The Full Monty is where GMO Pundit keeps all those extra details that would clog up the main GMO Pundit page. It should only be used by consenting adult GMO buffs who wish to tackle The Full Monty. The rest of us can move right along. First of all go to: gmopundit.blogspot.com and use the Blogsearch tool to find what you want (Puzzled by The Full Monty expression? go to http://www.worldwidewords.org/articles/monty.htm)
Here's a guide to all that's useful about animal feeds.
Labels: Commodity trade, Economics, Nutrition, Stock feeds
posted by GMO Pundit @ 7:20 AM
2 comments
This post, updated regularly, collects news on emerging farm technologies and innovation.
Labels: Innovation, Technology
posted by GMO Pundit @ 12:17 PM
1 comments
This post collects breaking news items and links on farming commodities and agricultural trade.
Pacific Business News are flagging expected higher yield for pushing production of sugarcane for sugar and seed in Hawaii at 29.8 million tons this season.This is 12 percent better than last year.
Business News say sugarcane growers intend to harvest 908,800 acres, down 1 percent from last year, but the yield forecast is for 32.8 tons per acre, four tons better than the last year. Thus fewer acres will produce more sugar if the forecast holds.
United States grain growers have planted 4- 15pc more land to hard red winter wheat than last year after prices rallied to reach 10-year highs.SOURCE: FarmProgress, Rural Press, USA
Kansas, the leading wheat state, has an estimated 10-15pc more HRW acres planted this year, while Oklahoma and Texas have about 5pc more.
Allan Fritz, Kansas State University professor of agronomy, says that state's higher acreage was "all driven by price".
"Just driving around the state, there's a lot of fields that would have been left open for summer crops that have been planted for wheat," Mr Fritz says.
Futures of HRW wheat, which is used to make bread, hit 10-year highs at the Kansas City Board of Trade last month at $US5.56 a bushel, driven by global supply concerns due in part to the devastating drought here in Australia.
Prices for December KCBT wheat settled at $US5.18 on Tuesday.
"Five dollars a bushel does not go unnoticed in the wheat world," says Travis Miller, associate head of the Department of Soil and Crop Sciences at Texas A&M University.
Australia’s wine glut has resulted in the first slide in value of year-on-year wine exports since the industry started keeping records in 1991.
The decline reflects entirely lower export prices, not volumes.
Average export price dropped to $A3.77 a litre - the lowest in nine years.
The figures were released yesterday by the Australian Wine and Brandy Corporation (AWBC).
Even so, wine exports still totalled $2.78 billion...
Will ethanol produce a bull market in corn?
By Darrell Jobman, Editor-in-Chief, TradingEducation.com 08.07.2006 CBOT commentary.
Selected Quote:
Demand bullish
But you can make a strong bullish case for corn on the demand side. The biggest factor, of course, is corn usage for ethanol. Major credit for that goes to high prices for energy, the reason for the weather watch on the coasts where many energy production and refinery facilities are located. USDA estimates 2.15 billion bushels of corn will be used for ethanol in the 2006-07 season, up almost 35% in just one year. Within just the last few years, ethanol has grown into a major outlet for corn, accounting for about 18 percent of corn usage in this year’s projections.As a result, total corn usage of 11.65 billion bushels estimated for this season is a billion bushels more than in 2004-05, and it would take another bumper crop of well over 11 billion bushels to maintain high stock levels. By the end of the 2006-07 season, USDA estimates corn carryover could be sliced about in half to just over 1 billion bushels. With the corn surplus evaporating, you can imagine what could happen to corn prices if there is a weather or other production problem in 2007 or 2008.
Studies by agricultural economists suggest it could mean a whole new dimension for a number of agricultural markets. Josh Roe at Kansas State University and Bob Jolly and Bob Wisner at Iowa State University have developed half a dozen scenarios about what could happen. With the price of ethanol at $2.11 per gallon, the average price from May 2005 through April 2006, an ethanol plant could afford to pay $4.29 a bushel for corn and still have a positive net margin in one of their scenarios.
Jump the price of ethanol to $3.00 per gallon, the going rate in early May, and the breakeven
price that ethanol plants can pay for corn is $6.69 a bushel in another scenario. These estimates are far above the average cash price of $1.74 a bushel that Iowa farmers received from 1996- 2006. If such a drastic rise seems unimaginable, think about what has happened to prices of crude oil, copper and a number of other commodities in the last year.If ethanol demand does drive up corn prices, it would likly increase corn acreage and decrease the area planted to other crops next year, boosting those prices as well. The Roe-Jolly-Wisner study projects that by 2012 U.S. farmers would need to plant almost 14 million more acres of corn than they did in 2005 to meet the demand of livestock feeders, ethanol plants and exporters if China is a corn importer. Unless acreage increases that much, competition for corn could become very intense from these three sources of buyers.
Cargill reports strong sales increase, solid profits for 2006
Carried by by Pete Hisey on 8/21/2006 for Meatingplace.com
Meating place are reporting that privately held Cargill Inc., Minnetonka, Minn., reported a $4.1 billion increase in revenues for fiscal 2006, with record earnings excluding one-time charges related to its majority ownership in The Mosaic Company, a major fertilizer supplier.
The item says altogether, the company reported revenues of $75.2 billion, up 6 percent and, excluding the one-time charge of $190 million, net earnings were $1.73 billion, up 13 percent from $1.53 billion a year ago, but t5hat fiscal 2005 earnings were higher, at $2.1 billion, including a one-time gain of $578 million related to Mosaic.
