Biology subjects

Ahmed, T.

Publications and source records attributed to Ahmed, T..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

A maternal high-fat diet predisposes to infant lung disease via increased neutrophil-mediated IL-6 trans-signaling

Poor maternal diet during pregnancy predisposes to severe lower respiratory tract infections (sLRI) in infancy, which in turn, increases childhood asthma risk, however the underlying mechanisms remain poorly understood. Here, we show that the offspring of high fat diet (HFD)-fed mothers ( HFD-reared pups) developed a sLRI following pneumovirus inoculation in early-life and subsequent asthma in later-life upon allergen exposure. Prior to infection, HFD-reared pups developed microbial dysbiosis and low-grade systemic inflammation (LGSI), characterized by hyper-granulopoiesis in the liver and elevated inflammatory cytokine expression, most notably IL-17A, IL-6 and sIL-6R (indicative of IL-6 trans-signaling) in the circulation and multiple organs, but most prominently the liver. Inhibition of IL-6 trans-signaling, using sgp130Fc transgenic mice or via specific genetic deletion of IL-6Ra on neutrophils, conferred protection against both diseases. Taken together, our findings suggest that a maternal HFD induces neonatal LGSI that predisposes to sLRI and subsequent asthma via neutrophil-mediated IL-6 trans-signaling.

immunology↗

bioRxiv2023

GABA(A) receptor activation drives GABARAP-Nix mediated autophagy to radiation-sensitize primary and brain-metastatic lung adenocarcinoma tumors

In non-small cell lung cancer (NSCLC) treatment, targeted therapies benefit only a subset of NSCLC, while radiotherapy responses are not durable and toxicity limits therapy. We find that a GABA(A) receptor activator, AM-101, impairs viability and clonogenicity of NSCLC primary and brain metastatic cells. Employing an ex vivo chip, AM-101 is as efficacious as the chemotherapeutic docetaxel, which is used with radiotherapy for advanced-stage NSCLC. In vivo, AM-101 potentiates radiation, including conferring a survival benefit to mice bearing NSCLC intracranial tumors. GABA(A) receptor activation stimulates a selective-autophagic response via multimerization of GABA(A) Receptor-Associated Protein (GABARAP), stabilization of mitochondrial receptor Nix, and utilization of ubiquitin-binding protein p62. A targeted-peptide disrupting Nix binding to GABARAP inhibits AM-101 cytotoxicity. This supports a model of GABA(A) receptor activation driving a GABARAP-Nix multimerization axis triggering autophagy. In patients receiving radiotherapy, GABA(A) receptor activation may improve tumor control while allowing radiation dose de-intensification to reduce toxicity. HighlightsO_LIActivating GABA(A) receptors intrinsic to lung primary and metastatic brain cancer cells triggers a cytotoxic response. C_LIO_LIGABA(A) receptor activation works as well as chemotherapeutic docetaxel in impairing lung cancer viability ex vivo. C_LIO_LIGABA(A) receptor activation increases survival of mice bearing lung metastatic brain tumors. C_LIO_LIA selective-autophagic response is stimulated by GABA(A) receptor activation that includes multimerization of GABARAP and Nix. C_LIO_LIEmploying a new nanomolar affinity peptide that abrogates autophagosome formation inhibits cytotoxicity elicited by GABA(A) receptor activation. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/569295v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1df2f4eorg.highwire.dtl.DTLVardef@19ac26forg.highwire.dtl.DTLVardef@1533986org.highwire.dtl.DTLVardef@e59653_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2023

