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Gravity flow of granular materials through a vertical channel
No full textGrains and powders are the second most widely used materials in industries
and daily life after simple fluids. There are a variety of granular materials such
as food grains, detergents, tablets and capsules, fertilizers, coal, and catalyst
pellets. They show both solid-like and fluid-like behaviour. Experiments reveal
unexpected features and exceptionally complex signatures in granular flows. Unlike simple fluids, their rheology is not well understood. Models based on particle
dynamics are available to simulate such flows. However, simulations at an industrial scale are computationally highly expensive because of handling extremely
large number of particles in a unit operation. Hence there is dire need of a constitutive theory which can predict the flow behaviour well. Since many decades,
researchers have attempted to develop theories for granular flows based on soil
plasticity, kinetic theory of dense gases, non-equilibrium statistical mechanics,
and non-local approaches. Unfortunately, a universally accepted constitutive
theory for granular flows is lacking.
In conclusion, the gravity flow chosen in the present work is appropriate
to examine the continuum models. None of the models, which were recently
developed and are examined here, has the ability to predict all the features well.
The lack of suitable boundary conditions is an another issue. This highlights the
need for more work to develop a universally accepted theory for granular flow.
Fluctuations in the wall stresses are observed in the simulations when periodic
boundary conditions are used in two directions. It remains to be seen whether
these features are preserved when such boundary conditions are not used and
the actual bin problem is solved. The results may have an important bearing on
the design of vertical vessels handling granular materials
Analysis of vocal sounds in asthmatic patients
No full textAround 334 million people have asthma worldwide. Asthma is an inflammatory disease of the airways which causes cough, breathlessness, chest tightness, and other peculiar sounds during breathing. The golden standard test spirometry is used to diagnose and monitor asthma. Spirometry is a lung function test that measures the time and volume of air a person can exhale after a deep inhalation. In general, patients repeat the test multiple times to get accurate readings, making it very time-consuming, and strenuous, especially for children and older people. A spirometer is also an expensive and bulky device that is not suitable for a home monitoring setup. Hence, a need for an easy and fast method exists. Sound-based analysis can be one such method. The motivation behind using sounds for monitoring and diagnosis of asthma originates from the sound production mechanism. In literature, non-speech sounds, namely, cough and breath recorded at the chest, have been explored. However, the analysis of speech and non-speech sounds recorded at the mouth is least investigated. Therefore, the work done in this thesis addresses this problem. For the analysis, we started with two tasks, namely classification and spirometry prediction for each sound category. Therefore, the thesis is divided into two parts.\\
Analysis of speech sounds
For speech sound analysis, classification between the asthmatic and healthy subjects and spirometry prediction tasks have been performed. Results of the classification and spirometry prediction task show that \textipa{/oU/} (as in 'Home') is the best for the classification task, whereas \textipa{/i:/} (as in 'Meet') is best for the spirometry prediction. Results of the classification task suggest that Mel-frequency cepstral coefficients (MFCC) statistics carry maximum information for the discrimination in the case of all speech sounds considered in this work. Spirometry variables prediction task results show that the low frequency carries more information in best-performing sound \textipa{/i:/}.\\
Analysis of non-speech sounds
Classification performed with non-speech sounds, cough, and breath, indicates that MFCC's are best, but interestingly, static MFCC coefficients are more informative than the velocity and acceleration coefficients. Breath performs the best for the classification task in the non-speech sound group. Further analysis of breath signal shows that discriminative information for classification is not uniform in the entire breath signal. Interestingly, the middle 50\% of the breath signal carries maximum information for the classification. To extract the middle 50\% of a breath, prior knowledge of breath boundaries is required. Therefore, we developed an unsupervised breath segmentation algorithm using dynamic programming. Classification results using predicted boundaries are found to be on par with the ground truth boundaries. Comparison of speech sounds and breath for the classification tasks shows that breath sound outperformed speech sounds. Experiments conducting for spirometry prediction tasks using non-speech sound indicate that breath performance is better than cough. In the spirometry prediction task, speech sounds outperformed the non-speech sounds.
