Immunoinformatic Identification of Potential Epitopes Against Shigellosis

Diarrhoeal diseases due to Shigellosis account for deaths of ~1.5 million children every year in developing countries. Outer membrane proteins (OMPs) of Gram negative bacteria have been shown to be excellent subunit vaccine candidates against various pathogens. However, effective immune response can be generated using specific immunogenic determinants or peptides instead of whole protein or pathogen. In the present study, we chose six OMPs of Shigella flexneri 2a to predict peptides with good antigenic potential. Various tools were used in a systematic flow to predict B- and T-cell epitopes. Stringent selection criteria were used for epitope screening to ensure generation of both arms of immunity. These epitopes are predicted to be effective against a significantly large population of the diarrhoea afflicted countries in Southeast Asia. Most of the predicted epitopes are located towards the outer exposed region of proteins. The epitopes were docked with respective MHC Class I and II molecules to study peptide–MHC interactions. In conclusion, we have predicted an epitope ensemble against Shigellosis which can be experimentally validated for its immunogenic efficacy. We also propose a systematic workflow for immune-optimization to design effective peptide vaccines.     

Gram positivity induced in Escherichia coli by chloroform-methanol treatment

Summary Extraction of lipid by chloroform-methanol from Escherichia coli induces Gram positivity in the cells of this bacterium. It has been observed that approximately 1.5 times more lipid is extracted from Escherichia coli than from Staphylococcus aureus by this treatment. An increase of 1.5–1.8 fold in the retention of dye has been evident in the case of S. aureus where as this was 70–90 fold in the case of E. coli, which is 1/4th of the normal retention by S. aureus. The more lipid present in the cell wall or cell membrane, the less retention of dye seems to be exhibited by the bacteria. This also substantiates our model for Gram reaction presented in a previous communication.     

Behaviour of catalase in some members of Chlorophyceae and Cyanophyceae

Summary The activation energy of catalase revealed statistically significant variations in Chlorophyceae and Cyanophyceae. The differences in two classes of algae may suggest a close catalase-chlorophyll relationship.     

A Mouse Geneticist’s Practical Guide to CRISPR Applications

CRISPR/Cas9 system of RNA-guided genome editing is revolutionizing genetics research in a wide spectrum of organisms. Even for the laboratory mouse, a model that has thrived under the benefits of embryonic stem (ES) cell knockout capabilities for nearly three decades, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 technology enables one to manipulate the genome with unprecedented simplicity and speed. It allows generation of null, conditional, precisely mutated, reporter, or tagged alleles in mice. Moreover, it holds promise for other applications beyond genome editing. The crux of this system is the efficient and targeted introduction of DNA breaks that are repaired by any of several pathways in a predictable but not entirely controllable manner. Thus, further optimizations and improvements are being developed. Here, we summarize current applications and provide a practical guide to use the CRISPR/Cas9 system for mouse mutagenesis, based on published reports and our own experiences. We discuss critical points and suggest technical improvements to increase efficiency of RNA-guided genome editing in mouse embryos and address practical problems such as mosaicism in founders, which complicates genotyping and phenotyping. We describe a next-generation sequencing strategy for simultaneous characterization of on- and off-target editing in mice derived from multiple CRISPR experiments. Additionally, we report evidence that elevated frequency of precise, homology-directed editing can be achieved by transient inhibition of the Ligase IV-dependent nonhomologous end-joining pathway in one-celled mouse embryos.     

Synthesis of fluorescent nucleoside analogs as probes for 2′-deoxyribonucleoside kinases

We are reporting on the synthesis of fluorescent nucleoside analogs with modified sugar moieties (e.g., sugars other than ribose and 2′-deoxyribose). Four novel derivatives of the fluorescent thymidine analog 6-methyl-3-(β-D-2′-deoxyribofuranosyl) furano-[2,3-d]pyrimidin-2-one were synthesized via Sonogashira reaction and subsequent copper-catalyzed cycloaddition. These compounds represent promising tools for studying nucleoside metabolism inside living cells, as well as for screening directed evolution libraries of 2′-deoxyribonucleoside kinases with new and improved activity for the corresponding nucleoside analogs.     

Targeted novel surface-modified nanoparticles for interferon delivery for the treatment of hepatitis B

The purpose of the present work was to develop hepatitis B surface antigen (HBsAg) surface-adsorbed cationic poly (d,l-lactic-co-glycolic acid) PLGA nanoparticles for interferon alpha (IFNα) delivery targeted to hepatocytes. Cationic PLGA nanoparticles loaded with IFNα were prepared using the double emulsification technique. Delipidated HBsAg was passively adsorbed on the surface of nanoparticles by using the simple dipping and drying method. Surface morphology and size distribution of nanoparticles were analyzed by scanning electron microscopy and dynamic light-scattering method, respectively. The biodistribution behavior of plain and HBsAg-coated (99m)Tc-tagged PLGA nanoparticles was also examined followed by intravenous injection. The results revealed that ～75% of the radioactivity was recovered in the liver after 4 h of injection that was nearly 3-fold greater in magnitude than the plain PLGA nanoparticles. These data demonstrated that the novel formulation of nanoparticles has potential application in hepatic-targeted drug delivery.     

New Pyrano-4H-benzo[g]chromene-5,10-diones with Antiparasitic and Antioxidant Activities

New pyranonaphthoquinone derivatives were synthesized and investigated for their activity against Trypanosoma brucei, Leishmania major, and Toxoplasma gondii parasites. The pentafluorophenyl derivative was efficacious against T. brucei with single digit micromolar EC₅₀ values and against T. gondii with even sub-micromolar values. The 3-chloro-4,5-dimethoxyphenyl derivative showed an activity against amastigotes of Leishmania major parasites comparable to that of amphotericin B. In addition, antioxidant activities were observed for the bromophenyl derivatives, and their redox behavior was studied by cyclovoltammetry. Anti-parasitic and antioxidative activities of the new naphthoquinone derivatives appear uncorrelated.