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Banerjee, A.

Publications and source records attributed to Banerjee, A..

At least 145 records · Page 8Linked to original sources

Preservation of neural synchrony at peak alpha frequency via global synaptic scaling compensates for white matter structural decline over adult lifespan

We propose that preservation of functional integration, estimated from measures of neural synchrony, is a key neurocompensatory mechanism associated with healthy human ageing. To support this proposal, we demonstrate how phase-locking at peak alpha frequency from Magnetoencephalography (MEG) data is invariant over lifespan in a large cohort of human participants, aged 18-88 years. Using empirically derived connection topologies from diffusion tensor imaging (DTI) data, we create an in-silico model of whole-brain alpha dynamics. We show that enhancing inter-areal coupling can cancel the effect of increased axonal transmission delay associated with age-related degeneration of white matter tracts and thus, preserve neural synchrony. Together with analytical solutions for non-biological all-to-all connection scenarios, our model establishes the theoretical principles by which frequency slowing with age, frequently observed in the alpha band in diverse populations, can be viewed as an epiphenomenon of the underlying neurocompensatory mechanisms.

neuroscience↗

A novel innate pathogen sensing strategy involving ubiquitination of bacterial surface proteins

Sensing of pathogens by ubiquitination is critical for maintaining cytosolic sanctity. However, universal ubiquitination targets on bacteria, especially of proteinaceous origin, remain unidentified. Here, we unveil a novel strategy, involving recognition of degron-like motifs for identification of first protein-based ubiquitination substrates on phylogenetically distinct bacteria. Such motifs can form a new class of intra-cytosolic pathogen associated molecular patterns (PAMPs) as their incorporation enables identification of non-ubiquitin targets by host Ub-ligases. We find SCFFBW7 E3-ligase, supported by the regulatory kinase, GSK3{beta}, is crucial for effective pathogen detection and clearance. This may explain the enhanced risk of infections in Chronic Lymphocytic Leukaemia patients bearing FBXW7 mutations. We conclude that exploitation of such ubiquitous pathogen sensing strategy allows conservation of cellular resources and boost anti-microbial immunity. One Sentence SummaryUbiquitination of bacterial surface proteins fosters sensing and clearance of diverse pathogens

microbiology↗

Region-specific KCC2 rescue by rhIGF-1 and oxytocin in a mouse model of Rett syndrome

Rett syndrome (RTT) is characterized by dysfunction in neuronal excitation/inhibition (E/I) balance, potentially impacting seizure susceptibility via deficits in K+/Cl- cotransporter 2 (KCC2) function. Mice lacking the Methyl-CpG binding protein 2 (MeCP2) recapitulate many symptoms of RTT, and recombinant human insulin-like growth factor-1 (rhIGF-1) restores KCC2 expression and E/I balance in MeCP2 KO mice. However, clinical trial outcomes of rhIGF-1 in RTT have been variable, and increasing its therapeutic efficacy is highly desirable. To this end, the neuropeptide oxytocin (OXT) is promising, as it also critically modulates KCC2 function during early postnatal development. We measured basal KCC2 expression levels in MeCP2 KO mice and identified three key frontal brain regions showing KCC2 alterations in young adult mice but not in postnatal P10 animals. We thus hypothesized that deficits in an IGF-1/OXT signaling crosstalk modulating KCC2 may occur in RTT during postnatal development. Consistently, we detected alterations of IGF-1 receptor (IGF-1R) and OXT receptor (OXTR) levels in those brain areas. rhIGF-1 and OXT treatments in KO mice rescued KCC2 expression in a region-specific and complementary manner. These results suggest that region-selective combinatorial pharmacotherapeutic strategies could be the most effective at normalizing E/I balance in key brain regions subtending the RTT pathophysiology.

neuroscience↗

Neural network modeling of differential binding between wild-type and mutant CTCF reveals putative binding preferences for zinc fingers 1-2

