Biology subjects

Jones, M.

Publications and source records attributed to Jones, M..

At least 73 records · Page 4Linked to original sources

bioRxiv2022

Cell-surface PD-L1 expression identifies a sub-population of distal epithelial cells enriched in idiopathic pulmonary fibrosis

Idiopathic lung fibrosis (IPF) is a fatal lung disease characterized by chronic epithelial injury and exhausted repair capacity of the alveolar compartment, associated with the expansion of cells with intermediate alveolar epithelial cell (AT2) characteristics. Using SftpcCreERT2/+: tdTomatoflox/flox mice, we previously identified a lung population of quiescent injury activated alveolar epithelial progenitors (IAAPs) marked by low expression of the AT2 lineage trace marker tdTomato (Tomlow), and characterized by high levels of Pd-l1 (Cd274) expression. This led us to hypothesize that a population with similar properties exists in the human lung. To that end, we used flow cytometry to characterize the CD274 cell surface expression in lung epithelial cells isolated from donor and end-stage IPF lungs. The identity and functional behavior of these cells were further characterized by qPCR analysis, in vitro organoid formation, and ex vivo precision-cut lung slices (PCLS). Our analysis led to the identification of a population of CD274pos cells expressing intermediate levels of SFTPC, which was expanded in IPF lungs. While donor CD274pos cells initiated clone formation, they did not expand significantly in 3D organoids in AT2-supportive conditions. However, an increased number of CD274pos cells was found in cultured PCLS. In conclusion, we demonstrate that, similar to the IAAPs in the mouse lung, a population of CD274 expressing cells exists in the normal human lung and this population is expanded in the IPF lung and in an ex vivo PCLS assay, suggestive of progenitor cell behavior.

cell biology↗

bioRxiv2022

A hierarchical genotyping framework using DNA melting temperatures applied to adenovirus species typing

Known genetic variation for a pathogen, in conjunction with post-PCR melting curve analysis, can be leveraged to provide increased taxonomic detail for pathogen identification in commercial molecular diagnostic tests. The increased taxonomic detail may be used by clinicians and public health decision makers to observe circulation patterns, monitor for outbreaks, and inform local testing practices. We propose a method for expanding the taxonomic resolution of PCR diagnostic systems by incorporating a priori knowledge of the assay design and publicly available sequence information into a genotyping classification model. For multiplexed PCR systems, this framework is generalized to incorporate information from multiple assays that react with different gene targets of the same pathogen to increase classification accuracy. To illustrate the method, a hierarchical classification model is developed for the BioFire(R) Respiratory 2.1 Panel and the BioFire(R) Respiratory 2 Panel (collectively the BioFire Respiratory Panels - highly multiplexed PCR diagnostic tests) to predict the species of human adenovirus (HAdV) from Adenovirus Detected test results. Performance of the classification model was characterized via a 10-fold cross-validation on a labeled dataset and exhibited 95% {+/-} 4% accuracy. The model was then applied to the BioFire(R) Syndromic Trends dataset, which contains deidentified patient test data from BioFire Respiratory Panels collected at over 100 sites across the globe since 2015. Adenovirus Detected test results in BioFire Syndromic Trends were classified to produce predicted prevalence of each HAdV species within the United States from 2018 through 2021. These results show a marked change in both the predicted prevalence for HAdV and the species makeup with the onset of the COVID-19 pandemic. In particular, HAdV-B decreased from a pre-pandemic predicted prevalence of up to 40% to less than 5% in 2021, while HAdV-A and HAdV-F species both increased in predicted prevalence. Author SummaryIn the diagnosis of infectious disease there is often a trade-off between time to result, cost, and the amount of information gained about the pathogen. We develop a method that can provide increased genotypic information about a pathogen in a test result, with no additional time or cost. Our method is applied to the BioFire Respiratory(R) 2.1 Panel and the BioFire Respiratory(R) 2 Panel to speciate positive test results for adenovirus. The method shows robust performance in correctly identifying the adenovirus species from the test results. We estimate the prevalence of each adenovirus species in the United States by applying this method to adenovirus positive test results in the BioFire Syndromic Trends network. This information can be used in near real-time to augment the Centers for Disease Control and Prevention efforts to monitor adenovirus species circulation. Our mathematical framework can be generalized to other genotyping applications.

