Biology subjects

Narayanan, S.

Publications and source records attributed to Narayanan, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Highly synchronized inhibition from Purkinje cells entrains cerebellar output in zebrafish

Cerebellar function, known to be important for motor learning and motor coordination, is mediated by efferent neurons that project to diverse motor areas. To understand cerebellar function, it is imperative to study how these efferent neurons integrate inputs from the principal neurons of the cerebellar cortex, the inhibitory Purkinje neurons (PNs). In zebrafish, PNs are bistable and we show here that bistability influences spike synchrony among PNs. Bistability also alters spike correlation with motor bouts. We asked how PN population synchrony influences Eurydendroid cells (ECs), which are postsynaptic targets of PNs and are the cerebellar efferent cells in zebrafish. Using optogenetics, we artificially modulated population synchrony of PNs over millisecond time scales and showed that under conditions of high synchrony, EC firing is briefly suppressed and entrained by PN spiking. However, the magnitude of such modulation is relatively small and indicates a strong combined influence of other synaptic inputs on EC spiking. Key PointsO_LICerebellar Purkinje neurons (PN) in larval zebrafish alter simple spike correlations with each other based on cellular state. C_LIO_LIThey also alter simple spike correlations with motor bouts as a function of state. C_LIO_LIWe altered PN population synchrony in a graded manner using optogenetics. C_LIO_LIPN targets are cerebellar efferent neurons, which in teleosts are called eurydendroid cells. C_LIO_LIWhen PN population is firing with high synchrony, eurydendroid cells are entrained better than when the PN input is asynchronous. C_LIO_LIThis can explain how PNs use bistability to modulate their influence on cerebellar output and ultimately, motor behavior. C_LI

neuroscience↗

bioRxiv2023

Klebsiella pneumoniae Co-infection Leads to Fatal Pneumonia in SARS-CoV-2-infected Mice

SARS-CoV-2 patients have been reported to have high rates of secondary Klebsiella pneumoniae infections. Klebsiella pneumoniae is a commensal that is typically found in the respiratory and gastrointestinal tracts. However, it can cause severe disease when a persons immune system is compromised. Despite a high number of K. pneumoniae cases reported in SARS-CoV-2 patients, a co-infection animal model evaluating the pathogenesis is not available. We describe a mouse model to study disease pathogenesis of SARS-CoV-2 and K. pneumoniae co-infection. BALB/cJ mice were inoculated with mouse-adapted SARS-CoV-2 followed by a challenge with K. pneumoniae. Mice were monitored for body weight change, clinical signs, and survival during infection. The bacterial load, viral titers, immune cell accumulation and phenotype, and histopathology were evaluated in the lungs. The co-infected mice showed severe clinical disease and a higher mortality rate within 48 h of K. pneumoniae infection. The co-infected mice had significantly elevated bacterial load in the lungs, however, viral loads were similar between co-infected and single-infected mice. Histopathology of co-infected mice showed severe bronchointerstitial pneumonia with copious intralesional bacteria. Flow cytometry analysis showed significantly higher numbers of neutrophils and macrophages in the lungs. Collectively, our results demonstrated that co-infection of SARS-CoV-2 with K. pneumoniae causes severe disease with increased mortality in mice.

immunology↗

bioRxiv2023

Maximum Mutational Robustness in Genotype-Phenotype Maps Follows a Self-similar Blancmange-like Curve

Phenotype robustness, defined as the average mutational robustness of all the genotypes that map to a given phenotype, plays a key role in facilitating neutral exploration of novel phenotypic variation by an evolving population. By applying results from coding theory, we prove that the maximum phenotype robustness occurs when genotypes are organised as bricklayers graphs, so called because they resemble the way in which a bricklayer would fill in a Hamming graph. The value of the maximal robustness is given by a fractal continuous everywhere but differentiable nowhere sums-of-digits function from number theory. Interestingly, genotype-phenotype (GP) maps for RNA secondary structure and the HP model for protein folding can exhibit phenotype robustness that exactly attains this upper bound. By exploiting properties of the sums-of-digits function, we prove a lower bound on the deviation of the maximum robustness of phenotypes with multiple neutral components from the bricklayers graph bound, and show that RNA secondary structure phenotypes obey this bound. Finally, we show how robustness changes when phenotypes are coarse-grained and derive a formula and associated bounds for the transition probabilities between such phenotypes.

