RIPPLiT and ChimeraTie: High throughput tools for understanding higher order RNP structures

Even after their discovery more than 60 years ago, little is known about how messenger RNAs (mRNAs) are packaged inside the cells. To ensure efficient and accurate delivery of the intended message to its proper destination, it is important to package the informational molecule in a way that protects it from premature degradation but also proper decoding at the destination. However, very little is known about the this fundamentally important step of mRNA packaging inside eukaryotic cells. To this end, we developed a novel approach, RIPPLiT (RNA ImmunoPrecipitation and Proximity Ligation in Tandem), to capture the 3D architecture of the ribonucleoprotein particles (RNPs) of interest transcriptome-wide. To begin with, we applied RIPPLiT to the exon-junction complex (EJC), a set of proteins stably bound to a spliced RNA. EJCs have been shown to interact with other proteins like SR- and SR-like to form megadalton sized complexes and help protect large regions of mRNAs. Thus, we hypothesized that these RNPs would provide an ideal system to elucidate the higher order organization of mRNPs. Preliminary analysis of data obtained from RIPPLiT consisted of “chimeric reads”, reads with multiple RNA fragments ligated together, which could not be analyzed with any of the existing bioinformatics tools. Thus, we developed a new bioinformatics suite, ChimeraTie, to map, analyze and visualize chimeric reads. Performing polymer analysis on chimeric reads obtained for hundreds of mRNAs, we were able to predict that mRNPs are linearly and densely packed into flexible rod-like structures before they undergo translation. In this thesis, along with the detailed biological conclusion, I have also provided a step-wise manual to perform RIPPLiT experiment and analyze the ensuing data using ChimeraTie

Defense against buffer overflow attack by software design diversity

A buffer overflow occurs during program execution when a fixed-size buffer has had too much data copied into it. This causes the data to overwrite into adjacent memory locations, and, depending on what is stored there, the behavior of the program itself might be affected; Attackers can select the value to place in the location in order to redirect execution to the location of their choice. If it contains machine code, the attacker causes the program to execute any arbitrary set of instructions---essentially taking control of the process. Successfully modifying the function return address allows the attacker to execute instructions with the same privileges as that of the attacked program; In this thesis, we propose to design software with multiple variants of the modules/functions. It can provide strong defense against the buffer overflow attack. A way can be provided to select a particular variant (implementation) of the module randomly when software is executed. This proves to be useful when an attacker designs the attack for a particular variant/implementation which may not be chosen in the random selection process during execution. It would be much difficult for the attacker to design an attack because of the different memory (stack-frame) layout the software could have every time it is executed

Experimental and Kinetic Modeling Studies of Selective Catalytic Reduction of NOx with NH3 on Fe- and Cu-Zeolite Monolithic Catalysts

The selective catalytic reduction (SCR) of NOx with NH3 is considered to be the most promising technique for the efficient reduction of highly detrimental NOx (to N2) emitted from diesel engine vehicles. Amongst the various catalysts available for SCR, Fe- and Cu-zeolite catalysts are found to be highly stable and efficient towards maximum NOx reduction over a wide temperature range. Cu-zeolites are more active at low temperatures ( 400 oC). We carried out a comprehensive experimental and kinetic modeling study of key SCR reactions on Fe- and Cu-zeolite catalysts and present a detailed understanding of mass transfer limitations and kinetics and mechanistic aspects of various SCR reactions on these catalysts. Experiments carried out on monolith catalysts having different washcoat loadings, washcoat thicknesses and lengths indicate the presence of washcoat (or pore) diffusion limitations at intermediate to high temperature range in all the SCR reactions. A detailed analysis of the effect of temperature on the transitions between various controlling regimes (kinetic, washcoat diffusion and external mass transfer) is presented. Agreement in the differential kinetics studies of NO oxidation and standard SCR (NO + O2 + NH3) reactions indicates NO oxidation is the rate determining step for standard SCR. A detailed kinetic model capturing key features of all the SCR reactions is developed. This model accurately predicts the experimentally observed NOx conversions over a wide temperature range and different feed conditions. Finally, a systematic study of various SCR reactions is carried out on a combined system of Fe- and Cu-zeolite monolithic catalysts to determine if a high NOx conversion could be sustained over a wider temperature range than with individual Fe- and Cu-zeolite catalysts. Amongst various configurations, a dual-layer catalyst with a thin Fe-zeolite layer on top of a thick Cu-zeolite layer resulted in a very high NOx removal efficiency over a broad temperature range of practical interest. The kinetic model accurately captures the experimental data with a combined system of Fe- and Cu-zeolite catalysts and provides further insights into the catalyst arrangements for maximum NOx reduction efficiency.Chemical and Biomolecular Engineering, Department o

Conceptual study of Dhamani - A critical review

Ayurveda is been practiced in India for at least 5000 years, but in present time it is becoming more popular in whole world due to its holistic approach. Acharyas has used an anatomical term Dhamani which is on controversial term. Ayurvedic text which are Ancient works in the field of Rachana presented by Acharya Sushruta, Charaka, Vaghbhata and other. Dhamani is a structure introduced by ducts with thin wall and carry Rasa all over the body i.e. Sharira. The term Dhamani generally used in same sense as Siras and Srotas. Interpretation of these Ayurvedic terminologies is confusing in many contexts. Acharya Sushruta clearly explained the constitution of the human body and difference between Sira (vein), Dhamani (artery), Srotas (capillaries). Dhamani is a specific anatomical structure by critically reviewing all possible literature both as per Ayurveda and modern science