molecular biology↗

bioRxiv2022

Characterization of alveolar epithelial lineage heterogeneity during the late pseudoglandular stage of mouse lung development

The specification, characterization, and fate of alveolar type 1 and type 2 (AT1 and 2) progenitors during embryonic lung development remains mostly elusive. In this paper, we build upon our previously published work on the regulation of airway epithelial progenitors by fibroblast growth factor receptor 2b (Fgfr2b) signalling during early (E12.5) and mid (E14.5) pseudoglandular lung development. Here, we looked at the regulation by Fgfr2b signalling on alveolar progenitors during late pseudoglandular/early canalicular (E14.5-E16.5) development. Using a dominant negative mouse model to conditionally inhibit Fgfr2b ligands at E16.5, we used gene array analyses to characterize a set of potential direct targets of Fgfr2b signalling. By mining published single-cell RNA sequence (scRNAseq) datasets, we showed that these Fgfr2b signature genes narrow on a discreet subset of AT2 cells at E17.5 and in adult lungs. Furthermore, we demonstrated that Fgfr2b signalling is lost in AT2 cells in their transition to AT1 cells during repair after injury. We also used CreERT2-based mouse models to conditionally knock-out the Fgfr2b gene in AT2 and in AT1 progenitors, as well as lineage label these cells. We found, using immunofluorescence, that in wildtype controls AT1 progenitors labeled at E14.5-E15.5 contribute a significant proportion to AT2 cells at E18.5; while AT2 progenitors labeled at the same time contribute significantly to the AT1 lineage. We show, using immunofluorescence and FACS-based analysis, that knocking out of Fgfr2b at E14.5-E15.5 in AT2 progenitors leads to an increase in lineage-labeled AT1 cells at E18.5; while the reverse is true in AT1 progenitors. Furthermore, we demonstrate that increased Fgfr signalling in AT2 progenitors reduces their contribution to the AT1 pool. Taken together, our results suggest that a significant proportion of AT2 and AT1 progenitors are cross-lineage committed during late pseudoglandular development, and that lineage commitment is regulated in part by Fgfr2b signalling. We have characterized a set of direct Fgfr2b targets at E16.5 which are likely involved in alveolar lineage formation. These signature genes concentrate on a subpopulation of AT2 cells later in development, and are downregulated in AT2 cells transitioning to the AT1 lineage during repair after injury in adults. Our findings highlight the extensive heterogeneity of alveolar cells by elucidating the role of Fgfr2b signalling in these cells during early alveolar lineage formation, as well as during repair after injury.

developmental biology↗

bioRxiv2021

Bacterial colonisation dynamics of household plastics in a coastal environment

Accumulation of plastics in the marine environment has widespread detrimental consequences for ecosystems and wildlife. Marine plastics are rapidly colonised by a wide diversity of bacteria, including human pathogens, posing potential risks to human health. Here, we investigate the effect of polymer type, residence time and estuarine location on bacterial colonisation of common household plastics, including pathogenic bacteria. To do so, we submerged five main household plastic types: low-density PE (LDPE), high-density PE (HDPE), polypropylene (PP), polyvinyl chloride (PVC) and polyethylene terephthalate (PET) at an estuarine site in Cornwall (U.K.) and tracked bacterial colonisation dynamics. Using both culture-dependent and culture-independent approaches, we found that bacteria rapidly colonised plastics irrespective of polymer type. While biofilm community composition changed with colonisation time, no difference was observed between polymer types. Likewise, the presence of pathogenic bacteria, quantified using the insect model Galleria mellonella, increased over a five-week period, with no consistent differences observed between polymer types. Pathogens isolated from plastic biofilms using Galleria enrichment included Serratia and Enterococcus species and harboured a wide range of antimicrobial resistance genes. Our findings show that plastics in coastal waters are rapidly colonised by a wide diversity of bacteria, including known human pathogens, independent of polymer type.

