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Doolittle W.F.,Dalhousie University | Zhaxybayeva O.,Environmental Proteomics NB Inc.
BioScience | Year: 2010

Metagenomics is a complex of research methodologies aimed at characterizing microbial communities and cataloging microbial diversity and distribution without isolating or culturing organisms. This approach will unavoidably engender new ways of thinking about microbial ecology that supplant the concept of "species." This concept-thanks to comparative-genomicshas in any case become increasingly unsustainable, either as a way of binning diversity or as a biological reality. Communities will become the units of evolutionary and ecological study. Although metagenomic methods will increasingly find uses in protistology and mycology, the emphasis so far has been, and our focus here will be, on prokaryotes (bacteria and archaea). © 2010 by American Institute of Biological Sciences.

Tuorto S.J.,Rutgers University | Brown C.M.,Environmental Proteomics NB Inc. | Bidle K.D.,Rutgers University | McGuinness L.R.,Rutgers University | Kerkhof L.J.,Rutgers University
PLoS ONE | Year: 2015

This report describes BioDry (patent pending), a method for reliably preserving the biomolecules associated with aquatic microbial biomass samples, without the need of hazardous materials (e.g. liquid nitrogen, preservatives, etc.), freezing, or bulky storage/sampling equipment. Gel electrophoresis analysis of nucleic acid extracts from samples treated in the lab with the BioDry method indicated that molecular integrity was protected in samples stored at room temperature for up to 30 days. Analysis of 16S/18S rRNA genes for presence/ absence and relative abundance of microorganisms using both 454-pyrosequencing and TRFLP profiling revealed statistically indistinguishable communities from control samples that were frozen in liquid nitrogen immediately after collection. Seawater and river water biomass samples collected with a portable BioDry "field unit", constructed from off-the-shelf materials and a battery-operated pumping system, also displayed high levels of community rRNA preservation, despite a slight decrease in nucleic acid recovery over the course of storage for 30 days. Functional mRNA and protein pools from the field samples were also effectively conserved with BioDry, as assessed by respective RT-PCR amplification and western blot of ribulose-1-5-bisphosphate carboxylase/oxygenase. Collectively, these results demonstrate that BioDry can adequately preserve a suite of biomolecules from aquatic biomass at ambient temperatures for up to a month, giving it great potential for high resolution sampling in remote locations or on autonomous platforms where space and power are limited. © 2015 Tuorto et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Hossain Z.,Agriculture and Agri Food Canada | Hossain Z.,Environmental Proteomics NB Inc. | Amyot L.,Agriculture and Agri Food Canada | McGarvey B.,Agriculture and Agri Food Canada | And 6 more authors.
PLoS ONE | Year: 2012

The eukaryotic translation elongation factor eEF-1Bβ1 (EF1Bβ) is a guanine nucleotide exchange factor that plays an important role in translation elongation. In this study, we show that the EF1Bβ protein is localized in the plasma membrane and cytoplasm, and that the transcripts should be expressed in most tissue types in seedlings. Sectioning of the inflorescence stem revealed that EF1Bβ predominantly localizes to the xylem vessels and in the interfascicular cambium. EF1Bβ gene silencing in efβ caused a dwarf phenotype with 38% and 20% reduction in total lignin and crystalline cellulose, respectively. This loss-of-function mutant also had a lower S/G lignin monomer ratio relative to wild type plants, but no changes were detected in a gain-of-function mutant transformed with the EF1Bβ gene. Histochemical analysis showed a reduced vascular apparatus, including smaller xylem vessels in the inflorescence stem of the loss-of-function mutant. Over-expression of EF1Bβ in an eli1 mutant background restored a WT phenotype and abolished ectopic lignin deposition as well as cell expansion defects in the mutant. Taken together, these data strongly suggest a role for EF1Bβ in plant development and cell wall formation in Arabidopsis. © 2012 Hossain et al.

Hannoufa A.,Agriculture and Agri Food Canada | Hossain Z.,Environmental Proteomics NB Inc.
Biocatalysis and Agricultural Biotechnology | Year: 2012

Carotenoids are plant secondary metabolites with a range of beneficial physiological, health and industrial traits. In this review, we summarize the carotenoid biosynthesis pathway and provide an update on research into its regulation in plants. We discuss some factors that determine the steady-state levels of carotenoids in different plant organs and tissues. These factors include the flux through the biosynthesis pathway, and how certain steps represent rate-limiting (bottlenecks), that were exploited in the metabolic engineering of carotenoids. In addition, we discuss carotenoid catabolism, storage and sequestration, and transcriptional and epigenetic regulation as factors affecting the rate of carotenoid accumulation. © 2012.

Campbell D.A.,Mount Allison University | Hossain Z.,Environmental Proteomics NB Inc. | Cockshutt A.M.,Mount Allison University | Cockshutt A.M.,Environmental Proteomics NB Inc. | And 6 more authors.
Photosynthesis Research | Year: 2013

All oxygenic photoautotrophs suffer photoinactivation of their Photosystem II complexes, at a rate driven by the instantaneous light level. To maintain photosynthesis, PsbA subunits are proteolytically removed from photoinactivated Photosystem II complexes, primarily by a membrane-bound FtsH protease. Diatoms thrive in environments with fluctuating light, such as coastal regions, in part because they enjoy a low susceptibility to photoinactivation of Photosystem II. In a coastal strain of the diatom Thalassiosira pseudonana growing across a range of light levels, active Photosystem II represents only about 42 % of the total Photosystem II protein, with the remainder attributable to photoinactivated Photosystem II awaiting recycling. The rate constant for removal of PsbA protein increases with growth light, in parallel with an increasing content of the FtsH protease relative to the substrate PsbA. An offshore strain of Thalassiosira pseudonana, originating from a more stable light environment, had a lower content of FtsH and slower rate constants for removal of PsbA. We used this data to generate the first estimates for in vivo proteolytic degradation of photoinactivated PsbA per FtsH6 protease, at ∼3.9 × 10-2 s-1, which proved consistent across growth lights and across the onshore and offshore strains. © 2013 Springer Science+Business Media Dordrecht.

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