Prevotella copri-linked effects of a therapeutic food for malnutrition

Preclinical and clinical studies are providing evidence that the healthy growth of infants and children reflects, in part, healthy development of their gut microbiomes1-5. This process of microbial community assembly and functional maturation is perturbed in children with acute malnutrition. Gnotobiotic animals, colonized with microbial communities from children with severe and moderate acute malnutrition, have been used to develop microbiome-directed complementary food (MDCF) formulations for repairing the microbiomes of these children during the weaning period5. Bangladeshi children with moderate acute malnutrition (MAM) participating in a previously reported 3-month-long randomized controlled clinical study of one such formulation, MDCF-2, exhibited significantly improved weight gain compared to a commonly used nutritional intervention despite the lower caloric density of the MDCF6. Characterizing the metagenome assembled genomes (MAGs) of bacterial strains present in the microbiomes of study participants revealed a significant correlation between accelerated ponderal growth and the expression by two Prevotella copri MAGs of metabolic pathways involved in processing of MDCF-2 glycans1. To provide a direct test of these relationships, we have now performed reverse translation experiments using a gnotobiotic mouse model of mother-to-offspring microbiome transmission. Mice were colonized with defined consortia of age- and ponderal growth-associated gut bacterial strains cultured from Bangladeshi infants/children in the study population, with or without P. copri isolates resembling the MAGs. By combining analyses of microbial community assembly, gene expression and processing of glycan constituents of MDCF-2 with single nucleus RNA-Seq and mass spectrometric analyses of the intestine, we establish a principal role for P. copri in mediating metabolism of MDCF-2 glycans, characterize its interactions with other consortium members including Bifidobacterium longum subsp. infantis, and demonstrate the effects of P. copri-containing consortia in mediating weight gain and modulating the activities of metabolic pathways involved in lipid, amino acid, carbohydrate plus other facets of energy metabolism within epithelial cells positioned at different locations in intestinal crypts and villi. Together, the results provide insights into structure/function relationships between MDCF-2 and members of the gut communities of malnourished children; they also have implications for developing future prebiotic, probiotic and/or synbiotic therapeutics for microbiome restoration in children with already manifest malnutrition, or who are at risk for this pervasive health challenge.

microbiology↗

bioRxiv2023

ER structural remodeling requires TAK1/ATAT1-induced microtubule acetylation

Dynamic changes in the endoplasmic reticulum (ER) morphology are central to maintaining cellular homeostasis. Microtubules (MT) facilitate the continuous remodeling of the ER network into sheets and tubules by coordinating with many ER-shaping protein complexes, although how this process is controlled by extracellular signals remains unknown. Here we report that TAK1, a kinase responsive to numerous growth factors and cytokines including TGF-{beta} and TNF-, triggers ER tubulation by activating TAT1, an MT-acetylating enzyme that enhances ER-sliding. We show that this TAK1/TAT-dependent ER remodeling promotes cell survival by actively downregulating BOK, an ER membrane-associated proapoptotic effector. While BOK is normally protected from degradation when complexed with IP3R, it is rapidly degraded upon their dissociation during the ER sheets-to-tubules conversion. These findings demonstrate a distinct mechanism of ligand-induced ER remodeling and suggest that the TAK1/TAT pathway may be a key target in ER stress and dysfunction.

cell biology↗

bioRxiv2023

The maternal microbiome regulates infant respiratory disease susceptibility via intestinal Flt3L expression and plasmacytoid dendritic cell hematopoiesis

Severe lower respiratory infection (sLRI) are a major cause of infant morbidity and mortality, and predispose to later chronic respiratory diseases such as asthma. Poor maternal diet during pregnancy is a risk factor for sLRI in the offspring. Here we demonstrate in mice that a maternal low-fibre diet (LFD) disrupts plasmacytoid and conventional dendritic cell (DC) hematopoiesis in the offspring, predisposing to sLRI and subsequent asthma. The LFD alters the composition of the maternal milk microbiome and assembling infant gut microbiome, ablating the induction of a developmental wave of the non-redundant DC growth factor Flt3L by neonatal intestinal epithelial cells. Therapy with a propionate-producing bacteria isolated from the milk of high-fibre diet-fed mothers, or supplementation with propionate, confers protection against sLRI by restoring gut Flt3L expression and pDC hematopoiesis. Our findings identify a microbiome-dependent Flt3L axis in the gut that regulates pDC hematopoiesis in early life and confers disease resistance. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=51 SRC="FIGDIR/small/522516v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@1a39990org.highwire.dtl.DTLVardef@1b6fe67org.highwire.dtl.DTLVardef@f8440dorg.highwire.dtl.DTLVardef@13bc67e_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2022

IL-33-induced neutrophilic inflammation and NETosis underlie rhinovirus-triggered exacerbations of asthma