ecology↗

bioRxiv2021

Mining hidden knowledge: Embedding models of cause-effect relationships curated from the biomedical literature

We explore the use of literature-curated signed causal gene expression and gene-function relationships to construct un-supervised embeddings of genes, biological functions, and diseases. Our goal is to prioritize and predict activating and inhibiting functional associations of genes, and to discover hidden relationships between functions. As an application, we are particularly interested in the automatic construction of networks that capture relevant biology in a given disease context. We evaluated several unsupervised gene embedding models leveraging literature-curated signed causal gene expression findings. Using linear regression, it is shown that, based on these gene embeddings, gene-function relationships can be predicted with about 95% precision for the highest scoring genes. Function embedding vectors, derived from parameters of the linear regression model, allow to infer relationships between different functions or diseases. We show for several diseases that gene and function embeddings can be used to recover key drivers of pathogenesis, as well as underlying cellular and physiological processes. These results are presented as disease-centric networks of genes and functions. To illustrate the applicability of the computed gene and function embeddings to other machine learning tasks we expanded the embedding approach to drug molecules, and used a simple neural network to predict drug-disease associations.

bioinformatics↗

bioRxiv2021

Identification of a new family of "megaphages" that are abundant in the marine environment

Megaphages - bacteriophages harbouring extremely large genomes - have recently been found to be ubiquitous, being described from a variety of microbiomes ranging from the animal gut to soil and freshwater systems. However, no complete marine megaphage has been identified to date. Here, using both short and long read sequencing, we assembled >900 high-quality draft viral genomes from water in the English Channel. One of these genomes included a novel megaphage, Mar_Mega_1 at >650 Kb, making it one of the largest phage genomes assembled to date. Utilising phylogenetic and network approaches, we found this phage represents a new family of bacteriophages. Genomic analysis showed Mar_Mega_1 shares relatively few homologues with its closest relatives, but, as with other mega-phages Mar_Mega_1 contained a variety of auxiliary metabolic genes responsible for carbon metabolism and nucleotide biosynthesis, including isocitrate dehydrogenase [NADP] and nicotinamide-nucleotide amidohydrolase [PncC] which have not previously been identified in megaphages. The results of this study indicate that phages containing extremely large genomes can be found in abundance in the marine environment and augment host metabolism by mechanisms not previously described.

microbiology↗

bioRxiv2021

RPRD Proteins Control Transcription in Human Cells

The regulation of transcription is an essential process that allows the cell to respond to various internal and external signals. RNA Polymerase II (Pol II) activity is controlled by a number of factors which bind to the C-terminal domain (CTD) of its largest subunit, RPB1, and stimulate or suppress RNA synthesis. Here, we demonstrate that CTD-interacting proteins, RPRD2, RPRD1B and RPRD1A act as negative regulators of transcription and their levels inversely correlate with the accumulation of nascent and newly transcribed RNA in human cells. We show that the RPRD proteins form mutually exclusive complexes with Pol II to coordinate their roles in transcriptional control. Our data indicate that RPRD2 exerts the most substantial impact on transcription and has the potential to alter key biological processes including the cellular stress response and cell growth.

molecular biology↗

bioRxiv2021

Pseudohypoxic HIF pathway activation dysregulates collagen structure-function in human lung fibrosis