evolutionary biology↗

bioRxiv2022

Learning Fast and Slow: Increased cortical plasticity leads to memory interference and enhanced hippocampal-cortical interactions

Our brain is continuously challenged by daily experiences. Thus, how to avoid systematic erasing of previously encoded memories? While it has been proposed that a dual-learning system with "slow" learning in the cortex and "fast" learning in the hippocampus could protect previous knowledge from interference, this has never been observed in the living organism. Here, we report that increasing plasticity via the viral-induced overexpression of RGS14414 in the prelimbic cortex leads to better one-trial memory, but that this comes at the price of increased interference in semantic-like memory. Indeed, electrophysiological recordings showed that this manipulation also resulted in shorter NonREM-sleep bouts, smaller delta-waves and decreased neuronal firing rates. In contrast, hippocampal-cortical interactions in form of theta coherence during wake and REM-sleep as well as oscillatory coupling during NonREM-sleep were enhanced. Thus, we provide the first experimental evidence for the long-standing and unproven fundamental idea that high thresholds for plasticity in the cortex protects preexisting memories and modulating these thresholds affects both memory encoding and consolidation mechanisms.

neuroscience↗

bioRxiv2022

Recombinant Human ACE2-Fc : A promising therapy for SARS-CoV2 infection

SARS-CoV2 entry is mediated by binding of viral spike-protein(S) to the transmembrane Angiotensin-Converting Enzyme-2 (ACE2) of the host cell. Thus, to prevent transmission of disease, strategies to abrogate the interaction are important. However, ACE2 cannot be blocked since its normal function is to convert the Angiotensin II peptide to Angiotensin(1-7) to reduce hypertension. This work reports a recombinant cell line secreting soluble ACE2-ectopic domain (MFcS2), modified to increase binding and production efficacy and fused to human immunoglobulin-Fc. While maintaining its enzymatic activity, the molecule trapped and neutralized SARS CoV2 virus in vitro with an IC50 of 64 nM. In vivo, with no pathology in the vital organs, it inhibited the viral load in lungs in SARS-CoV2 infected Golden-Syrian-hamster. The Intravenous pharmacokinetic profiling of MFcS2 in hamster at a dose of 5 mg/Kg presented a maximum serum concentration of 23.45 {micro}g/mL with a half-life of 29.5 hrs. These results suggest that MFcS2 could be used as an effective decoy based therapeutic strategy to treat COVID19. This work also reports usage of a novel oral-cancer cell line as in vitro model of SARS-Cov2 infection, validated by over expressing viral-defence pathways upon RNA-seq analysis and over-expression of ACE2 and TMPRSS upon growth in hyperglycaemic condition.

molecular biology↗

bioRxiv2022

Comprehensive preclinical evaluation of human-derived anti-poly-GA antibodies in cellular and animal models of C9ORF72 disease