BackgroundMany transcription factors (TFs), such as multi zinc-finger (ZF) TFs, have multiple DNA binding domains (DBDs) with multiple components, and deciphering the DNA binding motifs of individual components is a major challenge. One example of such a TF is CCCTC-binding factor (CTCF), a TF with eleven ZFs that plays a variety of roles in transcriptional regulation, most notably anchoring DNA loops. Previous studies found that CTCF zinc fingers (ZFs) 3-7 bind CTCFs core motif and ZFs 9-11 bind a specific upstream motif, but the motifs of ZFs 1-2 have yet to be identified. ResultsWe developed a new approach to identifying the binding motifs of individual DBDs of a TF through analyzing chromatin immunoprecipitation sequencing (ChIP-seq) experiments in which a single DBD is mutated: we train a deep convolutional neural network to predict whether wild-type TF binding sites are preserved in the mutant TF dataset and interpret the model. We applied this approach to mouse CTCF ChIP-seq data and, in addition to identifying the known binding preferences of CTCF ZFs 3-11, we identified a GAG binding motif for ZF1 and a weak ATT binding motif for ZF2. We analyzed other CTCF datasets to provide additional evidence that ZFs 1-2 interact with the motifs we identified, and we found that the presence of the motif for ZF1 is associated with Ctcf peak strength. ConclusionsOur approach can be applied to any TF for which in vivo binding data from both the wild-type and mutated versions of the TF are available, and our findings provide an unprecedently comprehensive understanding of the binding preferences of CTCFs DBDs.

genomics↗

BubR1 recruitment to the kinetochore via Bub1 enhances Spindle Assembly Checkpoint signaling

During mitosis, unattached kinetochores in a dividing cell activate the Spindle Assembly Checkpoint (SAC) and delay anaphase onset by generating the anaphase-inhibitory Mitotic Checkpoint Complex (MCC). These kinetochores generate the MCC by recruiting MCC constituent proteins, including BubR1. In principle, BubR1 recruitment to signaling kinetochores should increase its local concentration and promote MCC formation. However, in human cells BubR1 is mainly thought to sensitize the SAC to silencing; whether BubR1 localization to signaling kinetochores per se enhances SAC signaling activity remains unknown. Therefore, we used ectopic SAC activation systems (eSAC) to isolate two molecules that recruit BubR1 to the kinetochore: the checkpoint protein Bub1 and the KI and MELT motifs in the kinetochore protein KNL1, and observed their contribution to eSAC signaling. Our quantitative analyses and mathematical modeling show that the Bub1-mediated BubR1 recruitment to the human kinetochore promotes SAC signaling and highlight BubR1s dual role of directly strengthening the SAC and indirectly silencing it.

cell biology↗

Unsupervised characterization of dynamic functional connectivity reveals age-associated differences in temporal stability and connectivity states during rest and task

Understanding brain functions as an outcome of underlying neuro-cognitive network mechanisms in rest and task requires accurate spatiotemporal characterization of the relevant functional brain networks. Recent endeavours of the Neuroimaging community to develop the notion of dynamic functional connectivity is a step in this direction. A key goal is to detect what are the important events in time that delimits how one functional brain network defined by known patterns of correlated brain activity transitions into a "new" network. Such characterization can also lead to more accurate conceptual realization of brain states, thereby, defined in terms of time-resolved correlations. Nonetheless, identifying the canonical temporal window over which dynamic functional connectivity is operational is currently based on an ad-hoc selection of sliding windows that can certainly lead to spurious results. Here, we introduce a data-driven unsupervised approach to characterize the high dimensional dynamic functional connectivity into dynamics of lower dimensional patterns. The whole-brain dynamic functional connectivity states bearing functional significance for task or rest can be explored through the temporal correlations, both short and long range. The present study investigates the stability of such short- and long-range temporal correlations to explore the dynamic network mechanisms across resting state, movie viewing and sensorimotor action tasks requiring varied degrees of attention. As an outcome of applying our methods to the fMRI data of a healthy ageing cohort we could quantify whole-brain temporal dynamics which indicates naturalistic movie watching task is closer to resting state than the sensorimotor task. Our analysis also revealed an overall trend of highest short range temporal network stability in the sensorimotor task, followed by naturalistic movie watching task and resting state that remains similar in both young and old adults. However, the stability of neurocognitive networks in the resting state in young adults is higher than their older counterparts. Thus, healthy ageing related differences in quantification of network stability along task and rest provides a blueprint of how our approach can be used for cohort studies of mental health and neurological disorders.

