Biology subjects

John, M.

Publications and source records attributed to John, M..

18 recordsLinked to original sources

bioRxiv2026

ABC1K7: A 350-Myr chloroplast rheostat fine-tuned during coconut domestication

Perennial crops follow different domestication trajectories from annuals, yet the molecular basis of slow-variable domestication--subtle tuning of conserved regulatory hubs--remains poorly characterized. We reconstructed the evolutionary history of the chloroplast kinase ABC1K7 across 9 seed plant species spanning [~]350 Myr, employing PAML codon models, IQ-TREE robust codon models, and protein-level phylogenetic inference, with AlphaFold2 structural modeling. ABC1K7 was under extreme purifying selection ({omega} = 0.073-0.104) across all seed plants. In coconut, a single Y[->]F substitution at residue 652--located >30 [A] from the catalytic core in a predicted intrinsically disordered region--represents the only non-synonymous change differentiating coconut from 7 of 8 angiosperm orthologs, and exhibits perfect co-segregation with domestication traits across a 17-year breeding panel (n = 327). These findings provide population-level evidence consistent with the slow-variable domestication model, identifying ABC1K orthologs as targets for perennial crop improvement.

genomics↗

bioRxiv2026

MYC/MIZ1 suppression of lysosomal protein degradation drives immune evasion in pancreatic ductal adenocarcinoma

The MYC oncoprotein promotes immune evasion of pancreatic ductal adenocarcinoma (PDAC), but the underlying molecular mechanisms are not fully understood. Here we show that MYC protects PDAC tumors from CD4+ T cell-dependent elimination. Single cell sequencing shows that MYC suppression in tumor cells increases amino acid availability and broadly activates amino acid-responsive gene expression programs in immune cell populations. This occurs because MYC-driven uptake depletes free amino acids from tumor interstitial fluid and plasma, while MYC compromises macropinocytosis and autophagy, both of which depend on lysosomal protein degradation. MYC engages the POZ/BTB transcription factor MIZ1 to suppress lysosomal genes regulated by the TFE3/TFEB/MITF network or by free MIZ1, thereby inhibiting lysosomal protein degradation. An orthogonal genetic model enabling transient, selective inhibition of amino acid uptake in tumor cells recapitulates the effects of MYC depletion on amino acid levels in the tumor microenvironment and induces complete, CD4+ T cell-dependent tumor eradication with long-term survival. We propose that MYC-mediated, cell-autonomous disruption of lysosome function coupled to non-cell-autonomous protection from immune clearance allows MYC-low cells to benefit from MYC-high neighbors, such that intratumoral heterogeneity in MYC expression confers a selective advantage to the entire tumor. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/740267v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@140d2ccorg.highwire.dtl.DTLVardef@cf5f1borg.highwire.dtl.DTLVardef@6d132aorg.highwire.dtl.DTLVardef@10535e6_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2026

Profound CD4+ T-Cell Reprogramming by Melphalan-Driven Oxidative Stress in High-Risk Multiple Myeloma

T cell-based immunotherapies have become central to the treatment of multiple myeloma (MM), yet their efficacy depends on the functionality of endogenous T cells. How cumulative treatment exposure, particularly high-dose melphalan, together with disease-intrinsic high-risk features shapes T-cell composition and immune competence remains incompletely understood. Here, we analyzed T cell composition and function in bone marrow (BM) and peripheral blood (PB) samples from MM patients across different stages of their treatment journey using flow cytometry (BM, n=162; PB, n=1,733), single-cell RNA sequencing (n=19), and cytotoxicity assays (n=20). We reveal reduced overall T cell frequencies and CD4+/CD8+ T cell ratio, associated with lines of therapy and driven in part by depletion of naive CD4+ T cells in gene-expression defined high risk (HR) disease. Among therapeutic agents, melphalan exerted the strongest effects on T cell populations and induced pronounced redox stress in both T cells and myeloma cell lines. This oxidative stress signature was enriched in HR patients and was reversible with N-acetyl-L-cysteine treatment. Together, these findings identify immune dysregulation as a defining feature of HR MM that extends beyond tumor-intrinsic genomic alterations and is further shaped by treatment-induced remodeling of the BM microenvironment. Given the association between higher CD4+ T cell numbers and improved CAR-T cell outcomes, our data highlight the translational importance of treatment sequencing, particularly in HR MM. One Sentence SummaryMelphalan-induced redox stress depletes CD4+ naive T cells, particularly in patients with high-risk multiple myeloma.

