A joint subspace mapping between structural and functional brain connectomes.

Understanding the connection between the brain's structural connectivity and its functional connectivity is of immense interest in computational neuroscience. Although some studies have suggested that whole brain functional connectivity is shaped by the underlying structure, the rule by which anatomy constraints brain dynamics remains an open question. In this work, we introduce a computational framework that identifies a joint subspace of eigenmodes for both functional and structural connectomes. We found that a small number of those eigenmodes are sufficient to reconstruct functional connectivity from the structural connectome, thus serving as low-dimensional basis function set. We then develop an algorithm that can estimate the functional eigen spectrum in this joint space from the structural eigen spectrum. By concurrently estimating the joint eigenmodes and the functional eigen spectrum, we can reconstruct a given subject's functional connectivity from their structural connectome. We perform elaborate experiments and demonstrate that the proposed algorithm for estimating functional connectivity from the structural connectome using joint space eigenmodes gives competitive performance as compared to the existing benchmark methods with better interpretability.

Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast.

Translational control is essential in response to stress. We investigated the translational programmes launched by the fission yeast Schizosaccharomyces pombe upon five environmental stresses. We also explored the contribution of defence pathways to these programmes: The Integrated Stress Response (ISR), which regulates translation initiation, and the stress-response MAPK pathway. We performed ribosome profiling of cells subjected to each stress, in wild type cells and in cells with the defence pathways inactivated. The transcription factor Fil1, a functional homologue of the yeast Gcn4 and the mammalian Atf4 proteins, was translationally upregulated and required for the response to most stresses. Moreover, many mRNAs encoding proteins required for ribosome biogenesis were translationally downregulated. Thus, several stresses trigger a universal translational response, including reduced ribosome production and a Fil1-mediated transcriptional programme. Surprisingly, ribosomes stalled on tryptophan codons upon oxidative stress, likely due to a decrease in charged tRNA-Tryptophan. Stalling caused ribosome accumulation upstream of tryptophan codons (ribosome queuing/collisions), demonstrating that stalled ribosomes affect translation elongation by other ribosomes. Consistently, tryptophan codon stalling led to reduced translation elongation and contributed to the ISR-mediated inhibition of initiation. We show that different stresses elicit common and specific translational responses, revealing a novel role in Tryptophan-tRNA availability.

In-vivo protein nitration facilitates Vibrio cholerae cell survival under anaerobic, nutrient deprived conditions.

Protein tyrosine nitration (PTN), a highly selective post translational modification, occurs in both prokaryotic and eukaryotic cells under nitrosative stress. However, its physiological function is not yet clear. Like many gut pathogens, Vibrio cholerae also faces nitrosative stress, which makes its proteome more vulnerable to PTN. Here, we report for the first time in-vivo PTN in V. cholerae by immunoblotting and LC-ESI-MS/MS proteomic analysis. Our results indicated that in-vivo PTN in V. cholerae was culture media independent. Surprisingly, in-vivo PTN was reduced in V. cholerae proteome under anaerobic or hypoxic condition in a nutrient deprived state. Interestingly, intracellular nitrate content was more than the nitrite content in V. cholerae under anaerobic conditions. Additionally, biochemical measurement of GSH/GSSG ratio, activities of catalase and SOD, ROS and RNS imaging by confocal microscopy confirmed a relative intracellular oxidizing environment in V. cholerae under anaerobic conditions. This altered redox environment favors the oxidation of nitrite which may be generated from protein denitration enriching the intracellular nitrate pool. The cell survival of V. cholerae can finally be facilitated by nitrate reductase (NapA) utilizing that nitrate pool. Our cell viability study using wild type and ΔnapA strain of V. cholerae also supported the role of NapA mediated cell survival under nutrient deprived anaerobic conditions. In spite of having nitrate reductase (NapA), V. cholerae lacks any nitrite reductase (NiR). Hence, in-vivo nitration may provide an avenue for toxic nitrite storage and also may help in nitrosative stress tolerance mechanism preventing further unnecessary protein nitration in V. cholerae proteome.

Secretome analysis identified extracellular superoxide dismutase and catalase of Macrophomina phaseolina.

