Biology subjects

Bhandari, R.

Publications and source records attributed to Bhandari, R..

30 records · Page 2Linked to original sources

bioRxiv2022

Biotic and abiotic stress distinctly drive the phyllosphere microbial community structure

While the physiological and transcriptional response of the host to biotic and abiotic stresses have been intensely studied, little is known about the resilience of associated microbiomes and their contribution towards tolerance to these stresses. We evaluated the impact of one such abiotic stress, elevated tropospheric ozone (O3), under open-top chamber field conditions on host susceptibility and phyllosphere microbiome associated with pepper cultivars resistant and susceptible to Xanthomonas. Pathogen challenge resulted in distinct microbial community structures in both cultivars under an ambient environment. Elevated O3 alone affected microbial community structure associated with resistant cultivar but not the susceptible cultivar, indicating the role of host genotypic background in response to abiotic stress. Elevated O3 did not influence overall host susceptibility but did increase disease severity on the resistant cultivar, indicating a possible compromise in the resistance. Interestingly, combined stress resulted in a shift in microbial composition and structure like that observed with pathogen challenge alone. It indicates the possible prioritization of community response towards the most significant stress and pathogen being most influential regardless of the cultivar. Despite community composition differences, overall functional redundancy was observed in the phyllosphere community. To gain insights into community-level interactions, network topology assessment indicated a stable network with enhanced taxon connectedness upon pathogen challenge. However, an observation of destabilized random network with a shift in hub taxa in the presence of combined stress warrants future studies on the consequences of such unstable microbial communities on host response to pathogens in the face of climate change.

ecology↗

bioRxiv2022

Cellular, Molecular, and Enzymatic Signatures ofThrombi are Vascular Bed-Dependent

BackgroundThe contribution of arterial and venous thrombi to vascular remodeling is unclear. While catheter-extraction of thrombus in cerebrovascular accident (CVA) is time-sensitive, similar urgency is rare in managing venous thromboembolism (VTE). ObjectivesOur goal was to determine molecular cellular signatures of thrombus extracted by catheter from various vascular beds to gain insight into vascular remodeling. MethodsTwenty-five patients underwent catheter-directed thrombectomy (CDT), 13 for acute CVA, 8 for pulmonary embolism (PE), and 4 for deep vein thrombosis (DVT). Protein and RNA extracted from thrombus was evaluated by immunoblotting and sequencing, respectively. Thrombus-derived enzymes for which substrate is present in the blood vessel wall were examined for enzymatic activity. ResultsTime from symptom onset to thrombus extraction was 7.7 {+/-} 1.9 hours for CVA and 109 {+/-} 55 hours for VTE. Protein concentration, white blood cell and red blood cell content were all greater in venous compared with arterial thrombus while platelet content was similar. Both venous and arterial thrombus contained multiple Matrix Metalloproteinase (MMP) isoforms. MMP9 specific activity was greater in venous than in arterial thrombus (57 {+/-} 6 ng/mL.g protein-1 vs. 24 {+/-} 8 ng/mL.g protein-1, P=0.0051). ConclusionsArterial and venous thrombus have dissimilar phenotypes, each with biologically-active enzymes known to remodel blood vessels, and enzymatic activity proportional to the white blood cell content which increases with thrombus age. These data suggest a mechanistically-important role for early CDT to avoid the consequences of irreversible vascular remodeling. Condensed AbstractEmergent extraction of acute thrombus from arterial vascular beds restores limb and end-organ perfusion and is widely-accepted to be the standard of care. Extraction of thrombus from venous vascular beds, however, is rarely considered urgent, even though many patients subsequently develop debilitating symptoms. By capitalizing on privileged thrombus extracted from multiple vascular beds, we gained mechanistic insight regarding the cellular composition and cell-derived enzymes secreted from thrombus that may remodel the vessel wall. This study shows thrombi are biologically-active entities, continuously recruiting circulating cells that secrete enzymes both proportional to thrombus age and the time of patient presentation.

biochemistry↗

bioRxiv2021

Depth-resolved intersubject functional correlation of 7T BOLD signals reveals increased stimulus related information sharing across deep layers in premotor and parietal nodes for predictable actions

