Translating cancer research by synthetic biology

Synthetic biology concerns applying engineering principles to biological systems. Engineering properties such as fine tuning, novel specificity, and modularity could be components of a synthetic toolkit that can be exploited to explore various issues in cancer research such as elucidation of mechanisms and pathways, creating new diagnostic tools and novel therapeutic approaches. A repertoire of synthetic biology toolkits involving DNA, RNA and protein bio-parts, have been applied to address the issues of drug target identification, drug discovery and therapeutic treatment in cancer research, thereby projecting a new dimension in oncology research.     

Improved siRNA/shRNA functionality by mismatched duplex

siRNA (small interfering RNA) and shRNA (small hairpin RNA) are powerful and commonly used tools in biomedical research. Currently, siRNAs are generally designed as two 21 nt strands of RNA that include a 19 nt completely complementary part and a 2 nt overhang. However, since the si/shRNAs use the endogenous miRNA machinery for gene silencing and the miRNAs are generally 22 nt in length and contain multiple internal mismatches, we tested if the functionality can be increased by designing the si/shRNAs to mimic a miRNA structure. We systematically investigated the effect of single or multiple mismatches introduced in the passenger strand at different positions on siRNA functionality. Mismatches at certain positions could significantly increase the functionality of siRNAs and also, in some cases decreased the unwanted passenger strand functionality. The same strategy could also be used to design shRNAs. Finally, we showed that both si and miRNA structured oligos (siRNA with or without mismatches in the passenger strand) can repress targets in all individual Ago containing cells, suggesting that the Ago proteins do not differentiate between si/miRNA-based structure for silencing activity.     

Can plant defensins be used to engineer durable commercially useful fungal resistance in crop plants?

Plant defensins are cysteine-rich proteins that play an important role in defense against fungal pathogens. Because of their potent antifungal activity, they have a strong potential to be used for engineering disease resistance in crops. Significant advances have been made in elucidating their structure–activity relationships and modes of antifungal action. Their expression in transgenic plants provides resistance to fungal pathogens in crop plants. In this article, we review recent advances and offer future perspectives on the use of these proteins for engineering durable commercially useful disease resistance in transgenic crop plants.     

DNA-binding behavior of ruthenium(II) complexes containing both group 15 donors and 2,2':6',2''-terpyridine

Tetrafluoroborate salts of cationic ruthenium complexes [Ru(kappa(3)-tpy)(EPh(3))(2)Cl](+) (tpy=2,2':6',2'-terpyridine; E=P, 1 or As, 2) containing both the group 15 donor ligands and tpy and their representative substitution products are reported. Weak interaction {C-H...X (X=Cl, F and pi) and pi-pi interaction} studies revealed the presence of a double helical motif in complex 1, while the complex 2 assumes a single helical motif. Intercalative mode of interaction of the complexes 1 and 2 with calf thymus DNA (ctDNA) has been supported by absorption titration studies.     

Design of humanized antibodies: from anti-Tac to Zenapax

Since the introduction of hybridoma technology, monoclonal antibodies have become one of the most important tools in the biosciences, finding diverse applications including their use in the therapy of human disease. Initial attempts to use monoclonal antibodies as therapeutics were hampered, however, by the potent immunogenicity of mouse (and other rodent) antibodies in humans. Humanization technology has made it possible to remove the immunogenicity associated with the use of rodent antibodies, or at least to reduce it to an acceptable level for clinical use in humans, thus facilitating the application of monoclonal antibodies to the treatment of human disease. To date, nine humanized monoclonal antibodies have been approved for use as human therapeutics in the United States. In this paper, we describe procedures for antibody humanization with an emphasis on strategies for designing humanized antibodies with the aid of computer-guided modeling of antibody variable domains, using as an example the humanized anti-CD25 monoclonal antibody, Zenapax.     

pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes

MOTIVATION: There is a scarcity of efficient computational methods for predicting protein subcellular localization in eukaryotes. Currently available methods are inadequate for genome-scale predictions with several limitations. Here, we present a new prediction method, pTARGET that can predict proteins targeted to nine different subcellular locations in the eukaryotic animal species. RESULTS: The nine subcellular locations predicted by pTARGET include cytoplasm, endoplasmic reticulum, extracellular/secretory, golgi, lysosomes, mitochondria, nucleus, plasma membrane and peroxisomes. Predictions are based on the location-specific protein functional domains and the amino acid compositional differences across different subcellular locations. Overall, this method can predict 68-87% of the true positives at accuracy rates of 96-99%. Comparison of the prediction performance against PSORT showed that pTARGET prediction rates are higher by 11-60% in 6 of the 8 locations tested. Besides, the pTARGET method is robust enough for genome-scale prediction of protein subcellular localizations since, it does not rely on the presence of signal or target peptides. AVAILABILITY: A public web server based on the pTARGET method is accessible at the URL http://bioinformatics.albany.edu/~ptarget. Datasets used for developing pTARGET can be downloaded from this web server. Source code will be available on request from the corresponding author.     

Impact of Juvenile Stocking Size on the Major Carp Production in a Minor Reservoir,Bibinagar, India

The present study deals with the impact of juvenile stocking sizes of the major carp on production in a minor reservoir, Bibinagar, Nalgonda, India. Reservoir surface area equaled over 23.8 ha and water from the reservoir was used for irrigation and fisheries. Four experiments were conducted for 4 years from 2000–2001 to 2003–2004. The experiments were planned in such a way that every year juvenile stocking size was held constant and subsequent fish production analyzed. During the first year’s experiment (2000–2001) a stocking size of 25–30 mm (fry) was maintained. Similarly 50–55 (advanced fry), 75–80 mm (fingerling) and 100–105 mm (advanced fingerling) were stocked during 2001–2002, 2002–2003 and 2003–2004 respectively. Uniform yearly stocking densities (2000/ha) were established in each experiment in the month of July and fish were harvested in June of the subsequent year. Major carp production was enhanced with larger stocking size. Yearly productions equaled 144.00, 231.48, 632.91 and 1005.03 kg/ha/year with the above stocking sizes. Variation in stocking sizes had significant (P<0.05) effects on fish production. The number of fish per kg production decreased gradually with increases in stocking size with an average value of 3.97. Reservoir production of catla was the most abundant species, followed by rohu, common carp, mrigal and grass carp. These results show that stocking size has a great impact on fish production and the stocking of advanced fingerlings will provide maximum carp production in minor reservoirs in India.