Biology subjects

Dutta, A.

Publications and source records attributed to Dutta, A..

103 records · Page 6Linked to original sources

bioRxiv2019

The role of ANGIOGENIN, or lack thereof, in the generation of stress-induced tRNA halves and of smaller tRNA fragments that enter Argonaute complexes

Overexpressed Angiogenin (ANG) cleaves tRNA anticodons to produce tRNA halves similar to those produced in response to stress, but it is not clear whether endogenous ANG is essential for producing the stress-induced tRNA halves. It is also not clear whether smaller tRNA fragments (tRFs) are generated from the tRNA halves. Global short RNAseq experiments reveal that ANG over-expression selectively cleaves a subset of tRNAs (tRNAGlu, tRNAGly, tRNALys, tRNAVal, tRNAHis, tRNAAsp and tRNASeC) to produce tRNA halves and 26-30 bases long tRF-5s. Surprisingly, knockout of ANG reveals that the majority of stress-induced tRNA halves except 5 half from tRNAHisGTG and 3 half from tRNAAspGTC are ANG-independent, suggesting there are other RNases that can produce tRNA halves. The 17-25 bases long tRF-3s and tRF-5s that could enter into Argonaute complexes are not induced by ANG overexpression, suggesting that they are generated independently from tRNA halves. Consistent with this, knockout of ANG did not decrease tRF-3 levels or gene-silencing activity. Therefore ANG cleaves specific tRNAs, is not the only RNAse that creates tRNA halves and the shorter tRFs are not generated from the tRNA halves or from independent tRNA cleavage by ANG.

molecular biology↗

bioRxiv2019

Computational modeling of the photon transport, tissue heating, and cytochrome C oxidase absorption during transcranial near-infrared stimulation

Transcranial near-infrared stimulation (tNIRS) has been proposed as a tool to modulate cortical excitability. However, the underlying mechanisms are not clear where the heating effects on the brain tissue needs investigation due to increased near-infrared (NIR) absorption by water and fat. Moreover, the risk of localized heating of tissues (including the skin) during optical stimulation of the brain tissue is a concern. The challenge in estimating localized tissue heating is due to the light interaction with the tissues constituents, which is dependent on the combination ratio of the scattering and absorption properties of the constituent. Here, apart from tissue heating that can modulate the cortical excitability (\"photothermal effects\"); the other mechanism reported in the literature is the stimulation of the mitochondria in the cells which are active in the adenosine triphosphate (ATP) synthesis. In the mitochondrial respiratory chain, the complex IV, also named as the cytochrome c oxidase(CCO), is the unit four with three copper atoms. The absorption peaks of CCO are in the visible (420-450nm and 600-700nm) and the near-infrared (760-980nm) spectral region which have been shown to be promising for low level light therapy (LLLT), also known as \"photobiomodulation\". While much higher CCO absorption peaks in the visible spectrum can be used for the photobiomodulation of the skin, 810nm has been proposed for the non-invasive brain stimulation (using tNIRS) due to the optical window in the NIR spectral region. In this article, we applied a computational approach to delineate the \"photothermal effects\" from the \"photobiomodulation,\" i.e., to estimate the amount of light absorbed individually by each chromophore in the brain tissue (with constant scattering) and the related tissue heating. Photon migration simulations were performed for motor cortex tNIRS based on a prior work that used a 500mW cm-2 light source placed on the scalp. We simulated photon migration at 630nm and 700nm (red spectral region) and 810nm (near-infrared spectral region). We found a temperature increase in the scalp below 0.25 {degrees} C and a minimal temperature increase in the gray matter less than 0.04 {degrees} C at 810nm. Similar heating was found for 630nm and 700nm used for LLLT, so photothermal effects are postulated to be unlikely in the brain tissue.

biophysics↗

bioRxiv2019

Extrachromosomal circular DNA, microDNA, without canonical promoters produce short regulatory RNAs that suppress gene expression