Cancer Biology↗

bioRxiv2026

Design of a Conductive Hydrogel Coating to Improve Catheter-Tissue Coupling in Radiofrequency Ablation

Radiofrequency ablation is a mainstay of cardiac rhythm management despite high recurrence rates. Current radiofrequency ablation catheters are limited by poor contact with trabeculated cardiac tissue that promotes uneven heating with hot spots that cause collateral damage and regions of incomplete ablation that promote recurrence. Herein, we report on a conductive hydrogel coating of radiofrequency ablation catheters to improve tissue contact while promoting efficient energy transfer. A method was developed to graft a polyether urethane diacrylamide hydrogel to the distal tip of the catheter that maintained stable adhesion following drying, sterilization, and rehydration. The coating also remained intact after passage through an introducer sheath and 50 cycles of radiofrequency ablation at clinical power. The hydrogel-coated catheter demonstrated enhanced tissue contact that was dependent on hydrogel modulus. Hydrogel-mediated ablation prevented steam pop incidence and generated homogeneous lesions in an ex vivo ablation model; however, increased hydrogel conductivity is needed to achieve comparable lesion dimensions as the bare metal catheter and prevent coating damage at higher power. Collectively, these results establish a tunable hydrogel coating method that addresses limitations of conventional radiofrequency ablation and offers a promising approach to enhance the safety and efficacy of cardiac ablation therapies.

bioengineering↗

bioRxiv2025

Hepatocyte MLKL Drives Obesity-Driven Hepatocellular Carcinoma Progression via Mitochondrial Dysfunction Independent of Necroptosis in MASLD

Background and AimsMetabolic dysfunction-associated steatotic liver disease (MASLD) is a leading cause of hepatocellular carcinoma (HCC), particularly in obesity, yet mechanisms linking hepatocyte dysfunction to tumorigenesis remain unclear. Mixed lineage kinase domain-like protein (MLKL), the effector of necroptosis, is elevated in MASLD, but its hepatocyte-intrinsic role in obesity-driven MASLD-HCC is unknown. Approach and ResultsUsing a long-term Western diet (WD)-induced MASLD-HCC model in hepatocyte-specific MLKL knockout (MlklHepKO) mice, we defined MLKLs hepatocyte-intrinsic function. WD increased hepatocyte MLKL protein expression without detectable necroptosis activation, indicating a necroptosis-independent role. MLKL deficiency did not alter WD-induced inflammation, fibrosis, or liver injury but increased hepatic lipid accumulation while reducing lipotoxic lipid species and preserving mitochondrial function. WD-fed MlklHepKO mice developed fewer and smaller tumors with reduced incidence, multiplicity, proliferation, and stemness. Transcriptomic analysis revealed upregulation of mitochondrial oxidative phosphorylation pathways in MlklHepKO livers. WD suppressed the mitochondrial fusion protein and tumor suppressor MFN2, whereas MLKL deficiency restored MFN2 expression post-translationally. In HCC cells, MLKL deletion reduced proliferation, improved mitochondrial respiration, and decreased glycolysis; these effects were reversed by MFN2 deletion. MLKL localized to nuclear and mitochondrial compartments, consistent with organelle-intrinsic functions. The human MLKL inhibitor necrosulfonamide (NSA) suppressed HepG2 xenograft growth, and elevated MLKL expression in human HCC correlated with poorer overall survival. ConclusionsHepatocyte MLKL promotes MASLD-associated HCC through a non-necroptotic mechanism involving MFN2 suppression, impaired mitochondrial function, and increased tumor proliferation and stemness. These findings identify MLKL as a potential therapeutic target in MASLD-associated HCC.

cancer biology↗

bioRxiv2025

Biological landscape of acute illness in children in sub-Saharan Africa and South Asia

