Hot off the presses! Apr 01 Trends in Ecology & Evolution

The Apr 01 issue of the Trends in Ecology & Evolution is now up on Pubget (About Trends in Ecology & Evolution): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends in Ecology and Evolution 26(4):i (2011)
  
• Natural history collections as sources of long-term datasets
  - Trends in Ecology and Evolution 26(4):153-154 (2011)
  In the otherwise excellent special issue of Trends in Ecology and Evolution on long-term ecological research (TREE 25(10), 2010), none of the contributors mentioned the importance of natural history collections (NHCs) as sources of data that can strongly complement past and ongoing survey data. Whereas very few field surveys have operated for more than a few decades, NHCs, conserved in museums and other institutions, comprise samples of the Earth's biota typically extending back well into the nineteenth century and, in some cases, before this time. They therefore span the period of accelerated anthropogenic habitat destruction, climate warming and ocean acidification, in many cases reflecting baseline conditions before the major impact of these factors.
• The costs of describing the entire animal kingdom
  - Trends in Ecology and Evolution 26(4):154-155 (2011)
  
• Why research on traits of invasive plants tells us very little
  - Trends in Ecology and Evolution 26(4):155-156 (2011)
  
• Unfortunately, linguistic injustice matters
  - Trends in Ecology and Evolution 26(4):156-157 (2011)
  
• Social networking in the world of ants
  - Trends in Ecology and Evolution 26(4):157-158 (2011)
  
• Aboveground–belowground interactions: the way forward
  - Trends in Ecology and Evolution 26(4):158-159 (2011)
  
• The genes underlying the process of speciation
  - Trends in Ecology and Evolution 26(4):160-167 (2011)
  The long-standing goal of finding genes causing reproductive isolation is being achieved. To better link the genetics with the process of speciation, we propose that 'speciation gene' be defined as any gene contributing to the evolution of reproductive isolation. Characterizing a speciation gene involves establishing that the gene affects a component of reproductive isolation; demonstrating that divergence at the locus occurred before completion of speciation; and quantifying the effect size of the gene (i.e. the increase in total reproductive isolation caused by its divergence). Review of a sample of candidate speciation genes found that few meet these criteria. Improved characterization of speciation genes will clarify how numerous they are, their properties and how they affect genome-wide patterns of divergence.
• Addressing the threat to biodiversity from botanic gardens
  - Trends in Ecology and Evolution 26(4):168-174 (2011)
  Increasing evidence highlights the role that botanic gardens might have in plant invasions across the globe. Botanic gardens, often in global biodiversity hotspots, have been implicated in the early cultivation and/or introduction of most environmental weeds listed by IUCN as among the worst invasive species worldwide. Furthermore, most of the popular ornamental species in living collections around the globe have records as alien weeds. Voluntary codes of conduct to prevent the dissemination of invasive plants from botanic gardens have had limited uptake, with few risk assessments undertaken of individual living collections. A stronger global networking of botanic gardens to tackle biological invasions involving public outreach, information sharing and capacity building is a priority to prevent the problems of the past occurring in the future.
• Peto's Paradox: evolution's prescription for cancer prevention
  - Trends in Ecology and Evolution 26(4):175-182 (2011)
  The evolution of multicellularity required the suppression of cancer. If every cell has some chance of becoming cancerous, large, long-lived organisms should have an increased risk of developing cancer compared with small, short-lived organisms. The lack of correlation between body size and cancer risk is known as Peto's paradox. Animals with 1000 times more cells than humans do not exhibit an increased cancer risk, suggesting that natural mechanisms can suppress cancer 1000 times more effectively than is done in human cells. Because cancer has proven difficult to cure, attention has turned to cancer prevention. In this review, similar to pharmaceutical companies mining natural products, we seek to understand how evolution has suppressed cancer to develop ultimately improved cancer prevention in humans.
• Why intraspecific trait variation matters in community ecology
  - Trends in Ecology and Evolution 26(4):183-192 (2011)
  Natural populations consist of phenotypically diverse individuals that exhibit variation in their demographic parameters and intra- and inter-specific interactions. Recent experimental work indicates that such variation can have significant ecological effects. However, ecological models typically disregard this variation and focus instead on trait means and total population density. Under what situations is this simplification appropriate? Why might intraspecific variation alter ecological dynamics? In this review we synthesize recent theory and identify six general mechanisms by which trait variation changes the outcome of ecological interactions. These mechanisms include several direct effects of trait variation per se and indirect effects arising from the role of genetic variation in trait evolution.
• Evolution in structured populations: beyond the kin versus group debate
  - Trends in Ecology and Evolution 26(4):193-201 (2011)
  Much of the literature on social evolution is pervaded by the old debate about the relative merits of kin and group selection. In this debate, the biological interpretation of processes occurring in real populations is often conflated with the mathematical methodology used to describe these processes. Here, we highlight the distinction between the two by placing this discussion within the broader context of evolution in structured populations. In this review we show that the current debate overlooks important aspects of the interplay between genetic and demographic structuring, and argue that a continued focus on the relative merits of kin versus group selection distracts attention from moving the field forward.
• New paradigms for the evolution of beneficial infections
  - Trends in Ecology and Evolution 26(4):202-209 (2011)
  A longstanding paradigm predicts that microbial parasites and mutualists exhibit disparate evolutionary patterns. Parasites are predicted to promote arms races with hosts, rapid evolution and sexual recombination. By contrast, mutualists have been linked with beneficial coadaptation, evolutionary stasis and asexuality. In this review we discuss the recent surge of molecular data on microbes that are being used to test and reshape these ideas. New analyses reveal that beneficial microbes often share mechanisms of infection and defense with parasites, and can also exhibit rapid evolution and extensive genetic exchange. To explain these patterns, new paradigms must take into account the varied population biology of beneficial microbes, their potential conflicts with hosts, and the mosaic nature of genome evolution that requires locus-based tests to analyze the genetics of host adaptation.