Rhinovirus-induced neutrophil extracellular traps (NETs) contribute to acute asthma exacerbations, however the molecular factors that trigger NETosis in this context remain ill-defined. Here, we sought to implicate a role for IL-33, an epithelial cell-derived alarmin rapidly released in response to infection. In mice with chronic experimental asthma (CEA), but not naive controls, rhinovirus inoculation induced an early (1 day post infection; dpi) inflammatory response dominated by neutrophils, neutrophil-associated cytokines (IL-1, IL-1{beta}, CXCL1) and NETosis, followed by a later, type-2 inflammatory phase (3-7 dpi), characterized by eosinophils, elevated IL-4 levels, and goblet cell hyperplasia. Notably, both phases were ablated by HpARI (Heligmosomoides polygyrus Alarmin Release Inhibitor), which blocks IL-33 release and signalling. Instillation of exogenous IL-33 recapitulated the rhinovirus-induced early phase, including the increased presence of NETs in the airway mucosa, in a PAD4-dependent manner. Ex vivo IL-33-stimulated neutrophils from mice with CEA, but not naive mice, underwent NETosis, and produced greater amounts of IL-1/{beta}, IL-4, and IL-5. In nasal samples from rhinovirus-infected people with asthma, but not healthy controls, IL-33 levels correlated with neutrophil elastase and dsDNA. Our findings suggest that IL-33 blockade ameliorates the severity of an asthma exacerbation by attenuating neutrophil recruitment and the downstream generation of NETs.

immunology↗

bioRxiv2022

Comprehensive multi-omics characterization of gut microbiome extracellular vesicles reveals a connection to gut-brain axis signaling

Microbiota-gut-brain axis is an evident pathway of host-microbiota crosstalk that is linked to multiple brain disorders. Microbiota released extracellular vesicles (MEVs) has emerged as a key player in intercellular signaling in host microbiome communications. However, their role in gutbrain axis signaling is poorly investigated. Here, we performed a deep multi-omics profiling of MEVs content generated ex vivo and from stool samples in order to get some insights on their role in gut-brain-axis signaling. Metabolomics profiling identified a wide array of metabolites embedded in MEVs, including lipids, carbohydrates, amino acids, vitamins, and organic acids. Interestingly, many neurotransmitter-related compounds were detected inside MEVs, including arachidonyl-dopamine (NADA), gabapentin, glutamate and N-acylethanolamines. Next, we aimed to identify commensal microbes with psychobiotic activity. We isolated 58 Bacteroides strains assigned to four genera, 11 species, and 4 new species based on 16S rDNA sequencing. We performed whole genome sequencing of 18 representative isolates, followed by a comparative analysis of the structure of polysaccharide utilization loci (PUL) and glutamate decarboxylase (GAD), a genetic system involved in GABA production. Quantifying GABA was done using competitive ELISA, wherein three isolates (B. finegoldii, B. faecis, and B. caccae) showed high GABA production (4.5-7 mM range) in supernatant whereas 2.2 to 4 uM GABA concentration was detected inside microvesicles extracted using ultracentrifugation. To test the biodistribution of MEVs from the gut to other parts of the body, CACO-2, RIN-14 B, and hCMEC/D3 cells showed a capacity to internalize labeled MEVs through an endocytic mechanism. Additionally, MEVs exhibited a dose dependent paracellular transport through CACO-2 intestinal cells and hCMEC/D3 brain endothelial cells. In vivo results showed biodistribution of MEVs to liver, stomach and spleen. Overall, our results reveal the capabilities of MEVs to cross the intestinal and blood brain barriers to deliver their cargoes of neuroactive molecules to the brain as a new signaling mechanism in microbiota-gut-brain axis communications.

microbiology↗

bioRxiv2022

Delivery of loaded MR1 Monomer Results in Efficient Ligand Exchange to Host MR1 and Subsequent MR1T cell activation