Macrophomina phaseolina, a necrotrophic fungal pathogen is known to cause charcoal rot disease in food crops, pulse crops, oil crops and cotton and fibre crops. Necrotrophic fungi survive on dead plant tissue. It is well known that reactive oxygen species (ROS) are produced by the host plant during plant-pathogen interaction. However, it is still unclear how M. phaseolina can overcome the ROS-induced cellular damage. To mimic the invasion of M. phaseolina inside the plant cell wall, we developed solid substrate fermentation where M. phaseolina spore suspension was inoculated on a wheat bran bed and incubated for vegetative growth. To analyse the secretome of M. phaseolina after different day interval, its secretory material was collected and concentrated. Both superoxide dismutase (SOD) and catalase were detected in the secretome by zymogram. The presence of SOD and catalase was further confirmed by liquid chromatography based mass spectrometry. The physicochemical properties of M. phaseolina catalase in terms of stability towards pH, temperature, metal ions and chaotropic agent and inhibitors indicated its fitness at different environmental conditions. Apart from the production of catalase in SSF, the studies on this particular microorganism may also have significance in necrotrophic fungal pathogen and their susceptible host plant interaction.

High rise in carbonaceous aerosols under very low anthropogenic emissions over eastern Himalaya, India: Impact of lockdown for COVID-19 outbreak.

The present study has been conducted to investigate the relative changes of carbonaceous aerosols (CA) over a high altitude Himalayan atmosphere with and without (very low) anthropogenic emissions. Measurements of atmospheric organic (OC) and elemental carbon (EC) were conducted during the lockdown period (April 2020) due to global COVID 19 outbreak and compared with the normal period (April 2019). The interesting, unexpected and surprising observation is that OC, EC and the total CA (TCA) during the lockdown (OC: 12.1 ± 5.5 µg m-3; EC: 2.2 ± 1.1 µg m-3; TCA: 21.5 ± 10 µg m-3) were higher than the normal period (OC: 7.04 ± 2.2 µg m-3; EC: 1.9 ± 0.7 µg m-3; TCA: 13.2 ± 4.1 µg m-3). The higher values for OC/EC ratio too was observed during the lockdown (5.7 ± 0.9) compared to the normal period (4.2 ± 1.1). Much higher surface O3 during the lockdown (due to very low NO) could better promote the formation of secondary OC (SOC) through the photochemical oxidation of biogenic volatile organic compounds (BVOCs) emitted from Himalayan coniferous forest cover. SOC during the lockdown (7.6 ± 3.5 µg m-3) was double of that in normal period (3.8 ± 1.4 µg m-3). Regression analysis between SOC and O3 showed that with the same amount of increase in O3, the SOC formation increased to a larger extent when anthropogenic emissions were very low and biogenic emissions dominate (lockdown) compared to when anthropogenic emissions were high (normal). Concentration weighted trajectory (CWT) analysis showed that the anthropogenic activities over Nepal and forest fire over north-east India were the major long-distant sources of the CA over Darjeeling during the normal period. On the other hand, during lockdown, the major source regions of CA over Darjeeling were regional/local. The findings of the study indicate the immense importance of Himalayan biosphere as a major source of organic carbon.

Reactive nitrogen species induced catalases promote a novel nitrosative stress tolerance mechanism in Vibrio cholerae.

Vibrio cholerae faces nitrosative stress during successful colonization in intestine. Very little information is available on the nitrosative stress protective mechanisms of V. cholerae. Reports show that NorR regulon control two genes hmpA and nnrS responsible for nitric oxide (NO) detoxification in V. cholerae. In the present study we first time report a novel role of V. cholerae catalases under nitrosative stress. Using zymogram analysis of catalase we showed that KatB and KatG activity were induced within 30 min in V. cholerae in the presence of sodium nitroprusside (SNP), a NO donor compound. Surprisingly, V. cholerae cell survival was found to be decreased under nitrosative stress if catalase activities were blocked by ATz, a catalase inhibitor. Flow cytometry study was conducted to detect reactive oxygen species (ROS) and reactive nitrogen species (RNS) using DHE and DHR123, fluorescent probes respectively. Short exposure of SNP to V. cholerae did not generate ROS but RNS was detectable within 30 min. Total glutathione content was increased in V. cholerae cells under nitrosative stress. Furthermore, Superoxide dismutase (SOD) and Glutathione reductase (GR) activities remained unchanged under nitrosative stress in V. cholerae indicated antioxidant role of NO which could produce peroxynitrite. To investigate the role of catalase induction under nitrosative stress in V. cholerae, we conducted peroxynitrite reductase assay using cell lysates. Interestingly, SNP treated V. cholerae cell lysates showed lowest DHR123 oxidation compared to the control set. The extent of DHR123 oxidation was more in V. cholerae cell lysate when catalases were blocked by ATz.