neuroscience↗

Systematic genome-scale identification of host factors for SARS-CoV-2 infection across models yields a core single gene dependency; ACE2

SARS-CoV-2, depends on host cell components for replication, therefore the identification of virus-host dependencies offers an effective way to elucidate mechanisms involved in viral infection. Such host factors may be necessary for infection and replication of SARS-CoV-2 and, if druggable, presents an attractive strategy for anti-viral therapy. We performed genome wide CRISPR knockout screens in Vero E6 cells and 4 human cell lines including Calu-3, Caco-2, Hek293 and Huh7 to identify genetic regulators of SARS-CoV-2 infection. Our findings identified only ACE2, the cognate SARS-CoV-2 entry receptor, as a common host dependency factor across all cell lines, while all other host genes identified were cell line specific including known factors TMPRSS2 and CTSL. Several of the discovered host-dependency factors converged on pathways involved in cell signalling, lipid metabolism, immune pathways and chromatin modulation. Notably, chromatin modulator genes KMT2C and KDM6A in Calu-3 cells had the strongest impact in preventing SARS-CoV-2 infection when perturbed. Overall, the network of host factors that have been identified will be broadly applicable to understanding the impact of SARS-CoV-2 on human cells and facilitate the development of host-directed therapies. IN BRIEFSARS-CoV-2, depends on host cell components for infection and replication. Genome-wide CRISPR screens were performed in multiple human cell lines to elucidate common host dependencies required for SARS-CoV-2 infection. Only ACE2, the cognate SARS-CoV-2 entry receptor, was common amongst cell lines, while all other host genes identified were cell line specific, several of which converged on pathways involved in cell signalling, lipid metabolism, immune pathways, and chromatin modulation. Overall, a network of host factors was identified that will be broadly applicable to understanding the impact of SARS-CoV-2 on human cells and facilitate productive targeting of host genes and pathways. HIGHLIGHTS- Genome-wide CRISPR screens for SARS-CoV-2 in multiple human cell lines - Identification of wide-ranging cell-type dependent genetic dependencies for SARS-CoV-2 infection - ACE2 is the only common host factor identified across different cell types

systems biology↗

Differential ubiquitination as an effective strategy employed by Blood-Brain Barrier for prevention of bacterial transcytosis

The protective mechanisms of blood-brain barrier (BBB) prohibiting entry of blood borne pathogens and toxins into the central nervous system (CNS) is critical for maintenance of homeostasis in the brain. These include various forms of intracellular defence mechanisms which are vital to block bacterial transcytosis, the major route of trafficking adopted by meningeal pathogens to transit into the CNS. However, mechanistic details of the defence mechanisms and their exploitation to prevent bacterial meningitis remain unexplored. In this study, we established that brain endothelium driven ubiquitination acts as a major intracellular defence mechanism for clearance of S. pneumoniae, a critical neurotropic pathogen, during its transit through BBB. Our findings suggest that brain endothelium employs differential ubiquitination with either K48 or K63-Ub chain topologies as an effective strategy to target SPN towards diverse killing pathways. While K63-Ub decoration triggers autophagic killing, K48-Ub directs pneumococcus exclusively to the proteasome machinery. Indeed, time lapse fluorescence imaging involving proteasomal marker LMP2 revealed that in BBB, majority of the ubiquitinated SPN were cleared by proteasome. Fittingly, pharmacological inhibition of proteasome and autophagy pathway not only led to exclusive accumulation of K48-Ub and K63-Ub marked SPN, respectively, but also triggered significant increment in intracellular SPN burden. Moreover, genetic impairment of formation of either K48 or K63-Ub chain topology demonstrated that though both chain types play important roles in disposal of intracellular SPN, K48-Ub chains and subsequent proteasomal degradation has more pronounced contribution towards ubiquitinated SPN killing in brain endothelium. Collectively, these observations for the first time illustrated a pivotal role of differential ubiquitination in orchestrating a symphony of intracellular defence mechanisms blocking pathogen trafficking into the brain which could be further exploited to prevent bacterial CNS infections. IMPORTANCEAmong the different cellular barriers present in the human body, Blood-Brain Barrier (BBB) is unique as it not only provides structural integrity but also protects the central nervous system (CNS) from pathogen invasion. In recent past, ubiquitination, which is known to be involved in protein quality control and cellular homeostasis, has been proven to be critically involved in pathogen clearance. In this study, employing S. pneumoniae as a model CNS pathogen, we wanted to decipher the critical contribution of ubiquitination in protective mechanism of BBB while tackling bacterial entry into the CNS. Our results suggest, that BBB deploys differential ubiquitination as an effective strategy to prevent neurotropic bacterial trafficking into the brain. By portraying a comprehensive picture of ubiquitin coat on SPN, we figured out that different ubiquitin chain topologies formed on the pneumococcus dictated the selection of downstream degradative pathways, namely, autophagy and proteasomal machinery. Amongst these, contribution of proteasomal system in clearance of pneumococcus was found to be more pronounced. Overall our study revealed how BBB deploys differential ubiquitination as a strategy to trigger autophagy and proteasomal system, which work in tandem to ensure brains identity as an immunologically sterile site.

