Bio-nanocomposites for food packaging applications

Background
Accuracy in quantitative real-time RT-PCR is dependent on high quality RNA, consistent cDNA synthesis, and validated stable reference genes for data normalization. Reference genes used for normalization impact the results generated from expression studies and, hence, should be evaluated prior to use across samples and treatments. Few statistically validated reference genes have been reported in grapevine. Moreover, success in isolating high quality RNA from grapevine tissues is typically limiting due to low pH, and high polyphenolic and polysaccharide contents.

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An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development

Biotechnology-a sustainable alternative for chemical industry.

Usually the reference genes used in gene expression analysis have been chosen for their known or suspected housekeeping roles, however the variation observed in most of them hinders their effective use. The assessed lack of validated reference genes emphasizes the importance of a systematic study for their identification. For selecting candidate reference genes we have developed a simple in silico method based on the data publicly available in the wheat databases Unigene and TIGR.

/pdf/identification-and-validation-of-reference-genes-for-264cxr8ams.pdf

Identification and validation of reference genes for quantitative RT-PCR normalization in wheat

Hypoxia is important in both biomedical and environmental contexts and necessitates rapid adaptive changes in metabolic organization. Mammals, as air breathers, have a limited capacity to withstand sustained exposure to hypoxia. By contrast, some aquatic animals, such as certain fishes, are routinely exposed and resistant to severe environmental hypoxia. Understanding the changes in gene expression in fishes exposed to hypoxic stress could reveal novel mechanisms of tolerance that may shed new light on hypoxia and ischemia in higher vertebrates. Using cDNA microarrays, we have studied gene expression in a hypoxia-tolerant burrow-dwelling goby fish, Gillichthys mirabilis. We show that a coherent picture of a complex transcriptional response can be generated for a nonmodel organism for which sequence data were unavailable. We demonstrate that: (i) although certain shifts in gene expression mirror changes in mammals, novel genes are differentially expressed in fish; and (ii) tissue-specific patterns of expression reflect the different metabolic roles of tissues during hypoxia.

https://www.pnas.org/content/pnas/98/4/1993.full.pdf

Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis.

Gymnosperms and angiosperms are thought to have evolved from a common ancestor c. 300 million yr ago. The manner in which gymnosperms and angiosperms form seeds has diverged and, although broad similarities are evident, the anatomy and cell and molecular biology of embryogenesis in gymnosperms, such as the coniferous trees pine, spruce and fir, differ significantly from those in the most widely studied model angiosperm Arabidopsis thaliana. Molecular analysis of signaling pathways and processes such as programmed cell death and embryo maturation indicates that many developmental pathways are conserved between angiosperms and gymnosperms. Recent genomics research reveals that almost 30% of mRNAs found in developing pine embryos are absent from other conifer expressed sequence tag (EST) collections. These data show that the conifer embryo differs markedly from other gymnosperm tissues studied to date in terms of the range of genes transcribed. Approximately 72% of conifer embryo-expressed genes are found in the Arabidopsis proteome and conifer embryos contain mRNAs of very similar sequence to key genes that regulate seed development in Arabidopsis. However, 1388 loblolly pine (Pinus taeda) embryo ESTs (11.4% of the collection) are novel and, to date, have been found in no other plant. The data imply that, in gymnosperm embryogenesis, differences in structure and development are achieved by subtle molecular interactions, control of spatial and temporal gene expression and the regulating agency of a few unique proteins.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2007.02239.x