Extracellular matrix (ECM) stiffening with downstream activation of mechanosensitive pathways is strongly implicated in fibrosis. We previously reported that altered collagen nanoarchitecture is a key determinant of pathogenetic ECM structure-function in human fibrosis (Jones et al., 2018). Here, through human tissue, bioinformatic and ex vivo studies we show that hypoxia-inducible factor (HIF) pathway activation is a critical pathway for this process regardless of oxygen status (pseudohypoxia). Whilst TGF{beta} increased rate of fibrillar collagen synthesis, HIF pathway activation was required to dysregulate post-translational modification of fibrillar collagen, promoting bone-type cross-linking, altering collagen nanostructure, and increasing tissue stiffness. In vitro, knock down of Factor Inhibiting HIF (FIH) or oxidative stress caused pseudohypoxic HIF activation in normal fibroblasts. In contrast, endogenous FIH activity was reduced in fibroblasts from patients with lung fibrosis in association with significantly increased normoxic HIF pathway activation. In human lung fibrosis tissue, HIF mediated signalling was increased at sites of active fibrogenesis whilst subpopulations of IPF lung mesenchymal cells had increases in both HIF and oxidative stress scores. Our data demonstrate that oxidative stress can drive pseudohypoxic HIF pathway activation which is a critical regulator of pathogenetic collagen structure-function in fibrosis.

cell biology↗

bioRxiv2021

Non-coding RNAs Associated with Prader-Willi Syndrome Regulate Transcription of Neurodevelopmental Genes in Human Induced Pluripotent Stem Cells

Mutations and aberrant gene expression during cellular differentiation lead to neurodevelopmental disorders such as Prader-Willi syndrome (PWS) which results from the deletion of an imprinted locus on chromosome 15. We analysed chromatin-associated RNA in human induced pluripotent cells (iPSCs) upon depletion of hybrid small nucleolar long non-coding RNAs (sno-lncRNAs) and 5 snoRNA capped and polyadenylated long non-coding RNAs (SPA-lncRNAs) transcribed from the locus deleted in PWS. We found that rapid ablation of these lncRNAs affects transcription of specific gene classes. Downregulated genes contribute to neurodevelopment and neuronal maintenance while genes that are upregulated are predominantly involved in the negative regulation of cellular metabolism and apoptotic processes. Our data revealed the importance of SPA-lncRNAs and sno-lncRNAs in controlling gene expression in iPSCs and provided a platform for synthetic experimental approaches in PWS studies. We conclude that ncRNAs transcribed from the PWS locus are critical regulators of a transcriptional signature important for neuronal differentiation and development.

molecular biology↗

bioRxiv2021

INfrastructure for a PHAge REference Database: Identification of large-scale biases in the current collection of phage genomes

BackgroundWith advances in sequencing technology and decreasing costs, the number of bacteriophage genomes that have been sequenced has increased markedly in the last decade. Materials and MethodsWe developed an automated retrieval and analysis system for bacteriophage genomes, INPHARED (https://github.com/RyanCook94/inphared), that provides data in a consistent format. ResultsAs of January 2021, 14,244 complete phage genomes have been sequenced. The data set is dominated by phages that infect a small number of bacterial genera, with 75% of phages isolated only on 30 bacterial genera. There is further bias with significantly more lytic phage genomes than temperate within the database, resulting in ~54% of temperate phage genomes originating from just three host genera. Within phage genomes, putative antibiotic resistance genes were found in higher frequencies in temperate phages than lytic phages. ConclusionWe provide a mechanism to reproducibly extract complete phage genomes and highlight some of the biases within this data, that underpins our current understanding of phage genomes.

microbiology↗

bioRxiv2021

Dysregulation of NRSF/REST via EHMT1 is association with psychiatric disorders

Genetic evidence indicates disrupted epigenetic regulation as a major risk factor for psychiatric disorders, but the molecular mechanisms that drive this association are undetermined. EHMT1 is an epigenetic repressor that is causal for Kleefstra Syndrome (KS), a neurodevelopmental disorder (NDD) leading to ID, and is associated with schizophrenia. Here, we show that reduced EHMT1 activity decreases NRSF/REST protein leading to abnormal neuronal gene expression and progression of neurodevelopment in human iPSC. We further show that EHMT1 regulates NRSF/REST indirectly via repression of miRNA leading to aberrant neuronal gene regulation and neurodevelopment timing. Expression of a NRSF/REST mRNA that lacks the miRNA-binding sites restores neuronal gene regulation to EHMT1 deficient cells. Importantly, the EHMT1-regulated miRNA gene set with elevated expression is enriched for NRSF/REST regulators with an association for ID and schizophrenia. This reveals a molecular interaction between H3K9 dimethylation and NSRF/REST contributing to the aetiology of psychiatric disorders.

