Preserving Plants and Seeds With DNA Bar-Coding, Research Paper Example

Introduction

The world has experienced and is still experiencing extinction of some ecosystems, this calls for preservation of seeds to ensure continuity. Technologies like DNA barcode have been used to get the age of various seeds and plants during preservation and restoration exercises. Palm trees in olden desert sands grew and fulfilled almost every requirement of the ancient Jews. These people ate the palm tree dates; the palm juices were fermented to produce wine; the stem of the palm tree was utilized as construction timber; and the leaves were used to make beds, baskets, brooms, mats, ropes, and some furniture. The remarkable breakthrough of Date Palm Seeds, Phoenix dactylifera, that have been, established by scientific means to date has been quite a help in the field. The damage to the environment is an issue that cannot be ignored any more. These facts corresponding to a shortage of natural history specialists have made nations, organizations and governments to seek methods of preservation of seeds, thus seed banks were born. In fact, a lot of times for a particular group of organisms there is only one expert in the whole world and samples in the environment contain mixtures of organisms hard to identify. This is where standardized DNA regions or barcodes have been used to identify biological material from a variety of animals. The bar-coding technique has great potential in identifying plants and fungi although it faces a lot of challenges when applied to the different groups. In a lot of land plants, as well as fungi, the coxl is not a suitable area to be used for DNA bar-coding (Chase and Fay, 1). This is because the mitochondrial genes in this group evolve too slowly to allow for the discrimination between different species. In addition, in fungi, these are subject to duplications and so other options have been thought out.

There are two categories of potential DNA barcode users, and these are taxonomists, who want to use their methods to elucidate the limits of species. The other category is other scientists who are the end users of taxonomic concepts. In the latter, there is a need to create at least a basic form of bar-coding. Thus for this purpose plastid regions of DNA are perfectly suited. Basically the intention is an easily developed but coarse system based on a one parent inherited system. In some instances, this marker will not provide accurate identification but there is still a lot of utility while developing the system. When it comes to population genetic studies, they typically have a large number of freshly collected specimens at their disposal.

Here, quality of the DNA sample is not such a concern. However, it is on such high quality DNA samples that the bar-coding techniques depend on the most. To improve on the concept of species, there is a need to develop a more sophisticated approach to the system of bar-coding. This would include sequences from multiple independent markers, a multi locus barcode and a tool for the specific inference used to explore specific limits as well as identify gaps. The second bar code would improve on the base of information, which the cruder plastid and the mitochondrial bar-codes depend on. Most potential users of bar-coding techniques are not taxonomists (Chase.et.al, 3). In many circumstances, the users in other fields need a quick easy and largely accurate method for use in identification. In many cases, a relatively crude diagnosis would be quite acceptable. The taxonomists in DNA have argued would be less of a success for  reasons that the limits prescribed in species are a product of what we think more than what we know.

On the whole, system of bar-coding is a relatively new concept. It was developed for the purpose of giving rather fast, accurate, and automatic species identification. This is using standardized DNA tags as tools for identification. Some of the most important DNA bar-coding features are the universality as well as the specification of variations and ease of employment involved in the process (Vijayan, 1).

History of palm date seed-DNA barcode

Problem

Getting exact period of the endangered and very rare in the world ecosystem must be preserved.

Preservation

The age of seed which over two thousand years has not been available is attainable due to DNA testing and other technologies. The existence of this one tree discovered in Israel is the work of natural preservation mechanism and very little input was made by humans for its existence. DNA bar-coding comprises sequencing a typical region of DNA as an instrument for species recognition. However, there is no agreement on which areas should be utilized for bar coding land vegetation. An ultimate DNA barcode should be regularly retrievable with a solitary primer pair, be agreeable to bidirectional sequencing with less requirement for physical editing of sequence tracks, and provide maximal bias among different species of plants. This has been used by scientific studies to gauge the age of various plants and seed (Hebert, Cywinska, Ball, deWaard, pp 313-320). Existence of proper seed banks like FNGLA and MBC should be encouraged to ensure restoration and preservation of such seeds. The straight spongy trunk was shaped with a canopy of green leaves that outspread like a botanical star rupture. During barcode, sequencing quality and coverage are given essential approach so as to get accurate answers in regard to seeds and plants ages. The olden date palm tree, it has been recommended, is the oldest outgrowth bearing vegetation on earth. Palm trees mature worldwide from tropical rain forests to sandy deserts. The palm trees have been nurtured in grove plantings, since people comprehended the food worth of the dates and the striking appearance and coverage on the landscape of the barren region sands. They were often grown near an oasis as a supply of water, food, and shade. Historically the tropical, facade of palm vegetation was noted in olden documents, and on stone writings uncovered by archaeological discoveries and from multiple orientations. Palm tree imagery were minted and struck on ageless coins of the Romans and Greeks. The foliages were an economic reserve for the exporting of high value, edible dates into regions exterior the Middle East and Africa. These reasons are the compelling factor that preservation and seed banks must be in place to ensure restoration of date seeds.