While the brain regions involved in action observation are relatively well documented in humans and primates, how these regions communicate to help understand and predict actions remains poorly understood. Traditional views emphasized a feed-forward architecture in which visual features are organized into increasingly complex representations that feed onto motor programs in parietal and then premotor cortices where the matching of observed actions upon the observers own motor programs contributes to action understanding. Predictive coding models place less emphasis on feed-forward connections and propose that feed-back connections from premotor regions back to parietal and visual neurons represent predictions about upcoming actions that can supersede visual inputs when actions become predictable, with visual input then merely representing prediction errors. Here we leverage the notion that feed-back connections target specific cortical layers to help adjudicate across these views. Specifically, we test whether observing sequences of hand actions in their natural order, which permits participants to predict upcoming actions, triggers more feed-back input to parietal regions than seeing the same actions in a scrambled sequence that hinders making predictions. Using submillimeter fMRI acquisition at 7T, we find that watching predictable sequences triggers more action-related activity (as measured using intersubject functional correlation) in the parietal cortical area PFt at depths receiving feed-back connections (layers III and V/VI) than watching the exact same actions in scrambled and hence unpredictable sequence. In addition, functional connectivity analysis performed using intersubject functional connectivity confirms that these increased action-related signals in PFt could originate from ventral premotor region BA44. This data showcases the utility of intersubject functional correlation in combination with 7T MRI to explore the architecture of social cognition under more naturalistic conditions, and provides evidence for models that emphasize the importance of feed-back connections in action prediction.

neuroscience↗

bioRxiv2021

Ecdysone exerts biphasic control of regenerative signaling, coordinating the completion of regeneration with developmental progression

In Drosophila melanogaster, loss of regenerative capacity in wing imaginal discs coincides with an increase in systemic levels of the steroid hormone ecdysone, a key coordinator of their developmental progression. Regenerating discs release the relaxin hormone Dilp8, which limits ecdysone synthesis and extends the regenerative period. Here, we describe how regenerating tissues produce a biphasic response to ecdysone levels: lower concentrations of ecdysone promote local and systemic regenerative signaling, whereas higher concentrations suppress regeneration through the expression of broad splice isoforms. Ecdysone also promotes the expression of wingless during both regeneration and normal development through a distinct regulatory pathway. This dual role for ecdysone explains how regeneration can still be completed successfully in dilp8- mutant larvae: higher ecdysone levels increase the regenerative activity of tissues, allowing regeneration to reach completion in a shorter time. From these observations, we propose that ecdysone hormone signaling functions to coordinate regeneration with developmental progression. Summary StatementEcdysone coordinates regenerative activity with developmental progression through the biphasic, concentration-dependent activation, and suppression of regenerative signaling.

developmental biology↗

bioRxiv2020

Ecdysone regulates the Drosophila imaginal disc epithelial barrier, determining the duration of regeneration checkpoint delay

Regeneration of Drosophila imaginal discs, larval precursors to adult tissues, produces a systemic response, a regeneration checkpoint that coordinates regenerative growth with developmental progression. This regeneration checkpoint is coordinated by the release of the relaxin-family peptide Dilp8 from regenerating tissues. Secreted Dilp8 protein can be detected within the imaginal disc lumen. The disc epithelium separates from the lumen from the larval hemolymph and the targets for Dilp8 activity in the brain and prothoracic gland. Here we demonstrate that the imaginal disc epithelial barrier limits Dilp8 signaling and checkpoint delay. We also observe that the wing imaginal disc barrier becomes more restrictive during development, becoming impermeable only at end of the final larval instar. This change in barrier permeability is driven by the steroid hormone ecdysone and correlates with changes in localization of Coracle, a component of the septate junctions that is required for the late, impermeable epithelial barrier. Based on these observations, we propose that the imaginal disc epithelial barrier regulates the duration of the regenerative checkpoint, providing a mechanism by which tissue function can signal the completion of regeneration. Summary StatementEcdysone signaling directs the Drosophila third instar imaginal disc epithelial barrier to mature, becoming more restrictive. This mature barrier limits Dilp8 signaling and determines the duration of the regeneration checkpoint.

developmental biology↗

bioRxiv2020

IP6K1 upregulates the formation of processing bodies by promoting proteome remodeling on the mRNA cap

Inositol hexakisphosphate kinases (IP6Ks) are ubiquitously expressed small molecule kinases that catalyze the conversion of the inositol phosphate IP6 to 5-IP7. IP6Ks have been reported to influence cellular functions by protein-protein interactions independent of their enzymatic activity. Here, we show that IP6K1 regulates the formation of processing bodies (P-bodies), which are cytoplasmic ribonucleoprotein granules that serve as sites for storage of translationally repressed mRNA. Cells with reduced levels of IP6K1 display a dramatic reduction in the number of P-bodies, which can be restored by the expression of active or catalytically inactive IP6K1. IP6K1 does not localize to P-bodies, but instead facilitates the formation of P-bodies by promoting translation suppression. We demonstrate that IP6K1 is present on ribosomes, where it interacts with proteins that constitute the mRNA decapping complex - the scaffold protein EDC4, activator proteins DCP1A/B, and the decapping enzyme DCP2. IP6K1 also interacts with components of the eIF4F translation initiation complex - the scaffolding protein eIF4G1, the RNA helicase eIF4A2, and the cap binding protein eIF4E. The RNA helicase DDX6 and the eIF4E binding protein 4E-T are known to promote translation suppression to facilitate P-body formation. We show that IP6K1 binds to DDX6 and promotes the interaction of DDX6 and 4E-T with the cap binding protein eIF4E, and also enhances the binding between DDX6 and EDC4, thus acting to suppress mRNA translation and promote mRNA decapping. Our findings unveil IP6K1 as a novel facilitator of proteome remodelling on the mRNA cap, tipping the balance in favour of translation repression over initiation, and thus leading to the formation of P-bodies.

