Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets

BACKGROUND: tRFs, 14 to 32 nt long single-stranded RNA derived from mature or precursor tRNAs, are a recently discovered class of small RNA that have been found to be present in diverse organisms at read counts comparable to miRNAs. Currently, there is a debate about their biogenesis and function. RESULTS: This is the first meta-analysis of tRFs. Analysis of more than 50 short RNA libraries has revealed that tRFs are precisely generated fragments present in all domains of life (bacteria to humans), and are not produced by the miRNA biogenesis pathway. Human PAR-CLIP data shows a striking preference for tRF-5s and tRF-3s to associate with AGO1, 3 and 4 rather than AGO2, and analysis of positional T to C mutational frequency indicates these tRFs associate with Argonautes in a manner similar to miRNAs. The reverse complements of canonical seed positions in these sequences match cross-link centered regions, suggesting these tRF-5s and tRF-3s interact with RNAs in the cell. Consistent with these results, human AGO1 CLASH data contains thousands of tRF-5 and tRF-3 reads chimeric with mRNAs. CONCLUSIONS: tRFs are an abundant class of small RNA present in all domains of life whose biogenesis is distinct from miRNAs. In human HEK293 cells tRFs associate with Argonautes 1, 3 and 4 and not Argonaute 2 which is the main effector protein of miRNA function, but otherwise have very similar properties to miRNAs, indicating tRFs may play a major role in RNA silencing. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12915-014-0078-0) contains supplementary material, which is available to authorized users

Aerodynamic heating of the student rocket project-5 sounding rocket

Thesis (M.S.) University of Alaska Fairbanks, 2005This thesis deals with the calculation of the flow properties and heat transfer around the rocket nose cone for Student Rocket Project-5 (SRP-5). Governing differential equations are presented for this purpose, giving the fundamental relations between the skin temperature and flight history. The determination of all the required parameters in the equations is discussed, and the Runge-Kutta numerical method of integration is used to obtain the solution. A model to implement the above equations to predict skin temperature for the given trajectory was built in SIMULINK®. Individual sub-systems of the SIMULINK® model are used to calculate local tree-stream values, Reynolds number, heat absorption capacity and skin friction coefficient. The SIMULINK® model was used to predict the variation of the skin temperature for the SRP-5 flight trajectory. The simulation results also show comparisons of the different subsystem outputs with data provided by the contractor for the NASA Sounding Rocket Contract (NSROC).Introduction -- Governing equations -- Determination of parameters -- Simulink model -- Example problem -- Simulation and results -- Conclusion and future work -- References -- Appendices

Uplink power control in 4G LTE

The research is related to the Uplink power control for 4G LTE which is to evaluate the system performance using the coding in MATLAB. The primary objective of this thesis is to design a cellular network environment which has 1050 users which are distributed in seven cells with directional antennas. The total environment is set up in MATLAB and the performance is evaluated for different values of path-loss compensation factor. Considering the fractional compensation and full compensation the LTE system analysis is compared for both open loop power control system and closed loop power control system as well. The performance is evaluated with the uplink signal to noise to interference ratio which is measured. Using the Shannon capacity, the bit rate is calculated. The distribution of the users for closed loop power control algorithm is collaborated with the Nash equilibrium from microeconomics and conclusions are drawn

ChloroMitoSSRDB 2.00: More genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection

© The Author(s) 2015. Published by Oxford University Press. Organelle genomes evolve rapidly as compared with nuclear genomes and have been widely used for developing microsatellites or simple sequence repeats (SSRs) markers for delineating phylogenomics. In our previous reports, we have established the largest repository of organelle SSRs, ChloroMitoSSRDB, which provides access to 2161 organelle genomes (1982 mitochondrial and 179 chloroplast genomes) with a total of 5838 perfect chloroplast SSRs, 37 297 imperfect chloroplast SSRs, 5898 perfect mitochondrial SSRs and 50 355 imperfect mitochondrial SSRs across organelle genomes. In the present research, we have updated ChloroMitoSSRDB by systematically analyzing and adding additional 191 chloroplast and 2102 mitochondrial genomes. With the recent update, ChloroMitoSSRDB 2.00 provides access to a total of 4454 organelle genomes displaying a total of 40 653 IMEx Perfect SSRs (11 802 Chloroplast Perfect SSRs and 28 851 Mitochondria Perfect SSRs), 275 981 IMEx Imperfect SSRs (78 972 Chloroplast Imperfect SSRs and 197 009 Mitochondria Imperfect SSRs), 35 250 MISA (MIcroSAtellite identification tool) Perfect SSRs and 3211 MISA Compound SSRs and associated information such as location of the repeats (coding and non-coding), size of repeat, motif and length polymorphism, and primer pairs. Additionally, we have integrated and made available several in silico SSRs mining tools through a unified web-portal for in silico repeat mining for assembled organelle genomes and from next generation sequencing reads. ChloroMitoSSRDB 2.00 allows the end user to perform multiple SSRs searches and easy browsing through the SSRs using two repeat algorithms and provide primer pair information for identified SSRs for evolutionary genomics

