May 5, 2006

Production of Ecosystem Goods and the Generation and Maintenance of Biodiversity

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Brent Hulke's ecosystem service paper

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May 2, 2006

Veronica Justen's Eco Services Paper

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May 1, 2006

McKay's EcoServices Paper

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April 5, 2006

Steven McKay's Review

A summary of “Chapman, B.A., J.E. Bowers, F.A. Feltus, and A.H. Paterson. 2006. Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. Proceedings of the National Academy of Science 103(8): 2730-2735.�


While it has been recognized for some time that gene duplication, including entire genome duplication, as been a relatively common event throughout flowering plant evolution, many questions remain about when and why it might occur. One explanatory model is that upon duplication, one copy of a gene is free to evolve and acquire new functionality, whereas the other copy is conserved with no corresponding loss of functionality. If this model, referred to as “functional divergence,’ is accurate, then, over time, enhanced levels of variability due to mutation would accumulate among homoeologous genes, those genes derived from a single ancestral gene. An alternative model, known as “functional buffering,� proposes that multiple copies of genes can yield increased levels of gene expression. Both of these models are at odds with previous studies of induced gene duplication in which resulting organisms are apparently maladapted, and genes are often rapidly lost. Both models require that duplicated genes be retained, either for a long enough duration for one set of genes to evolve in the first case, or indefinitely in the second case. The authors of this study have investigated whether there is evidence for a relationship between gene evolution and gene copy number. To do so, they utilize the recently sequenced genomes of Arabidopsis (a mustard) and Oryza (rice).

As a first step, the authors applied computational matching programs to identify pairs of duplicated genes. In other words, they identified genes in multiple locations throughout the genome, which are clearly derived from a common gene, yet are likely to contain mutations. They also identified non-duplicated genes, which they label “singletons.� These were defined as genes found within a single genomic location and clearly derived from a single ancestral gene, yet which may contain mutations. Using subspecies and landraces, as well as related species, for comparative purposes, the authors were able to detect three genome duplication events in the development of the Arabidopsis genome and one in that of the rice genome. For example, the Arabidopsis genome was compared to those of Gossypium (cotton) and Brassica (canola, cabbage and relatives), and gene duplication events were identified as having occurred between the two speciation events of these taxa from the Arabidopsis lineage. Similarly, a gene duplication event was identified as having occurred after the Musa (banana) lineage split off from that of Oryza, and a second occurred before the Sorghum lineage split off from that of Oryza as well. Individual pairs of duplicated genes, paleologs, were attributed to particular events.

Then, small mutations known as single nucleotide polymorphisms (SNPs) were identified within homoeologous pairs of genes, and their locations within the genes were determined as well. Throughout the study, only genes located within known coding regions were analyzed, thus reflecting those portions of the genome upon which evolutionary pressures are likely to apply. Then, the SNPs associated with each gene of study were examined to determine whether they would encode for changes in the resulting amino acids. Those SNPs associated with singleton genes were more likely to result in amino acid substitutions than those SNPs associated with duplicated genes. In other words, despite mutations, duplicated genes were more likely to be functionally conserved than singleton genes. Additionally, the more recent the duplication event, the more likely that duplicated genes were functionally conserved, yet no such pattern is apparent for singleton genes. This suggests that duplicated genes tend to be preferentially conserved relative to singletons, but that over time, copies do continue to evolve to new functional types. In fact, further analysis of amino acid substitutions indicated that the changes were more benign within duplicated genes than within singletons.

The sizes and complexity of duplicated genes also appear to differ substantially from those of the singleton genes. Duplicated genes, on average, are longer than are singleton genes. Furthermore, larger portions of the duplicated genes are sensitive to mutations that would result in changes in amino acid synthesis. These two facts suggest that large, complex genes are more likely to be retained than smaller, simpler genes.

In a particularly clever analysis, the authors compared genes from Arabidopsis and Oryza with homoeologous genes from Gossypium and Musa, respectively, which diverged before the most recent gene duplication event. The Arabidopsis and Oryza genes were also compared to those from Brassica and Sorghum, respectively, which diverged after the most recent gene duplication event. These comparisons allowed for an assessment of whether rates of gene change are related to time since divergence. Genetic change was measured as the maximum detected length of identical codons, representing the longest identical stretch of expressed amino acids. By looking at singletons and duplicates separately, the authors were able to evaluate the rates of change in the two different classes. Additionally, the authors separately examined coding regions, which one would expect to be acted upon by evolutionary selection, and non-coding regions, which would be evolving randomly. Non-coding regions demonstrated a steady pattern of increasing differentiation over time (pre-duplication event versus duplication event versus post-duplication event) in both lineages. Within coded regions, however, genetic similarity was retained after gene duplication, both within Arabidopsis and Oryza, and between these two species and their close relatives Brassica and Sorghum. In other words, even after speciation events, duplicated genes were more likely to be conserved than singleton genes. The authors speculate that these long stretches of conserved code may be retained by gene repair, and that this may be more successful when there are multiple copies of these genes to serve as templates for the repair mechanisms.

