The Relationship between the UniProt Knowledgebase (UniProtKB) and the IntAct Molecular Interaction Databases

IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submission and all experimental information relating to binary protein-protein
interactions is entered into the IntAct database by curators, via a web-based editor. Interaction information is added to the SUBUNIT comment and the RP line of the relevant publication within the UniProtKB entry. There may be a single INTERACTION comment present within a UniProtKB entry, which conveys information relevant to binary protein-protein interactions. This is automatically derived from the IntAct database and is updated on a triweekly basis. Interactions can be derived by any appropriate experimental method but must be confirmed by a second interaction if resulting from a single yeast2hybrid experiment. For large-scale experiments, interactions are considered if a high confidence score is assigned by the authors. The INTERACTION line contains a direct link to IntAct that provides detailed information for the experimental support. These lines are not changed manually and any discrepancy is reported to IntAct for updates. There is also a database crossreference line within the UniProtKB entry i.e.: DR IntAct _UniProtKB AC, which directs the user to additional interaction data for that molecule. 
UniProt is supported by grants from the National Institutes of Health, European Commission, Swiss Federal Government and PATRIC BRC.
IntAct is funded by the European Commission under FELICS, contract number 021902 (RII3) within the Research Infrastructure Action of the FP6 "Structuring the European Research Area" Programme

Impacts of Embryonic Exposure to Cannabidiol or ∆9-Tetrahydrocannabinol on Zebrafish (Danio rerio) Frailty in F0 and F1 Generations

Exposure to cannabinoids during critical development periods has increased with epileptic children being commonly prescribed CBD for seizures and pregnant women taking it recreationally. Many studies have been done on the possible benefits and drawbacks of cannabinoid exposure on the human brain, but not much is known about how it can affect the developing brain long-term. To see the potential adverse effects of cannabinoid exposure during critical stages of development and discover potential developmental origins of disease in consuming cannabinoids during embryogenesis, zebrafish embryos (6-96 hours post fertilization) were exposed to varying concentrations of CBD (0.02, 0.1, 0.5 µM), THC (0.08, 0.4, 2 µM) and a control (0.05% DMSO). Exposed parents (F0) were bred to produce an F1 generation to see if effects were cross-generational. Effects of aging were assessed 30 months after exposure. As zebrafish age, increased incidents of kyphosis are observed as well as decreased physical activity. The aged male fish exposed to 0.1 µM CBD during embryogenesis rotated significantly more times than the aged control male fish, demonstrating a significant deviation from the expected age-related change. These changes were not observed in the female fish or at any other experimental concentration of CBD or THC. Furthermore, the aged male fish treated with 0.4 µM THC swam with significantly more mobility than the aged control male fish, showing a significant deviation in mobility from the expected age-related change in aged fish. This was not observed in the female fish or at any other experimental concentration of CBD or THC. Exposure to THC and CBD during embryogenesis did not significantly alter the expected increase in kyphosis in aged males or females, despite a visual trend of reduced curvature as concentrations of both cannabinoids decreased. These findings demonstrate that exposure to cannabinoids during critical development periods can cause significant effects on the long term health of zebrafish

Master of Science

thesisThe main objective of this work is to study different materials for the direct photosynthesis of hydrogen from water. A variety of photocatalysts such as titanium dioxide, titanium oxy-nitride, silicon carbide, and gallium nitride are being investigated by others for the clean production of hydrogen for fuel cells and hydrogen economy. Our approach was to deposit suitable metallic regions on photocatalyst nanoparticles to direct the efficient synthesis of hydrogen to a particular site for convenient collection. We studied different electrode metals such as gold, platinum, titanium, palladium, and tungsten. We also studied different solar cell materials such as silicon (p- and n-types), silicon carbide and titanium dioxide semiconductors in order to efficiently generate electrons under illumination. We introduced a novel silicon-based multilayer photosynthesis device to take advantage of suitable properties of silicon and tungsten to efficiently produce hydrogen. The device consisted of a silicon (0.5mm) substrate, a deposited atomic layer of Al2O3 (1nm), a doped polysilicon (0.1?m), and finally a tungsten nanoporous (5-10nm) layer acting as an interface electrode with water. The Al2O3 layer was introduced to reduce leakage current and to prevent the spreading of the diffused p-n junction layer between the silicon and doped polysilicon layers. The surface of the photoelectrode was coated with nanotext;ured tungsten nanopores (TNP), which increased the surface area of the electrodes to the electrolyte, assisting in electron-hole mobility, and acting as a photocatalyst. The reported device exhibited a fill factor (%FF) of 27.22% and solar-to-hydrogen conversion efficiency of 0.03174%. This thesis describes the structures of the device, and offers a characterization and comparison between different photoelectrodes