microbiology↗

Intronic regulation of SARS-CoV-2 receptor (ACE2) expression mediated by immune signaling and oxidative stress pathways

The angiotensin-converting enzyme 2 (ACE2) protein has been highly studied as a key catalytic regulator of the renin-angiotensin system (RAS), involved in fluid homeostasis and blood pressure modulation. In addition to its important physiological role as a broadly-expressed membrane-bound protein, ACE2 serves as a cell-surface receptor for some viruses - most notably, coronaviruses such as SARS-CoV and SARS-CoV-2. Differing levels of ACE2 expression may impact viral susceptibility and subsequent changes to expression may be a pathogenic mechanism of disease risk and manifestation. Therefore, an improved understanding of how ACE2 expression is regulated at the genomic and transcriptional level may help us understand not only how the effects of pre-existing conditions (e.g., chronic obstructive pulmonary disease) may manifest with increased COVID-19 incidence, but also the mechanisms that regulate ACE2 levels following viral infection. Here, we initially perform bioinformatic analyses of several datasets to generate hypotheses about ACE2 gene-regulatory mechanisms in the context of immune signaling and chronic oxidative stress. We then identify putative non-coding regulatory elements within ACE2 intronic regions as potential determinants of ACE2 expression activity. We perform functional validation of our computational predictions in vitro via targeted CRISPR-Cas9 deletions of the identified ACE2 cis-regulatory elements in the context of both immunological stimulation and oxidative stress conditions. We demonstrate that intronic ACE2 regulatory elements are responsive to both immune signaling and oxidative-stress pathways, and this contributes to our understanding of how expression of this gene may be modulated at both baseline and during immune challenge. Our work supports the further pursuit of these putative mechanisms in our understanding, prevention, and treatment of infection and disease caused by ACE2-utilizing viruses such as SARS-CoV, SARS-CoV-2, and future emerging SARS-related viruses. Author SummaryThe recent emergence of the virus SARS-CoV-2 which has caused the COVID-19 pandemic has prompted scientists to intensively study how the virus enters human host cells. This work has revealed a key protein, ACE2, that acts as a receptor permitting the virus to infect cells. Much research has focused on how the virus physically interacts with ACE2, yet little is known on how ACE2 is turned on or off in human cells at the level of the DNA molecule. Understanding this level of regulation may offer additional ways to prevent or lower viral entry into human hosts. Here, we have examined the control of the ACE2 gene, the DNA sequence that instructs ACE2 protein receptor formation, and we have done so in the context of immune stimulation. We have indeed identified a number of DNA on/off switches for ACE2 that appear responsive to immuno-logical and oxidative stress. These switches may fine-tune how ACE2 is turned on or off before, during, and/or after infection by SARS-CoV-2 or other related coronaviruses. Our studies help pave the way for additional functional studies on these switches, and their potential therapeutic targeting in the future.