Interest in extrachromosomal circular DNA (eccDNA) molecules has increased recently because of their widespread presence in normal cells across every species ranging from yeast to humans, their increased levels in cancer cells, and their overlap with oncogenic and drug-resistant genes. However, the majority of eccDNA (microDNA) are too small to carry protein coding genes. We have tested functional capabilities of microDNA, by creating artificial microDNA molecules mimicking known microDNA sequences and have discovered that they express functional small regulatory RNA including microRNA and novel si-like RNA. MicroDNA is transcribed in vitro and in vivo independent of a canonical promoter sequence. MicroDNA which carry miRNA genes form transcripts which are processed into mature miRNA molecules, through the endogenous RNA-interference pathway, which repress a luciferase reporter gene as well as endogenous mRNA targets of the miRNA. Further, microDNA containing sequences of exons repress the endogenous gene from which the microDNA was derived through the formation of novel si-like RNA. We also show that endogenous microDNA associate with RNA polymerases subunits POLR2H and POLR3F. Together, these results suggest that microDNA may modulate gene expression through the production of both known and novel regulatory small RNA.

molecular biology↗

bioRxiv2019

Lobule-specific dosage considerations for cerebellar transcranial direct current stimulation during healthy aging - a computational modeling study using age-specific MRI templates

The world population aged 60 years and older is expected to double between 2015 and 2050. Aging is associated with a decline in cognitive and motor performances which are a part of geriatric syndromes. Aging is also associated with the loss of cerebellar volume where the cerebellum has a considerable contribution in cognitive and motor functions. Therefore, cerebellar transcranial direct current stimulation (ctDCS) has been proposed to study and facilitate cerebellar function during aging. However, the one-size-fits-all approach used for ctDCS can lead to variability in the cerebellar lobule-specific dosing due to age-related changes in the cerebellar structure. Therefore, we investigated lobular electric field (EF) distribution during healthy aging for age groups of 18 to 89 years where computational modeling was based on age-appropriate human brain magnetic resonance imaging (MRI) templates (http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/). A fully automated open-source pipeline (Realistic vOlumetric-Approach to Simulate Transcranial Electric Stimulation - ROAST) was used for the age-group specific EF modeling. Then, we extracted the EF distribution at the 28 cerebellar lobules based on a spatially unbiased atlas (SUIT) for the cerebellum. Our computational results showed that the EF strength increased significantly at certain important cerebellar lobules (e.g., Crus I and Crus II relevant for cognitive function) contralateral (contra) to the targeted (ipsi) cerebellar hemisphere at an older age that reduced the ctDCS specificity. Specifically, two-way ANOVA showed that the lobules as well as the age-group (and their interaction term) had a significant effect (p<0.01). Post-hoc multiple comparison tests at Alpha=0.01 using Bonferroni critical values showed that Right (Ipsi) Crus I, Right (Ipsi) Crus II, Right (Ipsi) VI, Vermis VIIb, Vermis VIIIa, Right (Ipsi) VIIb, Left (Contra) VIIIb, Left (Contra) IX, Right (Ipsi) VIIIa, Right (Ipsi) VIIIb, Vermis VIIIb, Right (Ipsi) IX, and Vermis IX, and the age-group 18, 18.5, 19, 20-24, 45-49, 50-54, 70-74, 75-79, 85-89 years experienced higher electric field strength (>0.11V/m). Since there is a dichotomy between the sensorimotor cerebellum and the cognitive cerebellum, therefore, subject-specific MRI based head modeling for lobule-specific dosage considerations will be necessary for clinical translation of ctDCS to address geriatric cerebellar syndromes.

neuroscience↗

bioRxiv2019

A computational pipeline to determine lobular electric field distribution during cerebellar transcranial direct current stimulation