The authors then speculate that the two models of functional divergence and functional buffering may actually represent two ends of a spectrum of responses to gene duplication. They point out that even full-genome scans are unlikely to detect ancient duplicated genes that have long ago diverged beyond the point of recognition. They also acknowledge that they have focused on protein encoding genes rather than regulatory genes, which could exhibit different patterns of evolution and retention.

Finally, as a counterpoint to empirical evidence that gene duplication often yields maladaptive traits, the authors speculate that as time since gene duplication increases, continued accumulation of mutations is likely to decrease the benefits of functional buffering. Consequently, under such conditions, organisms may benefit to a greater degree from gene duplication. These additional benefits may actually result in something of a cyclic or periodic nature of gene duplication events, ultimately leading to increased genetic evolution.

March 27, 2006

Candida's Translation Paper

Candida Cabral
AGRO8280 - Spring 2006

Safety and Public Acceptance of Transgenic Products

Patrick Byrne is an Assistant Professor in the Dep. of Soil and Crop Science in the Colorado State University; he has many years of experience working with an agricultural biotechnology outreach program. Based on his experience he believes that “the process of reaching reasonable decisions on how to benefit from genetically engineered (GE) crops while avoiding their pitfalls� has being hindered by “pro� and “con� viewpoints in public debate. Here he highlights some areas he believes are significant on the topic of public acceptance and safety of transgenic crops
Public knowledge and attitudes about GE foods: Hollywood presents the impression that genetic engineering is dangerous and will direct to disaster, it is persuasive because of the public limited understanding about the technology. According to recent surveys in the U.S. less than 30% of consumers believed they had eaten GE food despite the fact that around 70% of the products available in supermarkets contain GE ingredients. A quarter of the customers think GE food is safe, another quarter disagrees and half was neutral or uncertain about safety. However, more than 40% believed in safety of GE food after were told about the amount of GE products available in the market, which to Byrne is an indication that regulation of the process is supported by consumers. Public acceptance varies among countries, while in the USA and Canada public is neutral, in Western Europe and Japan the public believes that the risk outweigh the benefits, but the opposite happens in China and Colombia. According to the literature it is due to some factors as natural risks are less feared than human-generated ones; new technologies are seem with caution; possibility of choice increases acceptance; trustworthy of people or institutions involved; and risk-benefit trade-off. Byrne believes that as more beneficial GE crops become more accepted they will be.
“Next generation� GE crops: “Golden Rice� is one example of nutritional enhancement; it was designed to ease vitamin A deficiency, which would be especially beneficial in developing countries. Another way to benefit consumers is increase the quality of oil profile in oil crops; nevertheless, differently from “Golden Rice� other technologies might be effective and less expensive to increase oil quality when computed costs of the regulation process. Among all the “next generation� GE crops, those engineered to produce pharmaceutical proteins, called “biopharm� crops, are seem with more caution by many groups, including farmers, nutritionists and food industry.
Broader Concerns about the current agricultural system: Sustainability of agricultural systems is included in the public debate, being GE crops part of the discussion about to develop a “sustainable rural landscape for the future�, as wrote Freckleton in a letter to Science in May of 2004. Not that GE crops alone will determine the sustainability of the actual agricultural system, but additional monitoring and evaluation of these systems is required by the public.
Concerns with GE crop regulation: Byrne states that “ensuring the existence of a credible regulatory process is the single most important factor in gaining public trust�, giving the lack of time, interest or technical background in the general public to evaluate GE crops safety. To make the process more effective the system should act in a proactive mode, keeping up if the technology and public concerns; the fragmented authority of the three agencies currently in charge of the regulation process (USDA, EPA and FDA) should be addressed; increasing transparency by making the regulatory decisions quickly available for the general public, and increase public participation in the process.
Hope for the future: Several developments are taken place recently to improve the U.S. regulatory system. For instance, the USDA’s intention to prepare an Environmental Impact Statement of its GE regulation process, revising expansion of its authority, regulation of biopharm crops grown in confined conditions, among others. Other initiative was doubling of funding for the Biotechnology Risk-Assessment Grants Program of USDA-CSREES, a program created to generate useful information to federal regulators of biotechnology in agriculture. Finally, publications are coming up with the concept of address “safety issues at the earliest stages of GE product conceptualization�, i.e., “during the design phase of GE crops to ensure that they meet national goals for food safety and agricultural sustainability�.
Byrnes conclude that “for society to benefit from GE crops, the most important step forward is to move away from polarized positions that have defined the transgenic debate so far, to positions of mutual respect that will allow a rational discussion of both the merits risks of the technology.�

Reference
Byrne, P. F. 2006. Safety and Public Acceptance of Transgenic Products Crop Sci. 46: 113-117.