Critical roles of CTP synthase N-terminal in cytoophidium assembly.

Several metabolic enzymes assemble into distinct intracellular structures in prokaryotes and eukaryotes suggesting an important functional role in cell physiology. The CTP-generating enzyme CTP synthase forms long filamentous structures termed cytoophidia in bacteria, yeast, fruit flies and human cells independent of its catalytic activity. However, the amino acid determinants for protein-protein interaction necessary for polymerisation remained unknown. In this study, we systematically analysed the role of the conserved N-terminal of Drosophila CTP synthase in cytoophidium assembly. Our mutational analyses identified three key amino acid residues within this region that play an instructive role in organisation of CTP synthase into a filamentous structure. Co-transfection assays demonstrated formation of heteromeric CTP synthase filaments which is disrupted by protein carrying a mutated N-terminal alanine residue thus revealing a dominant-negative activity. Interestingly, the dominant-negative activity is supressed by the CTP synthase inhibitor DON. Furthermore, we found that the amino acids at the corresponding position in the human protein exhibit similar properties suggesting conservation of their function through evolution. Our data suggest that cytoophidium assembly is a multi-step process involving N-terminal-dependent sequential interactions between correctly folded structural units and provide insights into the assembly of these enigmatic structures.

Effective knockdown of Drosophila long non-coding RNAs by CRISPR interference.

Long non-coding RNAs (lncRNAs) have emerged as regulators of gene expression across metazoa. Interestingly, some lncRNAs function independently of their transcripts - the transcription of the lncRNA locus itself affects target genes. However, current methods of loss-of-function analysis are insufficient to address the role of lncRNA transcription from the transcript which has impeded analysis of their function. Using the minimal CRISPR interference (CRISPRi) system, we show that coexpression of the catalytically inactive Cas9 (dCas9) and guide RNAs targeting the endogenous roX locus in the Drosophila cells results in a robust and specific knockdown of roX1 and roX2 RNAs, thus eliminating the need for recruiting chromatin modifying proteins for effective gene silencing. Additionally, we find that the human and Drosophila codon optimized dCas9 genes are functional and show similar transcription repressive activity. Finally, we demonstrate that the minimal CRISPRi system suppresses roX transcription efficiently in vivo resulting in loss-of-function phenotype, thus validating the method for the first time in a multicelluar organism. Our analysis expands the genetic toolkit available for interrogating lncRNA function in situ and is adaptable for targeting multiple genes across model organisms.

Multimodal control of transcription factor Pap1 in Schizosaccharomyces pombe under nitrosative stress.

Schizosaccharomyces pombe Pap1, a bZIP transcription factor, is highly homologous to the mammalian c-Jun protein that belongs to the AP1 family of transcriptional regulators. The role of transcription factor Pap1 has been extensively studied under oxidative stress. Two cysteine residues in Pap1p namely, C278 and C501 form disulfide linkage under oxidative stress resulting in nuclear accumulation. We first time showed the involvement of Pap1 in the protection against nitrosative stress. In the present study we show that pap1 deletion makes growth of S. pombe sensitive to nitrosative stress. pap1 deletion also causes delayed recovery in terms of mitotic index under nitrosative stress. Our flow cytometry data shows that pap1 deletion causes slower recovery from the slowdown of DNA replication under nitrosative stress. This is the first report where we show that Pap1 transcription factor is localized in the nucleus under nitrosative stress. From our study it is evident that nuclear localization of Pap1 under nitrosative stress was not due to reactive oxygen species formation.

The EJC binding and dissociating activity of PYM is regulated in Drosophila.

