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1.
Salt drying: a low-cost, simple and efficient method for storing plants in the field and preserving biological repositories for DNA diversity research.
Carrió, E, Rosselló, JA
Molecular ecology resources. 2014;(2):344-51
Abstract
Although a variety of methods have been optimized for the collection and storage of plant specimens, most of these are not suited for field expeditions for a variety of logistic reasons. Drying specimens with silica gel in polyethylene bags is currently the standard for field-sampling methods that are suitable for subsequent DNA extraction. However, silica-gel repositories are not readily available in remote areas, and its use is not very cost-effective for the long-term storage of collections or in developing countries with limited research budgets. Salting is an ancient and traditional drying process that preserves food samples by dehydrating tissues and inhibiting water-dependent cellular metabolism. We compared salt and silica-gel drying methods with respect to dehydration rates overtime, DNA quality and polymerase chain reaction(PCR) success to assess whether dry salting can be used as an effective plant preservation method for DNA analysis. Specimens from eleven plant species covering a variety of leaf structures, leaf thicknesses and water contents were analysed. Experimental work indicated that (i) levels of dehydration in sodium chloride were usually comparable to those obtained when silica gel was used, (ii) no spoilage, fungal or bacterial growth was observed for any of the species with all drying treatments and (iii) good yields of quality genomic DNA suitable for PCR applications were obtained in the salt-drying treatments. The preservation of plant tissues in commercial table salt appears to be a satisfactory, and versatile method that may be suitable in remote areas where cryogenic resources and silica repositories are not available.
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2.
Genome-wide comparative analysis of tonoplast intrinsic protein (TIP) genes in plants.
Regon, P, Panda, P, Kshetrimayum, E, Panda, SK
Functional & integrative genomics. 2014;(4):617-29
Abstract
Tonoplast intrinsic proteins (TIPs) play a vital role in water transport across membranes. In the present study, we performed a comparative analysis of TIP genes in ten plant species including both monocots and dicots. A total of 100 TIP aquaporin genes were identified, and their relationships among the plant species were analyzed. Phylogenetic analysis was performed to evaluate the relationship of these genes within the plant species. Based on the phylogenetic analysis results, TIPs were classified into five distinct arbitrary groups (group I to group V), which represented TIP2, TIP5, TIP4, TIP1, and TIP3, respectively. Group I represented the largest arbitrary group, followed by group IV, in the phylogenetic tree. The result clearly indicates that TIP2 and TIP1 are abundant aquaporins and highly related among the species. In the present review, a comparative study of gene structure analysis between dicots and monocots has been performed to analyze their structural variation. Most of the predicted motifs are conserved among the species, signifying an evolutionary relationship. The gene expression analysis indicated that the expression of TIP genes varies during different developmental stages and also during stressed conditions. The results indicated a great degree of evolutionary relationship and variation in the expression levels of TIPs in plants.
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3.
A review of starch-branching enzymes and their role in amylopectin biosynthesis.
Tetlow, IJ, Emes, MJ
IUBMB life. 2014;(8):546-58
Abstract
Starch-branching enzymes (SBEs) are one of the four major enzyme classes involved in starch biosynthesis in plants and algae, and their activities play a crucial role in determining the structure and physical properties of starch granules. SBEs generate α-1,6-branch linkages in α-glucans through cleavage of internal α-1,4 bonds and transfer of the released reducing ends to C-6 hydroxyls. Starch biosynthesis in plants and algae requires multiple isoforms of SBEs and is distinct from glycogen biosynthesis in both prokaryotes and eukaryotes which uses a single branching enzyme (BE) isoform. One of the unique characteristics of starch structure is the grouping of α-1,6-branch points in clusters within amylopectin. This is a feature of SBEs and their interplay with other starch biosynthetic enzymes, thus facilitating formation of the compact water-insoluble semicrystalline starch granule. In this respect, the activity of SBE isoforms is pivotal in starch granule assembly. SBEs are structurally related to the α-amylase superfamily of enzymes, sharing three domains of secondary structure with prokaryotic Bes: the central (β/α)8 -barrel catalytic domain, an NH2 -terminal domain involved in determining the size of α-glucan chain transferred, and the C-terminal domain responsible for catalytic capacity and substrate preference. In addition, SBEs have conserved plant-specific domains, including phosphorylation sites which are thought to be involved in regulating starch metabolism. SBEs form heteromeric protein complexes with other SBE isoforms as well as other enzymes involved in starch synthesis, and assembly of these protein complexes is regulated by protein phosphorylation. Phosphorylated SBEIIb is found in multienzyme complexes with isoforms of glucan-elongating starch synthases, and these protein complexes are implicated in amylopectin cluster formation. This review presents a comparative overview of plant SBEs and includes a review of their properties, structural and functional characteristics, and recent developments on their post-translational regulation.