MR1-restricted T cells have been implicated in microbial infections, sterile inflammation, wound healing and cancer. Similar to other antigen presentation molecules, evidence supports multiple, complementary MR1 antigen presentation pathways. To investigate ligand exchange pathways for MR1, we used MR1 monomers and tetramers loaded with 5-(2-oxopropylideneamino)-6-d-ribitylaminouracil (5-OP-RU) to deliver the antigen. Using MR1-deficient cells reconstituted with wild-type MR1 or MR1 molecules that cannot bind 5-OP-RU, we show that presentation of monomer-delivered 5-OP-RU is dependent on cellular MR1 and requires the transfer of ligand from the soluble molecule onto MR1 expressed by the antigen presenting cell. This mode of antigen delivery strengthens the evidence for post-ER ligand exchange pathways for MR1, which could represent an important avenue by which MR1 acquires antigens derived from endocytosed pathogens.

immunology↗

bioRxiv2022

Identification of Mfn2-S249 as a Phosphoregulatory Switch of Mitochondrial Fusion Dynamics

Mitochondrial remodeling is a fundamental process underlying cellular respiration and metabolism. Here we report TAK1 as a direct regulator of mitochondrial fusion. TAK1 is activated by a variety of mitogenic factors, cytokines and environmental stimuli, which we find induces rapid fragmentation through Mfn2 inactivation. TAK1 phosphorylates Mfn2 at Ser249, which inhibits the binding of GTP required for Mfn trans-dimerization and mitochondrial membrane fusion. Accordingly, expression of Mfn2-S249 phosphomimetics (Mfn2-E/D) constitutively promote fission whereas alanine mutant (Mfn2-A) yields hyperfused mitochondria and increased bioenergetics in cells. In mice, Mfn2-E knock-in yields embryonic lethality in homozygotes whereas heterozygotes are viable but exhibit increased visceral fat accumulation despite normal body weight and cognitive/motor functions compared to wildtype and Mfn2-A mice. Mature white adipocytes isolated from mutant mice reveal cell-autonomous TAK1-related effects on mitochondrial remodeling and lipid metabolism. These results identify Mfn2-S249 as a dynamic phosphoregulatory switch of mitochondrial fusion during development and energy homeostasis.

cell biology↗

bioRxiv2021

Genomic characteristics of recently recognized Vibrio cholerae El Tor lineages associated with cholera in Bangladesh, 1991-2017

Comparative genomic analysis of Vibrio cholerae El Tor associated with endemic cholera in Asia revealed two distinct lineages, one dominant in Bangladesh and the other in India. An in depth whole genome study of V. cholerae El Tor clinical strains isolated during endemic cholera in Bangladesh (1991 - 2017) included reference genome sequence data obtained online. Core genome phylogeny established using single nucleotide polymorphisms (SNPs) showed V. cholerae El Tor strains comprised two lineages, BD-1 and BD-2, which, according to Bayesian phylodynamic analysis, originated from paraphyletic group BD-0 around 1981. BD-1 and BD-2 lineages overlapped temporally but were negatively associated as causative agents of cholera 2004-2017. Genome wide association study (GWAS) revealed 140 SNPs and 31 indels, resulting in gene alleles unique to BD-1 and BD-2. Regression analysis of root to tip distance and year of isolation indicated early BD-0 strains at the base, whereas BD-1 and BD-2 subsequently emerged and progressed by accumulating SNPs. Pangenome analysis provided evidence of gene acquisition by both BD-1 and BD-2, of which six crucial proteins of known function were predominant in BD-2. BD-1 and BD-2 diverged and have distinctively different genomic traits, namely heterogeneity in VSP-2, VPI-1, mobile elements, toxin encoding elements, and total gene abundance. In addition, the observed phage-inducible chromosomal island-like element (PLE1), and SXT ICE elements (ICETET) in BD-2 presumably provided a fitness advantage for the lineage to outcompete BD-1 as the etiological agent of the endemic cholera in Bangladesh, with implications for global cholera epidemiology. ImportanceCholera is a global disease with specific reference to the Bay of Bengal Ganges Delta where Vibrio cholerae O1 El Tor, causative agent of the disease showed two circulating lineages, one dominant in Bangladesh and the other in India. Results of in-depth genomic study of V. cholerae associated with endemic cholera during the past 27 years (1991 - 2017) indicate emergence and succession of the two lineages, BD-1 and BD-2, arising from a common ancestral paraphylatic group, BD-0, comprising the early strains and short-term evolution of the bacterium in Bangladesh. Among the two V. cholerae lineages, BD-2 supersedes BD-1 and is predominant in the most recent endemic cholera in Bangladesh. The BD-2 lineage contained significantly more SNPs and indels, and showed richness in gene abundance, including antimicrobial resistance genes, gene cassettes, and PLE to fight against bacteriophage infection, acquired over time. These findings have important epidemic implications at a global scale.

