Dataset Information

Isolation of a thioesterase gene from the metagenome of a mountain peak, Apharwat, in the northwestern Himalayas.

ABSTRACT: The soil metagenome of Apharwat (latitude 34.209° and longitude 74.368°) was explored for the presence of esterase encoding genes using a cultivation-independent approach, metagenomics. Among the various protocols tested, the method developed by Wechter was found to be the best for metagenome isolation from the soil under investigation. The purity of the isolated metagenomic DNA was not suitable for gene cloning. To improve the yield and purity of isolated metagenomic DNA, isothermal amplification of the isolated metagenomic DNA using phi (?) polymerase in a strand displacement technique was performed. The amplified DNA was comparatively pure and the yield increased 50-fold. A metagenomic library was constructed in Escherichia coli (DH5?) using pUC19 as a vector with an average insert size ranging between 2 and 5 kb. Out of 10,000 clones generated, one clone carrying a ~1,870-bp insert hydrolysed tributyrin, indicating esterase activity. Sequence analysis revealed that the insert harboured three open reading frames (ORFs), of which ORF 3 encoded the esterase. Open reading frame 3 comprises 1,178 bp and encodes a putative 392 amino acid protein whose size correlates with most of the bacterial esterases. The esterase isolated in the present study is suggested to be a 4-methyl-3-oxoadipyl-CoA thioesterase (Accession No. JN717164.1), as it shows 60 % sequence similarity to the thioesterase gene of Pseudomonas reinekei (Accession No. ACZ63623.1) by BLAST, ClustalX and ClustalW analysis.

SUBMITTER: Sudan AK

PROVIDER: S-EPMC3563745 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:One of the main goals of ecological studies is to disentangle the dynamics that underlie the spatiotemporal distribution of biodiversity and further functions of the ecosystem. However, due to many ecological and geopolitical reasons, many remote areas with high plant species diversity have not been assessed using newly based analytical approaches for vegetation characterization. Here, we classified and characterized different vegetation types (i.e., major plant communities) based on indicator species and on the influence of different environmental gradients in the Himalayan mixed coniferous forest, Pakistan. For that, we addressed the following questions: Does the vegetation composition of the Himalayan mixed coniferous forest correlate with climatic, topographic, geographic, and edaphic variables? Is it possible to identify plant communities through indicator species in relation to environmental gradients using multivariate approaches? Can this multivariate be helpful for conservation planning? During four consecutive years we assessed the vegetation composition and environmental variables (21 variables divided in geographic, climatic, topographic, and edaphic groups) of 156 50 m-trasects between an elevation of 2000-4000 m. Using newly based analytical approaches for community characterization, we found a total of 218 plant species clustered into four plant communities with the influence of environmental gradients. The highest index of similarity was recorded between Pinus-Cedrus-Viburnum (PCV) and Viburnum-Pinus-Abies (VPA) communities, and the highest index of dissimilarity was recorded between PCV and Abies-Juniperus-Picea (AJP) communities. Among these four communities, highest number of plant species (156 species) was recorded in PCV, maximum alpha diversity (H' = 3.68) was reported in VPA, highest Simpson index (0.961) and Pielou's evenness (0.862) were reported in VPA and AJP. The edaphic gradients (i.e., organic matter, phosphorous, pH and soil texture) and climatic factors (temperature, humidity) were the strongest environmental gradients that were responsible for structuring and hosting the diverse plant communities in mixed coniferous forest. Finally, the Himalayan mixed coniferous structure is more influenced by the spatial turnover beta-diversity process (βsim) than by the species loss (nestedness-resultant, βsne). Our analysis of the vegetation structure along the environmental gradient in the Himalayan mixed coniferous forest supported by sophisticated analytical approaches reveled indicator species groups, which are associated to specific microclimatic zones (i.e., vegetation communities). Within this focus, we side with the view that these results can support conservation planning and management for similar and different areas providing mitigating and preventive measures to reduce potential negative impacts, such as anthropic and climatic.

Project description:Working equids play a central role in mountainous communities, but their work often goes unnoticed by the wider world, with sparse documentation of their role, value, or welfare - a state which often extends to their human counterparts. Communities living in the remote Manaslu Valley, Nepal, face a number of uncertainties, including extreme weather events due to the seasonal monsoon and, more recently, the construction of a new road network. Using semi-structured interviews, questionnaires, and Equine Assessment Research and Scoping (EARS) welfare assessments, we outline the specific role of pack mules in supporting the lives of local people, explain the nuanced links between human experience and mule welfare, and gain insight into how people living in this volatile environment manage uncertainty and risk. Mule work was felt to be the 'only option' for a sustainable livelihood for most mule owners although, in some cases, mules had enabled respondents to diversify their income. Mule owners with more husbandry experience did not own mules in more positive behavioural states, which may suggest a lack of generational knowledge and support networks. Short-term ongoing risks, such as the monsoon or unstable tracks, had a larger impact both financially and emotionally than the long-term but distant implications of the road construction. Mule owners must constantly balance the risk of working during the monsoon season, when conditions are treacherous but pay was higher, with losing valuable income but keeping themselves and their mules safe; they do, however, have a more mobile option for employment than non-owners. Mules enable a level of resilience and agility for communities living with constant uncertainty and change, which is only beginning to be recognised formally within the sustainable development sphere. Integration of animal welfare into the SDGs would allow humanitarian aid initiatives to strengthen support networks around working equids, which would greatly benefit the mules and humans alike.

Dataset Information

Isolation of a thioesterase gene from the metagenome of a mountain peak, Apharwat, in the northwestern Himalayas.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets