A computational docking study for prediction of binding mode of diospyrin and derivatives: Inhibitors of human and leishmanial DNA topoisomerase-I

A computational approach was utilized to study the relative binding modes of diospyrin (bisnaphthoquinonoid) with the crystal structure of human DNA-TopoI and the recently reported Leishmania donavani DNA-TopoI. Additionally, the binding site interactions of amino derivatives of diospyrin with human TopoI were studied extensively. Based on the docking results, binding modes of diospyrin with the human and leishmanial TopoI catalytic core were predicted. The parallel use of two efficient and predictive docking programs, GOLD and Ligandfit, allowed mutual validation of the predicted binding poses. A reasonably good correlation coefficient between the calculated docking scores and the experimentally determined cytotoxicity helped in validating the docking method. Furthermore, a structure-based pharmacophore model was developed for L. donavani DNA-TopoI inhibition which helped in elucidating the topological and spatial requirements of the ligand-receptor interactions. This study provides an understanding of the structural basis of ligand binding to the topoisomerase receptor, which may be used for the structure-based design of potent and novel ligands for anticancer and antileishmanial therapy. To our knowledge, this is the first report of a binding mode exploration study for diospyrin and its derivatives as inhibitors of the leishmanial and human TopoI enzymes.     

HPCA1 and HSL3: two plasma membrane proteins that probably cooperate to modulate H2O2 signalling under drought conditions

Plant Growth Regulation - Ion transporters are essential for plant growth and development, and play key roles not only in acquisition/ transportation of essential ions from the surrounding and...     

A Regional Ecological Risk Assessment of the Kaipara Harbour,New Zealand,Using a Relative Risk Model

A regional ecological risk assessment was conducted for the Kaipara Harbour catchment in New Zealand. The Relative Risk Model was used to prioritize management of the sources of stress and habitats of concern in the basin. Semi-structured interviews with 25 representative stakeholders were conducted to obtain the resource-users’ perspectives and to identify the regional stressor sources and receptor habitat data for the model. For this risk analysis we divided the catchment into nine ecological districts. Mixed-methodological approaches including content analysis, geospatial analysis, and source documentation were used to categorize source and habitat rankings, based on the relative abundance of each in the nine ecological districts. Risk characterization revealed that fishing pressure and tidal energy pose the largest sources of perceived risk to the catchment; shellfish and Maui dolphin habitats are the receptors estimated to be at greatest risk; and the Kaipara and Rodney ecological districts are the sub-regions estimated with the greatest combined risk. A Monte Carlo analysis confirmed the source inputs and revealed greater uncertainty than the estimated habitat input results. The results of this assessment can be used by policy-makers, conservation groups, and municipalities to inform the future management efforts in the harbor and catchment.     

Soil salinity: A serious environmental issue and plant growth promoting bacteria as one of the tools for its alleviation

Salinity is one of the most brutal environmental factors limiting the productivity of crop plants because most of the crop plants are sensitive to salinity caused by high concentrations of salts in the soil, and the area of land affected by it is increasing day by day. For all important crops, average yields are only a fraction – somewhere between 20% and 50% of record yields; these losses are mostly due to drought and high soil salinity, environmental conditions which will worsen in many regions because of global climate change. A wide range of adaptations and mitigation strategies are required to cope with such impacts. Efficient resource management and crop/livestock improvement for evolving better breeds can help to overcome salinity stress. However, such strategies being long drawn and cost intensive, there is a need to develop simple and low cost biological methods for salinity stress management, which can be used on short term basis. Microorganisms could play a significant role in this respect, if we exploit their unique properties such as tolerance to saline conditions, genetic diversity, synthesis of compatible solutes, production of plant growth promoting hormones, bio-control potential, and their interaction with crop plants.     