Hot off the presses! Feb 01 Trends in Ecology & Evolution

The Feb 01 issue of the Trends in Ecology & Evolution is now up on Pubget (About Trends in Ecology & Evolution): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends in Ecology and Evolution 26(2):i (2011)
  
• Basic research in evolution and ecology enhances forensics
  - Trends in Ecology and Evolution 26(2):53-55 (2011)
  In 2009, the National Research Council recommended that the forensic sciences strengthen their grounding in basic empirical research to mitigate against criticism and improve accuracy and reliability. For DNA-based identification, this goal was achieved under the guidance of the population genetics community. This effort resulted in DNA analysis becoming the 'gold standard' of the forensic sciences. Elsewhere, we proposed a framework for streamlining research in decomposition ecology, which promotes quantitative approaches to collecting and applying data to forensic investigations involving decomposing human remains. To extend the ecological aspects of this approach, this review focuses on forensic entomology, although the framework can be extended to other areas of decomposition.
• Academic strategies in a funding crisis: research competitor, ruderal or university teacher?
  - Trends in Ecology and Evolution 26(2):56-57 (2011)
  
• Recent developments in sociobiology and the scientific method
  - Trends in Ecology and Evolution 26(2):57-58 (2011)
  
• 'Linguistic injustice' is not black and white
  - Trends in Ecology and Evolution 26(2):58-59 (2011)
  
• Conservation science must engender hope to succeed
  - Trends in Ecology and Evolution 26(2):59-60 (2011)
  