genomics↗

bioRxiv2021

Use of eVLP-based vaccine candidates to broaden immunity against SARS-CoV-2 variants

Rapid emergence of SARS-CoV-2 variants is a constant threat and a major hurdle to reach heard immunity. We produced VBI-2905a, an enveloped virus-like particle (eVLP)-based vaccine candidate expressing prefusion spike protein from the Beta variant that contains several escape mutations. VBI-2905a protected hamsters against infection with a Beta variant virus and induced high levels of neutralizing antibodies against Beta RBD. In a heterologous vaccination regimen, a single injection of VBI-2905a in animals previously immunized with VBI-2902, a vaccine candidate expressing S from ancestral SARS-CoV-2, hamsters were equally protected against Beta variant infection. As an alternate strategy to broaden immunity, we produced a trivalent vaccine expressing the prefusion spike protein from SARS-CoV-2 together with unmodifed S from SARS-CoV-1 and MERS-CoV. Relative to immunity induced against the ancestral strain, the trivalent vaccine VBI-2901a induced higher and more consistent antibody binding and neutralizing responses against a panel of variants including Beta, Delta, Kappa, and Lambda, with evidence for broadening of immunity rather than just boosting cross-reactive antibodies.

immunology↗

bioRxiv2021

How Our Cells Become Our Selves: The Cellular Phylodynamic Biology of Growth and Development

Our lives begin with 1 cell, then 2, then 4, then the trillion cell adult, comprised of cell lineages, tissues, organs. How does this occur? Examination in numbers of cells, N, Cellular Phylodynamics, revealed two previously unappreciated processes: UNI-GROWTH, the slowing of growth that occurs as we become larger, caused by fewer cells dividing, captured by the Universal Mitotic Fraction and Universal Growth Equations, with accuracy confirmed for 13 species, including nematodes, mollusks, and vertebrates; and ALLO-GROWTH, the creation of body parts from Founder Cells, captured by the Cellular Allometric Growth Equation, which describes mitotic expansion by Cell-Heritable change in the Cell Cycle Time. These equations can generate cell lineage approximations, bringing the power of coalescent theory to developmental biology.

developmental biology↗

bioRxiv2021

Automated movement assessment in stroke rehabilitation

We are developing a system for long term Semi-Automated Rehabilitation At the Home (SARAH) that relies on low-cost and unobtrusive video-based sensing. We present a cyber-human methodology used by the SARAH system for automated assessment of upper extremity stroke rehabilitation at the home. We propose a hierarchical model for automatically segmenting stroke survivors movements and generating training task performance assessment scores during rehabilitation. The hierarchical model fuses expert therapist knowledge-based approaches with data-driven techniques. The expert knowledge is more observable in the higher layers of the hierarchy (task and segment) and therefore more accessible to algorithms incorporating high level constraints relating to activity structure (i.e. type and order of segments per task). We utilize an HMM and a Decision Tree model to connect these high level priors to data driven analysis. The lower layers (RGB images and raw kinematics) need to be addressed primarily through data driven techniques. We use a transformer based architecture operating on low-level action features (tracking of individual body joints and objects) and a Multi-Stage Temporal Convolutional Network(MS-TCN) operating on raw RGB images. We develop a sequence combining these complimentary algorithms effectively, thus encoding the information from different layers of the movement hierarchy. Through this combination, we produce a robust segmentation and task assessment results on noisy, variable and limited data, which is characteristic of low cost video capture of rehabilitation at the home. Our proposed approach achieves 85% accuracy in per-frame labeling, 99% accuracy in segment classification and 93% accuracy in task completion assessment. Although the methodology proposed in this paper applies to upper extremity rehabilitation using the SARAH system, it can potentially be used, with minor alterations, to assist automation in many other movement rehabilitation contexts (i.e. lower extremity training for neurological accidents).

neuroscience↗

bioRxiv2021

An enveloped virus-like particle vaccine expressing a stabilized prefusion form of the SARS-CoV-2 spike protein elicits potent immunity after a single dose.

