Biology subjects

Rajagopal, S.

Publications and source records attributed to Rajagopal, S..

29 records · Page 2Linked to original sources

bioRxiv2021

Steps to (s)-stereoisomers: Rationalization of a standard Short-chain dehydrogenase for the reduction of multiple pharmaceutical ketone intermediates

Short-chain dehydrogenases/reductases (SDRs) are a convenient class of enzymes used to synthesize enantiopure alcohols. Several studies describe native or engineered SDRs for converting substrates of interest using cost and time-intensive high-throughput approaches. The classification of SDRs is based on chain length and cofactor binding site. Of these, the shorter Classical and the longer Extended enzymes participate in ketoreduction. However, comparative analysis of various modelled SDRs reveals a length independent conserved N-terminal Rossmann fold and a variable C-terminus region for both types. The general hypothesis is that the latter domain influences the enzymes flexibility that may affect the observed promiscuity of the enzyme. We have used a machine learning algorithm on this flexible domain to build a rationale to screen promiscuous candidates. We have built a data set consisting of physicochemical properties derived from the amino-acid composition of enzymes to select closely associated promiscuous mesophilic enzymes. The resulting in vitro studies on pro-pharmaceutical substrates illustrate a direct correlation between the C-terminal lid-loop structure, enzyme melting temperature and the turnover number. We present a walkthrough for exploring promiscuous SDRs for catalyzing enantiopure alcohols of industrial importance.

biochemistry↗

bioRxiv2021

Beta-arrestin-mediated Angiotensin II type 1 Receptor Activation Promotes Pulmonary Vascular Remodeling in Pulmonary Hypertension

ObjectivesThe goal of this study was to test whether a {beta}-arrestin-biased agonist of the angiotensin II (AngII) type 1 receptor (AT1R), which acts as a vasodilator while not blocking cellular proliferation, would have positive effects compared to a balanced agonist, angiotensin II (AngII), or an antagonist, losartan, in pulmonary arterial hypertension (PAH). BackgroundPAH is a disease of abnormal pulmonary vascular remodeling whose treatment has focused on targeting vasoactive substances, such as inhibiting endothelin signaling and promoting prostacyclin signaling. PAH medical therapies are thought to primarily act as vasodilators, although they may also have effects on pulmonary vascular remodeling. There are a number of reports that blocking AT1R signaling can be beneficial in preclinical models of PAH. The AT1R is a G protein-coupled receptor (GPCR) that promotes vasoconstriction through heterotrimeric G proteins but also signals via {beta}-arrestins, which promote cardioprotective effects and vasodilation. MethodsWe compared the effects of a {beta}-arrestin-biased AT1R agonist, TRV120023 (TRV023), to a balanced agonist (AngII) and an antagonist (losartan) in preclinical PAH models. ResultsIn acute infusion studies, AngII increased right ventricular (RV) pressures while TRV023 did not. However, with chronic infusion in monocrotaline (MCT) PAH rats, TRV023 failed to improve hemodynamics or survival compared to AngII, while losartan significantly improved survival. Both TRV023 and AngII enhanced proliferation and migration of pulmonary artery smooth muscle cells (PASMCs) from PAH patients, which was associated with the promotion of proliferative MAP kinase signaling. Conclusions{beta}-arrestin-mediated AT1R signaling promotes vascular remodeling and worsens PAH, and suggests that the primary benefit of current PAH therapies is through pulmonary vascular reverse remodeling and not vasodilation.

molecular biology↗

bioRxiv2020

An accurate aging clock developed from the largest dataset of microbial and human gene expression reveals molecular mechanisms of aging

Accurate measurement of the biological markers of the aging process could provide an "aging clock" measuring predicted longevity and allow for the quantification of the effects of specific lifestyle choices on healthy aging. Using modern machine learning techniques, we demonstrate that chronological age can be predicted accurately from (a) the expression level of human genes in capillary blood, and (b) the expression level of microbial genes in stool samples. The latter uses the largest existing metatranscriptomic dataset, stool samples from 90,303 individuals, and is the highest-performing gut microbiome-based aging model reported to date. Our analysis suggests associations between biological age and lifestyle/health factors, e.g., people on a paleo diet or with IBS tend to be biologically older, and people on a vegetarian diet tend to be biologically younger. We delineate the key pathways of systems-level biological decline based on the age-specific features of our model; targeting these mechanisms can aid in development of new anti-aging therapeutic strategies.