genetics↗

Preclinical evaluation of a SARS-CoV-2 mRNA vaccine PTX-COVID19-B

Safe and effective vaccines are needed to end the COVID-19 pandemic caused by SARS-CoV-2. Here we report the preclinical development of a lipid nanoparticle (LNP) formulated SARS-CoV-2 mRNA vaccine, PTX-COVID19-B. PTX-COVID19-B was chosen among three candidates after the initial mouse vaccination results showed that it elicited the strongest neutralizing antibody response against SARS-CoV-2. Further tests in mice and hamsters indicated that PTX-COVID19-B induced robust humoral and cellular immune responses and completely protected the vaccinated animals from SARS-CoV-2 infection in the lung. Studies in hamsters also showed that PTX-COVID19-B protected the upper respiratory tract from SARS-CoV-2 infection. Mouse immune sera elicited by PTX-COVID19-B vaccination were able to neutralize SARS-CoV-2 variants of concern (VOCs), including the B.1.1.7, B.1.351 and P.1 lineages. No adverse effects were induced by PTX-COVID19-B in both mice and hamsters. These preclinical results indicate that PTX-COVID19-B is safe and effective. Based on these results, PTX-COVID19-B was authorized by Health Canada to enter clinical trials in December 2020 with a phase 1 clinical trial ongoing (ClinicalTrials.gov number: NCT04765436). One Sentence SummaryPTX-COVID19-B is a SARS-CoV-2 mRNA vaccine that is highly immunogenic, safe, and effective in preventing SARS-CoV-2 infection in mice and hamsters and is currently being evaluated in human clinical trials.

immunology↗

Conserved in 186 countries the RBD fraction of SARS CoV-2 S-protein with in-silicoT500S mutation strongly blocks ACE2 rejecting the viral spike; A Molecular-docking analysis.

SARS-CoV-2 developed global-pandemic with millions of infections/deaths. Blocker/inhibitor of ACE2 and viral-spikes Receptor-Binding-Domain RBD-blockers are helpful. Here, conserved RBD (CUTs) from 186-countries were compared with WUHAN-Hu-1 wild-type by CLUSTAL-X2 and Structural-alignment using Pymol. The RBD of ACE2-bound nCOV2 crystal-structure (2.68[A]) 6VW1 was analyzed by Haddock-PatchDock. Extensive structural study/trial to introduce point/double/triple mutations in the following locations (Y489S/Y453S/T500S/T500Y)/(Y489S,Y453S/Y489S,T500S/Y489S,T500Y/Y453S,T500S/Y453S, T500Y)/ (Y489S,Y453S,T500S/Y489S,Y453S,T500Y) of CUT4 (most-effective) were tested with Swiss-Model-Expacy. Blind-docking of mutated-CUTs to ACE2 (6VW1) by Haddock-Hawkdock was performed and optimally complete-rejection of nCOV2 to ACE2 was noticed. Further, competitive-docking/binding-analyses were done by PRODIGY. Present results suggest that compared to the wild-spike, CUT4 showed extra LYS31-PHE490/GLN42-GLN498 bonding and lack of TYR41-THR500 interaction (in wild H-bond:2.639[A]) with ACE2 RBD. Mutated-CUT4 strongly binds with the ACE2-RBD, promoting TYR41-T500S (H-bond: 2.0[A] and 1.8[A])/T500Y (H-bond:2.6[A]) interaction and complete inhibition of ACE2 RBD-nCOV2. Mutant combinations T500S,Y489S,T500S and Y489S,Y453S,T500Y mostly blocked ACE2. Conclusively, CUT4-mutant rejects whole glycosylated-nCoV2 pre-dock/post-dock/competitive-docking conditions.

bioinformatics↗

Radio-pathomic maps of cell density identify glioma invasion beyond traditional MR imaging defined margins