Restoration and preservation of date palm seed: conservation of plant genetic resources

Problem

Extinction and degradation of the world ecosystem are problems the universe as a whole, must seriously tackle if they value existence of inhabitants.

Conservation of the plant resources is achieved by either controlling the number of population or preserving the existing genetic resources. Preservation requires use of germplasm. These are the two contemporary means of conservation being undertaken. Era of conservation of genetic resources has been influenced by technology inventions and innovation. The capability of seeds to stay viable over extended periods of time is significant in preserving plant hereditary resources. Germination of a thirteen hundred year-old lotus seed has been recognized; however, other declarations of exceptional seed prolonged existence are controversial. During the mid 1960s excavation of Masada, a Herodian fortification overlooking the Dead Sea, constructed the second half of the initial century prior to the Common Era, shattered 70 Common Era, olden seeds were discovered under the rubble at the Northern Palace entrance. The seeds had been stored at room temperature for four decades; numerous seeds were found from this gathering in 2005, all from the similar archaeological region and botanically recognized as dates (Phoenix dactylifera L.) Radiocarbon dating of two date seeds under controls produced overlapping adjusted calendar ages of plus or minus 102 and plus or minus 13 years. Three remaining whole seeds were sowed after preparation in an enclosed site for sometimes. After two months, one of the seeds germinated. Its development over 2 years and 2 months demonstrated development alike that of usual date seedlings proliferated from modern seeds apart from  whitish spots on initial leaves signifying lack of chlorophyll, perhaps because of insufficiency of essential nutrients during first stages of germination. At a year and three months, the seedling was shifted into a bigger pot. Seed shell remains attaching to rootlets were radiocarbon-dated, consequential to calibrated calendar age of approximately 295 years and more. The dissimilarity in calendar ages between germinated and controls seed fragment emerges to be due to seedling development with amalgamation of two to three percent of modern carbon, which decreases the measured period by about 250 to 300 years. High summer conditions and low rainfall at Masada may have influenced the seeds outstanding longevity by decreasing free radical invention, an important ground of seed aging. The date palm was cultivated over 5 five thousand years ago, with the genotype of individual cultivar highly conserved through clonally transmission of offshoots. The Judean Dead Sea area was particularly eminent for its wide and high-quality date customs in the first century. Over the subsequence, two millennia, these extraordinary cultivars were misplaced, and by the untimely twentieth century comparatively few, low value date palms mostly circulated from seeds were documented. Preliminary genetic study of the germinated sprout and three influential date cultivars presently growing in Israel was performed with arbitrary amplified polymorphic DNA. Of nearly 400 specific DNA bands produced, over fifty percent were similar or monomorphic between the plantlet and Hayani of Egypt, Moroccan? Medjool, and Iraqi? Barhee cultivars. Polymorphic groups representing genetic divergences were greatest evaluated with Moroccan, roughly thirty five point three percent with fewer dissimilarities between Iraqi, sixteen point five percent and Egyptians nineteen point five percent cultivars. As yields of sexual duplication, seedlings vary from their progenitors and initial cultivar because each carries a unique genotype, half fatherly, half motherly derived. On the foundation of a single sampling of unknown origin, these statistics can, therefore, give limited information on the genotype of very old cultivars, but they are nonetheless significant because they may add to our comprehending of the contemporaneous Judean date inhabitants that enriched in the Dead Sea area 2000 years ago. Germination of olden seeds can offer valuable insight into the past of preservation and historic crops and has significant implications for seed banking and preservation. This case may also establish to be important to contemporary date palm cultivation. Preservation and conservation of seeds is essential for the existence and growth of the world ecosystem. There are challenges pertaining restoration, however, there are seed banks which have greatly considered those challenges and come up with various solutions (Eisner, pgs 1-2).