Development of efficacious single dose vaccines would substantially aid efforts to stop the uncontrolled spread of the COVID-19 pandemic. We evaluated enveloped virus-like particles (eVLPs) expressing various forms of the SARS-CoV-2 spike protein and several adjuvants in an effort to identify a COVID-19 vaccine candidate efficacious after a single dose. The eVLPs expressing a modified prefusion form of SARS-CoV-2 spike protein were selected as they induced the highest antibody binding titers and neutralizing activity after a single injection in mice. Formulation of SARS-CoV-2 S eVLPs with aluminum phosphate resulted in balanced induction of IgG2 and IgG1 isotypes and antibody binding and neutralization titers were undiminished for more than 3 months after a single immunization. A single dose of this candidate, VBI-2902a (prefusion S eVLPs formulated with aluminum phosphate), protected Syrian golden hamsters from challenge with SARS-CoV-2 and supports the on-going clinical evaluation of VBI-2902a as a potential single dose vaccine against COVID-19. HighlightsO_LIVBI-2902a is a VLP-based vaccine candidate against SARS-COV-2 C_LIO_LIVBI-2902a contains VLPs pseudotyped with a modified prefusion SARS-COV-2 S in Alum. C_LIO_LIVBI-2902a induces robust neutralization antibody response against SARS-COV-2 S C_LIO_LIVBI-2902a protects hamsters from SARS-CoV-2 induced lung inflammation C_LIO_LIA single dose of VBI-2902a provides protective benefit in hamsters C_LI

immunology↗

bioRxiv2021

Privacy Preserving RNA-Model Validation Across Laboratories

Reproducibility of results obtained using RNA data across labs remains a major hurdle in cancer research. Often, molecular predictors trained on one dataset cannot be applied to another due to differences in RNA library preparation and quantification. While current RNA correction algorithms may overcome these differences, they require access to all patient-level data, which necessitates the sharing of training data for predictors when sharing predictors. Here, we describe SpinAdapt, an unsupervised RNA correction algorithm that enables the transfer of molecular models without requiring access to patient-level data. It computes data corrections only via aggregate statistics of each dataset, thereby maintaining patient data privacy. Furthermore, SpinAdapt can correct new samples, thereby enabling evaluation of validation cohorts. Despite an inherent tradeoff between privacy and performance, SpinAdapt outperforms current correction methods that require patient-level data access. We expect this novel correction paradigm to enhance research reproducibility and patient privacy. Finally, SpinAdapt lays a mathematical framework that can be extended to other -omics modalities.

bioinformatics↗

bioRxiv2021

Nonsense Mediated RNA Decay Is a Unique Vulnerability of Cancer Cells with SF3B1 and U2AF1 Mutations

Nonsense-mediated RNA decay (NMD) is well recognized as an RNA surveillance pathway that targets aberrant mRNAs with premature translation termination codons (PTCs) for degradation; however, its molecular mechanisms and roles in health and disease remain incompletely understood. In this study, we developed a novel reporter system that can accurately measure NMD activity in individual cells. By carrying out a genome-wide CRISPR/Cas9 knockout screen using this reporter system, we identified novel NMD-promoting factors, including multiple components of the SF3B complex and other U2 spliceosome factors. Interestingly, we also found that cells with mutations in the U2 spliceosome genes SF3B1 and U2AF1--which are commonly found in myelodysplastic syndrome (MDS) and cancers--have overall attenuated NMD activity. Furthermore, we found that compared to wild type cells, SF3B1 and U2AF1 mutant cells are more sensitive to NMD inhibition, a phenotype that is accompanied by elevated DNA replication obstruction, DNA damage and chromosomal instability. Remarkably, the sensitivity of spliceosome mutant cells to NMD inhibition could be rescued by overexpression of RNase H1, which removes R-loops in the genome. Together, our findings shed new light on the functional interplay between NMD and RNA splicing and suggest a novel strategy for the treatment of MDS and cancers with spliceosome mutations.

