Local Alignment Refinement Using Structural Assessment

Homology modeling is the most commonly used technique to build a three-dimensional model for a protein sequence. It heavily relies on the quality of the sequence alignment between the protein to model and related proteins with a known three dimensional structure. Alignment quality can be assessed according to the physico-chemical properties of the three dimensional models it produces

Towards an Effective Multi-Stakeholder Consultation Process: Applying the Imagine Method in Context of Abu Dhabi’s Education Policy

This paper is concerned with the many interleaving issues that emerge when engaging multiple stakeholders in decision-making. Whilst recognising the intrinsic value of group work and keeping in mind the numerous issues that obstruct group work (including multiple roles for participants, bias due to domination and distortion emerging from uneven group inputs), we applied the Imagine method to propose a new framework - the ‘Multiple Formation Consultation Framework’ (MFCF) - for organising effective multi-stakeholder consultations along the Policy Sciences Framework. Our proposed framework was applied in the context of education policy in the Emirate of Abu Dhabi, where 24 small group formations were tasked and assessed in a systemic manner. Evidence from the exercise suggests that: (1) when moving participants from heterogeneous to homogenous groups, the working of the groups became more focused and the outcomes gained greater clarity in terms of the thinking of group members. (2) Yet, when groups moved from homogenous formations to heterogeneous, they became more inquisitive and explored broader aspects of the tasks at hand. (3) A repeat of the process over two-day period where different members of the groups experience both homogenous and heterogeneous formations back and forth (in order to capture the unique value emerging from each composition) have led to more efficient and effective working and outcomes of the groups

Genetic Structure in the Seabuckthorn Carpenter Moth (Holcocerus hippophaecolus) in China: The Role of Outbreak Events, Geographical and Host Factors

Understanding factors responsible for structuring genetic diversity is of fundamental importance in evolutionary biology. The seabuckthorn carpenter moth (Holcocerus hippophaecolus Hua) is a native species throughout the north of China and is considered the main threat to seabuckthorn, Hippophae rhamnoides L. We assessed the influence of outbreaks, environmental factors and host species in shaping the genetic variation and structure of H. hippophaecolus by using Amplified Fragment Length Polymorphism (AFLP) markers. We rejected the hypothesis that outbreak-associated genetic divergence exist, as evidenced by genetic clusters containing a combination of populations from historical outbreak areas, as well as non-outbreak areas. Although a small number of markers (4 of 933 loci) were identified as candidates under selection in response to population densities. H. hippophaecolus also did not follow an isolation-by-distance pattern. We rejected the hypothesis that outbreak and drought events were driving the genetic structure of H. hippophaecolus. Rather, the genetic structure appears to be influenced by various confounding bio-geographical factors. There were detectable genetic differences between H. hippophaecolus occupying different host trees from within the same geographic location. Host-associated genetic divergence should be confirmed by further investigation

Calcite-accumulating large sulfur bacteria of the genus Achromatium in Sippewissett Salt Marsh

Large sulfur bacteria of the genus Achromatium are exceptional among Bacteria and Archaea as they can accumulate high amounts of internal calcite. Although known for more than 100 years, they remain uncultured, and only freshwater populations have been studied so far. Here we investigate a marine population of calcite-accumulating bacteria that is primarily found at the sediment surface of tide pools in a salt marsh, where high sulfide concentrations meet oversaturated oxygen concentrations during the day. Dynamic sulfur cycling by phototrophic sulfide-oxidizing and heterotrophic sulfate-reducing bacteria co-occurring in these sediments creates a highly sulfidic environment that we propose induces behavioral differences in the Achromatium population compared with reported migration patterns in a low-sulfide environment. Fluctuating intracellular calcium/sulfur ratios at different depths and times of day indicate a biochemical reaction of the salt marsh Achromatium to diurnal changes in sedimentary redox conditions. We correlate this calcite dynamic with new evidence regarding its formation/mobilization and suggest general implications as well as a possible biological function of calcite accumulation in large bacteria in the sediment environment that is governed by gradients. Finally, we propose a new taxonomic classification of the salt marsh Achromatium based on their adaptation to a significantly different habitat than their freshwater relatives, as indicated by their differential behavior as well as phylogenetic distance on 16S ribosomal RNA gene level. In future studies, whole-genome characterization and additional ecophysiological factors could further support the distinctive position of salt marsh Achromatium

Long-term Results of Rectal Cancer Surgery with a Systematical Operative Approach

Surgical oncolog