Preservation of Seed banks

Some seeds have natural preservation mechanisms that can allow them to exist for very long and germinate after prevailing conditions are met. Seeds can be practical for decades or centuries. An article according to New York Times documented that a 2,000-year-old palm date seed from olden Israel, the Methuselah seed, sprouted and is growing. Not long, the Montgomery Botanical Center (MBC) and the Florida Nursery, Growers and Landscape Association (FNGLA) commemorated the anniversary of their Seed bank Project. The original idea for the Seed bank Project was first created by John DeMott of Redland Nursery, a close ally and strong enthusiast of MBC. The objectives of these organizations were to promote the preservation of endangered and rare palms and cycads by promoting seed production and seed circulation from Montgomery? collections to other regions. To create chances in South Florida for testing and growing species not yet recognized in the horticultural industry. Create opportunities for recognizing successful vegetation for the future South Florida surface industry. Promote educational and scientific opportunities on the flora produced from the circulation of the seeds.

FNGLA and MBC have tried very much to tackle seed bank issues such as creating restoration mechanisms that are viable and recognized by the stakeholders. They handle the crisis of scale by ensuring the few seeds are well preserved and distributed accordingly. These other concerns are also addressed viably; ambitious restoration programs need large volume of seeds to accomplish the project but there is a serious shortage also most seed banks are lacking the technological requirement as well as the facility to deliver landscape-scale refurbishment. Lack of adequate research information on the phenology of seed maturation and development; in addition, lack of research data on rare and endangered wild species and improper timing of seed collection. Lastly, failure to record or comprehend the quality and viability of seeds and failure to break seed dormancy along with deprived storage practices; further, Botanic gardens are not using their capacity adequately. The above concerns are considered factors failing most of the seed bank projects from flourishing (Terrace, pages 1-2).

An essential element of the MBC suggestion was the employing of a part-time seed bank manager to oversee the collecting, cleaning, and circulation of seed to FNGLA and to other botanically-oriented organizations. John deliberated the suggestion with Murray Corman of Garden of Delights to gauge if he could be interested in promoting such a program. This happened when Murray had been attempting to find ways to increase the diversity of species accessible to the South Florida Nursery firm. The MBC proposal was precisely what Murray had wanted. Murray immediately agreed with John as a huge supporter of the project and became one of the initial members of the fresh FNGLA Seed Bank Committee. In April 1998, Judy Kay, was appointed as the part-time Seed Bank director through the MBC/FNGLA Seed bank agenda. Murray Corman agreed to foster the Program by functioning with Judy Kay once very fortnight. With a priority inventory of species required by FNGLA, Murray and Judy spent every other Friday gathering seed from Montgomery? collections. Later in the year, Murray accepted a seed cleaning/consultant position through MBC. His tasks were to assist Judy with identifying which seeds to gather, when to gather the seeds, and how to gather them. The most outstanding in this project was the work of coordination that has helped them so much to maintain their functionality. With the monetary support of FNGLA, MBC was capable to harvest over 176,000 seeds from the gathering in 1998. More than 145,000 of these seeds, which signified more than 75 taxa (varieties, species, and cultivars), were circulated. Because of success and development of the Seed bank Project, MBC is currently capable to support and dispense large numbers of seeds to botanical gardens, and plant organizations throughout the universe. FNGLA is to be highly praised for supporting an activity with significant global impact. This organization has addressed issues concerning restoration of seeds and seed bank adequately.

Preservation techniques

Pyrolysis gas chromatography accumulation spectrometry acknowledged good carbohydrate conservation, whilst amino acid examination revealed roughly 90% loss of the initial protein amount or mass. In the York test, mass spectrometry-based results identified several tainted early peptides. Nuclear microsatellite locus examination permitted a cautious comparison of the hereditary profiles of both the olden samples with the contemporary varieties. The ability to convalesce microsatellite DNA has the capability to improve biomolecular scrutiny on ancient grape or palm seeds from an archaeological perspective. Although the study of five microsatellite loci could not assign the ancient examples to any world region or current cultivar, the results permit speculation that the substances from York were not planted locally, even as the remains from Supersano could symbolize a trace of acquaintances with the eastern Mediterranean.