ObjectiveCerebellar transcranial direct current stimulation (ctDCS) is challenging due to the complexity of the cerebellar structure. Therefore, our objective is to develop a freely available computational pipeline to perform cerebellar atlas-based electric field analysis using magnetic resonance imaging (MRI) guided subject-specific head modeling. MethodsWe present a freely available computational pipeline to determine subject-specific lobular electric field distribution during ctDCS. The computational pipeline can isolate subject-specific cerebellar lobules based on a spatially unbiased atlas (SUIT) for the cerebellum, and then calculates the lobular electric field distribution during ctDCS. The computational pipeline was tested in a case study using a subject-specific head model as well as using a Colin 27 Average Brain. The 5cmx5cm anode was placed 3 cm lateral to inion, and the same sized cathode was placed on the contralateral supraorbital area (called Manto montage) and buccinators muscle (called Celnik montage). A 4x1 HD-ctDCS electrode montage was also implemented for a comparison using analysis of variance (ANOVA). ResultsEta-squared effect size after three-way ANOVA for electric field strength was 0.05 for lobule, 0.00 for montage, 0.04 for head model, 0.01 for lobule*montage interaction, 0.01 for lobule* head model interaction, and 0.00 for montage*head model interaction in case of Enorm. Here, the electric field strength of both the Celnik and the Manto montages affected the lobules Crus II, VIIb, VIII, IX of the targeted cerebellar hemispheres while Manto montage had more bilateral effect. The HD-ctDCS montage primarily affected the lobules Crus I, Crus II, VIIb of the targeted cerebellar hemisphere. Our freely available computational modeling approach to analyze subject-specific lobular electric field distribution during ctDCS provided an insight into healthy human anodal ctDCS results

neuroscience↗

bioRxiv2018

The Germline Variants rs61757955 and rs34988193 are Predictive of Survival in Low Grade Glioma Patients

AbstractLow grade gliomas are invasive brain tumors that are difficult to completely resect neurosurgically. They often recur following resection and progress, resulting in death. Although previous studies have shown that specific germline variants increase the risk of tumor formation, no previous study has screened many germline variants to identify variants predictive of survival in glioma patients. In this study, we present an approach to identify the small fraction of prognostic germline variants from the pool of over four million variants that we variant called in The Cancer Genome Atlas whole exome sequencing and RNA sequencing datasets. We identified two germline variants that are predictive of poor patient outcomes by Cox regression, controlling for eleven covariates. rs61757955 is a germline variant found in the 3 UTR of GRB2 associated with increased KRAS signaling, CIC mutations, and 1p/19q co-deletion. rs34988193 is a germline variant found in the tumor suppressor gene ANKDD1a that causes an amino acid change from lysine to glutamate. This variant was found to be predictive of poor prognosis in two independent low grade glioma datasets and is predicted to be within the top 0.06% of deleterious mutations across the human genome. The wild type residue is conserved in all 22 other species with a homologous protein.\n\nImplicationsThis is the first study presenting an approach to screening many germline variants to identify variants predictive of survival and our application of this methodology revealed the germline variants rs61757955 and rs34988193 as being predictive of survival in low grade glioma patients.

cancer biology↗

bioRxiv2018

Lipid Droplet metabolism dependent microbial defense in pre-immune zebrafish embryos

Microbes present survival challenge to pre-immune embryos. Our study provides evidence for antimicrobial-secretion-based strategy of zebrafish embryos against microbes during pre-immune stages. Chorion prevents physical contact between embryos and microbes, yet microbes compromise embryonic survival through their secretions. Development of embryos in microbe-free medium involves secretion of pro-microbial compounds that bacteria utilize to accelarete growth. Embryo senses presence of microbes through microbial secretions. They respond by altering their secretions to include antimicrobial compounds along with regular pro-microbial ones. Upon sensing embryonic anti-microbial secretions, microbes too alter their secretions to include more potent toxins for embryos. In response to this embryos alter their secretions to include more potent antimicrobial compounds. Ability of embryos to secrete antimicrobial compounds is positively correlated with amount of lipid droplets (LDs) in them. Inhibition of LD metabolism prevents antimicrobial secretions by embryos. Thus, LDs protect zebrafish embryos from microbes. This manuscript establishes that pre-immune embryos employ dynamically evolving biochemical warfare to protect themselves from harmful microbes.