In eukaryotes, RNA processing events in the nucleus influence the fate of transcripts in the cytoplasm. The multi-protein exon junction complex (EJC) associates with mRNAs concomitant with splicing in the nucleus and plays important roles in export, translation, surveillance and localization of mRNAs in the cytoplasm. In mammalian cells, the ribosome associated protein PYM (HsPYM) binds the Y14-Mago heterodimer moiety of the EJC core, and disassembles EJCs, presumably during the pioneer round of translation. However, the significance of the association of the EJC with mRNAs in a physiological context has not been tested and the function of PYM in vivo remains unknown. Here we address PYM function in Drosophila, where the EJC core proteins are genetically required for oskar mRNA localization during oogenesis. We provide evidence that the EJC binds oskar mRNA in vivo. Using an in vivo transgenic approach, we show that elevated amounts of the Drosophila PYM (DmPYM) N-terminus during oogenesis cause dissociation of EJCs from oskar RNA, resulting in its mislocalization and consequent female sterility. We find that, in contrast to HsPYM, DmPYM does not interact with the small ribosomal subunit and dismantles EJCs in a translation-independent manner upon over-expression. Biochemical analysis shows that formation of the PYM-Y14-Mago ternary complex is modulated by the PYM C-terminus revealing that DmPYM function is regulated in vivo. Furthermore, we find that whereas under normal conditions DmPYM is dispensable, its loss of function is lethal to flies with reduced y14 or mago gene dosage. Our analysis demonstrates that the amount of DmPYM relative to the EJC proteins is critical for viability and fertility. This, together with the fact that the EJC-disassembly activity of DmPYM is regulated, implicates PYM as an effector of EJC homeostasis in vivo.

Unprecedented Strong Panchromic Absorption from Proton-Switchable Iridium(III) Azoimidazolate Complexes.

Two new heteroleptic iridium(III) complexes bearing an aryldiazoimidazole ligand are reported. These complexes differ structurally with respect to the protonation state of the imidazole ring, but can be independently accessed by varying the synthetic conditions. Their structures have been unequivocally confirmed by X-ray crystal structure analysis, with surprising differences in the structural parameters of the two complexes. The strongly absorbing nature of the free diazoimidazole ligand is enhanced in these iridium complexes, with the protonated cationic complex demonstrating extraordinarily strong panchromic absorption up to 700 nm. The absorption profile of the deprotonated neutral complex is blueshifted by about 100 nm and thus the interconversion between the two complexes as a function of the acidity/basicity of the environment can be readily monitored by absorption spectroscopy. Theoretical calculations revealed the origins of these markedly different absorption properties. Finally, the protonated analogue has been targeted as an acceptor material for organic photovoltaic (OPV) applications, and preliminary results are reported.

Detection of in vivo protein tyrosine nitration in petite mutant of Saccharomyces cerevisiae: consequence of its formation and significance.

Protein tyrosine nitration (PTN) is a selective post-translational modification often associated with physiological and pathophysiological conditions. Tyrosine is modified in the 3-position of the phenolic ring through the addition of a nitro group. In our previous study we first time showed that PTN occurs in vivo in Saccharomyces cerevisiae. In the present study we observed occurrence of PTN in petite mutant of S. cerevisiae which indicated that PTN is not absolutely dependent on functional mitochondria. Nitration of proteins in S. cerevisiae was also first time confirmed in immunohistochemical study using spheroplasts. Using proteosomal mutants Rpn10Δ, Pre9Δ, we first time showed that the fate of protein nitration in S. cerevisiae was not dependent on proteosomal clearing and probably played vital role in modulating signaling cascades. From our study it is evident that protein tyrosine nitration is a normal physiological event of S. cerevisiae.

Identification and characterization of domain-specific inhibitors of DENV NS3 and NS5 proteins by in silico screening methods.

