respiratory droplets. The coating acts as a physical barrier against a broad spectrum of viruses and bacteria, and rapidly neutralizes them, reducing the pathogen load by >99.99%. In mice, PCANS showed nasal retention for at least 8 h and was safe for daily administration. A single prophylactic dose of PCANS protected mice against supra-lethal dosages of a mouse-adapted H1N1 Influenza virus (PR8), reduced lung viral titer by >99.99%, improved survival, and suppressed pathological manifestations. Together, our data suggest PCANS as a promising daily-use prophylactic approach against current and emerging respiratory infections.

bioengineering↗

Characterization of the RBM15 protein binding with XCI-escaping long noncoding RNAs

The RNA binding motif 15 protein (RBM15) plays a critical role in post-transcriptional regulation. Its role in facilitating N6-methyladenosine (m6A) modification, specifically through guiding the writer complex (WTAP METTL13 METTL14) to DRACH sequence motifs, has been demonstrated for several classes of RNA, including long noncoding RNAs (lncRNAs). The structural mechanism that underlies how RBM15 interacts with RNA has yet to be elucidated. In this study, we mined and bioinformatically assessed publicly available genome-wide RNA 2D structural probing and RBP cross-linking and immunoprecipitation data to investigate how RBM15 interacts with RNA, with a focus on lncRNA transcripts. RBM15, which possesses three RNA recognition motifs (RRMs), primarily interacts with stem-loop structured RNA motifs. Structural modeling reveals RRMs 2 and 3 are coaxially stacked in solution; these two RRMs are responsible for driving RBM15s interaction with RNA. We further demonstrate this experimentally with two RNA hairpins, revealing low micromolar binding affinities. Altogether, this work provides insight into the structural mechanism by which RBM15 interacts with RNAs to govern biological function.

biochemistry↗

In Vivo Monitoring of Cellular Senescence by Photoacoustic and Fluorescence Imaging Utilizing a Nanostructured Organic Probe

Senescent cells accumulate in multiple age-related disorders, including cancer, exacerbating the pathological manifestations, and the eradication of these cells has emerged as a promising therapeutic strategy. Despite the impact of senescence in diseases, the development of tools to monitor the senescent burden in vivo remains a challenge due to their suboptimal specificity, translatability, and tissue penetrance. Here, we have designed a nanostructured organic probe (NanoJaggs) based on biocompatible indocyanine green dye (ICG) building blocks forming J-aggregates, which possess distinct spectral properties allowing both fluorescence and photoacoustic tomography (PAT) detection. We show that NanoJaggs are taken up by an active process of endocytosis and exhibit selective accumulation at the lysosomal compartment in several in vitro models for senescence. Finally, NanoJagg probe is validated in two in vivo studies including live PAT imaging and shows remarkable specificity to tumours with chemotherapy-induced senescence compared to untreated proliferative tumors. In vitro, ex vivo and in vivo all indicate that NanoJaggs are a clinically translatable tool for detection of senescence and their robust PAT signal makes them suitable for longitudinal monitoring of the senescent burden in solid tumors after chemo or radiotherapy.

cancer biology↗