Current MRI signatures of brain cancer often fail to identify regions of hypercellularity beyond the contrast enhancing region. Therefore, this study used autopsy tissue samples aligned to clinical MRIs in order to quantify the relationship between intensity values and cellularity, as well as to develop a radio-pathomic model to predict cellularity using MRI data. This study used 93 samples collected at autopsy from 44 brain cancer patients. Tissue samples were processed, stained for hematoxylin and eosin (HE) and digitized for nuclei segmentation and cell density calculation. Pre- and post-gadolinium contrast T1-weighted images (T1, T1C), T2 fluid-attenuated inversion recovery (FLAIR) images, and apparent diffusion coefficient (ADC) images calculated from diffusion imaging were collected from each patients final acquisition prior to death. In-house software was used to align tissue samples to the FLAIR image via manually defined control points. Mixed effect models were used to assess the relationship between single image intensity and cellularity for each image. An ensemble learner was trained to predict cellularity using 5 by 5 voxel tiles from each image, employing a 2/3-1/3 train-test split for validation. Single image analyses found subtle associations between image intensity and cellularity, with a less pronounced relationship within GBM patients. The radio-pathomic model was able to accurately predict cellularity in the test set (RMSE = 1015 cells/mm2) and identified regions of hypercellularity beyond the contrast enhancing region. We concluded that a radio-pathomic model for cellularity is able to identify regions of hypercellular tumor beyond traditional imaging signatures.

neuroscience↗

The archaeal triphosphate tunnel metalloenzyme SaTTM defines structural determinants for the diverse activities in the CYTH protein family

CYTH is a large protein superfamily that is conserved in all three domains of life with its unique triphosphate tunnel metalloenzyme (TTM) fold. Besides phosphatase functions, e.g. as RNA triphosphatase, inorganic polyphosphatase or thiamine triphosphatase, some CYTH orthologs cyclize nucleotide triphosphates to 3,5-cyclic nucleotides. So far, archaeal CYTH proteins are annotated as adenylyl cyclases although experimental evidence is lacking. To address this gap, we characterized a CYTH ortholog, SaTTM, from the crenarchaeote Sulfolobus acidocaldarius. Our initial in silico studies suggested a close relationship between archaeal CYTH enzymes and class IV adenylyl cyclases compared to the other CYTH-subclasses, but biochemical data showed no cyclic nucleotide production. Instead, our structural and functional analyses show a classical TTM behavior. The Ca2+-inhibited Michaelis complex indicates a two-metal ion reaction mechanism analogous to other TTMs. Different co-crystal structures of SaTTM further reveal conformational dynamics in SaTTM, let us to assume feedback inhibition in TTMs due to tunnel closure in the product state. Combining our structural insights with sequence-similarity network based in silico analysis, we further set out a firm molecular basis for distinguishing CYTH orthologs with phosphatase activities from class IV adenylyl cyclases. Major highlights- CyaB-like class IV adenylyl cyclase homologs in archaea are triphosphatases. - The co-crystal structure of SaTTM in sulfate and triphosphate bound state revealed conformational transition of the TTM tunnel during catalysis. - Atomic insights into TTM inhibition by calcium and pyrophosphate. - In silico and structure-function analysis revealed the molecular determinant for functional diversification among CYTH proteins.

biochemistry↗

MEG Oscillatory and Aperiodic neural dynamics contribute to different cognitive aspects of short-term memory decline through the lifespan

