Comparison of Modules of Wild Type and Mutant Huntingtin and TP53 Protein Interaction Networks: Implications in Biological Processes and Functions

Disease-causing mutations usually change the interacting partners of mutant proteins. In this article, we propose that the biological consequences of mutation are directly related to the alteration of corresponding protein protein interaction networks (PPIN). Mutation of Huntingtin (HTT) which causes Huntington's disease (HD) and mutations to TP53 which is associated with different cancers are studied as two example cases. We construct the PPIN of wild type and mutant proteins separately and identify the structural modules of each of the networks. The functional role of these modules are then assessed by Gene Ontology (GO) enrichment analysis for biological processes (BPs). We find that a large number of significantly enriched (p<0.0001) GO terms in mutant PPIN were absent in the wild type PPIN indicating the gain of BPs due to mutation. Similarly some of the GO terms enriched in wild type PPIN cease to exist in the modules of mutant PPIN, representing the loss. GO terms common in modules of mutant and wild type networks indicate both loss and gain of BPs. We further assign relevant biological function(s) to each module by classifying the enriched GO terms associated with it. It turns out that most of these biological functions in HTT networks are already known to be altered in HD and those of TP53 networks are altered in cancers. We argue that gain of BPs, and the corresponding biological functions, are due to new interacting partners acquired by mutant proteins. The methodology we adopt here could be applied to genetic diseases where mutations alter the ability of the protein to interact with other proteins.Comment: 35 pages, 10 eps figures, (Supplementary material and Datasets are available on request

Making India Literate, Fully and Functionally

Introduction Amid a pat for marching towards the measurable “Education for All” goals, the chastisement that India has the world\u27s largest illiterate population and that the poverty-stricken women in India will take 65 years to attain literacy should make all those who have stake in India\u27s development sit up and pull up their socks. A major thrust has been made in each decade since Independence to spread literacy in India. Major initiatives include Social Education (1952), Farmers\u27 Training and Functional Literacy Programme (1967–68), and National Adult Education Programme (1977–78). Then in 1988, the then Prime Minister Rajiv Gandhi inaugurated the ambitious National Literacy Mission (NLM) that envisaged making 30 million Indians literate by 1990 and 50 millions more literate by 1995. Using unprecedented techno-pedagogic inputs, NLM initiatives began across the country. The initiatives, especially NLM, bore results but they were less than satisfactory. An example from Gujarat makes it clear. A review,1 commissioned by the Government of Gujarat and carried out by Sardar Patel Institute of Economic and Social Research declared 15 out of 21 districts fully literate. Remarkably this review was commissioned when a government-commissioned review2 by Gujarat Institute of Development Research earlier in the same year reported less than satisfactory progress in the state\u27s Gandhinagar district. The ground reality was affirmed in 1999 when Action India, a non-government organisation floated by some well meaning influential non-resident Indians, identified literacy as an area to work in.&nbsp;Sam Pitroda,&nbsp;the technocrat credited with conceiving NLM, was the driving force behind Action India. By 2003, the Government of Gujarat which had claimed total literacy in 15 out of 21 districts, officially recognised the state\u27s literacy scene as one of the poorest in the country and appointed a core group headed by a UNESCO consultant to look into the problem. The idea, obviously, was to make future literacy initiatives more effective. NLM was followed up by PostLiteracy Programme in districts across the country. In 2009, the federal government floated another literacy initiative: Saakshar Bharat Mission (SBM). The Government of Gujarat tried to make the most of it and launched massive campaign to attain 100 per cent literacy on its Swarnim Gujarat (golden jubilee) celebration year, 2010. Sounds ambitious. But then that is how Prime Minister Narendra Modi appends his signature to projects. (He was the chief minister of Gujarat then.) Before the launch of SBM, India\u27s literacy rate was 65.4 per cent (Census2001). Census India-1951 had reported literacy figure of 18.3 per cent. This means an effective growth of a shade above 37 percentage points in 50 years! Kothari, et al4 report that actual figure could be 10 percentage points less, i.e., around 55 per cent. This makes the picture that much more dismal. DOI: 10.5281/zenodo.336691

Distributed C++ : Design and implementation

Distributed C++ is a learning tool developed to investigate distributed programming using the object paradigm. An extension is designed for C++, to enable the use of C++ in programming distributed applications. A user transparent interface is designed and implemented to create and manipulate remote objects on a network of workstations running the Unix operating system. The concept of remote classes is introduced and remote object invocation is implemented over a remote procedure call mechanism

Efficient Decoding of Topological Color Codes

Color codes are a class of topological quantum codes with a high error threshold and large set of transversal encoded gates, and are thus suitable for fault tolerant quantum computation in two-dimensional architectures. Recently, computationally efficient decoders for the color codes were proposed. We describe an alternate efficient iterative decoder for topological color codes, and apply it to the color code on hexagonal lattice embedded on a torus. In numerical simulations, we find an error threshold of 7.8% for independent dephasing and spin flip errors.Comment: 7 pages, LaTe

Antibiotic sensitivity of Vibrio parahaemolyticus strains

The strains of Vibrio parahaemolyticus isolated from water, sediment, plankton, fish and prawn of Cochin backwater were tested for sensitivity to ten antibiotics namely, ampicillin, chloramphenicol, gentamycin, kanamycin, neomycin, oxytetracycline, penicillin, polymyxin-B, streptomycin and sulphadiazine. Of the 120 isolates tested, 96.7 and 93.3% were sensitive to gentamycin and chloramphenicol respectively. No strain was sensitive to penicillin and only 5% were sensitive to kanamycin. Isolates from fish and prawn showed higher resistance to ampicillin and none of them was sensitive to kanamycin. Multiple resistant V. parahaemolyticus strains were more in prawn than in other samples