developmental biology↗

bioRxiv2018

Inference of splicing motifs through visualization of recurrent networks

Neural models have been able to obtain state-of-the-art performances on several genome sequence-based prediction tasks. Such models take only nucleotide sequences as input and learn relevant features on its own. However, extracting the interpretable motifs from the model remains a challenge. This work explores various existing visualization techniques in their ability to infer relevant sequence information learned by a recurrent neural network (RNN) on the task of splice junction identification. The visualization techniques have been modulated to suit the genome sequences as input. The visualizations inspect genomic regions at the level of a single nucleotide as well as a span of consecutive nucleotides. This inspection is performed based on modification of input sequences (perturbation-based) or the embedding space (back-propagation based). We infer features pertaining to both canonical and non-canonical splicing from a single neural model. Results indicate that the visualization techniques produce comparable performance for branchpoint detection. However, in case of canonical donor and acceptor junction motifs, perturbation based visualizations perform better than back-propagation based visualizations and vice-versa for non-canonical motifs.

bioinformatics↗

bioRxiv2018

A prognostic signature for lower-grade gliomas based on expression of long noncoding RNAs

Diffuse low-grade and intermediate-grade gliomas (together known as lower-grade gliomas, WHO grade II and III) develop in the supporting glial cells of brain and are the most common types of primary brain tumor. Despite a better prognosis for lower-grade gliomas, 70% of patients undergo high-grade transformation within 10 years, stressing the importance of better prognosis. Long non-coding RNAs (lncRNAs) are gaining attention as potential biomarkers for cancer diagnosis and prognosis. We have developed a computational model, UVA8, for prognosis of lower-grade gliomas by combining lncRNA expression, Cox regression and L1-LASSO penalization. The model was trained on a subset of patients in TCGA. Patients in TCGA, as well as a completely independent validation set (CGGA) could be dichotomized based on their risk score, a linear combination of the level of each prognostic lncRNA weighted by its multivariable cox regression coefficient. UVA8 is an independent predictor of survival and outperforms standard epidemiological approaches and previous published lncRNA-based predictors as a survival model. Guilt-by-association studies of the lncRNAs in UVA8, all of which predict good outcome, suggest they have a role in suppressing interferon stimulated response and epithelial to mesenchymal transition. The expression levels of 8 lncRNAs can be combined to produce a prognostic tool applicable to diverse populations of glioma patients. The 8 lncRNA (UVA8) based score can identify grade II and grade III glioma patients with poor outcome and thus identify patients who should receive more aggressive therapy at the outset.

genomics↗

bioRxiv2018

Topological Scoring of Protein Interaction Networks

It remains a significant challenge to define individual protein associations within networks where an individual protein can directly interact with other proteins and/or be part of large complexes, which contain functional modules. Here we demonstrate the topological scoring (TopS) algorithm for the analysis of quantitative proteomic analyses of affinity purifications. Data is analyzed in a parallel fashion where a bait protein is scored in an individual affinity purification by aggregating information from the entire dataset. A broad range of scores is obtained which indicate the enrichment of an individual protein in every bait protein analyzed. TopS was applied to interaction networks derived from human DNA repair proteins and yeast chromatin remodeling complexes. TopS captured direct protein interactions and modules within complexes. TopS is a rapid method for the efficient and informative computational analysis of datasets, is complementary to existing analysis pipelines, and provides new insights into protein interaction networks.

systems biology↗

bioRxiv2017

SpliceVec: distributed feature representations for splice junction prediction

Identification of intron boundaries, called splice junctions, is an important part of delineating gene structure and functions. This also provides valuable in-sights into the role of alternative splicing in increasing functional diversity of genes. Identification of splice junctions through RNA-seq is by mapping short reads to the reference genome which is prone to errors due to random sequence matches. This encourages identification of splicing junctions through computa-tional methods based on machine learning. Existing models are dependent on feature extraction and selection for capturing splicing signals lying in vicinity of splice junctions. But such manually extracted features are not exhaustive. We introduce distributed feature representation, SpliceVec, to avoid explicit and biased feature extraction generally adopted for such tasks. SpliceVec is based on two widely used distributed representation models in natural language processing. Learned feature representation in form of SpliceVec is fed to multi-layer perceptron for splice junction classification task. An intrinsic evaluation of SpliceVec indicates that it is able to group true and false sites distinctly. Our study on optimal context to be considered for feature extraction indicates inclusion of entire intronic sequence to be better than flanking upstream and downstream region around splice junctions. Further, SpliceVec is invariant to canonical and non-canonical splice junction detection. The proposed model is consistent in its performance even with reduced dataset and class-imbalanced dataset. SpliceVec is computationally efficient and can be trained with user defined data as well.