Hexanucleotide G4C2 repeat expansions in the C9ORF72 gene are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Dipeptide repeat proteins (DPRs) generated by translation of repeat-containing RNAs show toxic effects in vivo as well as in vitro and are key targets for therapeutic intervention. We generated human antibodies that bind DPRs with high affinity and specificity. Anti-GA antibodies engaged extra- and intracellular poly-GA and reduced aggregate formation in a poly-GA over-expressing human cell line. However, antibody treatment in human neuronal cultures synthesizing exogenous poly-GA resulted in the formation of large extracellular immune complexes and did not affect accumulation of intracellular poly-GA aggregates. Treatment with antibodies was also shown to directly alter the morphological and biochemical properties of poly-GA and to shift poly-GA/antibody complexes to more rapidly sedimenting ones. These alterations were not observed with poly-GP and have important implications for accurate measurement of poly-GA levels including the need to evaluate all centrifugation fractions and disrupt the interaction between treatment antibodies and poly-GA by denaturation. Targeting poly-GA and poly-GP in two mouse models expressing G4C2 repeats by systemic antibody delivery for up to 16 months was well-tolerated and led to measurable brain penetration of antibodies. Long term treatment with anti-GA antibodies produced improvement in an open field movement test in aged C9ORF72450 mice. However, chronic administration of anti-GA antibodies in AAV-(G4C2)149 mice was associated with increased levels of poly-GA detected by immunoassay and did not significantly reduce poly-GA aggregates or alleviate disease progression in this model. SignificanceImmunotherapy has been proposed for neurodegenerative disorders including Alzheimers or Parkinsons diseases. Recent reports using antibodies against poly-GA or active immunization suggested similar immunotherapy in ALS/FTD caused by repeat expansion in the C9ORF72 gene (1, 2). Here, we systematically characterized human antibodies against multiple DPR species and tested the biological effects of antibodies targeting poly-GA in different cellular and mouse models. Target engagement was shown in three independent cellular models. Anti-GA antibodies reduced the number of intracellular poly-GA aggregates in human T98G cells but not in cultured human neurons. Whereas chronic anti-GA treatment in BAC C9ORF72450 mice did not impact poly-GA levels and modestly improved one behavioral phenotype, poly-GA levels detected by immunoassays were increased and disease progression was unaltered in AAV-(G4C2)149 mice.

neuroscience↗

bioRxiv2021

Diffusely abnormal white matter converts to T2 lesion volume in the absence of acute inflammation

Diffusely abnormal white matter (DAWM), characterised by biochemical changes of myelin in the absence of frank demyelination, has been associated with clinical progression in secondary progressive MS (SPMS). However, little is known about changes of DAWM over time and their relation to focal white matter lesions (FWML). The objectives of this work were: 1) To characterize the longitudinal evolution of FWML, DAWM, and DAWM that transforms into FWML, and 2) To determine whether gadolinium enhancement, known to be associated with the development of new FWML, is also related to DAWM voxels that transform into FWML. Our data included 4220 MRI scans of 689 SPMS participants, followed for 156 weeks and 2677 scans of 686 RRMS participants, followed for 96 weeks. FWML and DAWM were segmented using a previously validated, automatic thresholding technique based on normalized T2 intensity values. Using longitudinally registered images, DAWM voxels at each visit that transformed into FWML on the last MRI scan as well as their overlap with gadolinium enhancing lesion masks were identified. Our results showed that the average yearly rate of conversion of DAWM-to-FWML was 1.27cc for SPMS and 0.80cc for RRMS. FWML in SPMS participants significantly increased (t=3.9; p=0.0001) while DAWM significantly decreased (t=-4.3 p<0.0001) and the ratio FWML:DAWM increased (t=12.7; p<0.00001). RRMS participants also showed an increase in the FWML:DAWM Ratio (t=6.9; p<0.00001) but without a significant change of the individual volumes. Gadolinium enhancement was associated with 7.3% and 18.7% of focal New T2 lesion formation in the infrequent scans of the RRMS and SPMS cohorts, respectively. In comparison, only 0.1% and 0.0% of DAWM-to-FWML voxels overlapped with gadolinium enhancement. We conclude that DAWM transforms into FWML over time, in both RRMS and SPMS. DAWM appears to represent a form of pre-lesional pathology that contributes to T2 lesion volume increase over time, independent of new focal inflammation and gadolinium enhancement.

neuroscience↗

bioRxiv2021

Repression of Hypoxia-Inducible Factor-1 Contributes to Increased Mitochondrial Reactive Oxygen Species Production in Diabetes