Cargill offers few details about results of its various businesses, which range from beef to biofuel, with its largest businesses in commodity crops and byproducts...
"Although the food ingredients and applications segment lagged the year-ago level, earnings advanced in several of Cargill's edible oils, sweeteners, meat and poultry businesses around the world," said Warren Staley, chief executive...
India: GM Cotton Cultivation Expected to Double in 2007
MUMBAI: The coming season, cultivation of genetically modified cotton in India is expected to double over the next year, said K F Jhunjhunwala, president of the East India Cotton Association here on August 10. The president further pointed out that farmers are opting for more disease-resistant seeds amid a rise in the total cotton production in the country.
Jhunjhunwala said that of the total area of 8.8 million hectares under the crop in the year to the end of Sept 2006, 1.3 million were planted with transgenic Bt cotton and the coming season it should be around 3.2 million hectares.
However the total area under cotton cultivation was likely to remain around 9 million hectares as over a period of time, Bt cotton may touch 70-75 percent of the production. The switchover to genetically modified seeds was seen as the main reason for the increase in production as it offered protection against major pests.
During 2002, India allowed farmers to plant transgenic cotton containing a gene from bacillus thuringiensis, a bacterium species, which causes lethal paralysis in the digestive tract of bollworm. Jhunjhunwala also informed that total cotton crop in the season ending September 2006 would be 24.5 million bales, slightly higher than the 24.3 million produced a year ago.
Further exports would surge to a record 4.5 to 5 million bales from 1 million during the same comparable period because of carryover stocks and a good harvest. Whereas production next year could easily touch 27 million bales, if there was a slight increase in yields, he added.Argentina Soybeans Forecast To Increase Due To Higher Profitability
FAS, USDA June 2006
Argentina’s 2006/07 soybean production is forecast at 41.3 million tons, up 2 percent from last
year, which is largely due to an increase in area. The USDA forecasts Argentina’s area at 15.4
million hectares, which is 3 percent above last year’s record yield of 15.0 million. Argentina’s
area has been steadily rising since the 1980’s, and there is evidence that this trend will continue
based on soybean profitability, agronomic practices, and seed technology. Soybeans remain the most profitable crop for grain and oilseed farmers across Argentina. \Additionally, biotechnology has resulted in increasingly shorter cycle soybeans, which have allowed double-cropping in areas previously planted with one crop per growing season. Further supporting the increase of soybean area, no-tillage practices have allowed areas to be cropped which were previously unsuitable for agriculture, such as in the expansion areas of the north and west. While area and production have increased, USDA forecasts Argentina’s soybean yield at 2.7 tons per hectare, which is unchanged from 2005/06 and 2004/05 soybean yields. (For more information, contact Nicole Wagner at 202-720-0882.)
The mealie vs Event 3 272
Mail and Guardian Online, RSA
Kevin Davie
02 June 2006 08:45
Ethanol, made from crops such as sugar cane and maize, is attracting interest internationally as a relatively benign, renewable energy source that is cost-effective at current oil prices The genetic modification (GM) battlefield has been extended to biofuels production, with South Africa featuring among a number of countries that are being asked to allow the import of GM maize to make ethanol.
The GM industry worldwide wants to use GM to boost the energy properties of crops for ethanol production, says an environmental lawyer.
Ethanol is attracting interest internationally as a relatively benign, renewable energy source that is cost- effective at current oil prices...
Syngenta South Africa, a subsidiary of the Swiss agrochemical giant, gave notice last month of its intention to seek commodity clearance to import its GM maize, Event 3 272, into South Africa to be used to produce ethanol.
Syngenta, which employs 19 000 people, is a market leader in GM [sic]. Its GM business, which includes a special seed to boost ethanol production, is growing revenue at 45%, says Jim Cramer of Thestreet.com.
GM is controlled in South Africa by the Genetically Modified Organisms Act of 1997. GM is used in both maize and soya cultivation for human consumption and for cotton and cotton oil for non-food use.
The application has been launched simultaneously in the United States, the European Union and China.
Environmental lawyer Mariam Mayet says Syngenta’s Event 3 272 application is the first GM application in the world for commercial approval for a non-food (fuel) use of a food crop (maize)...
...Freese and Mayet say the enzyme in Event 3 272 is derived from novel deep-sea organisms that have never been a part of the human food supply.
“Very little is known about organisms of the Archaea domain, as they were only recently discovered, and are ubiquitous mainly in inaccessible regions such as the deep sea.”...[sic! Freese and Mayer need to do their basic biology courses again;Pundit]
More vroom
Syngenta South Africa’s head of regulatory affairs, Kulani Machaba, said the application was for a commodity clearance, meaning that Event 3 272 will be imported and not grown in the country.
He said he could not see how Event 3 272 could contaminate the maize supply as it would not be grown in South Africa and would have to be ground at the port of entry.
He said Syngenta was ready to address concerns and that GM had to pass rigorous testing otherwise it would not be brought to market...
Syngenta’s public notice reads:
“This is to inform the public that an application for commodity clearance of genetically modified Event 3 272 maize has been submitted by Syngenta South Africa. Upon receiving official authorisation; Event 3 272 maize could be imported in South Africa.