cell biology↗

bioRxiv2020

A pyro-phosphodegron controls MYC polyubiquitination to regulate cell survival

The transcription factor MYC regulates cell survival and growth, and its level is tightly controlled in normal cells. Here, we report that serine pyrophosphorylation - an enigmatic posttranslational modification triggered by inositol pyrophosphate signaling molecules - controls MYC levels via regulated protein degradation. We find that endogenous MYC is stabilized and less polyubiquitinated in cells with reduced inositol pyrophosphates. We show that the inositol pyrophosphate 5-IP7 transfers its high-energy beta phosphate moiety to pre-phosphorylated serine residues in the central PEST domain of MYC. Pyrophosphorylation of MYC promotes its interaction with the E3 ubiquitin ligase FBW7, thereby enhancing MYC polyubiquitination and degradation. FBW7 can bind directly to the PEST domain of MYC in a pyrophosphorylation-dependent manner. A stabilized, pyrophosphorylation-deficient form of MYC increases cell death during growth stress in untransformed cells, and promotes cell proliferation in response to mitogens. Thus, control of MYC stability through a novel pyro-phosphodegron provides unexpected insight into the regulation of cell survival in response to environmental cues.

cell biology↗

bioRxiv2019

Does higher sampling rate (Multiband + SENSE) benefit the detection of task correlated BOLD for cognitive neuroscience applications at 3T?

Multiband (MB) or Simultaneous multi-slice (SMS) acquisition schemes allow the acquisition of MRI signals from more than one spatial coordinate at a time. Commercial availability has brought this technique within the reach of many neuroscientists and psychologists. Most early evaluation of the performance of MB acquisition employed resting state fMRI or the most basic tasks. In this study, we tested whether the advantages of using MB acquisition schemes generalize to group analyses using a cognitive task more representative of typical cognitive neuroscience applications. Twenty-three subjects were scanned on a Philips 3T scanner using five sequences up to eight-fold acceleration with MB-factors 1 to 4, SENSE factors up to 2 and corresponding TRs of 2.45s down to 0.63s, while they viewed (i) movies showing complex actions with hand object interactions and (ii) control movies without hand object interaction. Using random effects group-level, voxel-wise analysis we found that all sequences were able to detect the basic action observation network known to be recruited by our task. The highest t-values were found for sequences with MB4 acceleration. For the MB1 sequence, a 50% bigger voxel volume was needed to reach comparable t-statistics. The group-level t-values for resting state networks (RSNs) were also highest for MB4 sequences. Here the MB1 sequence with larger voxel size did not perform comparable to the MB4 sequence. Altogether, we can thus recommend the use of MB4 (and SENSE 1.5 or 2) on a Philips scanner when aiming to perform group-level analyses using cognitive block design fMRI tasks and voxel sizes in the range of cortical thickness (e.g. 2.7mm isotropic). While results will not be dramatically changed by the use of multiband, our results suggest that MB will bring a moderate but significant benefit.

neuroscience↗

bioRxiv2019

Challenges in assessing voxel-wise single-subject level benefits of MB acceleration

Multiband (MB) acceleration of functional magnetic resonance imaging has become more widely available to neuroscientists. Here we compare MB factors of 1, 2 and 4 while participants view complex hand actions vs. simpler hand movements to localize the action observation network. While in a previous study, we show that MB4 shows moderate improvements in the group-level statistics, here we explore the impact it has on single subject statistics. We find that MB4 provides an increase in p values at the first level that is of medium effect size compared to MB1, providing moderate evidence across a number of voxels that MB4 indeed improves single subject statistics. This effect was localized mostly within regions that belong to the action observation network. In parallel, we find that Cohens d at the single subject level actually decreases using MB4 compared to MB1. Intriguingly, we find that subsampling MB4 sequences, by only considering every fourth acquired volume, also leads to increased Cohens d values, suggesting that the FAST algorithm we used to correct for temporal auto-correlation may over-penalize sequences with higher temporal autocorrelation, thereby underestimating the potential gains in single subject statistics offered by MB acceleration, and alternative methods should be explored. In summary, considering the moderate gains in statistical values observed both at the group level in our previous study and at the single subject level in this study, we believe that MB technology is now ripe for neuroscientists to start using MB4 acceleration for their studies, be it to accurately map activity in single subjects of interest (e.g. for presurgical planning or to explore rare patients) or for the purpose of group studies.