Varying the length of dim nocturnal illumination differentially affects the pacemaker controlling the locomotor activity rhythm of Drosophila jambulina

Photic entrainment of animals in the field is basically attributed to their exposure to the dimly lit nights flanked by the dawn and dusk twilight transitions. This implicates the functional significance of the dimly lit nights as that of the twilight transitions. Recently, the authors have demonstrated that the dimly lit night at 0.0006 lux altered the attributes of the circadian rhythm of locomotor activity of Drosophila jambulina. The present study examined whether the durations of such dimly lit nights affect the entrainment and free-running rhythmicity of D. jambulina. Flies were subjected for 10 days to two types of 24-h lighting regimes in which the photophase (L) was at 10 lux for all flies but the scotophase, which varied in duration from 9 to 15 h, was either at 0 lux (D phase) for control flies or 0.0006 lux (the artificial starlight or S phase) for experimental flies. Thereafter, they were transferred to constant darkness (DD) to compare the after-effects of the dimly lit nights on the period (τ) of free-running rhythm in DD with that of the completely dark nights. Control flies were entrained by all LD cycles, but the experimental flies were entrained only by five LS cycles in which the duration of the S phases ranged from 10 to 14 h. The two LS cycles with very short (9 h) and long (15 h) S phases rendered the flies completely arrhythmic. Control flies started activity shortly before lights-on and continued well after lights-off. The experimental flies, however, commenced activity several hours prior to lights-on but ended activity abruptly at lights-off as the result of a negative masking effect of nocturnal illumination. Length of the midday rest was considerably shorter in the control than in the experimental flies in each lighting regime. The active phase in the control flies was predictably shortened; nonetheless, it was invariable in the experimental flies as the nights lengthened. Transfer from lighting regimes to DD initiated robust free-running rhythmicity in all flies including the arrhythmic ones subjected to LS cycles with 9 and 15 h of scotophases. The τ was profoundly affected by the nocturnal irradiance of the prior entraining lighting regime, as it was always shorter in the experimental than in the control flies. Thus, these results indisputably demonstrate the changes in fundamental properties of the circadian pacemaker of D. jambulina were solely attributed to the extremely dim nocturnal irradiance. This strain of D. jambulina is entrained essentially by the dimly lit natural nights, since it is never exposed to the prevailing photic cues such as the twilight transitions or bright photoperiod, owing to the dense vegetation of its habitat.     

Synthesis and evaluation of indole-based new scaffolds for antimicrobial activities--identification of promising candidates

Search for new antimicrobial agents led to the synthesis of series of N-1, C-3 and C-5 substituted bis-indoles. Their evaluation for antifungal and antibacterial activities resulted in the optimization of pyrrolidine/morpholine/N-benzyl moiety at the C-3 end and propane/butane/xylidine groups as linkers between two indoles for significant inhibition of microbial growth. Preliminary investigations have identified three highly potent antimicrobial agents. Dockings of these molecules in the active sites of lanosterol demethylase, dihydrofolate reductase and topoisomerase II indicate their strong interactions with these enzymes.     

Liver engraftment potential of hepatic cells derived from patient-specific induced pluripotent stem cells

Human induced pluripotent stem cells (iPSCs) are potential renewable sources of hepatocytes for drug development and cell therapy. Differentiation of human iPSCs into different developmental stages of hepatic cells has been achieved and improved during the last several years. We have recently demonstrated the liver engraftment and regenerative capabilities of human iPSC-derived multistage hepatic cells in vivo. Here we describe the in vitro and in vivo activities of hepatic cells derived from patientspecific iPSCs, including multiple lines established from either inherited or acquired liver diseases, and discuss basic and clinical applications of these cells for disease modeling, drug screening and discovery, gene therapy and cell replacement therapy.Key words: induced pluripotent stem cells (iPSCs), hepatic differentiation, liver ngraftment, disease modeling, drug testing, alpha-1 antitrypsin, liver cirrhosis, hepatocellular carcinoma, cell therapy     

Development of single-stranded DNA aptamers for specific Bisphenol a detection

The development of reagents with high affinity and specificity to small molecules is crucial for the high-throughput detection of chemical compounds, such as toxicants or pollutants. Aptamers are short and single-stranded (ss) oligonucleotides able to recognize target molecules with high affinity. Here, we report the selection of ssDNA aptamers that bind to Bisphenol A (BPA), an environmental hormone. Using SELEX process, we isolated high affinity aptamers to BPA from a 10(15) random library of 60 mer ssDNAs. The selected aptamers bound specifically to BPA, but not to structurally similar molecules, such as Bisphenol B with one methyl group difference, or 4,4'-Bisphenol with 2 methyl groups difference. Using these aptamers, we developed an aptamer-based sol-gel biochip and detected BPA dissolved in water. This novel BPA aptamer-based detection can be further applied to the universal and high-specificity detection of small molecules.