“Event 3 272 maize contains the amy797E gene derived from micro-organisms of the archeal order Thermococcales and the pmi gene from Escherichia coli. The amy797 E gene encodes the thermostable amy797E alpha-amylase enzyme, which catalyzes hydrolysis of starch into smaller and less complex carbohydrate molecules during the starch liquefaction step of the dry-grind ethanol process. The pmi gene encodes the PMI enzyme as a selectable marker. PMI allows transformed cells to use mannose as a primary carbon source during the process of regenerating plant material after transformation. [i.e. it avoids antibiotic resistance markers objected to by some critics]
“In those countries where Event 3272 maize will be cultivated, the grain will be used in the dry-grind fuel ethanol process. It is not intended to be used in other processing applications (for example wet-milling and dry-milling processes) or to be exported as a commodity crop. However, it cannot be excluded that the harvest originally intended to be used in the dry-grind fuel ethanol industry or the by-products of this processing could enter international trade routs at extremely low levels. This is not an application for cultivation or release into the environment.”-- Kevin Davie
Imports go home
GrainSA will be opposing Syngenta’s application to import Event 3 272, says Fanie Brink, not because it is anti-genetic modification (GM) or new technology, but because farmers cannot grow these mealies since this technology is yet to be approved for use as a cultivar in South Africa.
This means that South African farmers are competitively disadvantaged.
“We have no problem with GM,” says Brink, manager of industry services at GrainSA. “But farmers can’t plant that cultivar because it is not approved by the local Act.”
Brink says he suspects the new cultivar will be grown in the United States. This raises the prospect that South African farmers will be asked to compete against a cultivar that they are not permitted to grow and the heavily subsidised US maize farmer.
“We are trying to develop a biofuels industry to help both the emerging and commercial farmer,” says Brink. “[Importing Event 3 272] goes against all these plans.” -- Kevin Davie
Total use of all main ingredients (wheat, barley, maize, sorghum, oats, triticale, lupins, peas, faba beans, soybean meal, sunfl ower meal, canola meal, cottonseed meal, cottonseed, mill mix and rice pollard) in all demand regions in Australia is projected to increase from 8.9 million tonnes in 2003-04 to 10.5 million tonnes in 2007-08 largely refl ecting the projected growth in animal numbers over this period. The projected growth in feed use is expected to be driven by the cattle feedlot industry, with consumption of feed ingredients by this industry increasing by 29 per cent over the fi ve year period. Of the other industries, consumption of feed grains is forecast to increase by 12 per cent in the pig industry, 15 per cent in the broiler industry and 7 per cent in the dairy industry.
Over the projection period, demand for main feed ingredients is projected to increase strongly in northern New South Wales and Queensland, refl ecting the concentration of beef feedlot industries in these areas, and in the Victorian eastern, the New South Wales Hunter and the Queensland southern demand regions where the poultry meat industry is most heavily represented.
Around 30 per cent of all main feed ingredients consumed is projected to be used in each of New South Wales and Victoria, with the main feed ingredients used in Queensland accounting for just over 20 per cent of total Australian use.
In 2007-08, approximately 400 000 tonnes of feed, mainly wheat, lupins and barley, is projected to be shipped from Western Australia and South Australia to east coast regions, particularly Victoria and the Queensland central and New South Wales north and Sydney southern regions.
Labels: Commodity trade, Economics
posted by GMO Pundit @ 11:50 AM
0 comments
The threat to agriculture in Australian through dryland salinity is increasing at an alarming rate.
posted by GMO Pundit @ 2:19 PM
1 comments
This review examines some agronomic, economic, and environmental impacts of herbicide-resistant (HR) canola, soybean, corn, and wheat in Canada after 10 years of growing HR cultivars. The rapid adoption of HR canola and soybean suggests a net economic benefit to farmers. HR crops often have improved weed management, greater yields or economic returns, and similar or reduced environmental impact compared with their non-HR crop counterparts. There are no marked changes in volunteer weed problems associated with these crops, except in zero-tillage systems when glyphosate is used alone to control canola volunteers. Although gene flow from glyphosate-HR canola to indigenous populations of bird’s rape in eastern Canada has been measured, enrichment of hybrid plants in such populations should only occur when and where herbicide selection pressure is applied. Weed shifts as a consequence of HR canola have been documented, but a reduction in weed species diversity has not been demonstrated. Reliance on HR crops in rotations using the same mode-of-action-herbicide and/or multiple in-crop herbicide applications over time can result in intense selection pressure for weed resistance and consequently, greater herbicide use in the future to control HR weed biotypes.
"We believe that farm yields are poised for a further increase in the next few years now that canola hybrids are becomining more widely available. As can be seen from Figure 4, the yield of the best hybrid canola variety with a normal fatty acid profile was 128% of the check variety in the 2004 Prairie Canola Variety Trials. The yield of the best low linolenic hybrid was 106.4% of the check variety"
Biodiesel is the name of a clean burning alternative fuel, produced from domestic, renewable resources. Biodiesel contains no petroleum, but it can be blended at any level with petroleum diesel to create a biodiesel blend. It can be used in compression-ignition (diesel) engines with little or no modifications. Biodiesel is simple to use, biodegradable, nontoxic, and essentially free of sulfur and aromatics.
How is biodiesel made?
Biodiesel is made through a chemical process called transesterification whereby the glycerin is separated from the fat or vegetable oil. The process leaves behind two products -- methyl esters (the chemical name for biodiesel) and glycerin (a valuable byproduct usually sold to be used in soaps and other products).
Is Biodiesel the same thing as raw vegetable oil?
No! Fuel-grade biodiesel must be produced to strict industry specifications (ASTM D6751) in order to insure proper performance. Biodiesel is the only alternative fuel to have fully completed the health effects testing requirements of the 1990 Clean Air Act Amendments. Biodiesel that meets ASTM D6751 and is legally registered with the Environmental Protection Agency is a legal motor fuel for sale and distribution. Raw vegetable oil cannot meet biodiesel fuel specifications, it is not registered with the EPA, and it is not a legal motor fuel.