Neural communication or signal transmission in the brain propagates via distinct oscillatory frequency bands. With aging, the communication mediated by these frequency bands is hindered by noise, which arises from the increased stochastic variability in the baseline neural spiking. This increase in noise measured as 1/f power-law scaling reflects the global background noise and is often linked to impaired cognition in different tasks. In this study, we quantified the 1/f slope and intercept of MEG brain signal as a putative marker of neural noise and examined its effect on cognitive and metacognitive measures. We hypothesize that as neural communication becomes noisier with age, it impacts global information processing, whereas specific periodic features mediate local aspects of cognition. Using recently proposed parametric Fooof model, we first characterised the normative pattern of periodic and aperiodic features (temporal dynamics) across the lifespan, modelled via spectral peaks (Central frequency, power, bandwidth) and 1/f noise activity (slope and intercept) respectively. Secondly, how this Resting-State (RS) baseline shift in temporal dynamics of the signal is associated with various aspects of visual short-term memory (VSTM). Our results suggest that age-associated global change in noisy baseline affects global information processing and crucially impacts the oscillatory features, which relates to more local processing and selective behavioural measures in the VSTM task. Moreover, we suggest that the task-related differences observed across age groups are due to the baseline shift of periodic and aperiodic features. Significant statementAging is accompanied by the decline in cognitive functions and age itself is a major risk factor for Alzheimers Disease and other neurological conditions. Our study provides MEG 1/f aperiodic and periodic markers across the healthy adult lifespan and shows that different frequency bands and their spectral features mediate age-related changes across different brain regions, in multiple cognitive and metacognitive domains, which not only provides us with a better understanding of the aging process but would also help in better prevention of cognitive impairments. A clear characterization of the association between baseline MEG temporal dynamics, healthy aging and cognition, is established in this study.

neuroscience↗

Active microrheology using pulsed optical tweezers to probe viscoelasticity of Lamin A towards diagnosis of laminopathies

Lamins are nucleoskeletal proteins of mammalian cells that stabilize the structure and maintain the rigidity of the nucleus. These type V intermediate filament proteins which are predominantly of A and B types provide necessary tensile strength to the nucleus. Single amino acid missense mutations occurring all over the lamin A protein form a cluster of human diseases termed as laminopathies, a few of which principally affect the muscle and cardiac tissues responsible for load bearing functionalities of the body. One such mutation is lamin A350P which causes dilated cardiomyopathy in patients. It is likely that a change from alanine to proline in the -helical 2B rod domain of the protein might severely disrupt the propensity of the filaments to polymerise into functional higher order structures required to form a fully functional lamina with its characteristic elasticity. In this study, we validate for the very first time, the application of active microrheology employing oscillating optical tweezers to investigate any alterations in the visco-elastic parameters of the mutant protein meshwork in vitro, which might translate into possible changes in nuclear plasticity. We confirm our findings from this robust yet fast method by imaging both the wild type and mutant lamins using a super resolution microscope, and observe changes in the mesh size which explain our measured changes in the viscoelastic parameters of the lamins. This method could naturally be extended to conduct microrheological measurements on any intermediate filament protein or any protein endowed with elastic behavior, with minor schematic modifications, thus bearing significant implications in laminopathies and other diseases which are associated with changes in structural rigidity of any cellular organelle. SignificanceLamin A mutations produce an array of diseases termed as laminopathies which are primarily characterized by alteration of elastic behavior of the nucleus which in turn leads to defects in mechanotransduction. This is the first report in the lamin arena which shows a fast, accurate and direct quantification of elastic moduli of lamin A using optical tweezers-based microrheology. This has very significant implications and can be registered to be a robust and universal method that could also be suitably used for probing changes in elastic properties of any proteins or surfactants in a disease scenario such as SARS-Cov2 (Covid-19), which is pandemic at this time.

biophysics↗

Pyruvate oxidase as a key determinant of pneumococcal viability during transcytosis across the blood-brain barrier endothelium