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4.
Relationships between fatty acid composition and bile tolerance in lactobacillus isolates from plants and from non-plant materials.
Kimoto-Nira, H, Suzuki, S, Yakabe, T, Suzuki, C
Canadian journal of microbiology. 2012;(12):1396-404
Abstract
Twenty plant-derived and 18 non-plant-derived strains of Lactobacillus casei were compared for their growth in tryptone - yeast extract - glucose broth containing 0.3% bile by measuring absorbance at a wavelength of 620 nm after 24 h of incubation at 37 °C. Bile tolerance - a fundamental probiotic property - was calculated by dividing the experimental data by control values (growth without bile). We found that bile tolerance was strain specific but that the average bile tolerance of the plant-derived strains was significantly (P < 0.05) lower than that of the non-plant-derived strains tested. All tested strains could not deconjugate sodium taurocholate, indicating that the difference in bile tolerance was not due to the ability to deconjugate bile. The fatty acid compositions of the test strains with and without exposure to 0.3% bile were investigated, and a statistical correlation analysis between these compositions and their bile tolerance was conducted. The fatty acids correlated with bile tolerance differed between plant and non-plant lactobacilli. This is the first report to show that the origin (i.e., growth environment) of lactobacilli affects their fatty acid composition, which in turn, appears to be related to their bile tolerance.
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5.
Evolutionary and comparative analysis of MYB and bHLH plant transcription factors.
Feller, A, Machemer, K, Braun, EL, Grotewold, E
The Plant journal : for cell and molecular biology. 2011;(1):94-116
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Abstract
The expansion of gene families encoding regulatory proteins is typically associated with the increase in complexity characteristic of multi-cellular organisms. The MYB and basic helix-loop-helix (bHLH) families provide excellent examples of how gene duplication and divergence within particular groups of transcription factors are associated with, if not driven by, the morphological and metabolic diversity that characterize the higher plants. These gene families expanded dramatically in higher plants; for example, there are approximately 339 and 162 MYB and bHLH genes, respectively, in Arabidopsis, and approximately 230 and 111, respectively, in rice. In contrast, the Chlamydomonas genome has only 38 MYB genes and eight bHLH genes. In this review, we compare the MYB and bHLH gene families from structural, evolutionary and functional perspectives. The knowledge acquired on the role of many of these factors in Arabidopsis provides an excellent reference to explore sequence-function relationships in crops and other plants. The physical interaction and regulatory synergy between particular sub-classes of MYB and bHLH factors is perhaps one of the best examples of combinatorial plant gene regulation. However, members of the MYB and bHLH families also interact with a number of other regulatory proteins, forming complexes that either activate or repress the expression of sets of target genes that are increasingly being identified through a diversity of high-throughput genomic approaches. The next few years are likely to witness an increasing understanding of the extent to which conserved transcription factors participate at similar positions in gene regulatory networks across plant species.
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6.
Model evaluation of the phytoextraction potential of heavy metal hyperaccumulators and non-hyperaccumulators.