For entities seeking to adopt a definition of biodiesel for purposes such as federal or state statute, state or national divisions of weights and measures, or for any other purpose, the official definition consistent with other federal and state laws and Original Equipment Manufacturer (OEM) guidelines is as follows:
Biodiesel is defined as mono-alkyl esters of long chain fatty acids derived from vegetable oils or animal fats which conform to ASTM D6751 specifications for use in diesel engines. Biodiesel refers to the pure fuel before blending with diesel fuel. Biodiesel blends are denoted as, "BXX" with "XX" representing the percentage of biodiesel contained in the blend (ie: B20 is 20% biodiesel, 80% petroleum diesel).
A Brazilian company - Intech Engenharia & Meio Ambiente - will use microwave energy to produce biodiesel and cut production costs by up to 40pc.
Using the microwave approach, according to a wire service reports, it can reduce production costs and produce biodiesel from any type of oil.
An expansion project at American Biorefining Inc., a soy-based biodiesel plant in Bloomington, Ill., was nearing completion in March. At press time, production was expected to begin by mid-March, according to company President Tim Lee. “Everybody will be happy to see the thing fired up, that’s for sure,” he said.
The plant has been producing biodiesel since 1994. With the $2 million expansion, capacity will increase from 10 MMgy per year to 30 MMgy when running 24 hours a day, seven days a week. Fifteen more workers will be hired to work in the biodiesel plant, bringing the total number of employees to 25.
posted by GMO Pundit @ 9:39 PM
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GM Crop Animal Feeding Safety Testing and Crop Chemical Safety Profiling Papers.
Plant breeders have made and will continue to make important contributions toward meeting the need for more and better feed and food. The use of new techniques to modify the genetic makeup of plants to improve their properties has led to a new generation of crops, grains and their by-products for feed. The use of ingredients and products from genetically modified plants (GMP) in animal nutrition properly raises many questions and issues, such as the role of a nutritional assessment of the modified feed or feed additive as part of safety assessment, the possible influence of genetically modified (GM) products on animal health and product quality and the persistence of the recombinant DNA and of the ‘novel’ protein in the digestive tract and tissues of food-producing animals. During the last few years many studies have determined the nutrient value of GM feeds compared to their conventional counterparts and some have additionally followed the fate of DNA and novel protein. The results available to date are reassuring and reveal no significant differences in the safety and nutritional value of feedstuffs containing material derived from the so-called 1st generation of genetically modified plants (those with unchanged gross composition) in comparison with non-GM varieties. In addition, no residues of recombinant DNA or novel proteins have been found in any organ or tissue samples obtained from animals fed with GMP.
These results indicate that for compositionally equivalent GMP routine-feeding studies with target species generally add little to nutritional and safety assessment. However, the strategies devised for the nutritional and safety assessment of the 1st generation products will be much more difficult to apply to 2nd generation GMP in which significant changes in constituents have been deliberately introduced (e.g., increased fatty acids or amino acids content or a reduced concentration of undesirable constituents). It is suggested that studies made with animals will play a much more important role in insuring the safety of these 2nd generation constructs.
Keywords: Animal nutrition, feed, genetically modified plants, nutritional assessment, DNA, protein degradation
New varieties of plants resistant to pests and/or tolerant to specific herbicides such as maize, soybean, cotton, sugar beets, canola, have been recently developed by using genetic transformation (GT). These plants contain detectable specific active recombinant DNA (rDNA) and their derived protein. Since they have not been selected for a modification of their chemical composition, they can be considered as substantially equivalent to their parents or to commercial varieties for their content in nutrients and anti-nutritional factors. However, insect protected maize is less contaminated by mycotoxins than its parental counterpart conferring a higher degree of safety to animal feeds. The new feeds, grain and derivatives, and whole plants have been intensively tested in vivo up to 216 days for their safety and their nutritional equivalence for monogastric farm animals (pig, poultry) and ruminants (dairy cows, steers, lambs). The present article is based on the interpretation and the summary of the scientific results published in original reviewed journals either as full papers (33) or as abstracts (33) available through September 2003. For the duration of the experiments adapted to the species, feed intake, weight gain, milk yield and nutritional equivalence expressed as feed conversion and/or digestibility of nutrients have never been affected by feeding animals diets containing GT plants. In addition, in all the experimental animals, the body and carcass composition, the composition of milk and animal tissues, as well as the sensory properties of meat are not modified by the use of feeds derived from GT plants. Furthermore, the health of animals, their physiological characteristics and the survival rate are also not affected.
The presence of rDNA and derived proteins can be recognized and quantified in feeds in the case of glyphosate resistant soybean and canola and in the case of insect protected maize. However, rDNA has never been recovered either in milk, or in liver, spleen and muscles tissues of animals, or in rumen bacteria. On the basis of these data, it can be suggested that in vivo tests on high producing animals are necessary and sufficient to evaluate the safety and the nutritional value of new GT plants.