Childhood illnesses including pneumonia, diarrhoea and malaria are leading causes of hospitalisation and mortality in resource-limited settings. However, we lack understanding of whether systemic responses to such diverse clinical syndromes are shared or specific, how they are impacted by malnutrition and how they differ from well children. We performed multi-omic profiling of plasma proteins, and serum metabolites and lipids in acutely ill hospitalised and well children in sub-Saharan Africa and South Asia. Using network-based clustering and mixed-effects modelling, we identified common and syndrome-specific omics responses to acute illness. We found that malnutrition often modifies host responses to disease. Although the internal structure of individual omics modules was largely preserved between ill and well children, the interactions between these preserved modules were markedly reorganised during acute illness. Compared to well children, biological systems in hospitalised children were more interconnected, exhibiting denser cross-omics interactions. These findings reveal widespread multisystem mobilisation during paediatric acute illness, offer deeper mechanistic insights and highlight candidate pathways for therapeutic intervention in high-burden settings.

systems biology↗

bioRxiv2024

High KIR diversity in Uganda and Botswana children living with HIV

Killer-cell immunoglobulin-like receptors (KIRs) are essential components of the innate immune system found on the surfaces of natural killer (NK) cells. The KIRs encoding genes are located on chromosome 19q13.4 and are genetically diverse across populations. KIRs are associated with various disease states including HIV progression, and are linked to transplantation rejection and reproductive success. However, there is limited knowledge on the diversity of KIRs from Uganda and Botswana HIV-infected paediatric cohorts, with high endemic HIV rates. We used next-generation sequencing technologies on 312 (246 Uganda, 66 Botswana) samples to generate KIR allele data and employed customised bioinformatics techniques for allelic, allotype and disease association analysis. We show that these sample sets from Botswana and Uganda have different KIRs of different diversities. In Uganda, we observed 147 vs 111 alleles in the Botswana cohort, which had a more than 1 % frequency. We also found significant deviation towards homozygosity for the KIR3DL2 gene for both rapid (RPs) and long-term non-progressors (LTNPs)in the Ugandan cohort. The frequency of the bw4-80I ligand was also significantly higher among the LTNPs than RPs (8.9 % Vs 2.0%, P-value: 0.032). In the Ugandan cohort, KIR2DS4*001 (OR: 0.671, 95 % CI: 0.481-0.937, FDR adjusted Pc=0.142) and KIR2DS4*006 (OR: 2.519, 95 % CI: 1.085-5.851, FDR adjusted Pc=0.142) were not associated with HIV disease progression after adjustment for multiple testing. Our study results provide additional knowledge of the genetic diversity of KIRs in African populations and provide evidence that will inform future immunogenetics studies concerning human disease susceptibility, evolution and host immune responses.

genomics↗

bioRxiv2024

Stem rot affects the structure of rhizosphere microbiome in Berseem Clover (Trifolium alexandrinum)

Rhizosphere microbiome plays an essential role in maintaining plant health and productivity. Fungal and bacterial diseases may affect the rhizosphere-associated microbial communities and overall structure of plant microbiome. Here, we studied the effect of stem rot of berseem clover on the bacterial and fungal communities associated with the rhizosphere. We analyzed the rhizosphere-associated bacterial and fungal microbiome from healthy and infected berseem clover collected from three sampling sites by using 16S rRNA and ITS based Illumina sequencing metabarcoding approach. Microbiome analysis showed that healthy plants had higher bacterial and fungal diversity as compared to stem rot infected plants. At the genus level, bacterial genera Rhizobium and Comamonas were more abundant in healthy plants while Pantoea was more abundant in infected plants and fungal genera Sclerotinia, Fusarium and Cladorrhinum were more abundant in infected plants while Microdochium and Cladosporium were distinctively abundant in healthy Berseem. Functional characterization of bacterial and fungal microbiomes revealed that bacterial communities from infected plants showed more abundance of bacteria with functions replication and repair, enzyme families and biosynthesis of other secondary metabolites as compared to healthy plant microbiome and decreased in fungal groups including arbuscular mycorrhiza and soil saprotrophs and an increase in plant saprotrophs and fungal parasite-plant pathogens. This study provides comprehensive information about the structure and composition of bacterial and fungal communities associated with the berseem clover rhizosphere that could be utilized for future research on the control of stem rot of berseem clover.

