Measurement of AhR Ligands in the Tissues of Colon Cancer Patients with XRE Luciferase Reporter

The Aryl hydrocarbon receptor (AhR) ligands exhibiting modulating activity represents a new class of anticancer agents that can be directed towards several tumors. We have examined AhR expression in human colon cancer and adjacent non-tumor tissue. AhR expression level was about 2-7 times higher in tumor tissue samples than in the adjacent non-tumor samples (in 82% of all the samples). We were unable to find any increase of ABCG2 expression on the level of the transcription, while the expression of MDR2 was increased in half of the tumors compared to the levels of expression in normal adjacent tissue. We have used FICZ as a potent high affinity ligand of the AhR to calibrate the reporter cell line HEK293T-AhR-luc as a potent high affinity ligand of the AhR. The concentration of xenobiotic response element (XRE) ligands is higher, than in the blood of healthy people in 86% of the patients. The proposed test system will allow the use of the AhR ligand level as an additional diagnostic marker in the treatment of colon cancer

Isolation and Characterization of Human Colon Adenocarcinoma Stem-Like Cells Based on the Endogenous Expression of the Stem Markers.

BACKGROUND: Cancer stem cells\u27 (CSCs) self-maintenance is regulated via the pluripotency pathways promoting the most aggressive tumor phenotype. This study aimed to use the activity of these pathways for the CSCs\u27 subpopulation enrichment and separating cells characterized by the OCT4 and SOX2 expression. METHODS: To select and analyze CSCs, we used the SORE6x lentiviral reporter plasmid for viral transduction of colon adenocarcinoma cells. Additionally, we assessed cell chemoresistance, clonogenic, invasive and migratory activity and the data of mRNA-seq and intrinsic disorder predisposition protein analysis (IDPPA). RESULTS: We obtained the line of CSC-like cells selected on the basis of the expression of the OCT4 and SOX2 stem cell factors. The enriched CSC-like subpopulation had increased chemoresistance as well as clonogenic and migration activities. The bioinformatic analysis of mRNA seq data identified the up-regulation of pluripotency, development, drug resistance and phototransduction pathways, and the downregulation of pathways related to proliferation, cell cycle, aging, and differentiation. IDPPA indicated that CSC-like cells are predisposed to increased intrinsic protein disorder. CONCLUSION: The use of the SORE6x reporter construct for CSCs enrichment allows us to obtain CSC-like population that can be used as a model to search for the new prognostic factors and potential therapeutic targets for colon cancer treatment

High-Throughput Sequencing of Six Bamboo Chloroplast Genomes: Phylogenetic Implications for Temperate Woody Bamboos (Poaceae: Bambusoideae)

BACKGROUND: Bambusoideae is the only subfamily that contains woody members in the grass family, Poaceae. In phylogenetic analyses, Bambusoideae, Pooideae and Ehrhartoideae formed the BEP clade, yet the internal relationships of this clade are controversial. The distinctive life history (infrequent flowering and predominance of asexual reproduction) of woody bamboos makes them an interesting but taxonomically difficult group. Phylogenetic analyses based on large DNA fragments could only provide a moderate resolution of woody bamboo relationships, although a robust phylogenetic tree is needed to elucidate their evolutionary history. Phylogenomics is an alternative choice for resolving difficult phylogenies. METHODOLOGY/PRINCIPAL FINDINGS: Here we present the complete nucleotide sequences of six woody bamboo chloroplast (cp) genomes using Illumina sequencing. These genomes are similar to those of other grasses and rather conservative in evolution. We constructed a phylogeny of Poaceae from 24 complete cp genomes including 21 grass species. Within the BEP clade, we found strong support for a sister relationship between Bambusoideae and Pooideae. In a substantial improvement over prior studies, all six nodes within Bambusoideae were supported with ≥0.95 posterior probability from Bayesian inference and 5/6 nodes resolved with 100% bootstrap support in maximum parsimony and maximum likelihood analyses. We found that repeats in the cp genome could provide phylogenetic information, while caution is needed when using indels in phylogenetic analyses based on few selected genes. We also identified relatively rapidly evolving cp genome regions that have the potential to be used for further phylogenetic study in Bambusoideae. CONCLUSIONS/SIGNIFICANCE: The cp genome of Bambusoideae evolved slowly, and phylogenomics based on whole cp genome could be used to resolve major relationships within the subfamily. The difficulty in resolving the diversification among three clades of temperate woody bamboos, even with complete cp genome sequences, suggests that these lineages may have diverged very rapidly

