Design, engineering, and characterization of zinc finger nucleases

Zinc finger nuclease (ZFN)-mediated gene targeting is rapidly becoming a powerful tool for "gene editing" and "directed mutagenesis" of plant and mammalian genomes including the human genome. ZFN-mediated gene targeting provides molecular biologists with the ability to site-specifically manipulate and permanently modify plant and mammalian genomes. Facile production of ZFNs and rapid characterization of their in vitro sequence-specific cleavage properties are a pre-requisite before ZFN-mediated gene targeting can become an efficient and effective practical tool for widespread use in biotechnology. Here, we report the design, engineering, and rapid in vitro characterization of ZFNs that target specific endogenous sequences within two mouse genes (mTYR and mCFTR), and two human genes (hCCR5 and hDMPK), respectively. These engineered ZFNs recognize their respective cognate DNA sites encoded in a plasmid substrate in a sequence-specific manner and, as expected, they induce a double-strand break at the chosen target site.     

Effect of pretreatment of Cassia fistula Linn. leaf extract against subacute CCl4 induced hepatotoxicity in rats

CCl4 alone treatment (0.lml of liquid paraffin/100g body weight, ip) for 7 days followed by 0.l ml of CCl4 (in liquid parafiin/100g body weight, ip) from day 8 till day 14, caused a 16 fold increase in lipid peroxidation and a 50% reduction in catalase and glutathione reductase in liver tissue of rats accompanied by an increase in the activities of transaminases. alkaline phosphatase, lactate dehydrogenase and gamma - glutamyl transpeptidase in serum as compared to liquid paraffin treated control. Pretreatment of ethanolic leaf extract of C. fistula (500mg/kg body weight/day for 7 days) followed by CCl4 treatment (0.1 ml/100g body weight from day 8 till day 14) completely reversed back lipid peroxidation and the activities of catalase and glutathione reductase in the liver tissue towards normalcy. This treatment also reversed the elevated levels of the enzymes in the serum. Ethanolic leaf extract alone treatment did not produce any change in all the parameters studied. The results suggest antioxidant and hepatoprotective properties of C. fistula during its pretreatment against CCl4 induced hepatotoxicity.     

Structural analysis of Pseudomonas 1-aminocyclopropane-1-carboxylate deaminase complexes: insight into the mechanism of a unique pyridoxal-5'-phosphate dependent cyclopropane ring-opening reaction

1-Aminocyclopropane-1-carboxylate (ACC) deaminase is a pyridoxal 5'-phosphate (PLP) dependent enzyme catalyzing the opening of the cyclopropane ring of ACC to give alpha-ketobutyric acid and ammonia as the products. This ring cleavage reaction is unusual because the substrate, ACC, contains no abstractable alpha-proton and the carboxyl group is retained in the product. How the reaction is initiated to generate an alpha-carbanionic intermediate, which is the common entry for most PLP-dependent reactions, is not obvious. To gain insight into this unusual ring-opening reaction, we have solved the crystal structures of ACC deaminase from Pseudomonas sp. ACP in complex with substrate ACC, an inhibitor, 1-aminocyclopropane-1-phosphonate (ACP), the product alpha-ketobutyrate, and two d-amino acids. Several notable observations of these structural studies include the following: (1) a typically elusive gem-diamine intermediate is trapped in the enzyme complex with ACC or ACP; (2) Tyr294 is in close proximity (3.0 A) to the pro-S methylene carbon of ACC in the gem-diamine complexes, implicating a direct role of this residue in the ring-opening reaction; (3) Tyr294 may also be responsible for the abstraction of the alpha-proton from d-amino acids, a prelude to the subsequent deamination reaction; (4) the steric hindrance precludes accessibility of active site functional groups to the l-amino acid substrates and may account for the stereospecificity of this enzyme toward d-amino acids. These structural data provide evidence favoring a mechanism in which the ring cleavage is induced by a nucleophilic attack at the pro-S beta-methylene carbon of ACC, with Tyr294 as the nucleophile. However, these observations are also consistent with an alternative mechanistic possibility in which the ring opening is acid-catalyzed and may be facilitated by charge relay through PLP, where Tyr294 functions as a general acid. The results of mutagenesis studies corroborated the assigned critical role for Tyr294 in the catalysis.     

lH-Pyrazolo[3,4-b]quinolin-3-amine derivatives inhibit growth of colon cancer cells via apoptosis and sub G1 cell cycle arrest

A series of lH-pyrazolo[3,4-b]quinolin-3-amine derivatives were synthesized and evaluated for anticancer efficacy in a panel of ten cancer cell lines, including breast (MDAMB-231 and MCF-7), colon (HCT-116, HCT-15, HT-29 and LOVO), prostate (DU-145 and PC3), brain (LN-229), ovarian (A2780), and human embryonic kidney (HEK293) cells, a non-cancerous cell line. Among the eight derivatives screened, compound QTZ05 had the most potent and selective antitumor efficacy in the four colon cancer cell lines, with IC₅₀ values ranging from 2.3 to 10.2?µM. Furthermore, QTZ05 inhibited colony formation in HCT-116 cells in a concentration-dependent manner. Cell cycle analysis data indicated that QTZ05 caused an arrest in the sub G1 cell cycle in HCT-116 cells. QTZ05 induced apoptosis in HCT-116 cells in a concentration-dependent manner that was characterized by chromatin condensation and increase in the fluorescence of fluorochrome-conjugated Annexin V. The findings from our study suggest that QTZ05 may be a valuable prototype for the development of chemotherapeutics targeting apoptotic pathways in colorectal cancer cells.     