• Data archiving in ecology and evolution: best practices
  - Trends in Ecology and Evolution 26(2):61-65 (2011)
  Many ecology and evolution journals have recently adopted policies requiring that data from their papers be publicly archived. I present suggestions on how data generators, data re-users, and journals can maximize the fairness and scientific value of data archiving. Data should be archived with enough clarity and supporting information that they can be accurately interpreted by others. Re-users should respect their intellectual debt to the originators of data through citation both of the paper and of the data package. In addition, journals should consider requiring that all data for published papers be archived, just as DNA sequences must be deposited in GenBank. Data are another valuable part of the legacy of a scientific career and archiving them can lead to new scientific insights. Archiving also increases opportunities for credit to be given to the scientists who originally collected the data.
• Hypothesis testing in biogeography
  - Trends in Ecology and Evolution 26(2):66-72 (2011)
  Often, biogeography is applied only as a narrative addition to phylogenetic studies and lacks scientific rigour. However, if research questions are framed as hypotheses, biogeographical scenarios become testable. In this review, we explain some problems with narrative biogeography and show how the use of explicit hypotheses is changing understanding of how organisms came to be distributed as they are. Developing synergies between biogeography, ecology, molecular dating and palaeontology are providing novel data and hypothesis-testing opportunities. New approaches are challenging the classic 'Gondwana' paradigm and a more complicated history of the Southern Hemisphere is emerging, involving not only general drivers such as continental drift and niche conservatism, but also drowning and re-emergence of landmasses, biotic turnover and long-distance colonization.
• Vacant habitats in the Universe
  - Trends in Ecology and Evolution 26(2):73-80 (2011)
  The search for life on other planets usually makes the assumption that where there is a habitat, it will contain life. On the present-day Earth, uninhabited habitats (or vacant habitats) are rare, but might occur, for example, in subsurface oils or impact craters that have been thermally sterilized in the past. Beyond Earth, vacant habitats might similarly exist on inhabited planets or on uninhabited planets, for example on a habitable planet where life never originated. The hypothesis that vacant habitats are abundant in the Universe is testable by studying other planets. In this review, I discuss how the study of vacant habitats might ultimately inform an understanding of how life has influenced geochemical conditions on Earth.
• Animals and the invention of the Phanerozoic Earth system
  - Trends in Ecology and Evolution 26(2):81-87 (2011)
  Animals do not just occupy the modern biosphere, they permeate its structure and define how it works. Their unique combination of organ-grade multicellularity, motility and heterotrophic habit makes them powerful geobiological agents, imposing myriad feedbacks on nutrient cycling, productivity and environment. Most significantly, animals have 'engineered' the biosphere over evolutionary time, forcing the diversification of, for example, phytoplankton, land plants, trophic structure, large body size, bioturbation, biomineralization and indeed the evolutionary process itself. This review surveys how animals contribute to the modern world and provides a basis for reconstructing ancient ecosystems. Earlier, less animal-influenced biospheres worked quite differently from the one currently occupied, with the Ediacaran–Cambrian radiation of organ-grade animals marking a fundamental shift in macroecological and macroevolutionary expression.
• The evolution of the worldwide leaf economics spectrum
  - Trends in Ecology and Evolution 26(2):88-95 (2011)
  The worldwide leaf economic spectrum (WLES) is a strikingly consistent pattern of correlations among leaf traits. Although the WLES effectively summarizes variation in plant ecological strategies, little is known about its evolution. We reviewed estimates of natural selection and genetic variation for leaf traits to test whether the evolution of the WLES was limited by selection against unfit trait combinations or by genetic constraints. There was significant selection for leaf traits on both ends of the WLES spectrum, as well as significant genetic variation for these traits. In addition, genetic correlations between WLES traits were variable in strength and direction. These data suggest that genetic constraints have had a smaller role than selection in the evolution of the WLES.
• Dynamic disequilibrium of the terrestrial carbon cycle under global change
  - Trends in Ecology and Evolution 26(2):96-104 (2011)
  In this review, we propose a new framework, dynamic disequilibrium of the carbon cycles, to assess future land carbon-sink dynamics. The framework recognizes internal ecosystem processes that drive the carbon cycle toward equilibrium, such as donor pool-dominated transfer; and external forces that create disequilibrium, such as disturbances and global change. Dynamic disequilibrium within one disturbance–recovery episode causes temporal changes in the carbon source and sink at yearly and decadal scales, but has no impacts on longer-term carbon sequestration unless disturbance regimes shift. Such shifts can result in long-term regional carbon loss or gain and be quantified by stochastic statistics for use in prognostic modeling. If the regime shifts result in ecosystem state changes in regions with large carbon reserves at risk, the global carbon cycle might be destabilized.

