Search results for: pocket

Authors: Rauan Sakenov, Peter Bukovics, Peter Gaszler, Veronika Tokacs-Kollar, Beata Bugyi

Abstract:

FH2 (formin homology-2) domains of several proteins, collectively known as formins, including DAAM, DAAM1 and mDia1, promote G-actin nucleation and elongation. FH2 domains of these formins exist as oligomers. Chain dimerization by ring structure formation serves as a structural basis for actin polymerization function of FH2 domain. Proper single chain configuration and specific interactions between its various regions are necessary for individual chains to form a dimer functional in G-actin nucleation and elongation. FH1 and WH2 domain-containing formins were shown to behave as intrinsically disordered proteins. Thus, the aim of this research was to study structural dynamics of FH2 domain of DAAM. To investigate structural features of FH2 domain of DAAM, molecular dynamics simulation of chain A of FH2 domain of DAAM solvated in water box in 50 mM NaCl was conducted at temperatures from 293.15 to 353.15K, with VMD 1.9.2, NAMD 2.14 and Amber Tools 21 using 2z6e and 1v9d PDB structures of DAAM was obtained on I-TASSER webserver. Calcium and ATP bound G-actin 3hbt PDB structure was used as a reference protein with well-described structural dynamics of denaturation. Topology and parameter information of CHARMM 2012 additive all-atom force fields for proteins, carbohydrate derivatives, water and ions were used in NAMD 2.14 and ff19SB force field for proteins in Amber Tools 21. The systems were energy minimized for the first 1000 steps, equilibrated and produced in NPT ensemble for 1ns using stochastic Langevin dynamics and the particle mesh Ewald method. Our root-mean square deviation (RMSD) analysis of molecular dynamics of chain A of FH2 domains of DAAM revealed similar insignificant changes of total molecular average RMSD values of FH2 domain of these formins at temperatures from 293.15 to 353.15K. In contrast, total molecular average RMSD values of G-actin showed considerable increase at 328K, which corresponds to the denaturation of G-actin molecule at this temperature and its transition from native, ordered, to denatured, disordered, state which is well-described in the literature. RMSD values of lasso and tail regions of chain A of FH2 domain of DAAM exhibited higher than total molecular average RMSD at temperatures from 293.15 to 353.15K. These regions are functional in intra- and interchain interactions and contain highly conserved tryptophan residues of lasso region, highly conserved GNYMN sequence of post region and amino acids of the shell of hydrophobic pocket of the salt bridge between Arg171 and Asp321, which are important for structural stability and ordered state of FH2 domain of DAAM and its functions in FH2 domain dimerization. In conclusion, higher than total molecular average RMSD values of lasso and post regions of chain A of FH2 domain of DAAM may explain disordered state of FH2 domain of DAAM at temperatures from 293.15 to 353.15K. Finally, absence of marked transition, in terms of significant changes in average molecular RMSD values between native and denatured states of FH2 domain of DAAM at temperatures from 293.15 to 353.15K, can make it possible to attribute these formins to the group of intrinsically disordered proteins rather than to the group of intrinsically ordered proteins such as G-actin.

Keywords: FH2 domain, DAAM, formins, molecular modelling, computational biophysics

Procedia PDF Downloads 136

Authors: V. Jayanthi

Abstract:

Urbanization and pace of urbanization have increased tremendously in last few decades. More towns are now getting converted into cities. Urbanization trend is seen all over the world but is becoming most dominant in Asia. Today, the scale of urbanization in India is so huge that Indian cities are among the fastest-growing in the world, including Bangalore, Hyderabad, Pune, Chennai, Delhi, and Mumbai. Urbanization remains a single predominant factor that is continuously linked to the destruction of urban green spaces. With reference to Chennai as a case study, which is suffering from rapid deterioration of its green spaces, this paper sought to fill this gap by exploring key factors aside urbanization that is responsible for the destruction of green spaces. The paper relied on a research approach and triangulated data collection techniques such as interviews, focus group discussion, personal observation and retrieval of archival data. It was observed that apart from urbanization, problem of ownership of green space lands, low priority to green spaces, poor maintenance, enforcement of development controls, wastage of underpass spaces, and uncooperative attitudes of the general public, play a critical role in the destruction of urban green spaces. Therefore the paper narrows down to a point, that for a city to have a proper sustainable urban green space, broader city development plans are essential. Though rapid urbanization is an indicator of positive development, it is also accompanied by a host of challenges. Chennai lost a lot of greenery, as the city urbanized rapidly that led to a steep fall in vegetation cover. Environmental deterioration will be the big price we pay if Chennai continues to grow at the expense of greenery. Soaring skyscrapers, multistoried complexes, gated communities, and villas, frame the iconic skyline of today’s Chennai city which reveals that we overlook the importance of our green cover, which is important to balance our urban and lung spaces. Chennai, with a clumped landscape at the center of the city, is predicted to convert 36% of its total area into urban areas by 2026. One major issue is that a city designed and planned in isolation creates underused spaces all around the cities which are of negligence. These urban voids are dead, underused, unused spaces in the cities that are formed due to inefficient decision making, poor land management, and poor coordination. Urban voids have huge potential of creating a stronger urban fabric, exploited as public gathering spaces, pocket parks or plazas or just enhance public realm, rather than dumping of debris and encroachments. Flyovers need to justify their existence themselves by being more than just traffic and transport solutions. The vast, unused space below the Kathipara flyover is a case in point. This flyover connects three major routes: Tambaram, Koyambedu, and Adyar. This research will focus on the concept of urban voids, how these voids under the flyovers, can be used for place making process, how this space beneath flyovers which are neglected, can be a part of the urban realm through urban design and landscaping.