Liang, HM, Lin, TH, Chiou, JM, Yeh, KC
Environmental pollution (Barking, Essex : 1987). 2009;(6):1945-52
Abstract
Evaluation of the remediation ability of zinc/cadmium in hyper- and non-hyperaccumulator plant species through greenhouse studies is limited. To bridge the gap between greenhouse studies and field applications for phytoextraction, we used published data to examine the partitioning of heavy metals between plants and soil (defined as the bioconcentration factor). We compared the remediation ability of the Zn/Cd hyperaccumulators Thlaspi caerulescens and Arabidopsis halleri and the non-hyperaccumulators Nicotiana tabacum and Brassica juncea using a hierarchical linear model (HLM). A recursive algorithm was then used to evaluate how many harvest cycles were required to clean a contaminated site to meet Taiwan Environmental Protection Agency regulations. Despite the high bioconcentration factor of both hyperaccumulators, metal removal was still limited because of the plants' small biomass. Simulation with N. tabacum and the Cadmium model suggests further study and development of plants with high biomass and improved phytoextraction potential for use in environmental cleanup.
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Structures and functions of the extrinsic proteins of photosystem II from different species.
Enami, I, Okumura, A, Nagao, R, Suzuki, T, Iwai, M, Shen, JR
Photosynthesis research. 2008;(1-3):349-63
Abstract
This minireview presents a summary of information available on the variety and binding properties of extrinsic proteins that form the oxygen-evolving complex of photosystem II (PSII) of cyanobacteria, red alga, diatom, green alga, euglena, and higher plants. In addition, the structure and function of extrinsic PsbO, PsbV, and PsbU proteins are summarized based on the crystal structure of thermophilic cyanobacterial PSII together with biochemical and genetic studies from various organisms.
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8.
Seasonal variability of dry matter content and its relationship with shoot growth and nonstructural carbohydrates.
Palacio, S, Milla, R, Albuixech, J, Pérez-Rontomé, C, Camarero, JJ, Maestro, M, Montserrat-Martí, G
The New phytologist. 2008;(1):133-142
Abstract
This study assesses how different phases of shoot growth underlie seasonal change in leaf and stem dry matter content (LDMC and SDMC, respectively) of 12 woody Mediterranean species. The relationship between LDMC and nonstructural carbohydrate (NSC) concentrations is also explored and the seasonal vs interspecies variability of LDMC compared. LDMC, SDMC and shoot elongation rate (SER) were measured on a monthly basis for a minimum of 12 months. Bud growth rate (BGR) and NSC concentrations were also assessed in several of the study species. LDMC and SDMC decreased during shoot elongation in spring and increased in summer, showing a significant negative correlation with SER, but were unrelated to BGR. Half of the species analysed showed a positive relationship between LDMC and NSC. Seasonal fluctuations of LDMC within species were higher than interspecies differences, and species ranking was significantly affected by the month of sampling, except during winter months. Seasonal changes in LDMC and SDMC are mainly related to shoot elongation phenology, and NSC sink-source relationships between old and growing organs can explain this relationship in some species. Owing to the high seasonal variability in LDMC, it is recommended that samples for comparative purposes should be collected as close to the winter as possible.
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9.
Are plant populations seed limited? A critique and meta-analysis of seed addition experiments.
Clark, CJ, Poulsen, JR, Levey, DJ, Osenberg, CW
The American naturalist. 2007;(1):128-42
Abstract
We examine the relative importance of processes that underlie plant population abundance and distribution. Two opposing views dominate the field. One posits that the ability to establish at a site is determined by the availability of suitable microsites (establishment limitation), while the second asserts that recruitment is limited by the availability of seeds (seed limitation). An underlying problem is that establishment and seed limitation are typically viewed as mutually exclusive. We conducted a meta-analysis of seed addition experiments to assess the relative strength of establishment and seed limitation to seedling recruitment. We asked (1) To what degree are populations seed and establishment limited? (2) Under what conditions (e.g., habitats and life-history traits) are species more or less limited by each? (3) How can seed addition studies be better designed to enhance our understanding of plant recruitment? We found that, in keeping with previous studies, most species are seed limited. However, the effects of seed addition are typically small, and most added seeds fail to recruit to the seedling stage. As a result, establishment limitation is stronger than seed limitation. Seed limitation was greater for large-seeded species, species in disturbed microsites, and species with relatively short-lived seed banks. Most seed addition experiments cannot assess the relationship between number of seeds added and number of subsequent recruits. This shortcoming can be overcome by increasing the number and range of seed addition treatments.