Keys words: GM plants, Safety, Feeding value, Farm animals
Abstract
Genetically modified (GM) Bt corn, through the pest protection that it confers, has lower levels of mycotoxins: toxic and carcinogenic chemicals produced as secondary metabolites of fungi that colonize crops. In some cases, the reduction of mycotoxins afforded by Bt corn is significant enough to have an economic impact, both in terms of domestic markets and international trade. In less developed countries where certain mycotoxins are significant contaminants of food, Bt corn adoption, by virtue of its mycotoxin reduction, may even improve human and animal health. This paper describes an integrated assessment model that analyzes the economic and health impacts of two mycotoxins in corn: fumonisin and aflatoxin. It was found that excessively strict standards of these two mycotoxins could result in global trade losses in the hundreds of millions $US annually, with the US, China, and Argentina suffering the greatest losses. The paper then discusses the evidence for Bt corn’s lower levels of contamination of fumonisin and aflatoxin, and estimates economic impacts in the United States. A total benefit of Bt corn’s reduction of fumonisin and aflatoxin in the US was estimated at $23 million annually. Finally, the paper examines the potential policy impacts of Bt corn’s mycotoxin reduction, on nations that are making a decision on whether to allow commercialization of this genetically modified crop.
Keywords Bt corn - economic impacts - health impacts - mycotoxin reduction - regulatory policy
Aeschbacher, K., L. Meile, R. Messikommer and C. Wenk. (2002) Influence of genetically modified maize on performance and product quality of chickens. Proc. Soc. Nutr. Physiol. 11:196.
Séralini, G-E, Cellier, D and de Vendomois, JS (2007) New Analysis of a Rat Feeding Study with a Genetically Modified Maize Reveals Signs of Hepatorenal Toxicity. Archives of Environmental Contamination and Toxicology 2007
10.1007/s00244-006-0149-5 [Reanalysis of existing studies, funded by Greenpeace]. Further comment here
Spencer JD, Allee GL, Sauber TE. (2000) Growing-finishing performance and carcass characteristics of pigs fed normal and genetically modified low-phytate corn. J Anim Sci. 78:1529-36.
Variation for metabolite composition and content is often observed in plants. However, it is poorly understood to what extent this variation has a genetic basis. Here, we describe the genetic analysis of natural variation in the metabolite composition in Arabidopsis thaliana. Instead of focusing on specific metabolites, we have applied empirical untargeted metabolomics using liquid chromatography–time of flight mass spectrometry (LC-QTOF MS). This uncovered many qualitative and quantitative differences in metabolite accumulation between A. thaliana accessions. Only 13.4% of the mass peaks were detected in all 14 accessions analyzed. Quantitative trait locus (QTL) analysis of more than 2,000 mass peaks, detected in a recombinant inbred line (RIL) population derived from the two most divergent accessions, enabled the identification of QTLs for about 75% of the mass signals. More than one-third of the signals were not detected in either parent, indicating the large potential for modification of metabolic composition through classical breeding.
Chemical protection plays a decisive role in the resistance of plants against pathogens and herbivores. The so-called secondary metabolites, which are a characteristic feature of plants, are especially important and can protect plants against a wide variety of microorganisms (viruses, bacteria, fungi) and herbivores (arthropods, vertebrates). As is the situation with all defense systems of plants and animals, a few specialized pathogens have evolved in plants and have overcome the chemical defense barrier. Furthermore, they are often attracted by a given plant toxin. During domestication of our crop and food plants secondary metabolites have sometimes been eliminated. Taking lupins as an example, it is illustrated that quinolizidine alkaloids are important as chemical defense compounds and that the alkaloid-free varieties (ldquosweet lupinsrdquo), which have been selected by plant breeders, are highly susceptible to a wide range of herbivores to which the alkaloid-rich wild types were resistant. The potential of secondary metabolites for plant breeding and agriculture is discussed.
Labels: feeding trials
posted by GMO Pundit @ 3:50 PM
2 comments
This post was inspired by Cédric Feschotte and colleagues' paper just below and collects together comments about natural evolution of genes. Much of this topic is covered in GMO Pundit's Natural GMOs series, and collected links to this series are also given below (see Collected GMO Pundit Posts).
The emergence of new genes and functions is of central importance to the evolution of species. The contribution of various types of duplications to genetic innovation has been extensively investigated. Less understood is the creation of new genes by recycling of coding material from selfish mobile genetic elements. To investigate this process, we reconstructed the evolutionary history of SETMAR, a new primate chimeric gene resulting from fusion of a SET histone methyltransferase gene to the transposase gene of a mobile element. We show that the transposase gene was recruited as part of SETMAR 40-58 million years ago, after the insertion of an Hsmar1 transposon downstream of a preexisting SET gene, followed by the de novo exonization of previously noncoding sequence and the creation of a new intron. The original structure of the fusion gene is conserved in all anthropoid lineages, but only the N-terminal half of the transposase is evolving under strong purifying selection. In vitro assays show that this region contains a DNA-binding domain that has preserved its ancestral binding specificity for a 19-bp motif located within the terminal-inverted repeats of Hsmar1 transposons and their derivatives. The presence of these transposons in the human genome constitutes a potential reservoir of {approx}1,500 perfect or nearly perfect SETMAR-binding sites. Our results not only provide insight into the conditions required for a successful gene fusion, but they also suggest a mechanism by which the circuitry underlying complex regulatory networks may be rapidly established.