neuroscience↗

bioRxiv2021

Assortative Mating Biases Marker-based Heritability Estimators

Many complex traits are subject to assortative mating (AM), with recent molecular genetic findings confirming longstanding theoretical predictions that AM alters genetic architecture by inducing long range dependence across causal variants. However, all marker-based heritability estimators assume mating is random. We provide mathematical and simulation-based evidence demonstrating that both method-of-moments estimators and likelihood-based estimators produce biased estimates in the presence of AM and that common approaches to account for population structure fail to mitigate this bias. Then, examining height and educational attainment in the UK Biobank, we demonstrate that these biases affect real world traits. Finally, we derive corrected heritability estimators for traits under equilibrium AM.

genetics↗

bioRxiv2021

Hydroxycarboxylic acid receptor 2 (HCAR2/GPR109A) expression and signaling promotes the maintenance of an immunoinhibitory retinal environment

BackgroundExcessive oxidative stress and related chronic, sub-clinical inflammation is linked causally to the development and progression of degenerative diseases of the retina including diabetic retinopathy, age-related macular degeneration and glaucoma, leading causes of blindness worldwide. The above responses may be related directly to dysregulated retinal immunity and are potentiated by the combined actions of native retinal cells (e.g., retinal pigment epithelial (RPE) and microglial cells) and immune cells infiltrating from the periphery. Maintaining tight regulation of these cells such that effective control of pathogens is accomplished yet uncontrolled inflammation and consequent tissue damage is prevented is extremely important. However, the molecular mechanisms that control this delicate balance are poorly understood. We hypothesize that the hydroxycarboxylic acid receptor 2 (HCAR2/GPR109A) may play an important role. HCAR2/GPR109A has been shown to regulate immune cell responses that potentiate anti-inflammatory signaling upon its activation in various tissues as evidenced principally by suppressed pro-inflammatory cytokine secretion in various experimental model systems. We have demonstrated HCAR2/GPR109A expression in RPE, microglia and endothelial cells and, our in vitro studies support that the receptor elicits anti-inflammatory signaling in these cell types. However, the functional relevance of HCAR2/GPR109A expression and its activation in the retina of the living animal has not been demonstrated definitively. This is the purpose of the present study. MethodsRetinal function was evaluated temporally in wildtype (Hcar2/Gpr109a +/+, WT) and knockout (Hcar2/Gpr109 -/-, KO) mice via electroretinography (ERG). Fundoscopic imaging, spectral domain-optical coherence tomography (OCT), fluorescein angiography and post-mortem histological analyses were additionally performed to evaluate retinal health. Gene microarray, RT-qPCR studies, ingenuity analyses and proteome pathway mapping were performed to evaluate potential key differences in the molecular signatures of WT and KO mouse retinas. Leukostasis and flow cytometric assays were performed to demonstrate the in vivo impact of HCAR2/GPR109A expression and its therapeutic activation on pro-inflammatory immune cell trafficking in retina. ResultsLongitudinal studies revealed progressive anomalies in retinal morphology and function in HCAR2/GPR109A knockout mice that impacted the entire retina. Gene expression and protein interactome analyses revealed differences in gene and protein expression consistent with the increased immune reactivity and infiltration of bone-marrow derived immune cells detected in KO mouse retinas. Studies conducted in an acute model of retinal (endotoxin-induced) inflammation revealed that targeting the receptor via intraperitoneal administration of agonist, beta-hydroxybutyrate, limits immune cell activation, infiltration and related inflammation in WT retinas. ConclusionsThe present studies demonstrate a central role for HCAR2/GPR109A in regulating the complex interplay between resident retinal cells and peripheral immune cells and, the potential therapeutic utility that targeting the receptor holds with respect to preventing and treating inflammatory retinal diseases. HighlightsOxidative stress and inflammation are major causative factors in degenerative retinal diseases stemming from numerous causes (e.g., aging, diabetes, sickle cell). Thus, identifying new targets and developing strategies to counter these factors to prevent and treat retinal degeneration is important. The present in vivo study demonstrates convincingly the principal role of the hydroxycarboxylic acid receptor 2 (HCAR2/GPR109A) as a major regulator of retinal immune responses under normal conditions and therefore, as a target with extremely high potential for therapeutic modulation of these responses in retinal disease.