Implementation Paper Modern and Smart Logistic Vehicle Using Tracking and Security

The logistic organization structure have climbed beginning late with the improvement of global positioning system (GPS), helpful correspondence movements, sensor and remote structures association advancements. The collaborations of the administrators system are fundamental as they can add to a few points of enthusiasm, for example, proposing right places for getting clients, developing pay of truck drivers, reducing holding up time, vehicle downpours and besides compelling fuel utilization and from this time forward broadening the measure of treks the drivers can perform. The rule motivation driving this structure would supply required vehicles that would be utilized to meet client requests through the arranging, control and utilization of the noteworthy headway and cutoff of related data and associations from beginning to objective. Customer brings to the table start to finish security to client and supplier information by utilizing QR code thought. Customer is proposition of closest best specialist relationship as shown by client intrigue and recognize spam master network. Joint efforts association suggests the commitment and association of plan and direct structures to control the improvement and land masterminding of foul materials, work-in-process, and completed inventories at the most unimportant all out expense. Composed endeavours solidifies the relationship of enthusiasm organizing, stock, transportation, and the mix of warehousing, materials managing, and packaging, all joined all through an arrangement of workplaces

Deep sequencing of pre-translational mRNPs reveals hidden flux through evolutionarily conserved AS-NMD pathways [preprint]

Background The ability to generate multiple mRNA isoforms from a single gene by alternative splicing (AS) is crucial for the regulation of eukaryotic gene expression. Because different mRNA isoforms can have widely differing decay rates, however, the flux through competing AS pathways cannot be determined by traditional RNA-Seq data alone. Further, some mRNA isoforms with extremely short half-lives, such as those subject to translation-dependent nonsense-mediated decay (AS-NMD), may be completely overlooked in even the most extensive RNA-Seq analyses. Results RNA immunoprecipitation in tandem (RIPiT) of exon junction complex (EJC) components allows for the purification of post-splicing mRNA-protein particles (mRNPs) not yet subject to translation (pre-translational mRNPs) and translation-dependent mRNA decay. Here we compared EJC RIPiT-Seq to whole cell and cytoplasmic RNA-Seq data from HEK293 cells. Consistent with expectations, we found that the flux through known AS-NMD pathways is substantially higher than what is captured by RNA-Seq. We also identified thousands of previously unannotated splicing events; while many can be attributed to “splicing noise”, others are evolutionarily-conserved events that produce new AS-NMD isoforms likely involved in maintenance of protein homeostasis. Several of these occur in genes whose overexpression has been linked to poor cancer prognosis. Conclusions Deep sequencing of RNAs in post-splicing, pre-translational mRNPs provides a means to identify and quantify splicing events without the confounding influence of differential mRNA decay. For many known AS-NMD targets, the NMD-linked AS pathway dominates. EJC RIPiT-Seq also enabled identification of numerous conserved but previously unknown AS-NMD events

Environmental Monitoring & Impact Assessment of Wasni (BK) Dam

Maharashtra is one of the Indian states mostly relying on agriculture. The Government of Maharashtra has been giving utmost importance for developing irrigation green fields. Under its efforts, the State has formulated a few Irrigation Development Corporation (VIDC) has been formulated for increasing irrigation potential of Vidharbha region of Maharashtra. VIDC has undertaken a few major, medium and minor irrigation projects based on the yields from catchment areas of respective projects. For the urban Indian, the word ?irrigation? conjures up images of first Prime Minister of India, Jawaharlal Nehru, and the Bhakra Nangal Dam (Temples of Modern India) and the tribal ousts of the Narmada dam. These are diverse perspectives on the story of large irrigation infrastructure in India. In fact, in popular public perception, irrigation connote ?large irrigation infrastructure? rather than provision of irrigation services. Agriculture is the backbone of Amravati district, in which the command area of Wasni project is an integral part. Most of the people are poor and economically backward. The proposed command area or its vicinities are devoid of any assured irrigation facility, through Sapan River potential for a medium project flows just adjacent to these areas, with its waters being unutilized. Because of the scarcity of the water there is a need to do socio-economic impact of Wasni(BK) dam

Multidimensional Modeling of Direct Injection Diesel Engine with Split Multiple Stage Fuel Injections

AbstractIn the present study, an attempt has been made to predict the influence of split multiple stage fuel injection on a DI diesel engine performance and emission characteristics. The predictions have been made for both conventional continuous fuel injection as well as split multiple stage fuel injection. The analysis mainly emphasize on the prediction of SFC and NOx levels in a diesel engine for the above mentioned two fuel injection modes. These computational predictions can enhance the knowledge of the flow and combustion characteristics, which is of vital importance for the design and development of a high performance DI diesel engine. The aforementioned simulation work has been performed using a CFD code. It has been found that the split multiple stage fuel injection exhibits strong effects on combustion characteristics and provides controlled pressure and temperature inside the combustion chamber. It has also been seen that split multiple stage fuel injection significantly reduces the formation of NOx compared to that ofthe continuous fuel injection