Nature Reviews Genetics http://www.nature.com/nrg/current_issue/ Nature Publishing Group en © 2008 Nature Publishing Group Nature Reviews Genetics 1471-0056 © 2008 Nature Publishing Group permissions@nature.com Nature Reviews Genetics http://www.nature.com/includes/rj_globnavimages/nrg_logo.gif http://www.nature.com/nrg/ Plant genetic engineering for biofuel production: towards affordable cellulosic ethanol http://dx.doi.org/10.1038/nrg2336 Biofuels provide a potential route to avoiding the global political instability and environmental issues that arise from reliance on petroleum. Currently, most biofuel is in the form of ethanol generated from starch or sugar, but this can meet only a limited fraction of global fuel Plant genetic engineering for biofuel production: towards affordable cellulosic ethanol

Nature Reviews Genetics 9, 433 (2008). doi:10.1038/nrg2336

Author: Mariam B. Sticklen

Biofuels provide a potential route to avoiding the global political instability and environmental issues that arise from reliance on petroleum. Currently, most biofuel is in the form of ethanol generated from starch or sugar, but this can meet only a limited fraction of global fuel

]]> Plant genetic engineering for biofuel production: towards affordable cellulosic ethanol Mariam B. Sticklen doi:10.1038/nrg2336 Nature Reviews Genetics 9, 433 (2008) Nature Reviews Genetics 9 6 Review 433 443 Opposition to transgenic technologies: ideology, interests and collective action frames http://dx.doi.org/10.1038/nrg2338 Genetic engineering has enabled significant, accepted innovations in medicine and other fields. In agriculture, however, a global cognitive divide around 'genetically modified organisms' (GMOs) has limited the diffusion and scope of this technology. The framing of agricultural products of recombinant DNA technology as GMOs lacks Opposition to transgenic technologies: ideology, interests and collective action frames

Nature Reviews Genetics 9, 458 (2008). doi:10.1038/nrg2338

Author: Ronald J. Herring

Genetic engineering has enabled significant, accepted innovations in medicine and other fields. In agriculture, however, a global cognitive divide around 'genetically modified organisms' (GMOs) has limited the diffusion and scope of this technology. The framing of agricultural products of recombinant DNA technology as GMOs lacks

]]> Opposition to transgenic technologies: ideology, interests and collective action frames Ronald J. Herring doi:10.1038/nrg2338 Nature Reviews Genetics 9, 458 (2008) Nature Reviews Genetics 9 6 Perspective 458 463 Detecting genetic responses to environmental change http://dx.doi.org/10.1038/nrg2339 Changes in environmental conditions can rapidly shift allele frequencies in populations of species with relatively short generation times. Frequency shifts might be detectable in neutral genetic markers when stressful conditions cause a population decline. However, frequency shifts that are diagnostic of specific conditions depend on Detecting genetic responses to environmental change

Nature Reviews Genetics 9, 421 (2008). doi:10.1038/nrg2339

Authors: Ary A. Hoffmann & Yvonne Willi

Changes in environmental conditions can rapidly shift allele frequencies in populations of species with relatively short generation times. Frequency shifts might be detectable in neutral genetic markers when stressful conditions cause a population decline. However, frequency shifts that are diagnostic of specific conditions depend on

]]> Detecting genetic responses to environmental change Ary A. Hoffmann Yvonne Willi doi:10.1038/nrg2339 Nature Reviews Genetics 9, 421 (2008) Nature Reviews Genetics 9 6 Review 421 432 DNA methylation landscapes: provocative insights from epigenomics http://dx.doi.org/10.1038/nrg2341 The genomes of many animals, plants and fungi are tagged by methylation of DNA cytosine. To understand the biological significance of this epigenetic mark it is essential to know where in the genome it is located. New techniques are making it easier to map DNA DNA methylation landscapes: provocative insights from epigenomics

Nature Reviews Genetics 9, 465 (2008). doi:10.1038/nrg2341

Authors: Miho M. Suzuki & Adrian Bird

The genomes of many animals, plants and fungi are tagged by methylation of DNA cytosine. To understand the biological significance of this epigenetic mark it is essential to know where in the genome it is located. New techniques are making it easier to map DNA

]]> DNA methylation landscapes: provocative insights from epigenomics Miho M. Suzuki Adrian Bird doi:10.1038/nrg2341 Nature Reviews Genetics 9, 465 (2008) Nature Reviews Genetics 9 6 Review 465 476 Genetic approaches to crop improvement: responding to environmental and population changes http://dx.doi.org/10.1038/nrg2342 Crop production is threatened by global climate change, and recent demands for crops to produce bio-fuels have started to affect the worldwide supply of some of the most important foods. How can we support a growing human population in such circumstances? One potential solution is Genetic approaches to crop improvement: responding to environmental and population changes