As asthma is not curable, patients needs to be on continuous medication known as bronchodilaotrs
to reduce inflammation in the airways. But what kind of changes introduced due to airway change is not known. A linear discriminant-based analysis has been carried out to determine what kind of spectral changes occur in an asthmatic patient's sound before and after taking a bronchodilator. For this task, breath sounds have been chosen. It has been observed that frequency bands 400Hz-500Hz and 1480Hz -1900Hz are more sensitive to obstruction change in breath sound
Topics on Safety and Security of Power Systems
No full textIn this thesis, we investigate some of the problems concerning the safety and security of power systems. Since the operational safety of the power system itself is a vast area of research, we choose to investigate the problem of identifying transmission line outages in a power system due to their cascading nature and widespread blackouts they can cause. Therefore, it is important to identify such outages in the shortest time possible. With this motivation, we propose a state estimation-based sequential hypothesis testing procedure to localize the failed lines. The primary focus is on single-line outages as these are more frequently occurring failures. The state estimation (SE) is performed using conventional power measurements (SCADA) and synchronized phasor measurement units (PMUs). The idea is that if there is an outage, then this information is embedded in the state estimation results, and by analyzing this information one can infer the topology of the power system. The proposed framework involves various Kalman filter-based state estimation techniques followed by a generalized likelihood ratio testing procedure to locate the failed lines. This work considers both centralized and decentralized state estimation approaches. In a centralized approach, all the information from various parts of the power system is available to the system operator. However, in the decentralized approach, only limited information is considered to reduce the communication and computational overhead. The proposed algorithms are evaluated on the IEEE 14 and the IEEE 118 bus systems, and results show that all the high-risk line failures were identified quickly. Further, simulation results show that the use of PMUs enables accurate and quicker detection than conventional power measurements.
Furthermore, recent cyber-attacks on power grids highlight the necessity to protect the critical functionalities of a control center vital for the secure operation of a grid. Even in a distributed framework, one central control center acts as a coordinator in the majority of the control center architectures. Such a control center can become a prime target for cyber and physical attacks, and, hence, a single point failure can lead to a complete loss of visibility of the power grid. If the control center that runs the critical functions in a distributed computing environment is chosen randomly among the available control centers in a secure framework, the ability of the attacker to cause a single point failure can be reduced to a great extent. To achieve this, we propose a novel distributed hierarchy-based framework to secure critical functions related to the control center. The proposed framework ensures that the data aggregation and the critical functions are carried out at a random location and incorporates security features such as attestation and trust management to detect compromised agents. A theoretical result is provided on the evolution and convergence of the trust values in the proposed trust management protocol. It is also shown that the system is nominally robust so long as the number of compromised nodes is strictly less than one-half of the nodes minus 1. For demonstration, a Kalman filter-based state estimation using phasor measurements is used as the critical function to be secured. The proposed framework’s implementation feasibility is tested on a physical hardware cluster of Parallella boards mimicking the IEEE-5-bus-system. The framework is also validated using simulations on the IEEE 118 bus system. The experimental and simulation results show that the trust for compromised control centers nominally reduces with the number of attestations.Department of Science and Technology, Ministry of Human Resource Development, Robert Bosch Center for Cyber-Physical Systems (RBCCPS
Assessment and Monitoring Of Hydrometeorological Variables And Extreme Conditions for Present and Future Climate Change Scenarios
No full textMonitoring and assessment of Hydrological/hydrometeorological Variables (HVs) like
streamflow, soil moisture, precipitation, and temperature are essential for various applications
such as prediction/forecasting of natural hazards (e.g., droughts, floods, heatwaves,
and landslides). Often impediments arise due to scarcity of gauges and/or records,
which poses challenges for hydrological studies, especially in areas witnessing considerable
spatiotemporal variability in climate conditions and regions with high heterogeneity
in physiographical conditions (e.g., mountainous, hilly/undulating terrains). In recent
decades, climate change has been deemed to be the cause of the intensification of natural
hazards. Hence, effective monitoring of the associated HVs for the present conditions
and assessing their future projections are essential for devising appropriate risk mitigation
strategies and early warning systems. The thesis proposes novel methodologies for the
optimal design of ground-based networks monitoring various HVs in univariate and multivariate
frameworks (Chapters 2 to 4). Furthermore, to identify global hotspot areas that
could be prioritized for establishing/developing monitoring networks, the spatiotemporal
variability, and trends of wet, normal, and dry conditions are assessed, corresponding
to various accumulation periods (Chapter 5). Additionally, analysis was conducted at
global-, continental- and regional scales to assess the impacts of Meteorological Flash
Droughts (MFDs) and changes in their trends and hotspot regions for present and five
future CMIP6 climate change scenario
Studies on Mono- and Multi-valent Ion Storage Using Metal Phosphosulfide and Organic Carbonyl Compounds
No full textThe present study describes the results on inorganic and organic materials for energy
storage and sensors. It contains eight chapters including introduction, experimental and
summary sections. The first chapter gives a brief overview of energy storage systems, progress
and challenges associated with them along with a few possible solutions to tackle them. The
second chapter explains all the experimental details like chemicals used, syntheses procedures,
instruments used, and various processes and procedures used in this work.
The third chapter demonstrates the ion storage performance of copper phosphosulfide.