The dengue virus (DENV) infects approximately 400 million people annually worldwide causing significant morbidity and mortality. Despite advances in understanding the virus life cycle and infectivity, no specific treatment for this disease exists due to the lack of therapeutic drugs. In addition, vaccines available currently are ineffective with severe side effects. Therefore, there is an urgent need for developing therapeutics suitable for effective management of DENV infection. In this study, we adopted a drug repurposing strategy to identify new therapeutic use of existing FDA approved drug molecules to target DENV2 non-structural proteins NS3 and NS5 using computational approaches. We used Drugbank database molecules for virtual screening and multiple docking analysis against a total of four domains, the NS3 protease and helicase domains and NS5 MTase and RdRp domains. Subsequently, MD simulations and MM-PBSA analysis were performed to validate the intrinsic atomic interactions and the binding affinities. Furthermore, the internal dynamics in all four protein domains, in presence of drug molecule binding were assessed using essential dynamics and free energy landscape analyses, which were further coupled with conformational dynamics-based clustering studies and cross-correlation analysis to map the regions that exhibit these structural variations. Our comprehensive analysis identified tolcapone, cefprozil, delavirdine and indinavir as potential inhibitors of NS5 MTase, NS5 RdRp, NS3 protease and NS3 helicase functions, respectively. These high-confidence candidate molecules will be useful for developing effective anti-DENV therapy to combat dengue infection.Communicated by Ramaswamy H. Sarma.

Bringing revolution through quadcopter technology in the field of supplying medicine in the Himalayan regions of Uttarakhand: Case example of Pithoragarh.

BACKGROUND: Quadcopters are used in various forms in the civil arena, from crop insurance to agricultural drones, as loudspeakers for announcing government guidelines, resilience tools in infrastructure monitoring, real-time vehicle detection, etc. However, the usage of quadcopters and hexacopters in supplying medical aid to inhospitable and far-flung terrains is being studied and researched in less detail throughout the globe. AIM: This paper focuses on the basics of quadcopter technology in supplying medicines and its advantages to the affected patients who get life-saving medicines from earlier inaccessible roads. The efficacy of quadcopters in terms of time, economy, and manpower in supplying essential and inescapable medical supplies is exponentially high, especially in the Pithoragarh Region of Uttarakhand State, where the villages are not connected to the roads. METHODS: The road structure of the hilly terrain of Uttarakhand, India, was studied in detail to know the state of people who do not get access to life-saving drugs due to the non-availability of roads near them. RESULTS: The result informs us that the quad/hexacopter if used in abundance can provide a glimmer of hope to people in remote places. CONCLUSION: The quadcopter can provide hope to the residents of the Pithoragarh district of Uttarakhand, India, located in far-flung places devoid of basic medical facilities.

Validation of CRISPR activation system in Aedes cells using multicistronic plasmid vectors.

Aedes mosquitoes transmit several pathogens including flaviviruses to humans which result in high morbidity and mortality. Owing to adaptability and climate change, these mosquito vectors are predicted to establish in new geographical areas thus exposing larger populations to the risk of infection. Therefore, control of Aedes vector is necessary to prevent disease transmission. Recently, genetic approaches to vector control have shown promise; however, the tools and methods for manipulating the mosquito genome are rather limited. While CRISPR-Cas9 system has been adapted for gene editing purposes in Aedes mosquito, the dCas9-based transcription control of genes remain unexplored. In this study we report implementation of the CRISPR activation system in Aedes cells. For this we designed, constructed and tested a bi-partite plasmid-based strategy that allows expression of the dCas9-VPR and targeting guide RNA together with a reporter cassette. Quantitative analysis of the fluorescent reporter gene levels showed a robust over-expression validating CRISPR activation in Aedes cells. This strategy and the biological parts will be useful resource for synthetic transcription factor-based robust upregulation of Aedes genes for application of synthetic biology approaches for vector control.

ß-Cyclodextrin Stabilized Nanoceria for Hydrolytic Cleavage of Paraoxon in Aqueous and Cationic Micellar Media.

Beta-cyclodextrin (ß-CD) stabilized cerium oxide nanoparticles (ß-CD@CeO2 NPs) were synthesized through a hydrothermal route. The electronic properties, surface functional group, surface composition, size, and morphologies of the as-synthesized ß-CD@CeO2 NPs were characterized using UV-visible spectroscopy, FTIR analysis, high resolution X-ray photoelectron spectroscopy (HRXPS), high resolution transmission electron microscopy (HRTEM), and field emission scanning electron microscopy (FESEM). The pH-dependent variation of the ζ-potential of ß-CD@CeO2 NPs and the catalytic activity of the NPs for the hydrolysis of paraoxon were investigated. The observed pseudo-first-order rate constant (kobs) for the hydrolysis of paraoxon is increased with increasing pH and the ζ-potential of ß-CD@CeO2 NPs. The kinetics and mechanism of hydrolysis of paraoxon in the aqueous and cationic micellar media have been discussed.