Genome data have revealed great variation in the numbers of genes in different organisms, which indicates that there is a fundamental process of genome evolution: the origin of new genes. However, there has been little opportunity to explore how genes with new functions originate and evolve. The study of ancient genes has highlighted the antiquity and general importance of some mechanisms of gene origination, and recent observations of young genes at early stages in their evolution have unveiled unexpected molecular and evolutionary processes2. Johnson, M. E., Viggiano, L., Bailey, J. A., Abdul-Rauf, M., Goodwin, G.,
Gene duplication followed by adaptive evolution is one of the primary forces for the emergence of new gene function. Here we describe the recent proliferation, transposition and selection of a 20-kilobase (kb) duplicated segment throughout 15 Mb of the short arm of human chromosome 16. The dispersal of this segment was accompanied by considerable variation in chromosomal-map location and copy number among hominoid species. In humans, we identified a gene family (morpheus) within the duplicated segment. Comparison of putative protein-encoding exons revealed the most extreme case of positive selection among hominoids. The major episode of enhanced amino-acid replacement occurred after the separation of human and great-ape lineages from the orangutan. Positive selection continued to alter amino-acid composition after the divergence of human and chimpanzee lineages. The rapidity and bias for amino-acid-altering nucleotide changes suggest adaptive evolution of the morpheus gene family during the emergence of humans and African apes. Moreover, some genes emerge and evolve very rapidly, generating copies that bear little similarity to their ancestral precursors. Consequently, a small fraction of human genes may not possess discernible orthologues within the genomes of model organisms.3. Marques, A. C., Dupanloup, I., Vinckenbosch, N., Reymond, A. & Kaessmann,
“Retrocopied” genes were long viewed as evolutionary dead ends, with little functional relevance. Such a gene copy is generated by a circuitous route. First, a normal gene is copied to make a messenger RNA, which in the usual scheme of things is sent out of the cell nucleus, used to code for protein, and eventually destroyed. Once in a great while, though, the messenger RNA is “reverse transcribed,” coded back into a DNA sequence by the enzyme reverse transcriptase. It can then be inserted back into a chromosome, quite possibly a different chromosome than the one on which its parent gene resides. This process, which is driven by the legions of transposable elements that litter the genome, usually creates a functionless “retropseudogene,” stranded without a promoter and unable to be expressed.
But occasionally, the new gene copy recruits a promoter by, as yet, largely unknown mechanisms, and may thus potentially become functional, able to code for a protein. In the primate lineage, four such genes have been identified to date. In this issue, Henrik Kaessman and colleagues announce the discovery of seven more, and estimate that on average, one such new gene arises every million years. Many of these genes are expressed predominantly in the testes, where at least some of them probably substitute for X-chromosome genes that are inactivated during sperm development.
The authors first used bioinformatics methods to identify almost 4,000 retrocopies in the human genome. Retrocopied genes can be distinguished from their parents because the introns, or noncoding sequences, of the parent are edited out of the original messenger before retrocopying; thus, the DNA coding sequence is initially the same, but lacks the intervening introns of the parent. Of these 4,000, about 700 had not been disabled by mutations that interrupt the coding sequence. The number of other harmless mutations each had accumulated was then used to estimate the time each retrocopy was formed, based on molecular evolution theory that such neutral mutations occur at a predictable rate. While retrocopies have been created continuously over many millions of years of mammalian evolution, the authors' analysis showed a peak around 40 million years ago, after the emergence of primates, but before establishment of the human line. They estimate that 57 functional retrogenes arose in primates, about one per million years of primate evolution.
To pinpoint individual retrogenes, the authors first conducted an evolutionary simulation to estimate, based on sequence changes, which retrocopies were likely to still be functional. They found seven, which originated between 18 and 63 million years ago. These genes play a variety of roles in transcription and translation, as well as chromosome condensation and segregation, which occur just prior to cell division.
They next looked at expression patterns for these genes in 20 human tissues, and discovered that for all seven, expression was restricted mostly or entirely to the testes. Three of the seven genes were copied from genes on the X chromosome to Chromosome 1, 5, and 12, respectively. The authors suggest that such retrogenes functionally replace their silenced parental genes on the X chromosome during spermatogenesis, a resourceful maneuver that may enhance the reproductive fitness of the organism expressing them. This increase in fitness, in turn, preserves the functional retrocopy through natural selection. For two other genes, the authors also infer a function in spermatogenesis based on the parental gene function. One of these genes as well as the two remaining genes appear to have been selectively driven to evolve new or more adapted functional properties compared to their parents. Together, the results suggest that retrogenes were often recruited during primate evolution to enhance male germline functions. —Richard Robinson
In Drosophila guanche, P-homologous sequences were found to be located in a tandem repetitive array (copy number: 20-50) at a single genomic site. The cytological position on the polytene chromosomes was determined by in situ hybridization (chromosome O: 85C). Sequencing of one complete repeat unit (3.25 kilobases) revealed high sequence similarity between the central coding region comprising exons 0 to 2 and the corresponding section of the Drosophila melanogaster P element. The rest of the sequence has diverged considerably. Exon 3 has no coding function and the inverted repeats have disappeared. The P homologues of D. guanche apparently have lost their mobility but have retained the coding capacity for a protein similar to the 66-kDa P-element repressor of D. melanogaster. Divergence between different repeat units indicates early amplification of the sequence at this particular genomic site. The presence of a common P-element site at 85C in Drosophila subobscura, Drosophila madeirensis, and D. guanche suggests that clustering of the sequence at this location took place before the phylogenetic radiation of the three species.5. Kidwell, M. G. & Lisch, D. R. (2001) Evolution Int. J. Org. Evolution 55, 1–24.
The nature of the role played by mobile elements in host genome evolution is reassessed considering numerous recent developments in many areas of biology. It is argued that easy popular appellations such as "selfish DNA" and "junk DNA" may be either inaccurate or misleading and that a more enlightened view of the transposable element-host relationship encompasses a continuum from extreme parasitism to mutualism. Transposable elements are potent, broad spectrum, endogenous mutators that are subject to the influence of chance as well as selection at several levels of biological organization. Of particular interest are transposable element traits that early evolve neutrally at the host level but at a later stage of evolution are co-opted for new host functions.12. Deininger, P. L., Moran, J. V., Batzer, M. A.&Kazazian, H. H., Jr. (2003) Curr.