BackgroundExcessive production of mitochondrial reactive oxygen species (ROS) is a central mechanism for the development of diabetes complications. Recently, hypoxia has been identified to play an additional pathogenic role in diabetes. In this study, we hypothesized that ROS overproduction was secondary to the impaired responses to hypoxia due to the inhibition of hypoxia-inducible factor-1 (HIF-1) by hyperglycemia. MethodsThe dynamic of ROS levels was analysed in the blood of healthy subjects and individuals with type 1 diabetes after exposure to hypoxia (ClinicalTrials.gov registration no. NCT02629406). The relation between HIF-1, glucose levels, ROS production and its functional consequences were analyzed in renal mIMCD-3 cells and in kidneys of mouse models of diabetes. ResultsExposure to hypoxia increased circulating ROS in subjects with diabetes, but not in subjects without diabetes. High glucose concentrations repressed HIF-1 both in hypoxic cells and in kidneys of animals with diabetes, through a HIF prolyl-hydroxylase (PHD) - dependent mechanism. The impaired HIF-1 signaling contributed to excess production of mitochondrial ROS through increased mitochondrial respiration that was mediated by Pyruvate dehydrogenase kinase 1 (PDK1) and was followed by functional consequences. The restoration of HIF-1 function attenuated ROS overproduction despite persistent hyperglycemia, and conferred protection against apoptosis and renal injury in diabetes. ConclusionsWe conclude that the repression of HIF-1 plays a central role in mitochondrial ROS overproduction in diabetes and is a potential therapeutic target for diabetic complications. These findings are highly significant and timely since the first PHD inhibitor that can activate HIF-1 has been newly approved for clinical use.

cell biology↗

bioRxiv2021

Adaptable internal representations drive cerebellum-mediated predictive control of an innate behavior

The cerebellum is known to optimize behavioral responses via error minimization, yet how past sensory experience shapes cerebellar output is still poorly understood. We imaged cerebellar Purkinje cells (PCs) in larval zebrafish during a behavioral assay in which they learnt to expect the direction of optic flow stimulus. PCs encoded signals of expectation and a graded error signal when a deviant stimulus was encountered. The amplitude of the error signal scaled based on stimulus history over minute-timescales. Granule cells (GC) did not encode error, however, some GC types encoded putative expectation signals. When PC population-wide readouts of expectation and error signals were strong, swim latency was low and vice versa, indicating participation of these signals in motor planning. Consistent with this, lesioning the cerebellum abolished expectation-dependent modulation of swim latency. Based on these results we propose that PCs use expectation and error signals to acquire and update internal models of the world. HighlightsO_LILarval zebrafish learn to expect repeatedly encountered optic flow stimuli C_LIO_LIStimulus history over minutes contributes to an internal model of the sensory world C_LIO_LIPurkinje neuron activity encodes deviations from expected direction of optic flow C_LIO_LIThe cerebellum uses learnt expectations to generate lower latency swim responses C_LI

neuroscience↗

bioRxiv2020

Hypercholesterolemia Impairs Clearance of Extracellular DNA and Promotes Inflammation and Atherosclerotic Plaque Progression

Defects in clearance of extracellular DNA due to sub-optimal activity of DNase results in exacerbated inflammation and contributes to the pathophysiology of atherosclerosis and other inflammatory diseases. However, the physiological mechanisms that regulate systemic DNase levels and the basis of its functional impairment during disease are poorly understood. Using a mouse model of experimental increase in systemic extracellular DNA levels, we identify the existence of a physiologic DNA-induced DNase response. Importantly, hypercholesterolemia in mice impairs this critical DNA-induced DNase response through an endoplasmic reticulum stress-mediated mechanism with consequences in advanced atherosclerotic plaque progression including increased extracellular DNA accumulation, exacerbated inflammation, and development of pathological features of necrotic rupture-prone vulnerable plaques. From a translational standpoint in humans, we demonstrate that individuals with hypercholesterolemia have elevated systemic extracellular DNA levels and decreased plasma DNase activity. These data suggest that the restoration of DNA-induced DNase response could be a potential therapeutic strategy to promote inflammation resolution during hypercholesterolemia.