Home Away From Home

Home Away from Home is an e-Commerce application for short-term rentals of homes or apartments. This application presents a web portal for property owners to advertise their properties and lease them to renters for short-term stays. Its functionalities should include uploads, setting, auditing, property listings, bookings, payment processing, post-rental ratings, surveys, web mapping and more. The database maintains the home information required for a user to check and book the home. This Home Away From Home website is designed using the home rental website as examples, it contains all the information of renter, owner, admin. All the owners can post their properties on the website. All the information regarding the properties, owners and renters are stored in the database. Admin has the right to view the details of everything on the website. Software Requirements/ToolsOperating System : Windows 7 & laterWeb Technologies : HTML5, CSS3, Bootstrap,Scripting Languages : JavaScript, jQueryDatabase : MS SQLFramework : .NET ModulesAdmin ModuleOwner ModuleRenter Modul

Employee HR Connect Portal

Employee HR Connect Portal is essential in order to track employee time, project time. This portal can be hosted on any java based web server or application server and will be accessible via web-browsers. This portal is very user- friendly. Employee HR Connect Portal will be a useful tool to identify supply and demand of human resources. We have three main modules to maintain records of employee, department and project. Employee HR Connect Portal is very helpful for auditing. Through this portal we can judge the potentiality of the employee

Efficient Tumor Detection in MRI Brain Images

Detection of brain of tumor is a laborious task as it involves identification, segmentation followed by detection of the tumor. It is a very challenging task to envisage uncommon structures in the image of human brain[15].    An Image processing concept called MRI can be used to visualize different structures of human body. The Magnetic Resonance images (MRI) are used to detect the uncommon portions of human brain. This paper explores different noise removal methods accompanied by Balance-contrast enhancement technique (BCET) which results in increased accuracy. Segmentation followed by canny edge detection is performed on the improved images to detect the fine edges of the abnormalities present. The model attained an accuracy of at most 98% in detecting the tumor or the abnormality in a human brain which determines the effectiveness of the proposed model

StemCellNet: an interactive platform for network-oriented investigations in stem cell biology.

Stem cells are characterized by their potential for self-renewal and their capacity to differentiate into mature cells. These two key features emerge through the interplay of various factors within complex molecular networks. To provide researchers with a dedicated tool to investigate these networks, we have developed StemCellNet, a versatile web server for interactive network analysis and visualization. It rapidly generates focused networks based on a large collection of physical and regulatory interactions identified in human and murine stem cells. The StemCellNet web-interface has various easy-to-use tools for selection and prioritization of network components, as well as for integration of expression data provided by the user. As a unique feature, the networks generated can be screened against a compendium of stemness-associated genes. StemCellNet can also indicate novel candidate genes by evaluating their connectivity patterns. Finally, an optional dataset of generic interactions, which provides large coverage of the human and mouse proteome, extends the versatility of StemCellNet to other biomedical research areas in which stem cells play important roles, such as in degenerative diseases or cancer. The StemCellNet web server is freely accessible at http://stemcellnet.sysbiolab.eu

Integration of biomass formulations of genome-scale metabolic models with experimental data reveals universally essential cofactors in prokaryotes

The composition of a cell in terms of macromolecular building blocks and other organic molecules underlies the metabolic needs and capabilities of a species. Although some core biomass components such as nucleic acids and proteins are evident for most species, the essentiality of the pool of other organic molecules, especially cofactors and prosthetic groups, is yet unclear. Here we integrate biomass compositions from 71 manually curated genome-scale models, 33 large-scale gene essentiality datasets, enzyme-cofactor association data and a vast array of publications, revealing universally essential cofactors for prokaryotic metabolism and also others that are specific for phylogenetic branches or metabolic modes. Our results revise predictions of essential genes in Klebsiella pneumoniae and identify missing biosynthetic pathways in models of Mycobacterium tuberculosis. This work provides fundamental insights into the essentiality of organic cofactors and has implications for minimal cell studies as well as for modeling genotype-phenotype relations in prokaryotic metabolic networks.J.C.X. was sponsored by Fundação para a Ciência e Tecnologia, Portugal [Grant SFRH/BD/81626/2011]. This study was supported by the European Molecular Biology Laboratory, the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit, COMPETE 2020 (POCI-01–0145-FEDER-006684) and BioTecNorte operation (NORTE-01–0145-FEDER-000004) funded by European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte. This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant agreement no 686070