Archaeobotanical evidence of grape seed consists mainly of sodden, mineralized, and overdone seeds. Morphological dissimilarity can only hesitantly distinguish wild and cultured. In addition, in many cases, this bias relies more on circuitous evidence, such as the lack of wild palm seed in the geographic region, or on the archaeological notion and the period of time. Grape or palm date seeds and in exacting those that are waterlogged kept biomolecular information, which can offer greater detail on date culture dispersion and the wine trade. Genetics have sophisticated our perceptive of crop domestication, for instance, studies of modern grapes and other related seeds have revealed diversities brought about by human assortment. Ancient DNA restored from archaeological plant remains has also started to play a responsibility by shaping comprehension of past grape diffusion. With their morphology and arrangement specifically premeditated to store genetic data, seeds are a promising object for studies on olden biomolecules, in some scenarios germinating after a prolonged time. In grape or date seeds in particular, protection is additionally enhanced by the nature of the seeds and the high concentrations of antioxidant contents. Remarkable preservation of nucleic acids and lipids has been documented in fourteen hundred years old radish seeds by O’Donoghue. Previous effort on blackberry seeds and crab apple pips found in York revealed that the preservation is excellent for cellulose and lignin but only limited for proteins.

Taking into consideration that, in olden samples, DNA endurance may be associated with general biomolecular preservation, also analyzed proteins and carbohydrates from the same taster of archaeological seeds, applying multiple ways. Pyrolysis gas chromatography volume spectrometry was utilized to investigate carbohydrate conservation. Protein degradation was predictable observing amino acid concentration and racemisation and by express sequencing of preserved data.

The protein constituent represents an essential indicator of seed and grain worth. Pioneering examinations on archaeological cereal seeds; recommended that the investigation of proteins from olden grains could assist in comprehending of plant domestication, but this effort was hampered by the existing technology of that moment. However, the relevance of mass spectrometry to remnant bone samples has facilitated the identification and processing of single olden proteins, specifically osteocalcin, and collagen; Schweitzer but see also Buckley. Recently Solazzo was capable to identify protein remnants in archaeological potsherds, even as Hollemeyer used matrix helped laser ionization/ deposition time-of-flight mass spectrometry to investigate some remains of the 5,300-year-old Tyrolean mummy’s garments. The integration of a variety of technical enhancements has enabled sensitive and rapid identification of proteins content in small and complex organic samples. To test the effect of this ensemble of technologies for the investigation of archaeobotanical models and to typify the effects of long-term protein dilapidation processes, extracted and examined the proteins from olden grape seeds, using both electro spray ionization and MALDI (Akeret, Carrott, Mant, Jaques, Stewart, Reeves, pages 160 -161).

Biomolecular preservation

Py-GC/MS shows the high amount of both and 4-methyl-guaiacol and 4-methyl-catechol, considered signs of good preservation as the failure of methyl-side chains is usually linked to lignin degradation. The large quantity of the protein-derived components is lesser than is commonly found in waterlogged archaeological seeds.

Ancient protein deprivation is also confirmed by disperse smear available in the electrophoretic profile, as in the past reported by Shewry, and by the bulge in the nano-LC chromatogram, with inset of contemporary sample with level baseline. Most of the proteins acknowledged by mass spectrometry are accumulative proteins, which symbolize a source of nitrogen, carbon, and sulfur for the spurt. They are regularly present in huge amounts, in discrete accumulation called protein components, and their high early abundance in the seeds is almost certainly the crucial aspect for the perseverance of residual remains amenable to classification after centuries. Storage proteins are categorized by a high point of polymorphism, because of the presence of multigene categories and to post-translational alteration.

Definition

A bimolecular is any organic particle that is produced by a breathing organism, including big polymeric molecules such as polysaccharides, proteins, and nucleic acids also small molecules such as key metabolites, minor metabolites, and natural contents.

