Identification of key DNA elements involved in promoter recognition by Mxr1p, a master regulator of methanol utilization pathway in Pichia pastoris

Mxr1p (methanol expression regulator 1) functions as a key regulator of methanol metabolism in the methylotrophic yeast Pichia pastoris. In this study, a recombinant Mxr1p protein containing the N-terminal zinc finger DNA binding domain was overexpressed and purified from E coli cells and its ability to bind to promoter sequences of AOXI encoding alcohol oxidase was examined. In the AOXI promoter, Mxr1p binds at six different regions. Deletions encompassing these regions result in a significant decrease in AOXI promoter activity in vivo. Based on the analysis of AOXI promoter sequences, a consensus sequence for Mxr1p binding consisting of a core 5' CYCC 3' motif was identified. When the core CYCC sequence is mutated to CYCA, CYCT or CYCM (M = 5-methylcytosine), Mxr1p binding is abolished. Though Mxr1p is the homologue of Saccharomyces cerevisiae Adr1p transcription factor, it does not bind to Adr1p binding site of S. cerevisiae alcohol dehydrogenase promoter (ADH2UAS1). However, two point mutations convert ADH2UAS1 into an Mxr1p binding site. The identification of key DNA elements involved in promoter recognition by Mxr1p is an important step in understanding its function as a master regulator of the methanol utilization pathway in P. pastoris.

Enhancing 'Mobility' through Integrated Transportation and Traffic Management

During the course of preparation of a master plan for the transportation networks in Bangalore city, mapping the various initiatives and interventions planned towards addressing mobility, existing situation and implications of some of the proposed interventions was analysed. The inferences are based on existing transportation network; synthesis of various transportation related studies and proposed infrastructure initiatives (road works) in Bangalore. Broadly, they can be summarized as following five aspects: I. Need for ~Sreclassifying~T existing road networks (arterial and sub-arterial) with effective geospatial database in the back-end. II. The proposed Core Ring Road at surface grade may not be feasible. III. Current interventions encouraging more independent motorable transport by way of road widening, construction of underpasses, flyovers and grade-separators would not ease traffic congestion when addressed in isolation. IV. Factors affecting time and cost-overruns in infrastructure projects and ways to tackle are discussed. V. Initiatives required for addressing effective planning for operations recommended.

Delay constrained optimal relay placement for planned wireless sensor networks

In this paper, we study the problem of wireless sensor network design by deploying a minimum number of additional relay nodes (to minimize network design cost) at a subset of given potential relay locationsin order to convey the data from already existing sensor nodes (hereafter called source nodes) to a Base Station within a certain specified mean delay bound. We formulate this problem in two different ways, and show that the problem is NP-Hard. For a problem in which the number of existing sensor nodes and potential relay locations is n, we propose an O(n) approximation algorithm of polynomial time complexity. Results show that the algorithm performs efficiently (in over 90% of the tested scenarios, it gave solutions that were either optimal or exceeding optimal just by one relay) in various randomly generated network scenarios.

QoS Constrained Optimal Sink and Relay Placement in Planned Wireless Sensor Networks

We are given a set of sensors at given locations, a set of potential locations for placing base stations (BSs, or sinks), and another set of potential locations for placing wireless relay nodes. There is a cost for placing a BS and a cost for placing a relay. The problem we consider is to select a set of BS locations, a set of relay locations, and an association of sensor nodes with the selected BS locations, so that the number of hops in the path from each sensor to its BS is bounded by h(max), and among all such feasible networks, the cost of the selected network is the minimum. The hop count bound suffices to ensure a certain probability of the data being delivered to the BS within a given maximum delay under a light traffic model. We observe that the problem is NP-Hard, and is hard to even approximate within a constant factor. For this problem, we propose a polynomial time approximation algorithm (SmartSelect) based on a relay placement algorithm proposed in our earlier work, along with a modification of the greedy algorithm for weighted set cover. We have analyzed the worst case approximation guarantee for this algorithm. We have also proposed a polynomial time heuristic to improve upon the solution provided by SmartSelect. Our numerical results demonstrate that the algorithms provide good quality solutions using very little computation time in various randomly generated network scenarios.