As an anode for Li-ion battery, it delivers a high capacity and high cycling stability. The pre activated electrode delivers very high stable capacity. The capacity offered by the
phosphosulfide is higher than that of the corresponding phosphide and sulfide that indicates
the importance of the presence of both P and S in the structure. The mechanism as investigated
by in situ Raman spectroscopy and other ex situ techniques suggest a conversion reaction and
formation of a thick SEI like film on the electrode surface. As prepared material shows good
performance for Mg-ion battery with moderate rate capability. A further improvement in the
capacity and importantly the rate performance is achieved by utilizing a multiwall carbon
nanotube composite. The composite electrode further delivers high cycling stability at high
current rates. Moderate performance is observed for Al-ion battery which may be due to its
high charge to size ratio that makes the insertion / extraction process rather slow.
The fourth chapter utilizes organic carbonyl compounds as electrodes for mono- and
multi-valent metal ion batteries. A layer type, slight off planar polymer is synthesized from
benzoquinone and pyrrole and explored as a universal cathode for Li, Mg, Zn and Al-ion
batteries. Thousands of stable cycles are observed for all these systems even at very high
current rates and show excellent rate performance. For Li-ion battery, the cell performance is
studied at high rates of 10 A g-1 which takes only 22 s to charge and discharge. For Mg-ion
battery, an alternate alloy anode (AZ31) is explored, and 5000 cycles are observed even at a
high current rate of 2 A g-1
. Similarly, for Zn-ion battery, along with good rate performance, a
long-term stability of 20000 cycles is achieved at 2 A g-1
. More importantly, even for a more
difficult Al-ion system, thousands of stable cycles are obtained at high rates of 0.5 and 1 A g-1
with 100% capacity retention. A surface controlled pseudocapacitive contribution to the overall
capacity is responsible for such high performance in all the cases. The off planar geometry is
expected to facilitate ion diffusion process thereby resulting in high rate and high performance.
Ex situ infrared and X-ray photoelectron spectroscopy measurements show functional group
transformation during the ion storage process. Further, an organic dye, vat orange 11 consisting
of three conjugated anthraquinone units is studied for Mg- and Zn-ion batteries. It shows better
performance than that of a single anthraquinone unit highlighting the benefit of conjugation.
Different carbon additives and electrolytes are investigated further to achieve high performance
for Mg-ion battery. A capacity fading is observed for Zn-ion battery due to high solubility of
the dye in the electrolyte.
The fifth chapter explores a few non-nucleophilic electrolytes for Mg-ion batteries with
wide electrochemical stability window. It is observed that Mg(HMDS)2 and AlCl3 in a mixture
of glymes with ionic liquid additive shows high deposition/ dissolution efficiency with low
overpotentials and excellent oxidation stability on a few common substrates. Further, the
electrolyte speciation study is carried out with the help of Raman and 27Al NMR spectroscopy.
A non-aqueous Li-O2 battery is studied using tin phosphosulfide (SnPS3) as air cathode
in the sixth chapter. High cycling performance and low charge-discharge overpotential is
observed for the rGO composite as compared to the pristine material. High electronic
conductivity and high surface area of rGO is believed to enhance the performance and Li2O2 is
obtained as the discharge product.
The seventh chapter investigates the gas sensing applications and photodetection
activity of Cu3PS4. It is very sensitive towards NH3 gas compared to other analyte gases and
can detect as low as 17 ppb with a high response of 160 % for 10 ppm NH3. It shows a fast
response and excellent reversibility under ambient conditions. Good sensing properties for NO2
gas has been observed. Preliminary photodetector studies reveal that the phosphosulfide can be
used for UV-vis photodetection.