Keywords: landscape design, flyovers, public spaces, reclaiming lost spaces, urban voids

Procedia PDF Downloads 282

Authors: Kriti Jain, Sucha Singh Gill

Abstract:

Subsidies have been a major part of agricultural policies around the world, and more extensively since the green revolution in developing countries, for the sake of attaining higher agricultural productivity and achieving food security. But entrenched subsidies lead to distorted incentives and promote inefficiencies in the agricultural sector, threatening the viability of these very subsidies and sustainability of the agricultural production systems, posing a threat to the livelihood of farmers and laborers dependent on it. This paper analyzes the economic and ecological sustainability implications of prolonged input and output subsidies in agriculture by studying the case of Indian Punjab, an agriculturally developed state responsible for ensuring food security in the country when it was facing a major food crisis. The paper focuses specifically on the environmentally unsustainable cropping pattern changes as a result of Minimum Support Price (MSP) and assured procurement and on the resource use efficiency and cost implications of power subsidy for irrigation in Punjab. The study is based on an analysis of both secondary and primary data sources. Using secondary data, a time series analysis was done to capture the changes in Punjab’s cropping pattern, water table depth, fertilizer consumption, and electrification of agriculture. This has been done to examine the role of price and output support adopted to encourage the adoption of green revolution technology in changing the cropping structure of the state, resulting in increased input use intensities (especially groundwater and fertilizers), which harms the ecological balance and decreases factor productivity. Evaluation of electrification of Punjab agriculture helped evaluate the trend in electricity productivity of agriculture and how free power imposed further pressure on the extant agricultural ecosystem. Using data collected from a primary survey of 320 farmers in Punjab, the extent of wasteful application of groundwater irrigation, water productivity of output, electricity usage, and cost of irrigation driven electricity subsidy to the exchequer were estimated for the dominant cropping pattern amongst farmers. The main findings of the study revealed how because of a subsidy has driven agricultural framework, Punjab has lost area under agro climatically suitable and staple crops and moved towards a paddy-wheat cropping system, that is gnawing away the state’s natural resources like water table has been declining at a significant rate of 25 cms per year since 1975-76, and excessive and imbalanced fertilizer usage has led to declining soil fertility in the state. With electricity-driven tubewells as the major source of irrigation within a regime of free electricity and water-intensive crop cultivation, there is both wasteful application of irrigation water and electricity in the cultivation of paddy crops, burning an unproductive hole in the exchequer’s pocket. There is limited access to both agricultural extension services and water-conserving technology, along with policy imbalance, keeping farmers in an intensive and unsustainable production system. Punjab agriculture is witnessing diminishing returns to factor, which under the business-as-usual scenario, will soon enter the phase of negative returns to factor.

Keywords: cropping pattern, electrification, subsidy, sustainability

Procedia PDF Downloads 186

Authors: Ayla Hoeta

Abstract:

In a post-colonial Aotearoa New Zealand, solutions by rangatahi (youth) for rangatahi are essential as is civic participation and building economic agency in an increasingly tough economic climate. Upsouth was an online community crowdsourcing platform developed by The Southern Initiative, in collaboration with Itsnoon that provides rangatahi and whānau (family) a safe space to share lived experience, thoughts and ideas about local kaupapa (issues/topics) of importance to them. The target participants were Māori indigenous peoples and Pacifica groups, aged 14 - 21 years. In the Aotearoa New Zealand context, this participant group is not likely to engage in traditional consultation processes despite being an essential constituent in helping shape better local communities, whānau and futures. The Upsouth platform was active for two years from 2018-2019 where it completed 42 callups with 4300+ participants. The web platform collates the ideas, voices, feedback, and content of users around a callup that has been commissioned by a sponsor, such as Auckland Council, Z Energy or Auckland Transport. A callup may be about a pressing challenge in a community such as climate change, a new housing development, homelessness etc. Each callup was funded by the sponsor with Upsouths main point of difference being that participants are given koha (money donation) through digital wallets for their ideas. Depending on the quality of what participants upload, the koha varies between small micropayments and larger payments. This encouraged participants to develop creative and critical thinking - upskilling for future focussed jobs, enterprise and democratic skills while earning pocket money at the same time. Upsouth enables youth-led action and voice, and empowers them to be a part of a reciprocal and creative economy. Rangatahi are encouraged to express themselves culturally, creatively, freely and in a way they are free to choose - for example, spoken word, song, dance, video, drawings, and/or poems. This challenges and changes what is considered acceptable as community engagement feedback by the local government. Many traditional engagement platforms are not as consultative, do not accept diverse types of feedback, nor incentivise this valuable expression of feedback. Upsouth is also empowering for rangatahi, since it allows them the opportunity to express their opinions directly to the government. Upsouth gained national and international recognition for the way it engages with youth: winning the Supreme Award and the Accessibility and Transparency Award at Auckland Council’s 2018 Engagement Awards, becoming a finalist in the 2018 Digital Equity and Accessibility category of International Data Corporation’s Smart City Asia and Pacific Awards. This paper will fully contextualize the challenges of rangatahi and whānau civic engagement in Aotearoa New Zealand and then present a reflective case study of the Upsouth project, with examples from some of the callups. This is intended to form part of the Divided Cities 22 conference New Ground sub-theme as a critical reflection on a design intervention, which was conceived and implemented by the lead author to overcome the post-colonial divisions of Māori, Pacifica and minority ethnic rangatahi in Aotearoa New Zealand.

Keywords: rangatahi, youth empowerment, civic engagement, enabling, relating, digital platform, participation

Procedia PDF Downloads 81