neuroscience↗

bioRxiv2019

Recently emerged and diverse lineages of Xanthomonas perforans have independently evolved through plasmid acquisition and homologous recombination originating from multiple Xanthomonas species

Xanthomonas perforans is the predominant pathogen responsible for bacterial leaf spot of tomato and X. euvesicatoria of pepper in the southeast United States. Previous studies have indicated significant changes in the X. perforans population collected from Florida tomato fields over the span of two decades including a shift in race, diversification into three genetic groups, and host range expansion to pepper. Recombination originating from X. euvesicatoria was identified as the primary factor driving the diversification of X. perforans in Florida. The aim of this study was to genetically characterize X. perforans strains that were isolated from tomato and pepper plants grown in Alabama and compare them to the previously published genomes available from GenBank. Surprisingly, a maximum likelihood phylogeny coupled with a Bayesian analysis of population structure revealed the presence of two novel genetic groups in Alabama, which each harbored a different transcription activation-like effector (TALE). While one TALE, avrHah1, was associated with adaptation of X. perforans to pepper, the other was identified as a new class within the avrBs3 family, designated here as pthXp1. Examination of patterns of homologous recombination between X. perforans and other closely related Xanthomonas spp. indicated that the lineages identified here emerged in part through recent recombination events originating from xanthomonads associated with diverse hosts of isolation. Our results also suggest that the evolution of pathogenicity to pepper has likely emerged independently within X. perforans and in one lineage, was associated with the recombination-mediated remodeling of the Xps type II secretion and TonB transduction systems.\n\nImportanceThe emergence of novel pathogen lineages has important implications in the sustainability of genetic resistance as a disease management tool in agricultural ecosystems. In this study, we identified two novel lineages of X. perforans in Alabama. While one lineage was isolated from symptomatic pepper plants, confirming the host range expansion of X. perforans, the other lineage was isolated from tomato and acquired a novel transcription activation-like effector, pthXp1. Unlike AvrBs4, PthXp1overcomes Bs4-mediated resistance in tomato, indicating the evolution of this novel lineage towards fitness on this host. Our findings also show that different phylogenetic groups of the pathogen have experienced independent recombination events originating from multiple Xanthomonas species. This suggests a continuous gene flux between related xanthomonads associated with diverse plant hosts which results in the emergence of novel pathogen lineages and associated phenotypes, including host range expansion.

genomics↗

bioRxiv2018

Action perception recruits the cerebellum and is impaired in spinocerebellar ataxia patients

Our cerebellum has been proposed to generate prediction signals that may help us plan and execute our motor programs. However, to what extent our cerebellum is also actively involved in perceiving the action of others remains to be elucidated. Using fMRI, we show here that observing goal-directed hand actions of others bilaterally recruits cerebellar Lobules VI, VIIb and VIIIa. Moreover, whereas healthy subjects (n=31) were found to be able to discriminate subtle differences in the kinematics of observed limb movements of others, patients suffering from spinocerebellar ataxia type 6 (SCA6; n=21) were severely impaired in performing such tasks. Our data suggest that the human cerebellum is actively involved in perceiving the kinematics of the hand actions of others and that SCA6 patients deficits include a difficulty in perceiving the actions of other individuals. This finding alerts us to the fact that cerebellar disorders can alter social cognition. Given that impairments in social cognition have been reported to be one of the most debilitating consequences of neurological disorders, this finding may be relevant to improving the quality of life of patients and their families.

neuroscience↗

bioRxiv2018

Deacetylation of catalytic lysine in CDK1 is essential for Cyclin-B binding and cell cycle

Cyclin-dependent-kinases (CDKs) are essential for cell cycle progression. While dependence of CDK activity on Cyclin levels is established, molecular mechanisms that regulate their binding are less studied. Here, we show that CDKl:Cyclin-B interactions are regulated by acetylation, which was hitherto unknown. We demonstrate that cell cycle dependent acetylation of the evolutionarily conserved catalytic lysine in CDK1 or eliminating its charge state abrogates Cyclin-B binding. Opposing activities of SIRT1 and P300 regulate acetylation, which marks a reserved pool of CDK1. Our high resolution structural analyses into the formation of kinase competent CDK1: Cyclin-B complex have unveiled long-range effects of catalytic lysine in configuring the CDK1 interface for Cyclin-B binding. Cells expressing acetylation mimic mutant of Cdc2 in yeast are arrested in G2 and fail to divide. Thus, by illustrating cell cycle dependent deacetylation as a determinant of CDK1:Cyclin-B interaction, our results redefine the current model of CDK1 activation and cell cycle progression.

cell biology↗