Mobile elements make up large portions of most eukaryotic genomes. They create genetic instability, not only through insertional mutation but also by contributing recombination substrates, both during and long after their insertion. The combination of whole-genome sequences and the development of innovative new assays to test the function of mobile elements have increased our understanding of how these elements mobilize and how their insertion impacts genome diversity and human disease.13. Cordaux, R. & Batzer, M. A. (2006) Proc. Natl. Acad. Sci. USA 103, 1157–1158.
Despite being scarce in the human genome, active L1 retrotransposons continue to play a significant role in its evolution. Because of their recent expansion, many L1s are not fixed in humans, and, when present, their mobilization potential can vary among individuals. Previously, we showed that the great majority of retrotransposition events in humans are caused by highly active, or hot, L1s. Here, in four populations of diverse geographic origins (160 haploid genomes), we investigated the degree of sequence polymorphism of three hot L1s and the extent of individual variation in mobilization capability of their allelic variants. For each locus, we found one previously uncharacterized allele in every three to five genomes, including some with nonsense and insertion/deletion mutations. Single or multiple nucleotide substitutions drastically affected the retrotransposition efficiency of some alleles. One-third of elements were no longer hot, and these so-called cool alleles substantially increased the range of individual susceptibility to retrotransposition events. Adding the activity of the three elements in each individual resulted in a surprising degree of variation in mobilization capability, ranging from 0% to 390% of a reference L1. These data suggest that individual variation in retrotransposition potential makes an important contribution to human genetic diversity.Discovery of Hsmar1:
A confident consensus sequence for Hsmar1, the first mariner transposon recognized in the human genome, was generated using three genomic and 15 cDNA
sequences. It is thought to represent the ancestrally active copy that invaded an early primate genome. The consensus is 1287 base pairs (bp) long, has 30 bp
perfect inverted terminal repeats (ITRs), and encodes a 343 amino acid (aa) mariner transposase. Each copy has diverged from the consensus largely independently of the others and mostly neutrally, and most are now defective.
They differ from the consensus by an average of 7.8% in DNA sequence and 7.5 indels per kilobase, both of which values indicate that the copies were formed about 50 Myr ago. On average, only 20% of the 73 surmised CpG hypermutable sites in the consensus remain. A remarkable exception to this loss of functionality is revealed by a set of ten cDNA clones derived from a particular genomic copy that has diverged only 2.4% from the consensus, retained 54% of its hypermutable CpG pairs, and which has a full-length transposase open reading frame. The complete sequence of one of these cDNAs (NIB1543) indicates that the transposase gene of this copy may have been conserved because it is spliced to a human cellular gene encoding a SET domain protein. A specific PCR assay was used to reveal the presence of Hsmar1 copies in all primates examined representing all major lineages, but not in close relatives of primates. PCR fragments cloned and sequenced from a representative sample of primates confirmed that Hsmar1 copies are present in all major lineages, and also revealed another cecropia subfamily mariner in prosimians only, and a third highly divergent mariner present in the greater slow loris Nycticebus coucang. There are about 200 copies of Hsmar1 in the human genome, as well as +/-2400 copies of a derived 80 bp paired ITR structure and +/-4600 copies of solo ITRs. Thus, this transposon had a considerable insertional mutagenic effect on past primate genomes
Transposable elements of the mariner family are widespread among insects and other invertebrates, and initial analyses of their relationships indicated frequent occurrence of horizontal transfers between hosts. A specific PCR assay was used to screen for additional members of the irritans subfamily of mariners in more than 400 arthropod species. Phylogenetic analysis of cloned PCR fragments indicated that relatively recent horizontal transfers had occurred into the lineages of a fruit fly Drosophila ananassae, the horn fly Haematobia irritans, the African malaria vector mosquito Anopheles gambiae, and a green lacewing Chrysoperla plorabunda. Genomic dot-blot analysis revealed that the copy number in these species varies widely, from about 17,000 copies in the horn fly to three copies in D. ananassae. Multiple copies were sequenced from genomic clones from each of these species and four others with related elements. These sequences confirmed the PCR results, revealing extremely similar elements in each of these four species (greater than 88% DNA and 95% amino acid identity).
In particular, the consensus sequence of the transposase gene of the horn fly elements differs by just two base pairs out of 1,044 from that of the lacewing elements. The mosquito lineage has diverged from the other Diptera for over 200 Myr, and the neuropteran last shared a common ancestor with them more than 265 Myr ago, so this high similarity implies that these transposons recently transferred horizontally into each lineage. Their presence in only the closest relatives in at least the lacewing lineage supports this hypothesis. Such horizontal transfers provide an explanation for the evolutionary persistence and widespread distribution of mariner transposons. We propose that the ability to transfer horizontally to new hosts before extinction by mutation in the current host constitutes the primary selective constraint maintaining the sequence conservation of mariners and perhaps other DNA-mediated elements.