immunology↗

bioRxiv2020

Single Gyroid and Inverse b.c.c. Photonic Crystals in Bird Feathers

Vivid, saturated structural colors are conspicuous and important features of many animals. A rich diversity of three-dimensional periodic photonic nanostructures is found in the chitinaceous exoskeletons of invertebrates. Three-dimensional photonic nanostructures have been described in bird feathers, but they are typically quasi-ordered. Here, we report bi-continuous single gyroid {beta}-keratin and air photonic crystal networks in the feather barbs of blue-winged leafbirds (Chloropsis cochinchinensis sensu lato), which have evolved from ancestral quasi-ordered channel-type nanostructures. Self-assembled avian photonic crystals may serve as inspiration for multi-functional applications, as they suggest efficient, alternative routes to single gyroid synthesis at optical length-scales, which has been experimentally elusive.

evolutionary biology↗

bioRxiv2020

Whole genome sequencing based differentiation between re-infection and relapse in Indian patients with tuberculosis recurrence, with and without HIV co-infection

Differentiation between relapse and reinfection in cases with tuberculosis (TB) recurrence has important implications for public health, especially in patients with human immunodeficiency virus (HIV) co-infection. Forty-one paired M. tuberculosis isolates collected from 20 HIV-positive and 21 HIV-negative patients, who experienced TB recurrence after previous successful treatment, were subjected to whole genome sequencing (WGS) in addition to spoligotyping and mycobacterial interspersed repeat unit (MIRU) typing. Comparison of M. tuberculosis genomes indicated that 95% of TB recurrences in the HIV-negative cohort were due to relapse, while the majority of TB recurrences (75%) in the HIV-positive cohort was due to re-infection (P=0.0001). Drug resistance conferring mutations were documented in four pairs (9%) of isolates associated with relapse. The high contribution of re-infection to TB among HIV patients warrants further study to explore risk factors for TB exposure in the community.

genomics↗

bioRxiv2020

A dynamical extracellular matrix coat regulates moruloid-blastuloid transitions of ovarian cancer spheroids

SummaryOvarian cancer metastasizes into the peritoneum through dissemination of transformed epithelia as multicellular spheroids 1, 2. Harvested from the malignant ascites of patients, spheroids exhibit startling features of organization typical to homeostatic glandular tissues3: lumen surrounded by smoothly contoured, adhered, and immotile epithelia. Herein, we demonstrate that cells of specific ovarian cancer lines in suspension, aggregate into dysmorphic solid ‘moruloid’ clusters that permit intercellular movement and penetration by new cells. Moruloid clusters can coalesce to form bigger clusters. Upon further culture, moruloid clusters mature into ‘blastuloid’ spheroids with smooth contours, lumen and immotile cells. Blastuloid spheroids neither coalesce nor allow penetration by new cells. Ultrastructural examination reveals a basement membrane-like matrix coat on the surface of blastuloid, but not moruloid, spheroids: immunocytochemistry confirms the presence of extracellular matrix proteins: Collagen IV and Laminin-322. Enzymatic debridement of the coat results in a reversible loss of lumen and contour. Debridement also allows spheroidal coalescence and cell intrusion in blastuloid spheroids and enhances adhesion to peritoneal substrata. Therefore, the dynamical matrix coat regulates both the morphogenesis of cancer spheroids and their adhesive interaction with their substrata, affecting ultimately the progression of the disease.Results Survival of women afflicted with epithelial ovarian cancer (EOC) trails behind other gynecological malignancies, despite improvements in surgical-pharmacological approaches4,5. The morbidity associated with the disease is a consequence of its transcoelomic route of metastasis: transformed epithelia of the fallopian tubes and ovaries in the form of spheroids, eventually home and adhere to the mesothelial lining of the peritoneum, occasionally invade through the underlying collagenous extracellular matrix and form secondary metastatic foci around abdominal organs1, 6, 7. EOC spheroids impede the drainage of the fluid from the peritoneal cavity and alter its composition; in turn the fluid, now known as malignant ascites serves as a pro-tumorigenic milieu for the spheroids8, 9The formation and presence of spheroids within ascites of an ovarian cancer patient is strongly associated with recurrence of cancer and greater resistance to chemotherapy10. Therefore, in order to develop novel strategies to target spheroidal metastatic niche, it is essential to investigate mechanisms that underlie their morphogenesis. Several proteins have been proposed to mediate the adhesion between ovarian cancer epithelia that give rise to spheroids. These include transmembrane receptors such as CD4411, cell adhesion molecules, such as E-cadherin and N-cadherin12, matrix adhesion-inducing proteins such as integrins13, 14. Remarkably, a phase-contrast microscopic examination of spheroids from patients, or from aggregated epithelia of immortalized cancer lines cultured on low attachment substrata, shows features of morphogenetic organization: presence of a central lumen, radially arranged apposed epithelia and compacted surfaces. Such traits are cognate to organized morphogenesis within the glandular epithelial organs,15 which are built through principles that include, but are not limited to, cell-cell adhesion16, 17. In fact, loss of tissue architecture seen in tumorigenesis involves the disappearance of such morphogenetic traits (such as matrix adhesion and polarity)18, 19.In this manuscript, we investigate how these traits are recapitulated in a fluid metastatic context. Using spheroids from patients with high grade serous adenocarcinoma and ovarian cancer cell lines, we show that the development of a basement membrane (BM)-like coat of extracellular matrix is responsible for the compaction and stability of cancer spheroids, for decreasing the motility of cells within it and for generation of lumen. The coat, which is rapidly replenished by cells upon enzymatic debridement, also prevents the attachment of spheroids to matrix substrata. This may have significant implications for the build-up of the massive cellular fraction within the malignant ascites of patients afflicted with ovarian cancer.Competing Interest StatementThe authors have declared no competing interest.View Full Text