Nature Reviews Genetics 9, 444 (2008). doi:10.1038/nrg2342

Authors: Shin Takeda & Makoto Matsuoka

Crop production is threatened by global climate change, and recent demands for crops to produce bio-fuels have started to affect the worldwide supply of some of the most important foods. How can we support a growing human population in such circumstances? One potential solution is

]]> Genetic approaches to crop improvement: responding to environmental and population changes Shin Takeda Makoto Matsuoka doi:10.1038/nrg2342 Nature Reviews Genetics 9, 444 (2008) Nature Reviews Genetics 9 6 Review 444 457 Linkage disequilibrium — understanding the evolutionary past and mapping the medical future http://dx.doi.org/10.1038/nrg2361 Linkage disequilibrium — the nonrandom association of alleles at different loci — is a sensitive indicator of the population genetic forces that structure a genome. Because of the explosive growth of methods for assessing genetic variation at a fine scale, evolutionary biologists and human geneticists Linkage disequilibrium — understanding the evolutionary past and mapping the medical future

Nature Reviews Genetics 9, 477 (2008). doi:10.1038/nrg2361

Author: Montgomery Slatkin

Linkage disequilibrium — the nonrandom association of alleles at different loci — is a sensitive indicator of the population genetic forces that structure a genome. Because of the explosive growth of methods for assessing genetic variation at a fine scale, evolutionary biologists and human geneticists

]]> Linkage disequilibrium — understanding the evolutionary past and mapping the medical future Montgomery Slatkin doi:10.1038/nrg2361 Nature Reviews Genetics 9, 477 (2008) Nature Reviews Genetics 9 6 Review 477 485 Out of sequence: how consumer genomics could displace clinical genetics http://dx.doi.org/10.1038/nrg2374 The era of personalized medicine has arrived, but not in the way that many predicted. Rather than emerging as clinical tools derived from years of biomedical research that characterized the accuracy and clinical usefulness of genetic markers of increased disease risk, the first publicly Out of sequence: how consumer genomics could displace clinical genetics

Nature Reviews Genetics 9, 419 (2008). doi:10.1038/nrg2374

Authors: Morris W. Foster & Richard R. Sharp

The era of personalized medicine has arrived, but not in the way that many predicted. Rather than emerging as clinical tools derived from years of biomedical research that characterized the accuracy and clinical usefulness of genetic markers of increased disease risk, the first publicly

]]> Out of sequence: how consumer genomics could displace clinical genetics Morris W. Foster Richard R. Sharp doi:10.1038/nrg2374 Nature Reviews Genetics 9, 419 (2008) Nature Reviews Genetics 9 6 Research Highlight 419 419 Genomic medicine and developing countries: creating a room of their own http://dx.doi.org/10.1038/nrg2379 The notion that developing countries must wait for the developed world to make advances in science and technology that they later import at great cost is being challenged. We have previously argued that developing countries can harness human genetic variation to benefit their populations and Genomic medicine and developing countries: creating a room of their own

Nature Reviews Genetics 9, 487 (2008). doi:10.1038/nrg2379

Authors: Béatrice Séguin, Billie-Jo Hardy, Peter A. Singer & Abdallah S. Daar

The notion that developing countries must wait for the developed world to make advances in science and technology that they later import at great cost is being challenged. We have previously argued that developing countries can harness human genetic variation to benefit their populations and

]]> Genomic medicine and developing countries: creating a room of their own Béatrice Séguin Billie-Jo Hardy Peter A. Singer Abdallah S. Daar doi:10.1038/nrg2379 Nature Reviews Genetics 9, 487 (2008) Nature Reviews Genetics 9 6 Perspective 487 493 Advances in autism genetics: on the threshold of a new neurobiology http://dx.doi.org/10.1038/nrg2380 Nature Reviews Genetics9, 341–355 (2008)The first row in Table 1 on page 344 of this Review was incorrect; the corrected version is shown below.The authors apologize for this error. Advances in autism genetics: on the threshold of a new neurobiology

Nature Reviews Genetics 9, 493 (2008). doi:10.1038/nrg2380

Author: Brett S. Abrahams & Daniel H. Geschwind

Nature Reviews Genetics9, 341–355 (2008)The first row in Table 1 on page 344 of this Review was incorrect; the corrected version is shown below.The authors apologize for this error.

