Comparison of Methods Used for Aligning Protein Sequences

Comparing protein sequences is an essential procedure that has many applications in the field of bioinformatics. The recent advances in computational capabilities and algorithm design, simplified the comparison procedure of protein sequences from several databases. Various algorithms have emerged using state of the art approaches to match protein sequences based on structural and functional properties of the amino acids. The matching involves structural alignment, and this alignment may be global; comprising of the whole length of the protein, or local; comprising of the sub-sequences of the proteins. Families of related proteins are found by clustering sequence alignments. The frequency distributions of the amino acids within these different clusters define the sequence profile. The best alignment algorithm uses these profiles. In this thesis, we have studied different profile alignment algorithms where the cost function for comparing two profiles is changed. These are compared to the FFAS3 (Fold and Function Assignment) algorithm

Use of Technology in Segregating Occupational risks of Migrant and linking them with Services: Experiences from National AIDS Control Program for Migrants

Background: The migrant intervention in India was initiated during the National AIDS Control Program (NACP) Phase-2 (2002-2007). Even by the end of NACP Phase-3 (2010-11); the service uptake among migrants remained very low (14% referred for HIV testing, of which only 37% were tested). USAID PHFI-PIPPSE project in collaboration with the National AIDS Control Organization (NACO) developed a unique system called Migrant Service Delivery System (MSDS) to capture migrants profile with respect to their risk profile and to provide tailor made services to them.Description: MSDS is a web-based system, designed and implemented to increase service uptake among migrants through evidence based planning. 110 destination migrants Targeted Intervention (TI) from 11 states were selected for study with varied target populations in terms of occupations; to understand occupation related risk behaviors amongst the migrants. Occupation wise registration data of high risk vulnerable migrants were analyzed through MSDS for the period April 2014-June 2016. Analysis was made on specific indicators amongst these occupational groups to understand the risk behavior and their vulnerability to HIV and STI.Lessons Learned: Out of total migrants workers enrolled in MSDS HIV rate is found to be highest amongst Auto-Rickshaw (18.66%) followed by daily wage laborers (14.46%), loom workers (10.73%), industrial workers (10.04%) and construction workers (7.93%). With 45.14% positivity, industrial workers are found to be most vulnerable to Sexually Transmitted Infections (STIs) amongst all occupational categories followed by loom workers (16.28%), skilled worker (Furniture, Jeweler)(7.14%), daily wage laborers (5.45%) .Conclusion/Next Steps: MSDS is an effective tool to assess migrants’ risk and their vulnerability to HIV for designing evidence informed program. This system calls for a replication across all destination TIs by NACO for differential strategies for different occupation groups to ensure better yield through scientific planning of intervention among high risk and high vulnerable migrants.

Fos-expressing neuronal ensemble in rat ventromedial prefrontal cortex encodes cocaine seeking but not food seeking in rats

Neuronal ensembles in ventromedial prefrontal cortex (vmPFC) play a role in both cocaine and palatable food seeking. However, it is unknown whether similar or different vmPFC neuronal ensembles mediate food and cocaine seeking. Here, we used the Daun02 inactivation procedure to assess whether the neuronal ensembles mediating food and cocaine seeking can be functionally distinguished. We trained male and female Fos-LacZ rats to self-administer palatable food pellets and cocaine on alternating days for 18 days. We then exposed the rats to a brief nonreinforced food- or cocaine-seeking test to induce Fos and β-gal in neuronal ensembles associated with food or cocaine seeking, respectively and infused Daun02 into vmPFC to ablate the β-gal-expressing ensembles. Two days later, we tested the rats for food or cocaine seeking under extinction conditions. Although inactivation of the food-seeking ensemble did not influence food or cocaine seeking, inactivation of the cocaine-seeking ensemble reduced cocaine seeking but not food seeking. Results indicate that the neuronal ensemble activated by cocaine seeking in vmPFC is functionally separate from the ensemble activated by food seeking

Mouse and human islets survive and function after coating by biosilicification

Inorganic materials have properties that can be advantageous in bioencapsulation for cell transplantation. Our aim was to engineer a hybrid inorganic/soft tissue construct by inducing pancreatic islets to grow an inorganic shell. We created pancreatic islets surrounded by porous silica, which has potential application in the immunoprotection of islets in transplantation therapies for type 1 diabetes. The new method takes advantage of the islet capsule surface as a template for silica formation. Mouse and human islets were exposed to medium containing saturating silicic acid levels for 9-15 min. The resulting tissue constructs were then cultured for up to 4 wk under normal conditions. Scanning electron microscopy and energy dispersive X-ray spectroscopy was used to monitor the morphology and elemental composition of the material at the islet surface. A cytokine assay was used to assess biocompatibility with macrophages. Islet survival and function were assessed by confocal microscopy, glucose-stimulated insulin release assays, oxygen flux at the islet surface, expression of key genes by RT-PCR, and syngeneic transplant into diabetic mice

Temperature memory effect in two-way shape memory TiNi and TiNiCu springs

An incomplete thermal cycle upon heating in a shape memory alloy (arrested at a temperature between A s and A f ) induced a kinetic stop in the next complete thermal cycle. The kinetic stop temperature is closely related to the previous arrested temperature. This phenomenon is named temperature memory effect (TME). In this article, the TME in two-way shape memory TiNiCu and TiNi springs was investigated by performing either a single incomplete cycle, or a sequence of incomplete cycles. N points of temperatures could be memorized if N times of incomplete cycles on heating were performed with different arrested temperatures in a decreasing order. The capability is enhanced by performing repetitive incomplete cycles with the same temperature, and the TME can be eliminated by appropriate complete transformation cycle. The TME is originated from the relaxation of both the strain energy between martensite and coherent strain between parent phase and martensite.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43242/1/10853_2005_Article_5908.pd