...Arabidopsis thaliana (Arabidopsis) has been a widely researched organism for botanists and molecular biologists for over one-hundred years. Over this time Arabidopsis has become a useful tool for scientists across the globe. Its usefulness comes from the quick germination, small size and the ability to copiously produce seeds (Koornneef & Meinke, 2010). In addition to those attributes, the size of the genome makes Arabidopsis a useful tool for identifying genes and their functions. The Arabidopsis genome was fully sequenced in 2000 which led to the discovery of more than 25,000 genes. Of those genes, approximately 30% of those genes could not be assigned a function (The Arabidopsis Genome Initiative, 2000). To help maintain a database of the...
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...cited articles • Top downloaded articles • Our comprehensive search Auxin Biosynthesis and Its Role in Plant Development Yunde Zhao Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093-0116; email: yzhao@ucsd.edu Annu. Rev. Plant Biol. 2010.61:49-64. Downloaded from www.annualreviews.org by Cambridge University on 01/19/11. For personal use only. Annu. Rev. Plant Biol. 2010. 61:49–64 First published online as a Review in Advance on January 25, 2010 The Annual Review of Plant Biology is online at plant.annualreviews.org This article’s doi: 10.1146/annurev-arplant-042809-112308 Copyright c 2010 by Annual Reviews. All rights reserved 1543-5008/10/0602-0049$20.00 Key Words Arabidopsis, tryptophan, YUCCA, TAA1, flavin monooxygenase Abstract Indole-3-acetic acid (IAA), the main auxin in higher plants, has profound effects on plant growth and development. Both plants and some plant pathogens can produce IAA to modulate plant growth. Although the genes and biochemical reactions for auxin biosynthesis in some plant pathogens are well understood, elucidation of the mechanisms by which plants produce auxin has proven to be difficult. So far, no single complete pathway of de novo auxin biosynthesis in plants has been firmly established. However, recent studies have led to the discoveries of several genes in tryptophan-dependent auxin biosynthesis pathways. Recent findings have also determined that local auxin biosynthesis plays...
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...such as detoxification. Arabidopsis...
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...Introduction Ultraviolet (UV) radiation reaching the Earth’s surface has increased significantly over the last 20 years from increased ozone depletion. UV radiation is a component of sunlight that is divided into three parts: UVA (320-400nm), UV-B (280-320nm) and UVC (less than 280nm) [25]. Wavelength determines the transmission of UV radiation through the Earth’s atmosphere. UVC is completely absorbed by the atmospheric gases; UV-B radiation is absorbed by ozone layer and only a small amount reaches the Earth’s surface while UVA radiation is hardly absorbed. The decreased UV-B-filtering capacity of the ozone layer due to pollutants like chlorofluorocarbons (CFC), methylbromide and halons has increased the amount of solar UV-B radiation that plant life is exposed to [2]. A thorough understanding of the UV-B radiation levels is especially important in agriculture as its effects on crop species is essential to design crops that can produce food and other raw materials for the increasing world population. Increased UV-B exposure has the potential to damage DNA, generate reactive oxygen species (ROS) and disrupt cellular process in many plant species [10]. Specifically, the primary deleterious effects of increased UV-B occur on the efficiency of the photosynthetic apparatus and the reduction of photosynthetic genes. Damage to the thylakoid membrane and destruction of chlorophyll (Fig. 6) along with the decrease in the amount of photosynthesis are also attributed to over exposure...