The last chapter summarizes the thesis work and gives some future directions to
improve the performance further and design new systems. At the end, two appendixes are given
where an ionic liquid, 1-ethyl-3-vinylimidazoilum bis(fluorosulfonyl)imide (EVImFSI)
containing lithium bis(trifluorosulfonyl)imide (LiTFSI) is used as a wide potential window (~5
V) electrolyte for Li-ion battery and nickel phosphosulfide (NiPS3) is used as electrocatalyst
for electrochemical nitrogen reduction to ammonia (NH3)
Synthesis and Studies of Covalent Polydiacetylene Glycopolymers as Scaffolds to Uncover Intricate Carbohydrate-Protein Interactions
No full textOverall, the Thesis work establishes:
• Monomeric and multimeric ligand-lectin interactions occurring at cell surfaces that could be assessed using purified protein and cellular model system, namely, glycovesicles;
• Variation in the ligand density as a hallmark to switch the nature of the interaction between monomeric and multimeric ligand-lectin interactions;
• Sparsely populated ligand surfaces promote intermolecular aggregation of the ligand-lectin complex, whereas mostly or fully ligand-functionalized surfaces involve intracellular monomeric ligand-lectin complex formation;
• That the binding affinities between intra- and intervesicular modes are comparable, yet the intravesicular mode tend to have a higher binding affinity;
• That introduction of amphiphilicity through incorporating sugar moieties on PDA polymers is a viable approach to induce mesomorphism in PDA polymers;
• Structural characterization and modeling studies on lamellar arrangement and interdigitization of the glycolipids in the mesophase;
• Smectic layering which occurs commonly in glyco-PDAs. The mesophase temperature range and the structural ordering are observed to vary depending on the sugar moiet
Experimental investigation of syngas combustion using a novel two-stage combustor
No full textIn recent years, syngas has gained research interest as the focus shifts from fossil to renewable fuels. Syngas generated from biomass such as wood, agricultural residue, and paper is a promising fuel to achieve net-zero carbon emissions. It is mainly composed of CO, H2 and diluents such as CO2 and N2. The combustion characteristics of biomass-derived syngas significantly differ from the well-studied fuels in terms of calorific value, stoichiometric fuel-to-air ratio, ignition delay, and flammability limits. In the present study, a combination of catalytic and swirl combustion is explored using a two-stage combustor to achieve low emissions without losing combustion stability. The first stage is the catalytic stage, and the second stage is the swirl stage. A preheated and premixed syngas-air mixture (Фfirst = 4) is supplied to the first stage, where syngas is consumed partially. The remaining unburnt fuel is combusted using an oxidizer in the second stage. In this stage, the flame is stabilized by two co-centric swirling streams where the inner stream is the unburnt gases coming from the first stage, and the outer stream is the oxidizer. By changing the swirling direction of the streams, co and counter-swirl flames are obtained.
In this thesis, the experimental results are described in six parts organized as follows. The first part of the study investigates the catalytic combustion of syngas in the first stage at an equivalence ratio of 4. The transient temperature measurements show three distinct regions of catalytic combustion: kinetically controlled, light-off, and steady-state regions. It is found that the start-up time depends on the conductivity of the monolith placed inside the first stage. The NOx emission is found to be low (< 1 ppm) at the exit.
The second part of the study explores the lean unconfined co/counter-swirl flame stabilized in the second stage. Both flames can be stabilized at a higher flow rate, maintaining a constant overall equivalence ratio. Co-swirl creates a ‘U’-shaped flame, and counter-swirl creates a more distributed and compact flame. A low NOx concentration (< 20 ppm) is found in the flame; however, the CO emission is more than 10000 ppm.
In the third part, the emission characteristics are studied, with the second stage being confined. The emission, temperature, flame shape and noise are investigated at three overall equivalence ratios (Фoverall). The CO emission reduces drastically in the presence of confinement, and the emission is found to be ~10 when Фoverall = 0.55. The NOx emission is below 2 ppm for all cases. The shape of co and counter-swirl flames behave differently when Фoverall changes. Planar laser-induced fluorescence (PLIF) shows the radicals are well distributed over the combustor for co/counter-swirl flames at a higher equivalence ratio, unlike existing studies. Particle image velocimetry (PIV) indicates that the flame shape is related to the shape of the inner recirculation zone. The sound pressure level (SPL) for co/counter-swirl flames is ~110 dB. The frequency domain contains a dominating peak at all Фoverall. The high-speed OH* chemiluminescence (5 kHz) confirms that the combustion is exciting the axial mode of the combustor, which is captured in the noise data.
The sound pressure level can be reduced by changing the O2 concentration in the oxidiser stream. Thus, in the fourth part of the thesis, we investigate the effect of O2 concentration in the oxidizer stream on swirling flames, which is discussed in the fourth part. The OH* chemiluminescence intensity reduces, and flame height increases when O2 concentration decreases. The sound pressure level (SPL) also shows a decreasing trend with O2. The global luminosity calculated from high-speed chemiluminescence indicates that the peaks corresponding to axial mode and PVC are suppressed at low O2 concentrations. In terms of emissions, CO emission increases with a reduction in O2. The feasibility of achieving distributed combustion is assessed from emission, chemiluminescence intensity, SPL, and combustion stability. It is found that the co-swirl configuration is suitable for studying distributed combustion.
In the fifth part, we investigated the combustion dynamics for co and counter-swirl flames. The noise emitted by the combustor shows signatures of intermittency. Pressure signals can be divided into periodic and aperiodic zones, and aperiodic epochs randomly appear between periodic epochs. The high-speed OH* chemiluminescence unravels two motions of the combustion. One oscillates in the axial direction, and the other represents the precessing vortex core (PVC) motion. Axial fluctuation of heat release decreases with an increase in momentum ratio; however, the PVC motion remains prevalent. Interestingly, both fluctuations are suppressed when the oxygen percentage is reduced to 13.13%, indicating that low-oxygen dilution can be an effective strategy to reduce combustion instability.