]]> Advances in autism genetics: on the threshold of a new neurobiology Brett S. Abrahams Daniel H. Geschwind doi:10.1038/nrg2380 Nature Reviews Genetics 9, 493 (2008) Nature Reviews Genetics 9 6 Corrigendum 493 493 Cliff Tabin http://dx.doi.org/10.1038/nrg2381 The 2008 March of Dimes Prize in Developmental Biology has been awarded jointly to Cliff Tabin of Harvard Medical School and to Philip Beachy of the Institute for Stem Cell Biology and Regenerative Medicine at Stanford University and the Department of Developmental Biology at Stanford Cliff Tabin

Nature Reviews Genetics 9, 420 (2008). doi:10.1038/nrg2381

The 2008 March of Dimes Prize in Developmental Biology has been awarded jointly to Cliff Tabin of Harvard Medical School and to Philip Beachy of the Institute for Stem Cell Biology and Regenerative Medicine at Stanford University and the Department of Developmental Biology at Stanford

]]> Cliff Tabin doi:10.1038/nrg2381 Nature Reviews Genetics 9, 420 (2008) Nature Reviews Genetics 9 6 Research Highlight 420 420 Global challenges: A sense of identity helps stressed-out plants http://dx.doi.org/10.1038/nrg2384 Understanding how plants cope with stressful conditions is essential if we are to use genetic approaches to produce crops that grow well in harsh environments — an important goal as agriculture feels the effects of climate change. A recent study significantly advances our understanding of Global challenges: A sense of identity helps stressed-out plants

Nature Reviews Genetics 9, 414 (2008). doi:10.1038/nrg2384

Author: Louisa Flintoft

Understanding how plants cope with stressful conditions is essential if we are to use genetic approaches to produce crops that grow well in harsh environments — an important goal as agriculture feels the effects of climate change. A recent study significantly advances our understanding of

]]> Global challenges: A sense of identity helps stressed-out plants Louisa Flintoft doi:10.1038/nrg2384 Nature Reviews Genetics 9, 414 (2008) Nature Reviews Genetics 9 6 Research Highlight 414 414 Development: Extending the role of FGFs in the limb http://dx.doi.org/10.1038/nrg2385 It has been known for 50 years that the apical ectodermal ridge (AER) is essential for the development of the tetrapod limb along its proximal–distal (P–D) axis. Fifteen years ago it was shown that members of the fibroblast growth factor (FGF) family are the vital Development: Extending the role of FGFs in the limb

Nature Reviews Genetics 9, 416 (2008). doi:10.1038/nrg2385

Author: Tanita Casci

It has been known for 50 years that the apical ectodermal ridge (AER) is essential for the development of the tetrapod limb along its proximal–distal (P–D) axis. Fifteen years ago it was shown that members of the fibroblast growth factor (FGF) family are the vital

]]> Development: Extending the role of FGFs in the limb Tanita Casci doi:10.1038/nrg2385 Nature Reviews Genetics 9, 416 (2008) Nature Reviews Genetics 9 6 Research Highlight 416 417 In Brief http://dx.doi.org/10.1038/nrg2387 Yeast geneticsThe chemical genomic portrait of yeast: uncovering a phenotype for all genes.Hillenmeyer, M. E.et al. Science320, 362–365 (2008)In Saccharomyces cerevisiae, only ∼20% of genes are essential under optimal growth conditions. In Brief

Nature Reviews Genetics 9, 417 (2008). doi:10.1038/nrg2387

Yeast geneticsThe chemical genomic portrait of yeast: uncovering a phenotype for all genes.Hillenmeyer, M. E.et al. Science320, 362–365 (2008)In Saccharomyces cerevisiae, only ∼20% of genes are essential under optimal growth conditions.

]]> In Brief doi:10.1038/nrg2387 Nature Reviews Genetics 9, 417 (2008) Nature Reviews Genetics 9 6 Research Highlight 417 417 In brief http://dx.doi.org/10.1038/nrg2388 EpigeneticsSmall RNA-directed epigenetic natural variation in Arabidopsis thaliana.Zhai, J.et al. PLoS Genet.4, e1000056 (2008)This paper suggests that small interfering RNAs (siRNAs) have a widespread role in directing variation in DNA methylation patterns in In brief

Nature Reviews Genetics 9, 418 (2008). doi:10.1038/nrg2388

EpigeneticsSmall RNA-directed epigenetic natural variation in Arabidopsis thaliana.Zhai, J.et al. PLoS Genet.4, e1000056 (2008)This paper suggests that small interfering RNAs (siRNAs) have a widespread role in directing variation in DNA methylation patterns in

]]> In brief doi:10.1038/nrg2388 Nature Reviews Genetics 9, 418 (2008) Nature Reviews Genetics 9 6 Research Highlight 418 418 From the editors http://dx.doi.org/10.1038/nrg2389 Our planet is facing challenges that, if left unaddressed, are predicted to cause untold damage on a global scale. Environmental change is threatening ecosystems and food production, particularly in developing countries, a problem that is exacerbated by the increasing expansion of the human population. And From the editors