biochemistry↗

bioRxiv2021

A new murine Rpl5 (uL18) mutation provides a unique model of variably penetrant Diamond Blackfan Anemia

Ribosome dysfunction is implicated in multiple abnormal developmental and disease states in humans. Heterozygous germline mutations in genes encoding ribosomal proteins (RPs) are found in the majority of individuals with Diamond Blackfan anemia (DBA) while somatic mutations have been implicated in a variety of cancers and other disorders. Ribosomal protein-deficient animal models show variable phenotypes and penetrance, similar to human DBA patients. The spontaneous anemia remission observed in some DBA patients occurs via unknown mechanism(s) and has not been previously described in animal models. Here we characterized a novel ENU mouse mutant (Skax23m1Jus) with growth and skeletal defects, cardiac malformations and increased mortality. Following genetic mapping and whole exome sequencing, we identified an intronic Rpl5 mutation, which segregated with all affected mice. This mutation was associated with decreased ribosome generation, consistent with Rpl5 haploinsufficiency. Rpl5Skax23-Jus mutant animals had a profound delay in erythroid maturation and increased mortality at embryonic day E12.5, which improved by E14.5. Surviving mutant animals had a macrocytic anemia at birth as well as evidence of ventricular septal defect (VSD). Surviving adult and aged mice exhibited no hematopoietic defect or VSD. We propose that this novel Rpl5Skax23-Jus mutant mouse will be useful to study the factors influencing the variable penetrance and anemia remission that are observed in DBA.

developmental biology↗

bioRxiv2021

Phagocytosed polyhedrin-cytokine co-crystal nanoparticles provide sustained secretion of bioactive cytokines from macrophages

Many cells possess the ability to engulf and incorporate particles by phagocytosis. This active process is characteristic of microorganisms as well as higher order species. In mammals, monocytes, macrophages and microglia are among so-called professional phagocytes. In addition, cells such as fibroblast and chondrocytes are classified as non-professional phagocytes. Professional phagocytes play important roles in both the innate and adaptive immune response, wound healing and tissue homeostasis. Consequently, these cells are increasingly studied as targets and vectors of therapeutic intervention to treat a range of diseases. Professional phagocytes are notoriously difficult to transfect limiting their study and manipulation. Consequently, efforts have shifted towards the development of nanoparticles to deliver a cargo to phagocytic cells via phagocytosis. However, this approach carries significant technical challenges, particularly for protein cargos. We have focused on the development of nanoscale co-crystalline protein depots, known as PODS(R), that contain protein cargos, including cytokines. Here, we show that PODS are readily phagocytosed by non-professional as well as professional phagocytic cells and have attributes, such as highly sustained release of cargo, that suggest potential utility for the study and exploitation of phagocytic cells for drug delivery. Monocytes and macrophages that ingest PODS retain normal characteristics including a robust chemotactic response. Moreover, the PODS-cytokine cargo is secreted by the loaded cell at a level sufficient to modulate the behavior of surrounding non-phagocytic cells. The results presented here demonstrate the potential of PODS nanoparticles as a novel molecular tool for the study and manipulation of phagocytic cells and for the development of Trojan horse immunotherapy strategies to treat cancer and other diseases.

bioengineering↗

bioRxiv2020

Using a non-destructive sugar-feeding assay for sporozoite detection and estimating the extrinsic incubation period of Plasmodium falciparum in mosquito vectors