Streptococcus pneumoniae (SPN / pneumococcus), invades myriad of host tissues following efficient breaching of cellular barriers. However, strategies adopted by pneumococcus for evasion of host intracellular defences governing successful transcytosis across host cellular barriers remain elusive. In this study, using brain endothelium as a model host barrier, we observed that pneumococcus containing endocytic vacuoles (PCVs) formed following SPN internalization into brain microvascular endothelial cells (BMECs), undergo early maturation and acidification, with a major subset acquiring lysosome-like characteristics. Exploration of measures that would preserve pneumococcal viability in the lethal acidic pH of these lysosome-like vacuoles revealed a critical role of the two-component system response regulator, CiaR, which has been previously implicated in induction of acid tolerance response. Pyruvate oxidase (SpxB), a key sugar metabolizing enzyme that catalyses oxidative decarboxylation of pyruvate to acetyl phosphate, was found to contribute to acid stress tolerance, presumably via acetyl phosphate-mediated phosphorylation and activation of CiaR, independent of its cognate kinase CiaH. Hydrogen peroxide, the by-product of SpxB catalysed reaction, was also found to improve pneumococcal intracellular survival, by oxidative inactivation of lysosomal cysteine cathepsins, thus compromising the degradative capacity of the host lysosomes. Expectedly, a {Delta}spxB mutant was found to be significantly attenuated in its ability to survive inside the BMEC endocytic vacuoles, reflecting in its reduced transcytosis ability. Collectively, our studies establish SpxB as an important virulence determinant facilitating pneumococcal survival inside host cells, ensuring successful trafficking across host cellular barriers. AUTHOR SUMMARYEukaryotic cells which constitute host barriers have innate immune defences to restrict microbial passage into sterile compartments. This necessitates need for pathogens to devise strategies to evade these, for successful establishment of disease. In this study, by focussing on the blood-brain barrier endothelium, we investigate the mechanisms which enable the opportunistic pathogen Streptococcus pneumoniae to traverse host barriers. Pyruvate oxidase, a pneumococcal sugar metabolizing enzyme was found to play a critical role in this key event, owing to production of acetyl phosphate and hydrogen peroxide via its enzymatic activity. On one hand, acetyl phosphate, by contributing to activation of acid tolerance stress response, enabled pneumococci to maintain viability in the lethal acidic pH of the lysosome-like vacuoles inside brain endothelium. On the other, hydrogen peroxide, was found to oxidise and inactivate a subset of degradative lysosomal enzymes. This two-pronged approach, aided by pyruvate oxidase, enabled pneumococci to evade intracellular degradation for successful transcytosis across the endothelium. Thus, pyruvate oxidase is a key determinant of pneumococcal virulence and hence can potentially serve as a viable candidate for therapeutic interventions for better management of invasive pneumococcal diseases.

microbiology↗

Molecular and functional architecture of striatal dopamine release sites

Dopamine controls striatal circuit function, but its transmission mechanisms are not well understood. We recently showed that dopamine secretion requires RIM, suggesting that it occurs at active zone-like sites similar to conventional synapses. Here, we establish using a systematic conditional gene knockout approach that Munc13 and Liprin-, active zone proteins for vesicle priming and release site organization, are important for dopamine secretion. Correspondingly, RIM zinc finger and C2B domains, which bind to Munc13 and Liprin-, respectively, are needed to restore dopamine release in RIM knockout mice. In contrast, and different from conventional synapses, the active zone scaffolds RIM-BP and ELKS, and the RIM domains that bind to them, are expendable. Hence, dopamine release necessitates priming and release site scaffolding by RIM, Munc13, and Liprin-, but other active zone proteins are dispensable. Our work establishes that molecularly simple but efficient release site architecture mediates fast dopamine exocytosis.

neuroscience↗

Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome

The long non-coding RNA Xist exploits numerous effector proteins to progressively induce gene silencing across the X chromosome and form the inactive X (Xi)-compartment. The mechanism underlying formation of the chromosome-wide Xi-compartment is poorly understood. Here, we find that formation of the Xi-compartment is induced by [~]50 locally confined granules, where two Xist RNA molecules nucleate supra-molecular complexes (SMCs) of interacting proteins. Xist-SMCs are transient structures that concentrate rapidly recycling proteins in the X by increasing protein binding affinity. We find that gene silencing originates at Xist-SMCs and propagates across the entire chromosome over time, achieved by Polycomb-mediated coalescence of chromatin regions and aggregation, via its intrinsically disordered domains, of the critical silencing factor SPEN. Our results suggest a new model for X chromosome inactivation, in which Xist RNA induces macromolecular crowding of heterochromatinizing proteins near distinct sites which ultimately increases their density throughout the chromosome. This mechanism enables deterministic gene silencing without the need for Xist ribonucleoprotein complex-chromatin interactions at each target gene.

cell biology↗