Non-quantized minimum free energy in untranslated region exons

In an attempt to improve automated gene prediction in the untranslated region of a gene, we completed an in-depth analysis of the minimum free energy for 8,689 sub-genetic DNA sequences. We expanded Zhang's classification model and classified each sub-genetic sequence into one of 27 possible motifs. We calculated the minimum free energy for each motif to explore statistical features that correlate to biologically relevant sub-genetic sequences. If biologically relevant sub-genetic sequences fall into distinct free energy quanta it may be possible to characterize a motif based on its minimum free energy. Proper characterization of motifs can lead to greater understanding in automated genefinding, gene variability and the role DNA structure plays in gene network regulation.

Our analysis determined: (1) the average free energy value for exons, introns and other biologically relevant sub-genetic sequences, (2) that these subsequences do not exist in distinct energy quanta, (3) that introns exist however in a tightly coupled average minimum free energy quantum compared to all other biologically relevant sub-genetic sequence types, (4) that single exon genes demonstrate a higher stability than exons which span the entire coding sequence as part of a multi-exon gene and (5) that all motif types contain a free energy global minimum at approximately nucleotide position 1,000 before reaching a plateau. These results should be relevant to the biochemist and bioinformatician seeking to understand the relationship between sub-genetic sequences and the information behind them.

The application of Cd Se/ZnS quantum dots and confocal laser scanning microscopy for three-dimensional imaging of nanfibrous structures

This paper reports a fast, accurate, and non-destructive three-dimensional imaging approach based on using quantum dots and confocal laser scanning microscopy to get three-dimensional images of internal pore structure of the nanofibrous materials. A practical method of making the fiber fluorescent using quantum dots was applied before three-dimensional imaging by confocal laser scanning microscopy. Fibrous scaffolds with different porosity parameters produced by electrospinning and their three-dimensional pore structure was evaluated by this approach. Furthermore, the introduced approach can be used to measure the pore interconnectivity of the scaffold

Cross-strand disulfides in the non-hydrogen bonding site of antiparallel β-sheet (aCSDns): poised for biological switching

Forbidden disulfides are stressed disulfides found in recognisable protein contexts previously defined as structurally forbidden. The torsional strain of forbidden disulfides is typically higher than for structural disulfides, but not so high as to render them immediately susceptible to reduction under physionormal conditions. The meta-stability of forbidden disulfides makes them likely candidates as redox switches. Here we mined the Protein Data Bank for examples of the most common forbidden disulfide, the aCSDn. This is a canonical motif in which disulfide-bonded cysteine residues are positioned directly opposite each other on adjacent anti-parallel β-strands such that the backbone hydrogen bonded moieties are directed away from each other. We grouped these aCSDns into homologous clusters and performed an extensive physicochemical and informatic analysis of the examples found. We estimated their torsional energies using quantum chemical calculations and studied differences between the preferred conformations of the computational model and disulfides found in solved protein structures to understand the interaction between the forces imposed by the disulfide linkage and typical constraints of the surrounding β-sheet. In particular, we assessed the twisting, shearing and buckling of aCSDn-containing β-sheets, as well as the structural and energetic relaxation when hydrogen bonds in the motif are broken. We show the strong preference of aCSDns for the right-handed staple conformation likely arises from its compatibility with the twist, shear and Cα separation of canonical β-sheet. The disulfide can be accommodated with minimal distortion of the sheet, with almost all the strain present as torsional strain within the disulfide itself. For each aCSDn cluster, we summarise the structural and strain data, taxonomic conservation and any evidence of redox activity. aCSDns are known substrates of thioredoxin-like enzymes. This, together with their meta-stability, means they are ideally suited to biological switching roles and are likely to play important roles in the molecular pathways of oxidative stress.

Capacity building for post disaster construction and demolition waste management: a case of Sri Lanka

Purpose – The purpose of this paper is to present a theoretical framework for capacity building in post disaster construction and demolition (C&D) waste management at a national level to address the identified capacity gaps in managing disaster waste resulting from natural hazards.

Design/methodology/approach – Data were gathered through pilot interviews, case studies and expert opinion surveys representing government, non-government and other sector organisations involved in post disaster waste management.

Findings – The study revealed unavailability of a single point of responsibility and provision for disaster waste in existing policies and capacity constraints in prevailing peace time solid waste management practices which were identified as major capacity gaps. Establishment of a regulatory body and enforceable rules and regulations with necessary levels of capacities was identified and presented in a theoretical framework comprising of seven identified areas for capacity building in post disaster waste management.

Research limitations/implications – This study is limited to disaster C&D waste as debris generated from totally or partially damaged buildings and infrastructure as a direct impact of natural hazards or from demolished buildings and infrastructure at rehabilitation or early recovery stages. Waste generated during reconstruction phase of post disaster management cycle is not considered as disaster C&D waste for purposes of this study.

Originality/value – The research enabled analysis of existing capacities and presents approaches for capacity building for identified gaps in post disaster C&D waste management to attain sustainable post disaster waste management for future resilience.

Capacity gaps in post disaster construction & demolition waste management

Purpose – The purpose of this paper is to focus on the identification of the existing capacities of post disaster C&D waste management in developing countries, with a special emphasis on Sri Lanka to determine the capacity gaps and related influencing factors.

Design/methodology/approach – Multiple case studies and expert interviews were conducted to gather primary information on the existing capacities of disaster C&D waste management. Three case studies, including 15 individuals and six experts representing government, non-government institutions and others, were selected.

Findings – The results revealed the existing capacities, capacity gaps and influencing factors for post disaster C&D waste management in the areas of skills and confidence building, links and collaborations, continuity and sustainability, research and development, communication andcoordination, organisational implementation and investment in infrastructure.

Research limitations/implications – This study limited disaster C&D waste to debris generated from totally or partially damaged buildings and infrastructure as a direct impact of natural disasters orfrom demolished buildings and infrastructure at rehabilitation or at early recovery stages.

Originality/value – The research enabled an analysis of existing capacities and identified capacity gaps in post disaster C&D waste management with influencing factors developing countries.

Post disaster construction & demolition waste management: a Sri Lanka case study

The increasing nature of impacts from disasters has made post disaster management a key area of concern. The management of disaster waste is revealed as an area of least concern yet it presents momentous challenges for those with inadequate capacities due to the large volume and hazardous constituents created, specifically in developing countries. This paper aims to report the findings of post-disaster waste management strategies and challenges identified in Sri Lanka. Data was gathered through interviews with government and non-government organisations at national and local level. The lack of an established hierarchy and single point of responsibility, mandatory and enforceable rules and regulations; inadequate capacity and funds, and lack of communication and coordination were identified as gaps in post-disaster waste management. This enabled the identification of post-disaster waste management strategies, highlighting gaps that need to be addressed for effective C&D debris management for Sri Lanka’s future resilience.