Despite its epidemiological importance, the time Plasmodium parasites take to achieve development in the vector mosquito (the extrinsic incubation period, EIP) remains poorly characterized. A novel non-destructive assay designed to estimate EIP in single mosquitoes, and more broadly to study Plasmodium - Anopheles vectors interactions, is presented. The assay uses small pieces of cotton wool soaked in sugar solution to collect malaria sporozoites from individual mosquitoes during sugar feeding to monitor infection status over time. This technique has been tested across four natural malaria mosquito species of Africa and Asia, six parasite isolates of Plasmodium falciparum, and across a range of temperatures relevant to malaria transmission in field conditions. We find that monitoring individual infectious mosquitoes is feasible, although due to the frequency of mosquito sugar feeding and inter-individual variation in infection intensity, there is inherent risk that this technique will result in some false negatives. The sensitivity rate ranged from 0.27 to 0.81 depending on mosquito species and on infection intensity in mosquitoes used to collect saliva. Using this non-destructive technique, the estimated median extrinsic incubation period of P. falciparum at 27{degrees}C was 11 to 14 days depending on mosquito species and parasite isolate. Long-term individual tracking also revealed that sporozoite transfer onto cotton wool can occur at least until day 40 post-infection. In addition to contributing to a better understanding of EIP and mosquito to human transmission with implications for improving epidemiological models, this technique also allows to link different transmission traits at the mosquito individual level. As one example, we found a significant relationship between EIP and mosquito lifespan, with short individual EIP associated with short mosquito lifespan. Correlations between mosquito/parasite traits often reveal trade-offs and constraints and have important implications for understanding the evolution of parasite transmission strategies.

molecular biology↗

bioRxiv2020

Expression of type I interferon-associated genes at antiretroviral therapy interruption predicts HIV virological rebound

Although certain individuals with HIV infection can stop antiretroviral therapy (ART) without evidence of viral load rebound, the mechanisms under-pinning post-treatment control remain unclear. Twelve individuals who had received 12 months of ART from primary HIV infection and then undertook a TI were sampled at the time of stopping therapy. Using RNA-Seq we explored gene expression in CD4 T cells to look for evidence of a mechanism that might underpin virological rebound and lead to discovery of an associated biomarker. Using independent analysis tools, genes associated with the type I interferon response were strongly associated with a delayed time to viral rebound following TI. These are the first data we are aware of that link transcriptomic signatures associated with innate immunity with control following TI. While these results need to be confirmed in larger trials, they could help define a strategy for new therapies and identify new biomarkers for remission.

microbiology↗

bioRxiv2020

Flower Power: Floral reversion as a viable alternative to nodal micropropagation in Cannabis sativa.

The legalization of Cannabis sativa L. for recreational and medical purposes has been gaining global momentum, leading to a rise in interest in Cannabis tissue culture as growers look for large-scale solutions to germplasm storage and clean plant propagation. Mother plants used in commercial propagation are susceptible to insect pests and disease and require considerable space. While micropropagation can produce disease free starting material in less space, current published in vitro micropropagation methods are not robust and few report high multiplication rates. Further, these micropropagation methods rely on photoperiod-sensitive plants which can be maintained in a perpetual vegetative state. Current methods are not adaptable to long-term tissue culture of day-neutral cultivars, which cannot be maintained in perpetual vegetative growth. In this study, we chose to develop a micropropagation system which uses C. sativa inflorescences as starting materials. This study used two cannabis cultivars, two plant growth regulators (PGR; 6-benzylaminopurine and meta-topolin) at different concentrations, and two different numbers of florets. Here we show that floral reversion occurs from meristematic tissue in C. sativa florets and that it can be used to enhance multiplication rates compared to existing in vitro methods. Floret number was shown to have a significant impact on percent reversion, with pairs of florets reverting more frequently and producing healthier explants than single florets, while cultivar and PGR had no significant effect on percent reversion. Compared with our previously published nodal culture studies, the current floral reversion method produced up to eight times more explants per tissue culture cycle. Floral reversion provides a foundation for effective inflorescence-based micropropagation systems in C. sativa.

plant biology↗