Juglans regia L. protects against UVB induced apoptosis in human epidermal keratinocytes

The present study was aimed to investigate the photoprotective effect of the male flower of J. regia L. (MEJR) against ultraviolet-B induced apoptosis in human skin cells. Human skin epidermal keratinocytes were pretreated with the MEJR (80 µg/ml, has been selected after MTT assay), prior to 30 min UVB-irradiation at a dose of 20 mJ/cm². Mitochondrial membrane potential was evaluated using Rhodamine-123 staining; the % apoptosis by Hoechst staining and acridine orange staining; DNA damage was measured by comet assay. The levels of p53, Bax, Bcl-xL, Bcl-2, Cytochrome c, Caspase-9 and Caspase-3 expression in HaCaT cells were analyzed by western blotting and RT-PCR. Pretreatment with MEJR 80 µg/ml prior to UVB-irradiation significantly prevents apoptotic characteristics, DNA damage and loss of mitochondrial membrane potential. Thus, MEJR protects UVB-mediated human skin cells, by modulating the expression of apoptotic markers and UVB-induced DNA damage in HaCaT cells.     

Using public surveys to reliably and rapidly estimate the distributions of multiple invasive species on the Andaman archipelago

To effectively manage multiple biological invasions, information on their distributions must be generated rapidly and over large spatial scales. Using public surveys in a false‐positive occupancy framework, we reliably estimate the distributions of three synanthropic invasive species on the Andaman Islands.     

Thrombin-reactive polypeptides of platelets may regulate inhibition of thrombin by antithrombin

The central enzyme involved in blood coagulation and activation of platelets is the serine proteinase thrombin. The principal inhibitor of this proteinase in plasma is antithrombin. The mechanism of regulation of the thrombin-antithrombin reaction remains unknown. Two polypeptides of 74 and 55 kDa present on the platelet surface and in plasma are known to specifically enhance the activity of thrombin on different substrates. This study was undertaken to assess the effects of these platelet proteins on thrombin-antithrombin interaction. Direct measurements of residual thrombin activity in mixtures of thrombin and antithrombin, in the presence or absence of the platelet proteins, were made utilizing a specific chromogenic substrate. Under these conditions, when 60% of thrombin activity was inhibited by antithrombin in controls, 100% of enzyme activity was retained in the presence of the platelet proteins. When heparin was used in these assays, the rate of inhibition of thrombin by antithrombin was much more rapid and 62% of thrombin activity remained after 1 min. Under these conditions, the platelet proteins continued to protect thrombin from inactivation with 98% activity remaining at 1 min and 85% activity at 5 min. In contrast, the inhibition of trypsin by antithrombin was not affected by the platelet proteins. Additional studies in platelet aggregation showed that the platelet polypeptides have two effects on thrombin: (i) protection of the enzyme inhibition by antithrombin and (ii) stabilization of thrombin from loss of activity due to aging. The results suggest a novel role for the platelet proteins in hemostasis - regulation of the inhibition of thrombin by antithrombin.     

Going Beyond Lithium Hybrid Capacitors: Proposing a New High‐Performing Sodium Hybrid Capacitor System for Next‐Generation Hybrid Vehicles Made with Bio‐Inspired Activated Carbon

A novel sodium hybrid capacitor (NHC) is constructed with an intercalation‐type sodium material [carbon coated‐Na₃V₂(PO₄)₃, C‐NVP] and high surface area‐activated carbon derived from an eco‐friendly resource cinnamon sticks (CDCs) in an organic electrolyte. This novel NHC possesses a combination of high energy and high power density, along with remarkable electrochemical stability. In addition, the C‐NVP/CDC system outperforms present, well‐established lithium hybrid capacitor systems in all areas, and can thus be added to the list of candidates for future electric vehicles. A careful optimization of mass balance between electrode materials enables the C‐NVP/CDC cell to exhibit extraordinary capacitance performance. This novel NHC produces an energy density of 118 Wh kg^?1 at a specific power of 95 W kg^?1 and retains an energy density of 60 Wh kg^?1 with high specific power of 850 W kg^?1. Furthermore, a discharge capacitance of 53 F g^?1 is obtained from the C‐NVP/CDC cell at a 1 mA cm^?2 current density, along with 95% capacitance retention, even after 10 000 cycles. The sluggish kinetics of the Na ion battery system is successfully overcome by developing a stable, high‐performing NHC system.