Finally, in the last part of the study, the effect of momentum ratio (M), density ratio and heat-release rate on the flow field is studied in detail. For counter-swirl configuration, the flow field shows a drastic change at M = 1.7 as the vortex breakdown mode changes from bubble to conical form. The vortex breakdown mode influences the shape of the flame. In the bubble mode, the flame is distributed, whereas ‘V’-shaped for the conical mode.
Thus, the current study has led to an improved understanding of fuel-rich catalytic combustion and shape, dynamics, and flow field of co/counter-swirl flames under various conditions. The present study also establishes that the two-stage rich-catalytic lean-swirl stabilized combustor is suitable for stationary power production applications with ultra-low NOx and low CO emissions
Decoding Epigenetic Regulators in Cancer: Acetylation of HIF2A by Histone Acetyltransferase 1 (HAT1) is essential for executing hypoxia response in glioma
No full textGliomas are tumors of the central nervous system arising from glial cells. Based on the origin of the cell type, it can be astrocytoma, oligodendroglioma, and ependymoma. Astrocytoma is the most common type of glioma, further classified as Grades I, II, III, and IV. Grade IV tumor is also known as Glioblastoma (GBM) and is the most lethal and highly malignant brain tumor. Despite several medical interventions, the overall survival is very dismal, and half of the patients die within 15 months of diagnosis. The dismal picture of survival is further aggravated by the grim quality of life of GBM patients.
Advancement in high-throughput technologies coupled with bioinformatics tools has revolutionized cancer research. The vast implication of next-generation sequencing techniques has empowered us to explore the molecular pathways leading to the pathogenesis and therapy resistance of GBM. Screening based on the whole genome, whole-exome, and transcriptome sequencing has identified major signaling pathways responsible for gliomagenesis and has played a broader role in diagnosis and treatment regimens. The genetic and epigenetic screens have stratified GBM into molecular features like G-CIMP+/-, IDH mutant and wild type, and MGMT promoter methylated and unmethylated, and these features have proven to be exceptional prognostic markers. These integrated genetic and epigenetic screenings have also revealed the molecular heterogeneity present in GBM and identified genes responsible for the resistance and phenotypic plasticity of GBM cells. In the recent decade, further augmentation in sequencing techniques like ChiP-Seq, ATAC-Seq, FAIRE-Seq, and global methylation assay has enabled researchers to understand the epigenome of cancer cells. E.g., In GBM, promoter methylation of MGMT makes the cells sensitive to chemotherapeutic drugs. In addition to this, IDH mutation leads to a change in the global methylation pattern of GBM cells compared to non-IDH mutant samples. Besides these, the growing knowledge about the role of long noncoding RNAs in fine-tuning gene regulation has propelled the field of epigenetics in cancer development and progression. Advancements in proteomic technology have recently identified protein deregulation in glioma. It has also helped us understand the role of post-translational regulation in cancer initiation and progression. These shreds of epigenetic evidence also indicate that the players performing these epigenetic functions may get deregulated or non-functional in cancer. All this information intrigued us to explore the status of epigenetic regulators in glioma. Our studies illustrate the various aspects of epigenetic regulators in GBM, where our focus ranges from surfacing the epigenetic regulator's landscape in GBM, expanding regulation of a particular epigenetic regulator, HAT1, and the role of this protein towards glioma pathogenesis. This thesis is divided into two work-related chapters: Chapter 3 and chapter 4. In chapter 3, we performed extensive bioinformatic analyses to understand altered epigenetic regulators and the probable causes of their misregulation. In chapter 4, we identify HAT1 (histone Acetyltransferase 1) as one of the epigenetic regulators dysregulated in GBM that promotes gliomagenesis, proliferation, and migration via HIF2A.
Chapter 3: Integrative multi-omics analysis illustrates the genetic and epigenetic alterations of Epigenetic Regulators (ERs) in Glioblastoma.
Epigenetic regulators are the proteins that participate in nucleotide modifications, histone modifications, and chromatin remodeling. Recent studies have illustrated the importance of these proteins in maintaining the epigenome of a cell and their deregulation leading to various cancer. However, the molecular mechanism by which this particular class of proteins gets regulated remains elusive.