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...Growing Radish with GlucoseSection 3 May 19, 2015 Introduction The purpose of this experiment is to determine if glucose helps the germination of radish. Radish germinates fairly quickly if it is provided with proper growing conditions as well as care. Radish seeds can germinate within three to four days, but can take up to ten days. Factors such as lighting and temperature will affect the growth of the radish. Radishes are almost disease-free if they are grown properly. They need sunlight for at least six to eight hours in order for them to grow quickly without molding; however, rash seeds will germinate in partial sunlight as well. Many plants and seeds are unable to grow due to the build-up of high concentration of salt due to the salts from water (Weinheimer, 2001). Not having any types of sunlight or lighting can affect the germination rate as well as the seeds molding, depending on the temperature of the room. Radish seeds grow best in temperatures around 55 to 75 degrees Fahrenheit. These seeds should remain moist and should be watered when they are beginning to dry. Carbohydrates are an energy source and building blocks for organic molecules (Dekkers, Schuurmans, & Smeekens, 2004). Glucose is a simple sugar and is an important component for many types of life on earth. Glucose is a carbohydrate, which gives energy to living organisms. Since glucose is essential for life, the theory was that if glucose was used on the radish seeds, the germination process would...
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...able to pass that information to the others, and fungi play the role of the carrier transmitting that information. In 1983 Jack Schultz and Ian Baldwin conducted an experiment regarding plant communication. They used APHIDA to ingest leaves of a plant, and when it started, the plant reacted by transmitting a signal known as VOC and contains chemicals that are passed to nearby plants and this signal, the VOC when passed to other plants makes them react and protect themselves. I earlier said that plants “talk” with the aid of genetic information, this is something confirmed by Jim Westwood at the Virginia tech College of Agriculture and Life Sciences. He studied a parasitic plant called a dodder on two other specific plants Arabidopsis and Tomatoes. Dodder clings on to a plant and sucks it’s nutrients but Jim Westwood says that this interaction is much more complex than it looks, due to the transferring of genetic information that DNA carries. Transferring of mRNA, which tells which proteins should be coded. A parasite tricks the plant into reducing defense in order to start feeding from it. "The typical way that plants communicate is through chemicals that they release through their leaves and roots," says Westwood. "So to find out that there is an exchange of RNA" - the intermediary form of genetic information that fills the gap between DNA and proteins - "is a new concept that hasn't been explored at all. “Westwood said mRNA could turn into an "Achilles' heel...
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...CHAPTER 5 AN INTEGRATED SYSTEMS APPROACH TO CROP IMPROVEMENT G.L. HAMMER# AND D.R. JORDAN## # Agricultural Production Systems Research Unit (APSRU), School of Land and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia. ## Hermitage Research Station, Queensland Department of Primary Industries, Warwick, QLD 4370, Australia. E-mail: g.hammer@uq.edu.au Abstract. Progress in crop improvement is limited by the ability to identify favourable combinations of genotypes (G) and management practices (M) given the resources available to search among possible combinations in the target population of environments (E). Crop improvement can be viewed as a search strategy on a complex G×M×E adaptation or fitness landscape. Here we consider design of an integrated systems approach to crop improvement that incorporates advanced technologies in molecular markers, statistics, bio-informatics, and crop physiology and modelling. We suggest that such an approach can enhance the efficiency of crop improvement relative to conventional phenotypic selection by changing the focus from the paradigm of identifying superior varieties to a focus on identifying superior combinations of genetic regions and management systems. A comprehensive information system to support decisions on identifying target combinations is the critical core of the approach. We discuss the role of ecophysiology and modelling in this integrated systems approach by reviewing (i) applications in environmental...
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...biology is the expression of the genetic information in any call. It is a universal process that occurs in every cell. The genetic information is stored in the DNA. During gene expression DNA is transcript to RNA and these RNA are transcribed to proteins. Bioinformatics deals with the genetic information which involves collecting, analyzing, manipulating and predicting etc. For the functioning of bioinformatics it is essential to know the genetic information that is stored in DNA. Therefore sequencing of DNA, genes or genomes is the fundamental need in bioinformatics. Organisms that are used in biological experiments in laboratories are called ‘model organisms’, of which most genomes are sequenced at present (rat, yeast, Arabidopsis; plant model organism) These sequenced genomes could be analyzed using bioinformatics tools in order to identify genes of significance as in drought tolerance genes in plants etc. Information revealed from sequencing could be studied using bioinformatics tools to understand its underlying mechanisms and to generate models that could be used in further studies. This information could also be used in evolutionary studies, micro array analysis, identification of genetic disorders (Alzheimer’s disease, breast cancer, cystic fibrosis, spinal muscular atrophy etc.) Discoveries have revealed that despite of the universality of the central dogma the regulation mechanisms in cells tend to create variations in the results of the same...