Dormancy is a time in an organism’s life sequence when growth, progress, and physical activity are temporarily halted. This minimizes metabolic movement and, therefore, assists an organism to preserve energy.

An Ecosystem is biological surroundings consisting of all the living things in a particular region, as well as all the inorganic, physical mechanism of the surroundings with which the organisms interrelate, such as soil, air, water, and sunshine. It is all the living things in a given location, along with the biotic factors with which they interrelate.

Degraded is when being decreased in value and quality.

Phenology is the study of episodic plant and animal life phase events and how these are prejudiced by seasonal and inter annual differences in climate.

Archaeobotanical refers to study of olden plant remains: the scientific examination of excavated plant remains from the ancient period.

Chromatography refers to the study of the severance of a mixture by transient it in solution or postponement or as a vapor as in gas chromatography through a mode in which the components move at different rates.

Germination refers to the process whereby spores or seeds sprout and start to grow.

Electrophoretic:  Concerning to electrophoresis, the division of molecules according to their mass and electrical charge by passing an electric current to them.

Conclusion

Seed restoration and preservation has been most significant of seed banks. It is necessary to preserve endangered and rare seeds to preserve the history, and world ecosystem. All the   articles considered the existence of palm date seed after a period of 2000 years dormancy. That preservation and conservation are the only ways the ecosystem can be preserved and restored is not in doubt. Too many years have passed while the human race ignored this fact. People have to start realizing that their actions have consequences not only themselves, but on the things that are around them like the environment.

This is a fact, and no science or discovery can remedy this no matter how much research is put into the field. Bar-coding will go only so far as to give a classification of plants and animals that are in question. This could also help in understanding fundamentals not known before about a certain species. However, it is no substitute for a species if one goes extinct due to unfavorable environmental conditions. Seed restoration and preservation may go as far as to give a helping hand to the future of some plant species, but similarly people need to take active responsibility.

The agitation for the conservation of the environment is commendable, but the message is still not sinking in, or the governments may not be acting as quickly as they should. The enthusiasm they have at this time should have been what they were doing decades ago. If this were so, the world would be in a decidedly different situation right now, but it seems one has to compromise sometimes.

Works cited

Akeret ?, Carrott J, Mant J, Jaques D, Stewart G, Reeves B. Environmental samples. In: Reeves B, editor, 628 Low, Petergate, York. Assessment report on an archaeological excavation, York: York Archaeological Trust; 2006. pp. 16061.

Chase , Mark W. Barcoding of Plants and Fungi. Published by AAAS. Science VOL 325. Web. Retrieved on 3^rd May 2011 from http://www.barcoding.si.edu/PDF/ChaseFaySciencePublished.pdf.

Chase, Mark W. Salamin, Nicolas. Wilkinson, Mike. Dunwell, James. M. Kesanakurthi, Rao Prasad. Haidar, Nadia and Savolainen, Vincent. Land plants and DNA barcodes: short-term and long-term goals. doi:10.1098/rstb.2005.1720

Published online. Retrieved on 3rd May 2011 from http://www.bolinfonet.org/pdf/LandPlantsandDNAbarcodes-shorttermandlongtermgoals.pdf

Eisner, G. Germination, Genetics, and Growth of an Ancient Date Seed. Published by BREVIA. Retrieved on 31^st May 2011 from http://www1.biu.ac.il/File/date%20seed-science-june08.pdf

Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA Barcodes. Published online. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1691236/pdf/12614582.pdf

Terrence, Walters. The Mbc/Fngla Seed Bank: Seeds, Seeds, And More Seeds: The History Of The Mbc/Fngla Seedbank Program At Montgomery Botanical Center. January 2000 pages 1-2, retrieved on 1^st June 2011 from             http://www.montgomerybotanical.org/Pages/SeedBank_Article.htm.

Marshall D. R, in plant population Genetics, Breeding, and Genetic resources, Sinauer, Amherst MA, 1990, pp 367-388

Vijayan, K. & Tsou, C. H. DNA barcoding in plants: taxonomy in a new perspective. Current Science, VOL. 99, NO. 11, 10 December 2010. 1Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan. Retrieved on May 3^rd 2011 from http://www.ias.ac.in/currsci/10dec2010/1530.pdf