In this study, we have carried out an integrated bioinformatic analysis of epigenetic regulators (ERs) in various datasets to identify several genetic and epigenetic altered events among them in GBM. Alterations in the ERs include mutations, copy number variations (amplifications and deletions), and expression changes both at RNA and protein levels, and the probable causes of deregulation were assessed in our analysis. Whole exome sequencing data from the TCGA was analyzed to identify mutated ERs in GBM. We identified 13 ERs mutated in more than 2% of GBM samples. Integrated analysis of the transcriptome, copy number variation data, RPPA, Methylome, and miRNAome was carried out to identify ERs transcript differentially regulated in GBM compared to control samples and the putative mechanism behind this differential regulation. There were 236 ERs differentially regulated at the transcript level. Additional analysis of these 236 differentially regulated ERs disclosed that CyclinB-CDK1-FOXM1axis transcriptionally regulates the most significantly upregulated ERs. Besides this, around 50% of ERs are regulated by miRNAs, nearly 15% of ERs are deregulated because of promoter methylation, and around 10% by copy number variation. Analysis of proteome data from CPTAC identified differentially regulated proteins in GBM compared to control samples. We also found the concordance between the RNA and protein data, revealing the genes regulated at the protein level through post-translational modifications. To obtain insights into transformation and aggressiveness-related ERs in GBM, we analyzed the transcriptome data for ERs deregulation in the lower grade and GBM. 110 ERs were dysregulated in the lower grade and GBM and could be responsible for initial transformation and gliomagenesis. While 66 ERs were specifically deregulated in GBM, that might be responsible for aggressiveness and progression from lower to higher grade glioma. We also recognized 45 ERs uniquely expressed in recurrent GBM compared to the control and primary GBM samples. These differentially expressed ERs might give an extra edge to tumor cells in chemoresistance and radioresistance and could be implicated in tumor recurrence prediction. These gene-specific targeting could be used in combination with the standard therapy of GBM to prevent a recurrence.
Chemoresistance and radioresistance of GBM, eventually leading to its recurrence, is also attributed to Glioma stem-like cells (GSCs). Hence, we compared the transcriptomic data of neural stem cells, Glioma stem-like cells (GSCs), and differentiated glioma cells to identify GSCs-specific ERs. We found one ER specifically upregulated and seven downregulated in GSCs compared to NSCs and DGCs. The upregulated ER, USP46, is a deubiquitinating enzyme and its silencing led to a reduction in sphere formation of MGG8 and 1035 GSCs cells in neural stem cell media. Upon qPCR analysis, it was revealed that ablation of USP46 leads to a reduction in the level of GSCs-specific reprogramming factors SOX2 and POU3F2. In this study, we also sought mutant ERs association with the survival of the patients. We carried out a univariate cox regression analysis for the ERs mutated in more than two percent of GBM samples; however, we did not find any significant association between the mutation and survival of GBM patients. In a similar analysis with the differentially regulated ERs in GBM, we identified 15 ERs expressions to be significantly associated with the survival of GBM patients. To further strengthen this observation, we carried out a multivariate cox regression analysis for these 15 ERs, and out of 15, one ER, i.e., PRDM14, showed significant association with overall survival of GBM patients and was found to be an excellent prognostic marker that was able to predict survival independent of other GBM prognostic markers.
Chapter 4: HAT1-dependent acetylation of HIF2A at Lysine 512 and Lysine 596 promotes its stability and confers oncogenic function.
From the previous study, we found that HAT1 was one of the top upregulated ER. It was found to be upregulated in various other GBM datasets analyzed. These findings led us to speculate whether upregulation has any pathophysiologic function in GBM and, if yes, how it is advantageous to GBM cells. Keeping these objectives in mind, we tried to explore the physiological role of HAT1 in GBM biology. Our analysis revealed that expression of HAT1 is significantly associated with tumor aggressiveness and overall survival in both GBM and lower-grade astrocytoma. In vitro experiments after silencing of HAT1 indicated its oncogenic function in GBM. HAT1 silencing induced apoptosis and reduced proliferative and migratory capacity of GBM cells LN299 and U87. HAT1, a type B histone acetyltransferase, acetylates histone H4 at K5 and K12 positions and helps in replication-dependent chromatin assembly. It has also been shown to promote homologous recombination in DNA repair. Very few reports also implicate its role in tumorigenesis.
In this study, we tried to explore the pathological role of HAT1 in GBM biology. We did transcriptome analysis in control and HAT1 silenced conditions. We found 1020 genes to be differentially regulated in HAT1 silenced conditions. Functional enrichment analysis identified hypoxia signaling as one of the most significantly depleted pathways in the HAT1 silenced condition. Further experiments revealed no change in the protein level expression of HIF1A in the HAT1-compromised condition. However, a drastic reduction in the HIF2A level indicated that HAT1 specifically regulates HIF2A protein stability and activity. Thus, we identified HIF2A as a novel target of HAT1.