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...Vitamin B6 is a water soluble vitamin present in many forms in human diet. Vitamin B6 has an essential role as cofactor for many metabolic enzymes (1). Vitamin b6 is a complex of six vitamers pyridoxal, pyridoxamine, pyridoxine, pyradoxamine 5-phosphate, pyridoxine 5 phosphate and pyridoxal 5 phosphate which is active form as human vitamin. Human have to take vitamin B6 from diet because they can’t synthesize it DE novo (2). Vitamin B6 has been known to have important role as antioxidant and have properties to increase stress tolerance in plants and in humans it is closely associated with functions of nervous, immune, and endocrine systems (2, 3). It also possesses a role in metabolic process of proteins, lipids and carbohydrates. Its deficiency is associated with cardiovascular disorders and neurological diseases and lead to infant abnormalities which are increasing in Asian countries and Pakistanis being in south Asian population have quite high rates of coronary heart disease (4), As abundance of this vitamin in edible parts of plants is insufficient to meet recommended daily allowance i.e. 1-3 mg/day(5). Wheat (Triticum aestivum) is the most important and considered cereal crop for major part of global population. Wheat is considered to be chief crop in Pakistan, contributing around 10.3 % to agricultural sector (6). Globally wheat provides around 55% carbohydrate, and 20% of calories consumed worldwide (7). With a huge progress in metabolic engineering of crops in Pakistan...
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...Introduction Wheat (Triticum aestivum) is the most important and considered cereal crop for major part of global population. In Pakistan, wheat is most important crop of agricultural economy. It is grown each year on 8.3 million hectares that is 36% of total area cropped in Pakistan. It accounts for 40% of total value added of major crops. It is essential part of diet for population as it contributes 60% of daily diet of common masses in Pakistan. Average per capita consumption is around 125kg and possess a central position in agricultural policies of government. If area under wheat crop remains same then wheat requirement would be about about 34.25 million tonnes in 2030. It means additional 10 million tonnes wheat have to be produced during next 20 years. It would require to improve national average yield from 2.8 to 3.8 t/ha (2030). There is 60% yield gap in wheat that is required to be tapered. There are several agronomic, physiological, political and managerial factors responsible for low yield in Pakistan. Among them ill management is more conspicuous of all. Since management skills vary from area to area, productivity also vary from region to region. In addition there is yield gap between progressive and common farmers which may attribute to several ignorance factors. Conventional plant breeding has been practicing successfully since 1960’s for production of improved wheat varieties but has limited potential to meet such a great challenge with limited gene pool. Genetic...
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...succumbed to greening as there are 130,000 acres of abandoned orange groves in the state of Florida alone. The future looks grim with these two factors threatening Florida’s largest agricultural crop, yet up-and-coming technology may be the answer to the prayers of many. Genetically Modified Organisms, or GMO’s, have been used in agriculture to increase crop yields or ensure that the crop will survive in more difficult conditions. This technology may very well be utilized to create citrus trees immune to greening. Scientists are currently attempting to solve the puzzle, and the solution may have been found. Researchers from the University of Florida have attempted modifying an orange tree so that it contains one precise gene from the Arabidopsis plant. This gene may aid in protecting orange trees from greening if “stacked” with another gene that is also resistant to the disease but fights it in a different way. Another use of biotechnology to battle HLB has been devised by Southern Gardens, a division of U.S. Sugar Corporation. Their method involves the modification of a citrus tree’s genome so that it holds a gene found in spinach plants; the gene creates a protein that causes the tree to be an unfit environment for the bacteria. This variation of citrus tree was planted in both Florida and Texas and it will be determined if the experiment was successful anywhere from 2018 to 2020. Hope for curing this monstrous epidemic lies in the use of biotechnology. Whether an orange comes...