plant biology↗

bioRxiv2023

permGWAS2: Enhanced and Accelerated Permutation-based Genome-Wide Association Studies

MotivationPermutation-based significance thresholds have been shown to be a robust alternative to Bonferroni-based significance thresholds in genome-wide association studies (GWAS). However, the implementation of permutation-based thresholds is computationally demanding. The recently published method permGWAS introduced a batch-wise approach using 4D tensors to efficiently compute permutation-based GWAS. However, running multiple univariate tests in parallel leads to many repetitive computations and increased computational resources. More importantly, the previous version of permGWAS does not take into account the population structure when permuting the phenotype. ResultsWe propose permGWAS2, an improved and accelerated version that uses a block matrix decomposition to optimize computations, thereby reducing redundant computations. It also introduces an alternative permutation strategy that takes into account the population structure during permutation. We show that this improved framework provides a more streamlined approach to performing permutation-based GWAS with a lower false discovery rate compared to the previous version and the traditional Bonferroni correction. AvailabilitypermGWAS2 is open-source and publicly available on GitHub for download: https://github.com/grimmlab/permGWAS.

bioinformatics↗

bioRxiv2022

A high-throughput sequencing approach identifies immunotherapeutic targets for bacterial meningitis in neonates

BackgroundWorldwide, Escherichia coli is the leading cause of neonatal Gram-negative bacterial meningitis, but full understanding of the pathogenesis of this disease is not yet achieved. Moreover, to date, no vaccine is available against bacterial neonatal meningitis. MethodsHere, we used Transposon Sequencing of saturated banks of mutants (TnSeq) to evaluate E. coli K1 genetic fitness in murine neonatal meningitis. We identified E. coli K1 genes encoding for factors important for systemic dissemination and brain infection, and focused on products with a likely outer-membrane or extra-cellular localization, as these are potential vaccine candidates. We used in vitro and in vivo models to study the efficacy of active and passive immunization. ResultsWe selected for further study the conserved surface polysaccharide Poly-{beta}-(1-6)-N-Acetyl Glucosamine (PNAG), as a strong candidate for vaccine development. We found that PNAG was a virulence factor in our animal model. We showed that both passive and active immunization successfully prevented and/or treated meningitis caused by E. coli K1 in neonatal mice. We found an excellent opsonophagocytic killing activity of the antibodies to PNAG and in vitro these antibodies were also able to decrease binding, invasion and crossing of E. coli K1 through two blood brain barrier cell lines. Finally, to reinforce the potential of PNAG as a vaccine candidate in bacterial neonatal meningitis, we demonstrated that Group B Streptococcus, the main cause of neonatal meningitis in developed countries, also produced PNAG and that antibodies to PNAG could protect in vitro and in vivo against this major neonatal pathogen. InterpretationAltogether, these results indicate the utility of a high-throughput DNA sequencing method to identify potential immunotherapy targets for a pathogen, including in this study a potential broad-spectrum target for prevention of neonatal bacterial infections. FundingsANR Seq-N-Vaq, Charles Hood Foundation, Hearst Foundation. Groupe Pasteur Mutualite

microbiology↗

bioRxiv2022

Efficient Permutation-based Genome-wide Association Studies for Normal and Skewed Phenotypic Distributions

MotivationGenome-wide Association Studies (GWAS) are an integral tool for studying the architecture of complex genotype and phenotype relationships. Linear Mixed Models (LMMs) are commonly used to detect associations between genetic markers and the trait of interest, while at the same time allowing to account for population structure and cryptic relatedness. Assumptions of LMMs include a normal distribution of the residuals and that the genetic markers are independent and identically distributed - both assumptions are often violated in real data. Permutation-based methods can help to overcome some of these limitations and provide more realistic thresholds for the discovery of true associations. Still, in practice they are rarely implemented due to its high computational complexity. ResultsWe propose permGWAS, an efficient linear mixed model reformulation based on 4D-tensors that can provide permutation-based significance thresholds. We show that our method outperforms current state-of-the-art LMMs with respect to runtime and that a permutation-based threshold has a lower false discovery rate for skewed phenotypes compared to the commonly used Bonferroni threshold. Furthermore, using permGWAS we re-analysed more than 500 Arabidopsis thaliana phenotypes with 100 permutations each in less than eight days on a single GPU. Our re-analyses suggest that applying a permutation-based threshold can improve and refine the interpretation of GWAS results. AvailabilitypermGWAS is open-source and publicly available on GitHub for download: https://github.com/grimmlab/permGWAS.