cell biology↗

bioRxiv2020

LAG3 is a Central Regulator of NK Cell Cytokine Production

Natural killer (NK) cells are innate effectors, which play a crucial role in controlling viral infections. Administration of IFN- has shown promising results as a therapeutic, controlling HIV, and chronic viral hepatitis. However the downstream mechanisms by which IFN- mediates its anti-viral effects is largely unknown. In this investigation, we evaluated the impact of IFN- on peripheral blood NK cells from healthy donors. High dimensional flow cytometry analysis of NK cell surface receptors following exposure to IFN- showed an increased expression of the check point inhibitor LAG3. Further characterization revealed that LAG3 was expressed in a subset of NK cells with high expression of activation and maturation markers. Assessment of metabolic pathways showed that LAG3+ NK cells had enhanced rates of glycolysis and glycolytic capacity, suggesting that it is a primed effector subset with enhanced glucose metabolism. Inhibition of LAG3 on NK cells using antibody in vitro resulted in a profound increase in secretion of cytokines IFN-{gamma}, TNF-, MIP-1 and MIP-1{beta}, without affecting the cytotoxic activity. Taken together, these results showed that LAG3 is a negative regulator of cytokine production by mature NK cells.

immunology↗

bioRxiv2020

Crystal structure of calcium bound outer membrane phospholipase A (OmpLA) from Salmonella typhi and in silico anti-microbial screening

Antimicrobial resistance is widespread in Salmonella infections that affect millions worldwide. Salmonella typhi and other Gram-negative bacterial pathogens encode an outer membrane phospholipase A (OmpLA), crucial for their membrane integrity. Further, OmpLA is implicated in pathogen internalization, haemolysis, acid tolerance, virulence and sustained infection in human hosts. OmpLA is an attractive drug target for developing novel anti-microbials that attenuate virulence, as the abrogation of OmpLA encoding pldA gene causes loss of virulence. Here, we present the crystal structure of Salmonella typhi OmpLA in dimeric calcium bound activated state at 2.95 [A]. Structure analysis suggests that OmpLA is a potential druggable target. Further, we have identified and shortlisted small molecules that bind at the dimer interface using structure based in silico screening, docking and molecular dynamics. While it requires further experimental validation, anti-microbial discovery targeting OmpLA from gram-negative pathogens offers an advantage as OmpLA is required for virulence.

biophysics↗

bioRxiv2019

Conversion of Diffusely Abnormal White Matter to Focal Lesions is Linked to Progression in Secondary Progressive Multiple Sclerosis