Hot off the presses! Dec 01 Trends in Ecology & Evolution

The Dec 01 issue of the Trends in Ecology & Evolution is now up on Pubget (About Trends in Ecology & Evolution): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends in Ecology and Evolution 25(12):i (2010)
  
• Light pollution as a biodiversity threat
  - Trends in Ecology and Evolution 25(12):681-682 (2010)
  
• Swarm intelligence in plant roots
  - Trends in Ecology and Evolution 25(12):682-683 (2010)
  
• Astrobiology in Antarctica
  - Trends in Ecology and Evolution 25(12):683-684 (2010)
  
• Community ecology: stasis, evolution or revolution?
  - Trends in Ecology and Evolution 25(12):684-685 (2010)
  
• Names are key to the big new biology
  - Trends in Ecology and Evolution 25(12):686-691 (2010)
  Those who seek answers to big, broad questions about biology, especially questions emphasizing the organism (taxonomy, evolution and ecology), will soon benefit from an emerging names-based infrastructure. It will draw on the almost universal association of organism names with biological information to index and interconnect information distributed across the Internet. The result will be a virtual data commons, expanding as further data are shared, allowing biology to become more of a 'big science'. Informatics devices will exploit this 'big new biology', revitalizing comparative biology with a broad perspective to reveal previously inaccessible trends and discontinuities, so helping us to reveal unfamiliar biological truths. Here, we review the first components of this freely available, participatory and semantic Global Names Architecture.
• Assessing rapid evolution in a changing environment
  - Trends in Ecology and Evolution 25(12):692-698 (2010)
  Climate change poses a serious threat to species persistence. Effective modelling of evolutionary responses to rapid climate change is therefore essential. In this review we examine recent advances in phylogenetic comparative methods, techniques normally used to study adaptation over long periods, which allow them to be applied to the study of adaptation over shorter time scales. This increased applicability is largely due to the emergence of more flexible models of character evolution and the parallel development of molecular technologies that can be used to assess adaptive variation at loci scattered across the genome. The merging of phylogenetic and population genetic approaches to the study of adaptation has significant potential to advance our understanding of rapid responses to environmental change.
• Making statistics biologically relevant in fragmented landscapes
  - Trends in Ecology and Evolution 25(12):699-704 (2010)
  The biological impacts of habitat fragmentation are routinely assessed using standard statistical modelling techniques that are used across many ecological disciplines. However, to assess the biological relevance of fragmentation impacts, we must consider an extra, spatial dimension to the standard statistical model: the biological importance of a significant and well supported model with large effect sizes crucially depends on the configuration of habitat within the study area. We argue that mapping the outputs from statistical models across a study area generates biologically meaningful estimates of fragmentation impacts. Integrating traditional statistical approaches with geographic information systems will facilitate rigorous comparisons of fragmentation impacts between taxa, studies and ecosystems.
• Adaptation genomics: the next generation
  - Trends in Ecology and Evolution 25(12):705-712 (2010)
  Understanding the genetics of how organisms adapt to changing environments is a fundamental topic in modern evolutionary ecology. The field is currently progressing rapidly because of advances in genomics technologies, especially DNA sequencing. The aim of this review is to first briefly summarise how next generation sequencing (NGS) has transformed our ability to identify the genes underpinning adaptation. We then demonstrate how the application of these genomic tools to ecological model species means that we can start addressing some of the questions that have puzzled ecological geneticists for decades such as: How many genes are involved in adaptation? What types of genetic variation are responsible for adaptation? Does adaptation utilise pre-existing genetic variation or does it require new mutations to arise following an environmental change?
• Species differences in responses to captivity: stress, welfare and the comparative method
  - Trends in Ecology and Evolution 25(12):713-721 (2010)
  Approximately 26 billion animals, spanning over 10 000 species, are kept on farms and in zoos, conservation breeding centers, research laboratories and households. Captive animals are often healthier, longer-lived and more fecund than free-living conspecifics, but for some species the opposite is true. Captivity is a very long way from the ideal 'common garden' often assumed by evolutionary and ecological researchers using data for captive animals. The use of comparative methods to investigate the fundamental biological causes of these species differences would help to improve husbandry and enclosure design, and might even reveal relationships between susceptibilities to poor captive welfare and susceptibilities to anthropogenic threat in the wild. Studies of these species differences could also inspire and facilitate 'evo-mecho' research into the functions of behavioral control mechanisms.