cell biology↗

bioRxiv2020

Structure of the ancestral TRPY1 channel from Saccharomyces cerevisiae reveals mechanisms of modulation by lipids and calcium

Transient Receptor Potential (TRP) channels have evolved in eukaryotes to control various cellular functions in response to a wide variety of chemical and physical stimuli. This large and diverse family of channels emerged in fungi as mechanosensitive osmoregulators. The Saccharomyces cerevisiae vacuolar TRP yeast 1 (TRPY1) is the most studied TRP channel from fungi, but the molecular details of channel modulation remain elusive so far. Here, we describe the full-length cryo-electron microscopy structure of TRPY1 at 3.1 [A] resolution. The structure reveals a distinctive architecture for TRPY1 among all eukaryotic TRP channels with an evolutionarily conserved and archetypical transmembrane domain, but distinct structural folds for the cytosolic N- and C-termini. We identified the inhibitory phosphatidylinositol 3-phosphate (PI(3)P) lipid binding site, which sheds light into the lipid modulation of TRPY1 in the vacuolar membrane. The structure also exhibited two Ca2+-binding sites: one in the cytosolic side, implicated in channel activation, and the other in the vacuolar lumen side, involved in channel inhibition. These findings, together with data from molecular dynamics simulations, provide structural insights into the basis of TRPY1 channel modulation by lipids and Ca2+.

biophysics↗

bioRxiv2020

The early evolution of oral poliovirus vaccine is shaped by strong positive selection and tight transmission bottlenecks

The evolution of circulating vaccine-derived polioviruses (cVDPV) from components of the live-attenuated oral poliovirus vaccine (OPV) presents a major challenge to global polio eradication. This process has largely been characterized by consensus sequencing of isolates collected from routine surveillance, and little is known about the early evolution of OPV within vaccinated hosts. These early events are critical steps in the progression of OPV to cVDPV. Here, we use whole genome, high depth of coverage sequencing to define the evolutionary trajectories of monovalent type 2 OPV in a cluster-randomized trial of polio vaccines in Matlab, Bangladesh. By sequencing 416 longitudinal samples from 219 mOPV2 recipients and 81 samples from 52 household contacts, we were able to examine the extent of convergent evolution in vaccine recipients and track the amount of viral diversity transmitted to new hosts. Using time-series data from a synchronized point of vaccine administration, we identify strong positive selection of reversion mutations at three known attenuating sites within two months post-vaccination. Beyond these three recognized "gate-keeper" mutations, we identify 19 mutations that exhibit significant parallelism across vaccine recipients, providing evidence for early positive selection not previously detected by phylogenetic inference. An analysis of shared genetic variants in samples from vaccinated individuals and their household contacts suggests a tight effective bottleneck during transmission. The absence of positively selected variants among household contacts across the cohort suggests that this tight bottleneck limits the transmission of these early adaptive mutations. Together, our results highlight the distinct evolutionary dynamics of live attenuated virus vaccines and have important implications for the success of novel OPV2 and other next generation approaches. SignificanceThe emergence of circulating vaccine-derived polioviruses (cVDPV) through evolution of the oral polio vaccine (OPV) poses a significant obstacle to global eradication. Understanding the genetic changes in OPV that occur as it evolves and transmits in populations is important for preventing future cVDPV outbreaks. Little is known about the early events in VDPV evolution and the selective forces that drive them. We used high depth-of-coverage genome sequencing to assess the within-host evolutionary dynamics of monovalent type 2 OPV in a vaccine trial in Matlab, Bangladesh. We leverage longitudinal sampling from vaccine recipients and household contacts to identify mutations that arise in parallel across individuals and estimate the size of the transmission bottleneck. We find evidence for strong positive selection on key sites in the capsid and the 5 noncoding region, many of which have not been previously identified. Our results also suggest that narrow transmission bottlenecks can constrain the spread of mutations selected within individuals. These results provide important insights into how OPV variants spread in populations and are highly relevant for ongoing poliovirus surveillance and the design of improved polio vaccines.

microbiology↗