Nature Reviews Genetics 9, 413 (2008). doi:10.1038/nrg2389

Our planet is facing challenges that, if left unaddressed, are predicted to cause untold damage on a global scale. Environmental change is threatening ecosystems and food production, particularly in developing countries, a problem that is exacerbated by the increasing expansion of the human population. And

]]> From the editors doi:10.1038/nrg2389 Nature Reviews Genetics 9, 413 (2008) Nature Reviews Genetics 9 6 From The Editors 413 413 Gene regulation: Opening promoters to flexible expression http://dx.doi.org/10.1038/nrg2390 In a simple world, nucleosomes would behave as roadblocks to transcription, to be lifted whenever access by RNA polymerase was required. A paper that surveys the pattern of nucleosome occupancy at yeast promoters shows that nucleosome patterns might, in fact, help to modulate gene expression, Gene regulation: Opening promoters to flexible expression

Nature Reviews Genetics 9, 416 (2008). doi:10.1038/nrg2390

Author: Tanita Casci

In a simple world, nucleosomes would behave as roadblocks to transcription, to be lifted whenever access by RNA polymerase was required. A paper that surveys the pattern of nucleosome occupancy at yeast promoters shows that nucleosome patterns might, in fact, help to modulate gene expression,

]]> Gene regulation: Opening promoters to flexible expression Tanita Casci doi:10.1038/nrg2390 Nature Reviews Genetics 9, 416 (2008) Nature Reviews Genetics 9 6 Research Highlight 416 416 Genomics: Annotating with proteomes http://dx.doi.org/10.1038/nrg2391 The more genome sequences we have, the greater the need for accurate and efficient annotation. Proteomics offers a way of doing this that guarantees accuracy — if a protein is detected, then there must be a gene that encodes it. Two new proteomics studies have Genomics: Annotating with proteomes

Nature Reviews Genetics 9, 418 (2008). doi:10.1038/nrg2391

Author: Patrick Goymer

The more genome sequences we have, the greater the need for accurate and efficient annotation. Proteomics offers a way of doing this that guarantees accuracy — if a protein is detected, then there must be a gene that encodes it. Two new proteomics studies have

]]> Genomics: Annotating with proteomes Patrick Goymer doi:10.1038/nrg2391 Nature Reviews Genetics 9, 418 (2008) Nature Reviews Genetics 9 6 Research Highlight 418 418 Global challenges: One gene, lots of rice http://dx.doi.org/10.1038/nrg2392 Understanding the genetic basis of crop yield has been thought to require the identification of many genes of small effect. New research has uncovered an important exception to this rule — a rice locus that has a major effect on several aspects of yield.Many Global challenges: One gene, lots of rice

Nature Reviews Genetics 9, 415 (2008). doi:10.1038/nrg2392

Author: Patrick Goymer

Understanding the genetic basis of crop yield has been thought to require the identification of many genes of small effect. New research has uncovered an important exception to this rule — a rice locus that has a major effect on several aspects of yield.Many

]]> Global challenges: One gene, lots of rice Patrick Goymer doi:10.1038/nrg2392 Nature Reviews Genetics 9, 415 (2008) Nature Reviews Genetics 9 6 Research Highlight 415 415 Genomics: Top billing for platypus genome http://dx.doi.org/10.1038/nrg2393 Given the unique position of the platypus in the evolutionary history of mammals, the sequencing of its genome has been eagerly anticipated. A draft genome for this fascinating creature has now appeared in Nature. This and five concurrently published papers in Genome Research Genomics: Top billing for platypus genome

Nature Reviews Genetics 9, 416 (2008). doi:10.1038/nrg2393

Author: Louisa Flintoft

Given the unique position of the platypus in the evolutionary history of mammals, the sequencing of its genome has been eagerly anticipated. A draft genome for this fascinating creature has now appeared in Nature. This and five concurrently published papers in Genome Research

]]> Genomics: Top billing for platypus genome Louisa Flintoft doi:10.1038/nrg2393 Nature Reviews Genetics 9, 416 (2008) Nature Reviews Genetics 9 6 Research Highlight 416 417 Evolution: A gene is born http://dx.doi.org/10.1038/nrg2394 There are various ways to explain how new genes can come about — exon shuffling, gene duplication and retroposition being just a few. But how are truly novel genes born out of a sequence that was previously non-coding? Using a comparative genomics approach, a research Evolution: A gene is born

Nature Reviews Genetics 9, 415 (2008). doi:10.1038/nrg2394

Author: Tanita Casci

There are various ways to explain how new genes can come about — exon shuffling, gene duplication and retroposition being just a few. But how are truly novel genes born out of a sequence that was previously non-coding? Using a comparative genomics approach, a research

]]> Evolution: A gene is born Tanita Casci doi:10.1038/nrg2394 Nature Reviews Genetics 9, 415 (2008) Nature Reviews Genetics 9 6 Research Highlight 415 415