The present study demonstrates that HIF2A and HAT1 physically interact inside the cell. We also proved that HAT1 acetylates HIF2A, and loss of HAT1-dependent acetylation causes destabilization and degradation of HIF2A via proteasomal degradation. In addition to this, we also find that abrogation of HAT1 leads to a reduction in global acetylation of cells suggesting HAT1 may play a significant role in maintaining the acetylome pool of a cell. Through LC-MS/MS approach, we found several acetylated lysine residues of HIF2A. We zeroed in on three Lysine residues around the oxygen-dependent degradation domain (ODD) of HIF2A as putative targets of HAT1. These were K385, K512, and K596. We mutated lysine (K) to Glutamine (Q, an acetylation mimic) of all three residues individually by site-directed mutagenesis. Subsequent experiments revealed that K512Q and K596Q mutants did not show any change in the protein level in HAT1 silenced condition compared to shNT, thus making the HIF2A protein more stable. However, K385Q mutants failed to stabilize in the HAT1 condition, similar to HIF2A Wt. Therefore, for the first time, we show HIF2A as the target of HAT1, which leads to an effective hypoxia response in glioma.
Though the oxygen-dependent regulation of HIF1A and HIF2A is similar, both proteins act on the same HIF response element, and both have overlapping targets like VEGF; however, they have selective target specificity based on the tissue and cell-type expression of HIF alpha subunits. For example, HIF1A primarily promotes glucose consumption and glycolysis, while HIF2A promotes the storage of fatty acids. Moreover, knockdown and overexpression studies of HIF1A and HIF2A in VHL deficient clear cell renal cell carcinoma cell line indicated that HIF2A but not HIF1A is responsible for tumor growth. HIF2A has also been found to promote the transcription of OCT4 and NANOG, implicating its role in pluripotency and stem cell maintenance. Moreover, HIF2A is expressed explicitly in the CD133 positive subpopulation of glioblastoma, and neuroblastoma cells, whereas HIF1A levels were similar in both tumorigenic and nontumorigenic cells implying the specific role of HIF2A in cancer stem cells maintenance. Existing literature information about HIF2A and the interaction of HAT1 with HIF2A compelled us to investigate the role of HAT1 in the reprogramming and maintenance of Glioma stem cells. Our results show that HAT1 is essential for DGC reprogramming as HAT1 silenced condition resulted in reduced neurosphere formation. Rescue experiments using acetylation mimic mutants (K512 and K596) of HIF2A enabled the DGCs to reprogram efficiently even in HAT1 silenced conditions implying HAT1 mediated acetylation of HIF2A promotes hypoxia response in GSCs.
In addition to this, we also investigated the probable reason for the robust expression of HAT1 in GBM. Upon inhibitor screening of oncogenic signaling pathways, we identified Wnt/β-catenin as a transcriptional regulator of HAT1. This observation was further validated using HAT1 promoter luc experiments in FH535 (a Wnt signaling inhibitor), LiCl (Wnt signaling activator) treatment, or in the silenced and overexpressed condition of β-catenin.
Thus, our study identifies that HAT1 modulates hypoxia response through HIF2A stabilization and is responsible for gliomagenesis and the promotion of glioma reprogramming and glioma stem-like cells maintenance
Dynamics of river plumes in the Bay of Bengal
No full textThe Bay of Bengal (BoB) receives a large amount of freshwater through runoff from sev-
eral rivers along its border. This large freshwater gain has severe implications on the
dynamics and thermodynamics of the BoB as well as on the regional climate. Several
studies have indicated that the freshwater from rivers is an important parameter in de-
termining the observed structure of the Sea Surface Salinity (SSS) and its variability in
the northern BoB. There are several studies dedicated to understand the movement and
export pathways of freshwater in the bay. However, there have been no attempts to in-
vestigate the fate of the discharge from individual rivers in the bay. Seasonal changes
in the BoB circulation take place by virtue of both direct forcing from the seasonally
reversing winds and remote forcing from the equator. The effects of wind forcing (both
direct and remote) on the movement of river plumes in the bay have not yet been re-
ported. This thesis explores various aspects of the dynamics of river plumes due to four
largest rivers in the BoB namely, Ganga-Brahmaputra (GB), Irrawaddy (IR), Godavari
(GD) and Mahanadi-Brahmani (MB). A numerical ocean circulation model was setup
to conduct idealized experiments in which a river plume was isolated from other major
sources of salinity (Other rivers and surface freshwater flux from the atmosphere) and was
subjected to different wind forcing scenarios namely wind forcing over the entire model
domain, no wind forcing, wind forcing over the equatorial region and wind forcing over
the Bay of Bengal. Results from experiment with Ganga-Brahmaputra river and wind
forcing applied over the entire model domain were used to validate the model against
observations of sea surface temperature, SSS and surface currents.
Dynamics of GB plume was investigated using experiments with only GB river and
four different wind forcing scenarios. Experiment with only GB river and winds over the
entire model domain revealed that GB plume drifts upstream (upstream) during spring.