Objectives1) To automatically segment focal white matter lesions (FWML) and Diffusely abnormal white matter (DAWM), i.e. regions of diffuse abnormality observed on conventional (T2-weighted) MRI and characterize their longitudinal volumetric and normalized T1-weighted (T1w) intensity evolution, 2) To assess associations of FWML and DAWM with Expanded Disability Status Scale (EDSS) and confirmed disability progression (CDP).\n\nMethodsData includes 3951 timepoints of 589 SPMS participants followed for three years. FWML and DAWM were automatically segmented using a 2-weighted-intensity thresholding technique. Screening DAWM volumes that transformed into FWML at the last visit (DAWM-to-FWML) and normalized T1w intensities (as a marker of severity of damage) in those voxels were calculated.\n\nResultsFWML volume significantly increased and DAWM volume significantly decreased as disease duration increased (p<0.001). Global EDSS scores were positively associated with FWML volumes (p=0.002), but not with DAWM volumes. Median volume of DAWM-to-FWML was significantly higher in patients who progressed (2.75 vs 1.70 cc; p<0.0001), and represented 14% of the total DAWM volume at screening, compared to 10% in patients who did not progress (p=0.001). Normalized T1w intensity values of DAWM-to-FWML were negatively associated with CDP status (p<0.00001).\n\nConclusionDAWM transformed into FWML over time, and this transformation was significantly associated with clinical progression. DAWM voxels that transformed had greater normalized T1w intensity decrease over time, in keeping with relatively greater tissue damage evolution. Evaluation of DAWM in progressive MS provides a useful measure to evaluate therapies that aim to protect this at-risk tissue with the potential to slow progression.

neuroscience↗

bioRxiv2019

Automated Separation of Diffusely Abnormal White Matter from Focal White Matter Lesions on MRI in Multiple Sclerosis

BackgroundPrevious histopathology and MRI studies have addressed the differences between focal white matter lesions (FWML) and diffusely abnormal white matter (DAWM) in multiple sclerosis (MS). These two categories of white matter T2-weighted (T2w) hyperintensity show different degrees of demyelination, axonal loss and immune cell density on histopathology, potentially offering distinct correlations with symptoms.\n\nObjectives1) To automate the separation of FWML and DAWM using T2w MRI intensity thresholds and to investigate their differences in magnetization transfer ratios (MTR), which are sensitive to myelin content; 2) to correlate MTR values in FWML and DAWM with normalized signal intensity values on fluid attenuated inversion recovery (FLAIR), T2w, and T1-weighted (T1w) contrasts, as well as with the ratio of T2w/T1w normalized values, in order to determine whether these normalized intensities can be used as myelin-sensitive markers when MTR is not available.\n\nMethodsUsing similar 3T MRI protocols, 2 MS cohorts of 20 participants each were scanned in 2 centers, including: 3D T1w (MP2RAGE), 3D FLAIR, 2D T2w, and 3D magnetization-transfer (MT) contrasts. We used the first dataset to develop an automated technique to separate FWML from DAWM and the second one to validate the automation of the technique. We applied the automatic thresholds to both datasets and assessed the overlap of the manual and the automated masks using Dice kappa. We also assessed differences in mean MTR values between NAWM, DAWM and FWML, using manually and automatically derived masks in both datasets. Finally, we used the mean intensity of manually-traced areas of NAWM on T2w images as the normalization factor for each MRI contrast, and compared these with the normalized-intensity values obtained using automated NAWM (A-NAWM) masks as the normalization factor. Paired t-tests assessed the MTR differences across tissue types. Wilcoxon Signed Rank test and paired t-tests assessed FWML and DAWM differences in manual and automated derived volumes. Pearson correlations assessed the relationship between MTR and normalized intensity values in the manual and automated derived masks.\n\nResultsThe mean Dice-kappa values for dataset 1 were: 0.8 for DAWM masks and 0.7 for FWML masks. In dataset 2, mean dice-kappa values were: 0.8 for DAWM and 0.8 for FWML. Also, manual and automated DAWM and FWML volumes were not significantly different in both datasets. MTR values (expressed as mean and standard deviation, arbitrary units) were significantly lower in manually derived FWML compared with DAWM in both datasets: 1) FWML: 37.1 {+/-} 3.2 vs DAWM: 43.3 {+/-} 2.1; t=13.2; p<0.0001, and 2) FWML: 32.5 {+/-} 3.9 vs DAWM: 38.8 {+/-} 1.7; t=9.8; p<0.0001. Similar results were obtained using the automatic derived masks in both datasets: 1) FWML: 35.8 {+/-} 2.8 vs DAWM: 43.1 {+/-} 1.6; t=15.3; p<0.0001, and 2) FWML: 31.3 {+/-} 3.1 vs DAWM: 38.1 {+/-} 1.5; t=12.8; p<0.0001. MTR was also significantly lower in manually derived DAWM masks compared with normal appearing white matter (NAWM) in both datasets: 1) NAWM: 46.7 {+/-} 1.3; t=10.1; p<0.0001, and 2) NAWM: 39.3 {+/-} 0.8; t=3.1; p=0.003. Similar results were obtained using the automatic derived masks in both datasets: 1) NAWM: 46.3 {+/-} 1.1; t=13.7; p<0.0001, and 2) NAWM: 39.9 {+/-} 1.1; t=9.6; p<0.0001.\n\nIn both datasets, manually derived FWML and DAWM MTR values showed significant correlations with normalized FLAIR (r=-0.35 to -0.67; p=0.06 to <0.0001), T2w (r=-0.60 to -0.72; p=0.003 to <0.0001), T1w/T2w (r=0.63 to 0.77; p=0.002 to <0.0001), and T1w (r=0.77 to 0.92; p<0.0001) intensities. Finally, normalized intensity values obtained using automatic derived masks were significantly correlated with the manually derived values in both datasets.\n\nConclusionsThe separation of FWML and DAWM on MRI scans of MS patients using automated intensity thresholds on T2w images is feasible. MTR values are significantly lower in FWML than DAWM, and DAWM values are significantly lower than NAWM, reflecting potentially greater demyelination within focal lesions. Normalized intensity values of different MRI contrasts exhibit a significant correlation with MTR values in both tissues of interest and could be used as a proxy to assess demyelination when MTR images are not available.