Key environmental determinants of global and regional richness and endemism patterns for a wild bee subfamily

10.1007/s10531-017-1432-7Biodiversity and Conservation272287-30

Inferring diversity patterns along an elevation gradient from stacked SDMs: A case study on Mesoamerican ferns

An enduring challenge in ecology is to characterise and understand species richness patterns in tropical regions. Species richness maps produced by stacking species distribution model (SDM) range maps could prove useful in this regard, but little attention has been given to this approach. Here we generate a species richness map by stacking the ranges of 86 Mesoamerican fern species modelled by MaxEnt from field data collected by the Sampled Red List Index for Plants project. Predicted species richness showed a hump-backed relationship with elevation, peaking at mid-elevation (1800–2000 m). A remarkably similar pattern was observed in a field survey conducted to validate the approach. Predicted species richness was also low in sites with high water deficits, as previously shown in the fern literature. Beta-diversity in the lowlands was greatest between sites with strongly contrasting water deficits, further emphasising the importance of this environmental variable. The stacked SDM approach was thus able to reproduce broad biogeographical patterns of species richness, despite many of the fern species being represented by fewer than 20 samples.Microsoft Researc

Inferring diversity patterns along an elevation gradient from stacked SDMs: A case study on Mesoamerican ferns

An enduring challenge in ecology is to characterise and understand species richness patterns in tropical regions. Species richness maps produced by stacking species distribution model (SDM) range maps could prove useful in this regard, but little attention has been given to this approach. Here we generate a species richness map by stacking the ranges of 86 Mesoamerican fern species modelled by MaxEnt from field data collected by the Sampled Red List Index for Plants project. Predicted species richness showed a hump-backed relationship with elevation, peaking at mid-elevation (1800–2000 m). A remarkably similar pattern was observed in a field survey conducted to validate the approach. Predicted species richness was also low in sites with high water deficits, as previously shown in the fern literature. Beta-diversity in the lowlands was greatest between sites with strongly contrasting water deficits, further emphasising the importance of this environmental variable. The stacked SDM approach was thus able to reproduce broad biogeographical patterns of species richness, despite many of the fern species being represented by fewer than 20 samples.Microsoft Researc

Economics and Employment Generation of Bamboo-Based Enterprises: A Case Study from Eastern Bangladesh

In the last decade non-timber forest products (NTFPs) and their associated goods have received much attention from researchers and development workers for their perceived socio-economic importance and potential, particularly in developing countries. It has been increasingly recognized that promoting the use, production and sustainable harvesting of such kinds of products could also contribute to forest conservation in the long run. However, since the development process has progressed in most regions, alternatives or substitutes of such products have become available on the markets, and it will be difficult for these nature-based products to exist without additional product values. A market survey was conducted in an urban fringe of north-eastern Bangladesh to investigate NTFP-based product diversity, and marketing patterns and challenges. Further information was collected from sellers and consumers to understand their views on probable future strategies to sustain the markets of these products. A total of 38 NTFP and NTFP-based secondary products were recorded from 25 NTFP shops, including 16 permanent, 7 temporary (or semi-permanent) and 2 mobile shops. The greatest demand was observed for bamboo and cane-based products, for which supply suffered due to the scarcity of raw materials. A decreasing trend in the consumption of NTFP-based articles for urban domestic use was also reported from the sellers. To cope with the competitive markets, sellers were found to place more emphasis on creative marketing, durability and appearance of their products. The study concluded that active government support is needed for the sustenance of this industry in a changing global perspective. This could be in the form of technical advancement in the production process, improvement of existing product supply chains and skill development of the workers which will not only secure the future of these products but also provide an essential means for the survival of this industry and for thousands of people living from it. © 2010 Steve Harrison, John Herbohn