With the onset of summer monsoon in June, freshwater from GB flows southward along the east coast of India. As the monsoon progresses, the plume detaches from the coast
and spreads eastward over the open ocean. By the end of summer monsoon, GB plume
occupies all of the head bay, but remains confined to the north of 16◦ N. During winter
monsoon (November-February), the plume flows southward, assisted by the East India
Coastal Current (EICC) along the east coast of India. In the central bay, plume recedes
northward during winter monsoon. In the absence of winds, GB plume flows southward
along the coast of India throughout the year. Remote forcing from the equator channelizes
the GB discharge southward along the coast of India throughout the year. Response of
GB plume to winds over only BoB is similar to the winds over the entire model domain.
Geostrophy controls the behavior of the plume during spring and winter. During summer
monsoon, downstream expansion of the plume is due to geostrophy whereas its expansion
over the open ocean occurs under the influence of winds.
Experiments with only IR river and wind forcing over the entire model domain show
that IR plume expands southward during spring. During summer monsoon, IR plume
flows rapidly towards southeast in the form of a narrow jet of freshwater that accumu-
lates over the shelf along the eastern boundary of the Andaman Sea. During winter
monsoon, IR plume flows northward along the coast of Myanmar and spreads westward
over the open ocean in the northern BoB. In the absence of winds, IR discharge flows
downstream throughout the year. In response to equatorial forcing, IR plume flows down-
stream throughout the year with accelerated flow occurring in April-May and November-
December. Wind over only BoB invoke a response from IR plume that is similar when the
winds are present over the entire model domain. Analysis of momentum balances inside
the plume shows that IR plume is completely driven by winds during summer monsoon.
Geostrophy controls the movement of the plume during spring and winter monsoon. This
is also the first time that the investigations of IR plume are being reported.
Experiments with only Godavari (GD) river show that the GD discharge drifts north-
ward (upstream) along the coast of India throughout February-June because of the pole-
ward EICC. Throughout July-September, GD discharge spreads offshore (first southward
and then eastward) because of the breakdown of EICC into two opposing flows and the
presence of eddies along the coast of India. During October-January, GD plume expands
southward along the coast of India due to the equatorward EICC. In the absence of winds,
GD discharge flows downstream (southward) throughout the year. In response to equatorial forcing, GD plume expands southward during April-August and November-January
and northwards during September-October and February-March. BoB winds invoke a
response similar to the winds over entire domain. Dispersion of the GD plume during
summer monsoon occurs under the influence of geostrophy with an added assistance of
wind friction whereas that during spring and winter monsoon is largely controlled by only
geostrophy.
Experiments conducted with only MB river show that MB plume expands upstream
due to poleward EICC during spring. During summer monsoon, EICC splits into two
opposite flows and the convergence of these two opposing legs carries MB discharge south-
ward and then pushes it offshore. During winter monsoon, EICC carries MB discharge
southward. In the absence of winds, MB discharge flows downstream throughout the year.
In response to equatorial winds, MB discharge drifts upstream during February-March
and downstream during April-December. In September, reversal of EICC spreads MB
discharge offshore. Response of MB plume to winds only over the BoB closely matches to
the response to winds over all of the model domain. Winds augment the offshore expan-
sion of the plume during spring and summer whereas geostrophy controls the downstream
expansion during winter monsoon.
This study makes several key contributions to our understanding of the behavior of
freshwater plumes due to four largest rivers in the BoB. The principle contribution of
the study is the characterization of the seasonal orientation of the freshwater plumes due
to these rivers. This helps us better understand the fate of the discharge from each of
these rivers in the bay. This study also reports the response of these river plumes to
different wind forcing scenarios of the bay and highlights the importance of each of these
scenarios. Our experiments provide an insight into the mechanisms responsible for the
seasonal dispersion of the freshwater from these rivers in the bay. The results obtained
from this study are relevant to our understanding of the salinity structure of the BoB and
to the dynamical processes resulting from this structure
Analytical Results on Disorder effects on Polaritons and Barrier Crossing Problems
No full textDisorder plays a significant role in the study of numerous fields of research in chemistry.
Whether it is a more that 80 years old classic problem like Kramers’ escape rate or the current interest in polaritons, disorder needs to be accounted in realistic modelling of systems. Recently, modifying chemistry by using setups like Fabry-Perot cavity has been attracting attention of chemists experimentally and theoretically. Theoretical models analytically solved so far do not account for the disorder in system. We analytically solve for the most used Tavis-Cumming Hamiltonian but with disorder. We report the effects of disorder on observables like the energies of polaritonic states, the line-shape of the spectra to name a few. Another problem for which we provide analytical results is the barrier crossing problem for a particle experiencing non-Gaussian noise. For such a system, the primary observation we report is that the rate of escape depends on the full shape of the potential energy and not just on the barrier height