systems biology↗

bioRxiv2020

Biased agonists of the chemokine receptor CXCR3 differentially drive formation of Gαi:β-arrestin complexes

G-protein-coupled receptors (GPCRs), the largest family of cell surface receptors, signal through the proximal effectors G proteins and {beta}-arrestins to influence nearly every biological process. Classically, the G protein and {beta}-arrestin signaling pathways have largely been considered separable. Recently, direct interactions between G protein and {beta}-arrestin have been described and suggest a distinct GPCR signaling pathway. Within these newly described G:{beta}-arrestin complexes, Gi/o, but not other G protein subtypes, have been appreciated to directly interact with {beta}-arrestin, regardless of canonical GPCR G protein subtype coupling. However it is unclear how biased agonists differentially regulate this newly described Gi:{beta}-arrestin interaction, if at all. Here we report that endogenous ligands (chemokines) of the GPCR CXCR3, CXCL9, CXCL10, and CXCL11, along with two small molecule biased CXCR3 agonists, differentially promote the formation of Gi:{beta}-arrestin complexes. The ability of CXCR3 agonists to form Gi:{beta}-arrestin complexes does not correlate well with either G protein signaling or {beta}-arrestin recruitment. Conformational biosensors demonstrate that ligands that promoted Gi:{beta}-arrestin complex formation generated similar {beta}-arrestin conformations. We find these Gi:{beta}-arrestin complexes can associate with CXCR3, but not with ERK. These findings further support that Gi:{beta}-arrestin complex formation is a distinct GPCR signaling pathway and enhance our understanding of biased agonism.

biochemistry↗

bioRxiv2019

Maximization of non-nitrogenous metabolite production in E. coli using population systems biology

The E. coli metabolome is an interconnected set of enzymes that has measurable kinetic parameters ascribed for the production of most of its metabolites. Flux Balance Analysis (FBA) or Ordinary Differential Equation (ODE) models are used to increase product yield using defined media. However, they either give a range (FBA) or exact amount (ODE) of metabolite yield which isnt true as the transcriptome diversity of individual cells isnt considered. We formulate the metabolic-behaviour of individual cells by using a POpulation SYstems-Biology ALgorithm (POSYBAL) which predicts multiple-gene knockouts for increasing industrially relevant metabolites. We validate this prediction for producing isobutanol (Heterogenous metabolite) and shikimate (Homogenous metabolite) where, the product-yield was increased by 40 times (~2000 ppm) and 42 times (~3000 ppm) respectively. Also, we introduce a nitrogen-swap in standard media to its low-nitrogen counterpart during post-growth phase to redistribute flux towards non-nitrogenous pathways for increasing overall product-yield. Further, our model shows growth-phase diversity in bacterial population even under normal glucose-uptake, portraying a real-world scenario of diverse and robust environment thus, making it evolutionarily favourable to threats such as anti-bacterial attack.

bioengineering↗

bioRxiv2019

APOE4 status is related to differences in memory-related brain function in asymptomatic older adults: Baseline analysis of the PREVENT-AD task fMRI dataset

Episodic memory decline is one of the earliest symptoms of late-onset Alzheimers Disease (AD) and older adults with the apolipoprotein E e4 (+APOE4) genetic risk factor for AD may exhibit altered patterns of memory-related brain activity years prior to initial symptom onset. In the current study we report the baseline episodic memory task fMRI results from the PRe-symptomatic EValuation of Experimental or Novel Treatments for Alzheimers Disease (PREVENT-AD) study in Montreal, Canada, in which 327 healthy older adults, within 15 years of the parents conversion to AD, were scanned. During the task fMRI protocol volunteers were scanned as they encoded and retrieved object-location spatial source associations. The task was designed to discriminate between brain activity related to successful spatial source recollection and failures in spatial source recollection, with memory for only item (object) memory. Multivariate task-related partial least squares (task PLS) was used to test the hypothesis that +APOE4 adults with a family history of AD would exhibit altered patterns of brain activity in the recollection-related memory network, comprised of medial frontal, parietal and medial temporal cortices, compared to APOE4 non-carriers (-APOE4). We also tested for group differences in the correlation between event-related brain activity and memory performance in +APOE4 compared to -APOE4 adults using behavioral-PLS (B-PLS). We found group similarities in memory performance and in task-related brain activity in the recollection network. However, the B-PLS results indicated there were group differences in brain activity-behavior correlations in ventral occipito-temporal, medial temporal, and medial prefrontal cortices during episodic encoding. These findings are consistent with previous literature on the influence of APOE4 on brain activity and provide new perspective on potential gene-based differences in brain-behavior relationships in people with parental history of AD. Future research should further investigate the potential to distinguish risk of AD development based on memory performance and associated patterns of brain activity.

neuroscience↗

bioRxiv2019

Noncanonical scaffolding of Gαi and β-arrestin by G protein-coupled receptors

G-protein-coupled receptors (GPCRs) enable cells to sense and respond appropriately to hormonal and environmental signals, and are a target of ~30% of all FDA-approved medications. Canonically, each GPCR couples to distinct G proteins, such as Gs, Gi, Gq or G12/13, as well as {beta}-arrestins. These transducer proteins translate and integrate extracellular stimuli sensed by GPCRs into intracellular signals through what are broadly considered separable signalling pathways. However, the ability of G proteins to directly interact with {beta}-arrestins to integrate signalling has not previously been appreciated. Here we show a novel interaction between Gi protein family members and {beta}-arrestin. Gi:{beta}-arrestin complexes were formed by all GPCRs tested, regardless of their canonical G protein isoform coupling, and could bind both GPCRs as well as the extracellular signal-regulated kinase (ERK). This novel paradigm of Gi:{beta}-arrestin scaffolds enhances our understanding of GPCR signalling.

cell biology↗

bioRxiv2019

Pathogen-encoded evasion of CXCL10 and T cell responses

Clearance of intracellular pathogens, such as Leishmania (L.) major, depends on a well-regulated adaptive T cell response. Here we describe a pathogen-encoded mechanism to alter T cell recruitment by suppressing CXCL10, a chemokine that recruits CD4+ and CD8+ T cells by signaling through the CXCR3 receptor. L. major suppresses CXCL10 through the virulence factor and protease, glycoprotein-63 (gp63). GP63 cleaves CXCL10 after amino acid A81, impairing T-cell chemotaxis in vitro. GP63 from either extracellular promastigotes or intracellular amastigotes is capable of cleaving CXCL10. Consistent with CXCL10 cleavage during infection, we observed GP63-mediated impairment of activated CD8+ T-cells in the draining lymph nodes of C57BL/6JWT mice. Correspondingly, in C57BL/6JWT mice, gp63 deletion resulted in slower lesion development and a smaller maximum lesion size. However, infection in C57BL/6Jcxcr3-/- mice revealed the delay to lesion development required CXCR3 signaling. Finally, Salmonella enterica and Chlamydia trachomatis infection also suppress CXCL10, demonstrating convergent evolution of this immune evasion strategy in diverse intracellular pathogens. Understanding mechanisms of CXCL10 evasion may facilitate the development of novel therapeutic strategies to treat intracellular pathogens. Author SummaryLeishmaniasis is an infectious disease that affects over one million people annually. It is caused by intracellular parasites that have evolved to evade the hosts attempts to eliminate the parasite. The most common form of disease, cutaneous leishmaniasis, causes disfiguring skin lesions if the host immune system does not appropriately respond to the infection. A family of molecules called chemokines are critical for the recruitment of specific subsets of immune cells required to eliminate infection. Here, we demonstrate a novel mechanism that the parasite Leishmania (L.) major employs to disrupt the immune response by interfering with chemokine signaling. By this strategy, L. major uses a protease to cleave chemokines known to recruit T-cells required for fighting off infection. We show that L. major cleavage of these immune signals changes the recruitment of CD8+ T-cells and alters disease progression in mice. Finally, we observe that multiple common human intracellular pathogens, including Chlamydia trachomatis and Salmonella enterica, interfere with the same chemokines, suggesting a strong selective pressure to avoid this component of the immune response. Our study provides new insights into how intracellular pathogens interact with the host immune response to enhance pathogen survival and exacerbate disease outcomes.