bioinformatics↗

bioRxiv2021

Pan-tissue and -cancer analysis of ROR1 and ROR2 transcript variants identify novel functional significance for an alternative splice variant of ROR1

BackgroundROR1/2 are putative druggable targets increasing in significance in translational oncology. Expression of ROR1/2 mRNA and transcript variants has not been systematically examined thus far. MethodsROR1/2 transcript variant sequences, signal peptides for cell surface localisation, and mRNA and transcript variant expression were examined in 34 transcriptomic datasets including 33 cancer types and 54 non-diseased human tissues. ResultsROR1/2 have four and eight transcript variants respectively. ROR1/2 mRNA and transcript variant expression was detected in various non-diseased tissues. Our analysis identifies predominant expression of ROR1 transcript variant ENST00000545203, which lacks a signal peptide for cell surface localisation, rather than the predicted principal variant ENST00000371079. ENST00000375708 is the predominantly expressed transcript variant of ROR2. ConclusionROR1/2 expression in healthy human tissues should be carefully considered for safety assessment of targeted therapy. Studies exploring the function and significance of the predominantly expressed ROR1 transcript variant ENST00000545203 are warranted.

cancer biology↗

bioRxiv2021

Phylogeny of the Formicoxenus genus-group (Hymenoptera: Formicidae) reveals isolated lineages of Leptothorax acervorum in the Iberian Peninsula predating the Last Glacial Maximum

The Formicoxenus genus-group comprises six genera within the tribe Crematogastrini. The group is well known for repeated evolution of social parasitism among closely related taxa and cold-adapted species with large distribution ranges in the Nearctic and Palearctic regions. Previous analyses based on nuclear markers (ultraconserved elements, UCEs) and mitochondrial genes suggest close relationship between Formicoxenus Mayr, 1855, Leptothorax Mayr, 1855 and Harpagoxenus Forel, 1893. However, scant sampling has limited phylogenetic assessment of these genera. Also, previous phylogeographic analyses of L. acervorum (Fabricius, 1793) have been limited to its West-Palearctic range of distribution, which has provided a narrow view on recolonization, population structure and existing refugia of the species. Here, we inferred the phylogenenetic history of genera within the Formicoxenus genus-group and reconstructed the phylogeography of L. acervorum with more extensive sampling. We employed four datasets consisting of whole genomes and sequences of the COI. The topologies of previous nuclear and our inferences based on mitochondrial genomes were overall congruent. Further, Formicoxenus may not be monophyletic. We found several monophyletic lineages that do not correspond to the current species described within Leptothorax, especially in the Nearctic region. We identified a monophyletic L. acervorum lineage that comprises both Nearctic and Palearctic locations. The most recent expansion within L. acervorum probably occurred within the last 0.5 Ma with isolated populations predating the Last Glacial Maximum (LGM), which are localized in at least two refugial areas (Pyrenean and Northern plateau) in the Iberian Peninsula. The patterns recovered suggest a shared glacial refugium in the Iberian Peninsula with cold-adapted trees that currently share high-altitude environments in this region.

evolutionary biology↗

bioRxiv2021

Towards prevention of re-entrant arrhythmias: Injectable hydrogel electrodes enable direct capture of previously inaccessible cardiac tissues