bioinformatics↗

bioRxiv2017

Global Gene Repression By Dicer-Independent tRNA Fragments

tRNA derived RNA fragments (tRFs) is an emerging group of small RNAs as abundant as miRNAs, and yet their roles are not well understood. Here, we focus on endogenous tRFs (18-22 bases) derived from 3 end of human mature tRNAs (tRF-3) and their functions in gene repression. tRF-3 levels increase upon parental tRNA over-expression or tRNA induction by c-Myc oncogene activation. Elevated tRF-3 levels lead to repression of target genes with a sequence complementary to the tRF-3 in the 3 UTR. The tRF-3-mediated repression is Dicer-independent, Argonaute-dependent and the targets are recognized by 5 seed sequence rules similar to miRNAs. Furthermore, tRF-3s associate with GW proteins in P-bodies. RNA-seq identifies the endogenous target genes of tRF-3s that are specifically repressed upon tRF-3 induction. Overall, our analysis shows Dicer-independent tRF-3s, generated upon tRNA upregulation such as c-Myc overexpression, regulate gene expression globally through Argounate via seed sequence matches.

molecular biology↗

bioRxiv2017

mlh3 separation of function and endonuclease defective mutants display an unexpected effect on meiotic recombination outcomes

Mlh1-Mlh3 is an endonuclease hypothesized to act in meiosis to resolve double Holliday junctions into crossovers. It also plays a minor role in eukaryotic DNA mismatch repair (MMR). To understand how Mlh1-Mlh3 functions in both meiosis and MMR, we analyzed in bakers yeast 60 new mlh3 alleles. Five alleles specifically disrupted MMR, whereas one (mlh3-32) specifically disrupted meiotic crossing over. Mlh1-mlh3 representatives for each separation of function class were purified and characterized. Both Mlh1-mlh3-32 (MMR+, crossover-) and Mlh1-mlh3-45 (MMR-, crossover+) displayed wild-type endonuclease activities in vitro. Msh2-Msh3, an MSH complex that acts with Mlh1-Mlh3 in MMR, stimulated the endonuclease activity of Mlh1-mlh3-32 but not Mlh1-mlh3-45, suggesting that Mlh1-mlh3-45 is defective in MSH interactions. Whole genome recombination maps were constructed for two mlh3 mutants with opposite separation of function phenotypes, and an endonuclease defective mutant. Unexpectedly, all three showed increases in the number of non-crossover events that were not observed in mlh3{Delta}. Our observations provide a structure-function map for Mlh3 that reveals the importance of protein-protein interactions in regulating Mlh1-Mlh3s enzymatic activity. They also illustrate how defective meiotic components can alter the fate of meiotic recombination intermediates, providing new insights for how meiotic recombination pathways are regulated.\n\nAuthor SummaryDuring meiosis, diploid germ cells that become eggs or sperm undergo a single round of DNA replication followed by two consecutive chromosomal divisions. The segregation of chromosomes at the first meiotic division is dependent in most organisms on at least one genetic exchange, or crossover event, between chromosome homologs. Homologs that do not receive a crossover frequently undergo non-disjunction at the first meiotic division, yielding gametes that lack chromosomes or contain additional copies. Such events have been linked to human disease and infertility. Recent studies suggest that the Mlh1-Mlh3 complex is an endonuclease that resolves recombination intermediates into crossovers. Interestingly, this complex also acts as a matchmaker in DNA mismatch repair (MMR) to remove DNA replication errors. How does one complex act in two different processes? We investigated this question by performing a mutational analysis of the bakers yeast Mlh3 protein. Five mutations were identified that disrupted MMR but not crossing over, and one mutation disrupted crossing over while maintaining MMR. Using a combination of biochemical and genetic analyses to further characterize these mutants we illustrate the importance of protein-protein interactions for Mlh1-Mlh3s activity. Importantly, we illustrate how defective meiotic components can alter the outcome of meiotic recombination events. They also provide new insights in our understanding of the basis of infertility syndromes.

genetics↗