March 25, 2006

Haiyan Jia: Translation Paper

Haiyan Jia
Agro 8280
Spring 2006

A PINOID-Dependent Binary Switch in Apical-Basal PIN Polar Targeting Directs Auxin Efflux
By: Friml, Jifi, Yang, Xiong, Michniewicz, Marta, Weijers, Dolf, Quint, Ab, Tietz, Olaf, Benjamins, René, Ouwerkerk, Pieter B. F., Ljung, Karin, Sandberg, Göran, Hooykaas, Paul J. J., Palme, Klaus, Offringa, Remko
Science, 0036-8075, October 29, 2004, Vol. 306, Issue 5697

Translated Version:

Plant Knows Where to Stick PINs in Its Body

This article in Science reports that auxin plays an essential role in many key facets of plant growth and development. Auxin (also called plant hormone or phytohormone) is a group of plant growth materials. For instance, auxin can influence plant growth according to gravity and light, positioning of leaf primordia, and the setup of stem cell niches. Auxin has different local concentrations and thus determines these processes. Auxin is directly transported from biosynthesis sits to action sties in shoot and root, which produced various auxin concentrations. As a result, polar auxin transport is dependent on the non-symmetric localization of proteins called “PINFORMED� (PIN) auxin transport helpers.
Tissue type determines where PIN proteins are located and how polar auxin transport is directed. For example, in the central part of the root, PIN proteins are in the bottom portion and auxin is transported downward. Since the PIN protein localization is very important to polar auxin transport, plant scientists have tried to study what controls the localization of PIN proteins in plant cells. Friml et al. find that the serine-threonine kinase PINOID (PID) determines PIN protein localization in Arabidopsis (which is a model organism in plant science research). Apical localization of PIN is positively related to levels of PID activity.

Arabidopsis mutants carrying a defective PINFORMED1 (pin1) gene produce “pin-like� inflorescences lacking proimordia. These pin1 mutants have reduced auxin transport. Pin-like inflorescences can be induced in wild-type plants by inhibitors of polar auxin transport. These mutant inflorescences can make primodia if auxin is applied. Thus pin1 mutant plants can respond to auxin.
The product of pin1 gene is a transmembrane protein similar to bacterial transporter proteins. Eight PIN-like proteins are found in Arabidopsis and involved in auxin transport. It is still unknown whether PIN proteins per se transport auxin or they facilitate the transport.
It has been difficult to study the defective pinoid (pid) mutants. Pid mutants have similar phenotype of inflorescence as pin1 mutants but only slightly reduces auxin transport. Earlier work proposes that PID and PIN function together and PID may also regulate auxin signaling negatively.
The article by Friml et al. confirms that PID controls auxin transport. Their study finds that PIN1 is on the apical membranes of Arabidopsis shoot cells where pid has normal expression. On the other hand, PIN1 is mistargeted to the bottom membranes of shoot cells in pid mutant plants. This results in auxin defect at primordial emergence site, producing shoots without leaves or flowers. They also find similar results in root.


To explain the data they find, the authors proposed a model that PID kinase works as a switch that controls PIN protein localization. PIN is directed to the apical membrane in cells where PID is above threshold level while it accumulates in cellular bottom membrane in cells lacking PID.
More questions regarding PID function need to be solved although Friml et al. confirm PID’s function on polar auxin transport regulation, such as what proteins the PID kinase phosporylate. And there may be lots of different types of PIN-PID interactions. An accurate measurement of auxin levels in situ will be critical for clarifying the role of PINS and PIDs in auxin transport. However, Friml et al. clearly prove that PID is essential in regulating polar transport and they improve our understanding of the establishment of plant cellular polarity.


March 24, 2006

Jennifer Flynn

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Alex Rigor's translation paper

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March 23, 2006

Veronica Justen: translation paper

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pdf writing

If anyone needs their paper encoded in .pdf (makes it easier to download) you can use the website below to make a pdf. Just follow the instructions on the site.

http://www.pdfonline.com/convert_pdf.asp

Brent Hulke's translation paper

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Adriana Telias: translation paper

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APS 8280 Blog

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