Re-entrant arrhythmias--the leading cause of sudden cardiac death--are caused by diseased myocardial tissue and consequent delayed myocardial conduction. Access to the coronary veins that cross the "culprit" scar regions where re-entry originates can provide improved pacing to these delayed regions, offering a novel opportunity to prevent ventricular arrhythmias and circumvent the need for painful defibrillation, risky cardiac ablation, or toxic and often ineffective antiarrhythmic medications. However, there are no pacing electrodes which are small or focal enough to navigate these tributaries. To address this need, we have developed an injectable conductive hydrogel that can fill the epicardial coronary veins and their mid-myocardial tributaries. When connected to a standard pacing lead, these injected hydrogels can be converted into flexible electrodes that directly pace the previously inaccessible mid-myocardial tissue. In our two-component system, hydrogel precursor solutions can be injected through a dual lumen catheter in a minimally invasive deployment strategy to provide direct access to the diseased regions with precision and ease. Mixing of the two solutions upon injection into the vein activates redox-initiated crosslinking of the gel for rapid in situ cure without an external stimulus. An ex vivo porcine model was used to identify the requisite viscosity and cure rate for gel retention and homogeneity. Ionic species added to the hydrogel precursor solutions conferred conductivity above target myocardium values that was retained after implantation. Successful in vivo deployment demonstrated that the hydrogel electrode filled the anterior interventricular vein with extension into the septal (mid-myocardial) venous tributaries to depths far more distal and refined than any current technologies allow. In addition to successful capture and pacing of the heart, analysis of surface ECG tracings revealed a novel pacing observation highly specific for and suggestive of capture of extensive swaths of septal myocardial tissue. This is the first report of an injectable electrode used to successfully pace the mid-myocardium and mimic physiologic conduction. Furthermore, in vivo cardiac electroanatomical mapping studies in an ablation scar model showed uniform capture along the hydrogel in the vessels as well as increased capture area compared to point pacing. Collectively, these findings demonstrate that this injectable hydrogel electrode can be deployed to scarred regions of the heart to provide a reliable pacing modality that most closely resembles native conduction with the potential to eliminate delayed myocardial conduction and associated re-entry. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC="FIGDIR/small/467102v2_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@1577526org.highwire.dtl.DTLVardef@cc510dorg.highwire.dtl.DTLVardef@1dd426eorg.highwire.dtl.DTLVardef@1346aab_HPS_FORMAT_FIGEXP M_FIG C_FIG One Sentence SummaryInjectable hydrogel electrodes achieve pacing that mimics physiologic conduction by capturing midmyocardial tissue

bioengineering↗

bioRxiv2021

RNA inhibits dMi-2/CHD4 chromatin binding and nucleosome remodelling

The ATP-dependent nucleosome remodeller Mi-2/CHD4 broadly modulates epigenetic landscapes to repress transcription and to maintain genome integrity. Here we use individual nucleotide resolution crosslinking and immunoprecipitation (iCLIP) to show that Drosophila Mi-2 associates with thousands of mRNA molecules in vivo. Biochemical data reveal that recombinant dMi-2 preferentially binds to G-rich RNA molecules using two intrinsically disordered regions of previously undefined function. Pharmacological inhibition of transcription and RNase digestion approaches establish that RNA inhibits the association of dMi-2 with chromatin. We also show that RNA inhibits dMi-2-mediated nucleosome mobilization by competing with the nucleosome substrate. Importantly, this activity is shared by CHD4, the human homolog of dMi-2, strongly suggesting that RNA-mediated regulation of remodeller activity is an evolutionary conserved mechanism. Our data support a model in which RNA serves to protect actively transcribed regions of the genome from dMi-2/CHD4- mediated establishment of repressive chromatin structures.

molecular biology↗

bioRxiv2020

Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence

BackgroundGenetic variations across the SARS-CoV-2 genome may influence transmissibility of the virus and the hosts anti-viral immune response, in turn affecting the frequency of variants over-time. In this study, we examined the adjacent amino acid polymorphisms in the nucleocapsid (R203K/G204R) of SARS-CoV-2 that arose on the background of the spike D614G change and describe how strains harboring these changes became dominant circulating strains globally. MethodsDeep sequencing data of SARS-CoV-2 from public databases and from clinical samples were analyzed to identify and map genetic variants and sub-genomic RNA transcripts across the genome. ResultsSequence analysis suggests that the three adjacent nucleotide changes that result in the K203/R204 variant have arisen by homologous recombination from the core sequence (CS) of the leader transcription-regulating sequence (TRS) rather than by stepwise mutation. The resulting sequence changes generate a novel sub-genomic RNA transcript for the C-terminal dimerization domain of nucleocapsid. Deep sequencing data from 981 clinical samples confirmed the presence of the novel TRS-CS-dimerization domain RNA in individuals with the K203/R204 variant. Quantification of sub-genomic RNA indicates that viruses with the K203/R204 variant may also have increased expression of sub-genomic RNA from other open reading frames. ConclusionsThe finding that homologous recombination from the TRS may have occurred since the introduction of SARS-CoV-2 in humans resulting in both coding changes and novel sub-genomic RNA transcripts suggests this as a mechanism for diversification and adaptation within its new host.