microbiology↗

bioRxiv2019

Sex differences in the neural correlates of age-related episodic memory decline

Aging is associated with episodic memory decline and alterations in memory-related brain function. However, it remains unclear if age-related memory decline is associated with similar patterns of brain aging in women and men. In the current task fMRI study, we tested the hypothesis that there are sex differences in the effect of age and memory performance on brain activity during episodic encoding and retrieval of face-location associations (spatial context memory). Forty-one women and 41 men between the ages of 21 to 76 years participated in this study. Between-group multivariate partial least squares (PLS) analysis of the fMRI data was conducted to directly test for sex-group differences and similarities in age-related and performance-related patterns of brain activity. Our behavioural analysis indicated no significant sex differences in retrieval accuracy on the fMRI tasks. In relation to performance effects, we observed similarities and differences in how retrieval accuracy related to brain activity in women and men. Both sexes activated dorsal and lateral prefrontal cortex (PFC), inferior parietal cortex (IPC) and left parahippocampal gyrus (PHG) at encoding and this supported subsequent memory performance. However, there were sex differences in retrieval activity in these same regions and in lateral occipital-temporal and ventrolateral PFC. In relation to age effects, we observed sex differences in the effect of age on memory-related activity within PFC, IPC, PHG and lateral occipital-temporal cortices. Overall, our findings suggest that the neural correlates of age-related spatial context memory decline differ in women compared to men.

neuroscience↗

bioRxiv2019

Age- and reserve-related increases in fronto-parietal and anterior hippocampal activity during episodic encoding predict subsequent memory

Remembering associations between encoded items and their contextual setting is a feature of episodic memory. Although this ability deteriorates with age in general, there is substantial variability in how older individuals perform on episodic memory tasks. This variability may stem from genetic and/or environmental factors related to reserve, allowing some individuals to compensate for age-related decline through differential recruitment of brain regions. In this fMRI study, we tested predictions related to reserve and compensation in a large adult lifespan sample (N=154). We used multivariate Behaviour Partial Least Squares (B-PLS) analysis to examine how age, retrieval accuracy, and a proxy measure of reserve, impacted brain activity patterns during spatial and temporal context encoding and retrieval. Reserve modulated age-related compensatory brain responses in ventral visual, temporal, and fronto-parietal regions during memory encoding as a function of task demands. Activity in inferior parietal, medial temporal, and ventral visual regions were strongly impacted by age at encoding and retrieval, but were also related to individual differences in reserve. Our findings are consistent with the concepts of reserve and compensation and suggest that reserve may mitigate age-related decline by modulating compensatory brain responses in the aging brain.

neuroscience↗

bioRxiv2016

Dissecting the role of non-coding RNAs in the accumulation of amyloid and tau neuropathologies in Alzheimer’s disease

BackgroundGiven multiple studies of brain microRNA (miRNA) in relation to Alzheimers disease (AD) with few consistent results and the heterogeneity of this disease, the objective of this study was to explore their mechanism by evaluating their relation to different elements of Alzheimers disease pathology, confounding factors and mRNA expression data from the same subjects in the same brain region.\n\nResultsWe report analyses of expression profiling of miRNA (n=700 subjects) and lincRNA (n=540 subjects) from the dorsolateral prefrontal cortex of individuals participating in two longitudinal cohort studies of aging. Evaluating well-established (miR-132, miR-129), we confirm their association with pathologic AD in our dataset, and then characterize their in disease role in terms of neuritic {beta}-amyloid plaques and neurofibrillary tangle pathology. Additionally, we identify one new miRNA (miR-99) and four lincRNA that are associated with these traits. Many other previously reported associations of microRNA with AD are associated with the confounders quantified in our longitudinal cohort. Finally, by performing analyses integrating both miRNA and RNA sequence data from the same individuals (525 samples), we characterize the impact of AD associated miRNA on human brain expression: we show that the effects of miR-132 and miR-129-5b converge on certain genes such as EP300 and find a role for miR200 and its target genes in AD using an integrated miRNA/mRNA analysis.\n\nConclusionsOverall, miRNAs play a modest role in human AD, but we observe robust evidence that a small number of miRNAs are responsible for specific alterations in the cortical transcriptome that are associated with AD.

neuroscience↗