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...Nowhere is the impact of the grand biological unification more evident than in the eukaryotes, where the genomic sequences of three model systems are already available (budding yeast, Saccharomyces cerevisiae, completed in 1996 (ref. 1); the nematode worm Caenorhabditis elegans, completed in 1998 (ref. 2); and the fruitfly Drosophila melanogaster, completed earlier this year3) and two more (the flowering plant Arabidopsis thaliana4 and fission yeast Schizosaccharomyces pombe) are imminent. The complete genomic sequence of the human genome is expected in a year or two, and the sequence of the mouse (Mus musculus) will likely follow shortly thereafter. The first comparison between two complete eukaryotic genomes (budding yeast and worm5) revealed that a surprisingly large fraction of the genes in these two organisms displayed evidence of orthology. About 12% of the worm genes (~18,000) encode proteins whose biological roles could be inferred from their similarity to their putative orthologues in yeast, comprising about 27% of the yeast genes (~5,700). Most of these proteins have been found to have a role in the ‘core biological processes’ common to all eukaryotic cells, such as DNA replication, transcription and metabolism. A three-way comparison among budding yeast, worm and fruitfly shows that this relationship can be extended; the same subset of yeast genes generally have recognizable homologues in the fly genome6. Estimates of sequence and functional conservation between...
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...genetics and developmental biology has been possible. * When the primary research goal is to understand broad biological principles, the organism chosen for study is called a model organism. * Researchers select model organisms that are representative of a larger group, suitable for the questions under investigation, and easy to grow in the lab. * For study of the connections between genes and development, suitable model organisms have short generation times and small genomes that are suitable for genetic analysis. * Model organisms used in developmental genetics include the fruit fly Drosophila melanogaster, the nematode Caenorhabditis elegans, the mouse Mus musculus, the zebra fish Danio rerio, and the plant Arabidopsis thaliana....
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...results (Chang et al., 2013). Recent studies mainly focus on gene expression profiling in potato plants infected with the virus using microarray method (Table 1). Also, several other studies have demonstrated different aspect of this interaction such as classification of genes based on biotic and abiotic stresses, changes in plant basal metabolism, protein synthesis, growth and photosynthetic processes (Table S1). Despite the vast efforts in simplification of regulation patterns of the genes in plants (caused by biotic and abiotic stresses), there isn't any general picture which describes gene expression outlines during plant-virus interaction. Majority of the data about plant-virus interaction have been limited to particular plant model, Arabidopsis, (Postnikova and Nemchinov, 2012; Rodrigo et al., 2012) and negligible have been shown about important and commercial plants such as potato. The aim of this study is to identify a robust set of genes involved in resistant to the important potato viruses; PVY, PVA and PLRV using meta-analysis of the publicly available microarray data sets. Also, the main outcome of our investigation have produced a list of common and specific genes along with regulatory networks involved in potato plant during interaction with different viruses. ...
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...created by the staff at the Museum of Zoology at the University of Michigan -- collecting the natural history, classification, species characteristics, conservation biology, and distribution information of thousands of species of animals Animal Genome Size Database -- created by Dr. T. Ryan Gregory of the University of Guelph in Canada -- publishing genome size estimates for vertebrate and invertebrate animals Animal Science Image Gallery -- a work of the United States Federal Government -- containing images, animations, and video for classroom and outreach learning Bioinformatic Harvester -- a bioinformatic meta search engine at KIT Karlsruhe Institute of Technology -- working for human, mouse, rat, zebrafish, drosophila and arabidopsis thaliana information Catalogue of Life -- compiled with sectors provided by 52 taxonomic databases from around the world -- planned to become a comprehensive catalogue of all known species of organisms on Earth Earth Human STR Allele Frequencies Database (EHSTRAFD) -- the natural step in managing populational data reported for Short Tandem Repeat (STR) loci from all over the world... Encyclopedia of Life (EOL) -- with senior officers from Harvard University and other organizations -- a free, online collaborative encyclopedia intended to document all of the 1.8 million species of living organisms...
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