neuroscience↗

bioRxiv2019

How helpful are the protein-protein interaction databases and which ones?

Protein-protein interactions (PPIs) are critical, and so are the databases and tools (resources) concerning PPIs. But in absence of systematic comparisons, biologists/bioinformaticians may be forced to make a subjective selection among such protein interaction databases and tools. In fact, a comprehensive list of such bioinformatics resources has not been reported so far. For the first time, we compiled 375 PPI resources, short-listed and performed preliminary comparison of 125 important ones (both lists available publicly at startbioinfo.com), and then systematically compared human PPIs from 16 carefully-selected databases. General features have been first compared in detail. The coverage of experimentally verified vs. all PPIs, as well as those significant in case of disease-associated and other types of genes among the chosen databases has been compared quantitatively. This has been done in two ways: outputs manually obtained using web-interfaces, and all interactions downloaded from the databases. For the first approach, PPIs obtained in response to gene queries using the web interfaces were compared. As a query set, 108 genes associated with different tissues (specific to kidney, testis, and uterus, and ubiquitous) or diseases (breast cancer, lung cancer, Alzheimers, cystic fibrosis, diabetes, and cardiomyopathy) were chosen. PPI-coverage for well-studied genes was also compared with that of less-studied ones. For the second approach, the back-end-data from the databases was downloaded and compared. Based on the results, we recommend the use of STRING and UniHI for retrieving the majority of experimentally verified protein interactions, and hPRINT and STRING for obtaining maximum number of total (experimentally verified as well as predicted) PPIs. The analysis of experimentally verified PPIs found exclusively in each database revealed that STRING contributed about 71% of exclusive hits. Overall, hPRINT, STRING and IID together retrieved ~94% of total protein interactions available in the databases. The coverage of certain databases was skewed for some gene-types. The results also indicate that the database usage frequency may not correlate with their advantages, thereby justifying the need for more frequent studies of this nature.

bioinformatics↗