The cellular and molecular biology of conifer embryogenesis

Clonal production of loblolly pine (Pinus taeda L) through somatic embryogenesis has the potential to meet the increasing industrial demands for high-quality uniform raw materials A major barrier to the commercialization of this technology is the low quality of the resulting embryos Twenty-five newly initiated loblolly pine genotypes were followed through the process of liquid culture establishment, embryo maturation, germination, and retrieval from cryogenic storage A maturation medium, capable of promoting the development of loblolly pine somatic embryos that can germinate, is presented that combines 1/2 P6 modified salts, 2% maltose, 13% polyethylene glycol 8000 (PEG), 5 mg/l abscisic acid (ABA), and 25 g/l Gelrite A procedure for converting and acclimating germinants to growth in soil and greenhouse conditions is also described A set of somatic seedlings, produced from the maturation medium, showed 100% survival when planted in a field setting Somatic seedlings showed normal yearly growth relative to standard seedlings from natural seed The quality of the resulting embryos was examined and compared to that of zygotic embryos using such parameters as morphology, dry weight, germination performance, and gene expression All of the observations that were made support the conclusion that even with the new maturation medium somatic embryos grow approximately only halfway through the normal sequence of development and then prematurely discontinue growth

/pdf/improving-loblolly-pine-somatic-embryo-maturation-comparison-58pv94aq5j.pdf

Improving loblolly pine somatic embryo maturation: comparison of somatic and zygotic embryo morphology, germination, and gene expression

Our experimental results of using Mg(OH)2 nanoparticles as an antibacterial agent are reported in this study. The antibacterial behavior of Mg(OH)2 nanoparticles in liquid culture and in paper sheets was investigated. The colony forming units (CFU) counting and the headspace gas chromatography (HS-GC) measurement were used to determine the cell viability. Results indicate that Mg(OH)2 nanoparticles are effective antibacterial agent against Escherichia coli (E. coli) and Burkholderia phytofirmans, and the OH− and Mg2+ ions in Mg(OH)2 water suspension were found not to be the reason for killing the bacteria. Mg(OH)2 nanoparticles could be added directly to wood pulp to make paper sheets, whose antibacterial efficiency increased with the increase of the nanoparticle amount. The possible mechanism of antibacterial effect of Mg(OH)2 nanoparticles is discussed.

Investigation of Mg(OH) 2 nanoparticles as an antibacterial agent

The process of embryogenesis in gymnosperms differs in significant ways from the more widely studied process in angiosperms. To further our understanding of embryogenesis in gymnosperms, we have generated Expressed Sequence Tags (ESTs) from four cDNA libraries constructed from un-normalized, normalized, and subtracted RNA populations of zygotic and somatic embryos of loblolly pine (Pinus taeda L.). A total of 68,721 ESTs were generated from 68,131 cDNA clones. Following clustering and assembly, these sequences collapsed into 5,274 contigs and 6,880 singleton sequences for a total of 12,154 non-redundant sequences. Searches of a non-identical amino acid database revealed a putative homolog for 9,189 sequences, leaving 2,965 sequences with no known function. More extensive searches of additional plant sequence data sets revealed a putative homolog for all but 1,388 (11.4%) of the sequences. Using gene ontologies, a known function could be assigned for 5,495 of the 12,154 total non-redundant sequences with 13,633 associations in total assigned. When compared to ∼72,000 sequences in a collated P. taeda transcript assembly derived from >245,000 ESTs derived from root, xylem, stem, needles, pollen cone, and shoot ESTs, 3,458 (28.5%) of the non-redundant embryo sequences were unique and thereby provide a valuable addition to development of a complete loblolly pine transcriptome. To assess similarities between angiosperm and gymnosperm embryo development, we examined our EST collection for putative homologs of angiosperm genes implicated in embryogenesis. Out of 108 angiosperm embryogenesis-related genes, homologs were present for 83 of these genes suggesting that pine contains similar genes for embryogenesis and that our RNA sampling methods were successful. We also identified sequences from the pine embryo transcriptome that have no known function and may contribute to the programming of gene expression and embryo development.

John Cairney

Papers

The cellular and molecular biology of conifer embryogenesis

Improving loblolly pine somatic embryo maturation: comparison of somatic and zygotic embryo morphology, germination, and gene expression

Investigation of Mg(OH) 2 nanoparticles as an antibacterial agent

Expressed sequence tags from loblolly pine embryos reveal similarities with angiosperm embryogenesis.

Antibacterial study of Mg(OH)2 nanoplatelets