Identification of dephosphorylated sites in the proximity of recurrent mutations in PP2A targets

Protein Phosphatase 2A (PP2A), a major serine/threonine phosphatase, is known to be involved in the wide range of cellular functions in many cell types. Notably, PP2A’s tumor suppressor function has a great potential for therapeutic use in cancer patients. However, understanding basic functions as well as translational potential of PP2A is complex and is at its infancy. Identification of PP2A targets, and especially target sites nearby the recurrent mutations can potentially provide insights on PP2A’s function in the context of cancer. Thus, the focus of this thesis was to identify target sites which are directly or indirectly dephosphorylated by PP2A and thereby map the sites nearby the significant recurrent mutations in cancer samples. Thesis presented here in made use of in-house as well as published phosphosproteomics datasets to identify the potential targets of PP2A. A protein was considered as a target of PP2A if its phosphopeptide was significantly regulated as assessed either from student’s t-test or alternatively defined in respective publications. In order to identify the significantly mutated residues as compared to background mutation rate, ActiveDriver methodology was employed in this study. ActiveDriver tests the null hypotheses given mutational, intrinsic disorder and phosphosite information. The null hypothesis assumes that mutations in protein sequences follows Poisson distribution. As an example of PP2A target identification process, an in-house generated B56 dataset of PP2A phosphpoproteomics dataset was used. Two sided students t-test was performed to find differentially regulated peptides and the analysis revealed 1249 out of 6739 peptides were statistically significant (unadjusted p value < 0.05). Volcano plot and heatmap for the analysis of B56 dataset were used to visualise most significant peptides. A comprehensive dataset of non-redundant phosphosites from various PP2A phosphoproteomics datasets (three groups of PP2A families) was built to reflect the broader coverage of PP2A targets. ActiveDriver analysis on cBioportal pancancer study revealed that there were 19 genes with 248 active regions (p-value < 0.05). Similar analysis on COSMIC mutational dataset revealed 57 genes with 2,723 active regions (p-value < 0.05). Network analysis was carried out on proteins having at least one significant active region. The resulting protein-protein interaction network from STRING database for the target list of proteins after ActiveDriver analysis is significantly enriched as compared to any random network and it was also significant (5e-15). Functional enrichment analysis also provided strong evidence among those analysis and PPI enrichment p- value also significant in both cases. Based on false discovery rate, biological and molecular function among the selected genes also showed significant. This mutational study provides better understand to identify target sites which are directly or indirectly dephosphorylated by PP2A and thereby likely provide potential clues for mechanisms of action for PP2A function

Poor fish farmers' accessibility to credits: A review

Fisheries sector contributes about 5.3% to GDP and about 6% of the export earnings of Bangladesh. There are about 4.1 million ha of inland water bodies in Bangladesh. However, over last two decades the catch from inland capture fishery has decreased due to filling of wet lands and other anthropogenic reasons. Accordingly, the production of inland fish has decreased not only for the decrease of water bodies but also due to irrational catch of fish fries, brood fishes and use of current nets for fishing. Significant responses from the fisheries entrepreneurs have not been received for the small loan scheme of the Bangladesh Bank. The bank could not disburse more than Tk. 500 million under the scheme. The total revolving credit under the scheme was Tk. 1,000 million with the assistance from the World Bank. The business houses having fixed assets of value not more than Tk. 10 million will be eligible to borrow from this fund. About Tk. 0.2-5.0 million can be borrowed as term loan and working capital from Bangladesh Bank through commercial banks. The loan was given to the commercial banks at 5% interest (bank rate) and the commercial banks shall also bridge finance to the entrepreneurs at a lower rate of interest. Working capital time limit is for a maximum of 1 year with half yearly rest, mid-term loan maximum of 3 years in 5 installments and with 6 months grace period and long-term loan maximum of 5 years in 9 installments with 6 months grace period