microbiology↗

bioRxiv2019

Relapse prevention through health technology program reduces hospitalization in schizophrenia

ImportancePsychiatric hospitalization is a major driver of cost in the treatment of schizophrenia. Symptom relapses are a frequent cause of hospitalization and both are primary source of burden to patients and their supporters.\n\nObjectiveTo determine whether a novel, multicomponent, and technology-enhanced approach to relapse prevention in outpatients following a psychiatric hospitalization could reduce days spent in a hospital after discharge.\n\nDesignThe Improving Care and Reducing Cost (ICRC) study was a quasi-experimental clinical trial in outpatients with schizophrenia conducted between February 2013 and April 2015 at 10 different sites in the US. Data were obtained from 89 participants who received usual relapse prevention services, followed by a second cohort of 349 participants who received the technology-enhanced relapse prevention program. Both groups were followed for 6 months.\n\nSettingOutpatient setting.\n\nParticipantsPatients were between 18 and 60 years old; had a diagnosis of schizophrenia, schizoaffective disorder, or psychotic disorder not otherwise specified; and were currently hospitalized or had been hospitalized within the past 30 days.\n\nInterventionPatients received usual care or a technology-enhanced relapse prevention program during a 6-month period after discharge.\n\nMain Outcome(s) and Measure(s)Days spent in a psychiatric hospital during 6 months after discharge.\n\nResultsThe study included 438 patients. Control participants (N = 89; 37 females) were enrolled first and received usual care for relapse prevention, and followed by 349 participants (128 females) who received technology-enhanced relapse prevention. Days of hospitalization were reduced by 4 days (Mean days: b = -4.25, 95% CI: -8.29; -0.21, P = 0.039) during follow-up in the intervention condition compared to control.\n\nConclusions and RelevanceThe reduction in days spent in the hospital for participants in the technology-informed relapse prevention program compared to those who received usual care, and the previously reported high satisfaction and usability suggest that technology-enhanced relapse prevention is an effective and feasible way to reduce rehospitalization days among patients with schizophrenia.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSCan rehospitalizations in schizophrenia be prevented at reduced cost by innovative mobile technology-delivered interventions?\n\nFindingsIn this clinical trial with 438 patients, a technology-enhanced relapse prevention program compared to usual services reduced an average of four days of hospitalization per patient during the first 6 months following an index hospitalization.\n\nMeaningRelapse prevention through a health technology may improve care while reducing costs associated with hospitalization.

neuroscience↗

bioRxiv2018

Shared Polygenicity detection using Elastic Nets: SHARPEN

Current research suggests that hundreds to thousands of single nucleotide polymorphisms (SNPs) with modest effect sizes contribute to the genetic basis of many disorders, a phenomenon labeled as polygenicity. Additionally, many such disorders demonstrate polygenic overlap, in which risk alleles are shared at associated genetic loci. However, there are currently no well-developed statistical methods that can be utilized to detect specific subsets of SNPs involved in the shared polygenicity of phenotypes. In this paper, we illustrate how elastic nets, with appropriate adaptation in selecting the penalty parameter, can be utilized for narrowing the range of SNPs involved in shared polygenicity. We first develop the method when individual-level data from genomewide association studies (GWASs) are available; we also extend the approach so that it can be used when only summary level data from GWASs are available. We illustrate and assess the performance of the proposed methods using extensive simulations, and by applying the methods to summary level data from a pair of related GWASs with fasting glucose level and BMI as the phenotypes.

genetics↗