Bayesian Adaptive Beamformer for Robust Electromagnetic Brain Imaging of Correlated Sources in High Spatial Resolution.

Reconstructing complex brain source activity at a high spatiotemporal resolution from magnetoencephalography (MEG) or electroencephalography (EEG) remains a challenging problem. Adaptive beamformers are routinely deployed for this imaging domain using the sample data covariance. However adaptive beamformers have long been hindered by 1) high degree of correlation between multiple brain sources, and 2) interference and noise embedded in sensor measurements. This study develops a novel framework for minimum variance adaptive beamformers that uses a model data covariance learned from data using a sparse Bayesian learning algorithm (SBL-BF). The learned model data covariance effectively removes influence from correlated brain sources and is robust to noise and interference without the need for baseline measurements. A multiresolution framework for model data covariance computation and parallelization of the beamformer implementation enables efficient high-resolution reconstruction images. Results with both simulations and real datasets indicate that multiple highly correlated sources can be accurately reconstructed, and that interference and noise can be sufficiently suppressed. Reconstructions at 2-2.5mm resolution (  âˆ¼  150K voxels) are possible with efficient run times of 1-3 minutes. This novel adaptive beamforming algorithm significantly outperforms the state-of-the-art benchmarks. Therefore, SBL-BF provides an effective framework for efficiently reconstructing multiple correlated brain sources with high resolution and robustness to interference and noise.

Effect of thermal annealing on an emissive layer containing a blend of a small molecule and polymer as host for application in OLEDs.

In order to improve the performance of OLEDs, a host-guest mixture was used as an emissive layer. To have better host properties, a mixture of different materials with suitable properties can also be used as a host. In this study, we used a mixture of a polymer and a small molecule as the host and studied the effect of thermal annealing on the emissive layer properties by using Ir(ppy)3 as the emitter. UV-visible absorption, steady-state and time-resolved photoluminescence, scanning electron microscopy, atomic force microscopy, and optical microscopic studies were performed to study the film properties. Devices were fabricated and their current-voltage and luminance-voltage characteristics were studied. Charge-carrier mobility in the devices was studied by dark CELIV and transient electroluminescence methods. We show that, below the glass transition temperature of the polymer, the small molecules formed aggregates due to thermal annealing, which was beneficial for the device performance in the lower-temperature range, mainly due to the improved electron mobility. However, this aggregate formation was detrimental in the higher-temperature range, as it led to inefficient energy transfer due to the increased pure phase formation. At temperatures above the glass transition temperature of the polymer, the small molecules were seen to be distributed more uniformly into the polymer matrix. However, as a result of the degradation of the polymer property due to degradation of the primary chain of the phenyl ring of the polymer, this uniform distribution was not of any use and the device performance deteriorated.

Multi-tasking deep network for tinnitus classification and severity prediction from multimodal structural MR images.

Objective:Subjective tinnitus is an auditory phantom perceptual disorder without an objective biomarker. Fast and efficient diagnostic tools will advance clinical practice by detecting or confirming the condition, tracking change in severity, and monitoring treatment response. Motivated by evidence of subtle anatomical, morphological, or functional information in magnetic resonance images of the brain, we examine data-driven machine learning methods for joint tinnitus classification (tinnitus or no tinnitus) and tinnitus severity prediction.Approach:We propose a deep multi-task multimodal framework for tinnitus classification and severity prediction using structural MRI (sMRI) data. To leverage complementary information multimodal neuroimaging data, we integrate two modalities of three-dimensional sMRI-T1 weighted (T1w) and T2 weighted (T2w) images. To explore the key components in the MR images that drove task performance, we segment both T1w and T2w images into three different components-cerebrospinal fluid, grey matter and white matter, and evaluate performance of each segmented image.Main results:Results demonstrate that our multimodal framework capitalizes on the information across both modalities (T1w and T2w) for the joint task of tinnitus classification and severity prediction.Significance:Our model outperforms existing learning-based and conventional methods in terms of accuracy, sensitivity, specificity, and negative predictive value.