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10.
Growth of plants on TBT-contaminated harbour sludge and effect on TBT removal.
Novak, J, Trapp, S
Environmental science and pollution research international. 2005;(6):332-41
Abstract
BACKGROUND Worldwide, large amounts of sediments have to be dredged annually from waterways and harbours. These sediments are sometimes polluted with a variety of toxic compounds. In some countries, including Belgium, the load with the biocide tributyltin (TBT) from ship coatings prohibits the dumping of harbour sludge into the sea. Land-based dumping is a commonly used alternative. OBJECTIVE This research investigated the feasibility to use land-deposited harbour sludge for plant production. In a field trial, the growth of 38 more or less salt-tolerant plant species on low and high TBT-contaminated sediments was studied. The elimination of TBT from sludge with and without vegetation was compared. The uptake of TBT and its degradation products di- and monobutyltin (DBT and MBT) into harvest products under field conditions was determined. EXPERIMENTAL SET-UP: Sediments dredged in May 2003 from the brackish waters of the port of Antwerp were analysed in the laboratory for soil texture, pH, electroconductivity, sodium, magnesium, potassium, calcium, ammonium, nitrate, total nitrogen, chloride, sulphur and the organotins TBT, DBT and MBT. The sediments were lagooned for one year to dewater, desalinate and improve their structure. Salt-tolerant domestic and wild plants were selected and sown in May 2004. In August 2004, plants were harvested and the produced biomass was determined. Samples were taken from vegetated and non-vegetated top and bottom sediments and from plants growing above soil and analysed for TBT, DBT and MBT. RESULTS The fresh sediments showed a good supply with nutrients and a neutral pH, but were rather saline (EC 14 mS cm(-1) of the saturated paste extract). The salinity decreased to 3.7 mS cm(-1) during lagoonation. The high and the low contaminated sediment had initially 43 and 1.6 mg TBT kg(-1) dry weight, respectively. Besides TBT, several other contaminants were present in the sediments at critical levels. The biomass production of the plant species from the field trial ranged from 0.2 to 13 tons dry mass per hectare. Plants performing excellently were barley, sorghum, rape seed, a clover/grass mix and reed. If at all, a positive influence of TBT on plant growth was seen. TBT was degraded significantly faster (>40%) below barley. The uptake of TBT, DBT and MBT into stem and leaves of reed, grass and clover was very low, but measurable and not related to concentrations in soil. No uptake of TBT or its metabolites into corn of barley was found. DISCUSSION This study confirmed former results: the toxicity of TBT to higher plants is low, and even high levels in soils would not be a hindrance for crop production. The removal of TBT seemed to be increased by both lagooning and plant growth, although the target values for sea dumping in use in certain European countries were not reached. A plausible explanation for the faster degradation of TBT under vegetation is that oxygen is a limiting factor, and plants dewater the soil, thus aerating it. The uptake of the organotins TBT, DBT and MBT into harvest products is probably due to attached soil particles. CONCLUSIONS To summarize, barley was the optimal species: it grew very well despite the salinity of the dredged sediments, it had a significantly positive effect on TBT removal; it showed no measurable uptake of TBT or the other butyltins into the harvested product; and it is a cash crop well established in European agriculture. OUTLOOK The amounts of dredged sediments are high, and good soils are becoming increasingly rare. The feasibility of using dredged sediments for non-food production, such as energy crops, should be investigated by a critical risk assessment.