A substantial fraction of vertebrate and invertebrate genomes is composed of mobile elements and their derivatives. One of the most intensively studied transposon families, the P elements of Drosophila, was thought to exist exclusively in the genomes of dipteran insects. Based on the data provided by the human genome project, in 2001 our group has identified a P element-homologous sequence in the human genome. This P element-homologous human
gene, named Phsa, is 19,533 nucleotides long, comprises six exons and five introns, and encodes a protein of still unknown function with a length of 903 amino acid residues. The N-terminal THAP domain of the putative Phsa protein shows similarities to the site-specific DNA-binding domain of the Drosophila P element transposase. In the present study, FISH analysis and the screening of a human lambda genomic library revealed a single copy of Phsa located on the long
arm of chromosome 4, upstream of a gene coding for the hypothetical protein DKFZp686L1814. The same gene arrangement was found for the homologous gene Pgga in the genome of chicken, thus, displaying Pgga at orthologous position on the long arm of chromosome 4. The single-copy gene status and the absence of terminal inverted repeats and target-site duplications indicate that Phsa and Pgga constitute domesticated stationary sequences. In contrast, a considerable
number of P-homologous sequences with terminal inverted repeats and intact target-site duplications could be identified in zebrafish, strongly indicating that Pdre elements were mobile within the zebrafish genome. Pdre elements are the first P-like transposons identified in a vertebrate species. With respect to Phsa, gene expression studies showed that Phsa is expressed in a broad range of human tissues, suggesting that the putative Phsa protein plays a not yet understood but essential role in a specific metabolic pathway. We demonstrate that P-homologous DNA sequences occur in the genomes of 21 analyzed vertebrates but only as rudiments in the rodents. Finally, the evolutionary history of P element-homologous vertebrate sequences is discussed in the context of the "molecular domestication" hypothesis versus the "source gene hypothesis."
In humans, at least 45% of the genome belong to transposable elements, and a number of single-copy genes seem to have originated from them. Until now, 48 domesticated human genes probably originating from up to 39 different transposon copies could be identified (Hagemann and Pinsker 2001; International Human Genome Sequencing Consortium 2001; Nekrutenko and Li 2001). Most of them originated from DNA transposons, although only about 6% of the human transposable elements belong to this transposon type.
Molecular Domestication History of P-Homologous Sequences
Two hypotheses have been discussed to explain active P element transposons in some dipteran species and stationary P element transposon–derived sequences in others. The "domestication hypothesis" considers those stationary sequences as degenerated transposons that have lost the structural features necessary for transposition like terminal inverted repeats and, thus, are not able to move any more. In some cases, these now immobile transposon derivates have acquired a novel function and represent a stable functional component within their host genome (Pinsker et al. 2001). In contrast, the "source gene hypothesis" argues for an evolutionary scenario in which active P element transposons are direct descendants of an ancient source gene that gave rise to a transposon by acquisition of terminal inverted repeats.
In zebrafish, P-homologous sequences are spread throughout the genome, indicating their transposable activity and contributing to two different scenarios that can be observed within the zebrafish genome: the terminally truncated Pdre sequences represent immobile components of the genome, whereas Pdre2 and the analyzed internally deleted copies show structural features typical for DNA transposons. Quite contrary features can be described for Phsa in human and Pgga in chicken, where they represent stationary single-copy genes. Phsa, Pgga, and the P-homologous mouse and rat rudiments are located at orthologous positions, thus, favoring the "source gene hypothesis." Although the immobile terminally truncated Pdre elements are located at paralogous positions compared with Pgga and the mammalian P-homologous sequences, the data obtained from zebrafish do not support the "source gene hypothesis." They indicate that P-homologous sequences as immobile and subsequently stable components of the genome were generated by "molecular domestication." As a consequence of this explanation, the domestication event of the Phsa/Pgga sequence has occurred by immobilization of an active transposon within a common ancestor before the separation of mammalians and birds about 310 MYA (Nelson 1996).
P-homologous sequences are not the only examples of domesticated transposons. A considerable number of domesticated transposable-element copies now contribute to transcriptionally regulatory elements or to protein-coding regions of cellular genes (Smit 1999, International Human Genome Sequencing Consortium 2001, Jordan et al. 2003). The high number of known transposon-derived domesticated genes provides further evidence that the stable vertebrate P-homologous sequences were recruited as novel genes from their respective host genomes by "molecular domestication" of a former active transposon copy.
Labels: Genetics, Plant Science
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Allergies reach epidemic levels in Europe: experts
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I teach graduate/undergrad courses in food science, food safety, biotechnology and microbiology at the University of Melbourne. My basic training is a first degree in biochemistry and chemistry, and graduate training to Ph.D. level in applied molecular genetics. My doctoral thesis topic was on production of an animal feed supplement using genetically manipulated bacteria. My recent publications (some noted below) have been on epidemics caused by bacterial pathogens, published in high-ranking journals. My current area of research is food risk analysis and management. The most important of these risks are microbes in food and microbial products that are toxic. Zaia A et al . Molecular tests can allow confirmation of invasive meningococcal disease when isolates yield atypical maltose, glucose or gamma-glutamyl peptidase test results. Pathology. 2005 Oct;37(5):378-9. Homan WL, Tribe D, et al Multilocus sequence typing scheme for Enterococcus faecium. J Clin Microbiol. 2002 Jun;40(6):1963-71. Willems RJ,et al . Variant esp gene as a marker of a distinct genetic lineage of vancomycin-resistant Enterococcus faecium spreading in hospitals. Lancet. 2001 Mar 17;357(9259):853-5.
Agrifood Awareness Australia is an industry initiative, established to increase public awareness of, and encourage informed debate about, gene technology. Agrifood Awareness Australia is committed to providing quality, factual information on the use of gene technology in agriculture, and the implications this may have on the entire food chain.