Hot off the presses! Dec 01 Trends Plant Sci

The Dec 01 issue of the Trends Plant Sci is now up on Pubget (About Trends Plant Sci): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends Plant Sci 15(12):i (2010)
  
• Viral trans-dominant manipulation of algal sphingolipids
  - Trends Plant Sci 15(12):651-655 (2010)
  Emiliania huxleyi is the host for the coccolithovirus (EhV), which is responsible for the demise of large oceanic blooms formed by this alga. The EhV-86 virus genome sequence has identified several genes apparently involved in sphingolipid metabolism. Recently, an unusual glucosylceramide from E. huxleyi infected with EhV-86 was isolated, implicating sphingolipids in the lysis of this alga. However, the EhV-86-encoded genes contain only a subset of the activities required to generate the novel sphingolipid, implying that its synthesis is the result of coordinated interactions between algal- and viral-encoded biosynthetic enzymes. Here, we discuss the likely role for EhV-86 open reading frames (ORFs) in the synthesis of novel sphingolipids and also consider the concept of the trans-dominant manipulation of lipid metabolism.
• Membrane rafts in plant cells
  - Trends Plant Sci 15(12):656-663 (2010)
  Over the past five years, the structure, composition and possible functions of membrane raft-like domains on plant plasma membranes (PM) have been described. Proteomic analyses have indicated that a high proportion of proteins associated with detergent-insoluble membranes (DIMs), supposed to contain raft-like domains isolated from the PM, might be involved in signalling pathways. Recently, the dynamic association of specific proteins with the DIM fraction upon environmental stress has been reported. Innovative imaging methods have shown that lateral segregation of lipids and proteins exists at the nanoscale level in the plant PM, correlating detergent insolubility and membrane-domain localization of presumptive raft proteins. These data suggest a role for plant rafts as signal transduction platforms, similar to those documented for mammalian cells.
• Plant molecular stress responses face climate change
  - Trends Plant Sci 15(12):664-674 (2010)
  Environmental stress factors such as drought, elevated temperature, salinity and rising CO2 affect plant growth and pose a growing threat to sustainable agriculture. This has become a hot issue due to concerns about the effects of climate change on plant resources, biodiversity and global food security. Plant adaptation to stress involves key changes in the '-omic' architecture. Here, we present an overview of the physiological and molecular programs in stress adaptation focusing on how genes, proteins and metabolites change after individual and multiple environmental stresses. We address the role which '-omics' research, coupled to systems biology approaches, can play in future research on plants seemingly unable to adapt as well as those which can tolerate climatic change.
• Landscape genetics of plants
  - Trends Plant Sci 15(12):675-683 (2010)
  Landscape genetics is the amalgamation of landscape ecology and population genetics to help with understanding microevolutionary processes such as gene flow and adaptation. In this review, we examine why landscape genetics of plants lags behind that of animals, both in number of studies and consideration of landscape elements. The classical landscape distance/resistance approach to study gene flow is challenging in plants, whereas boundary detection and the assessment of contemporary gene flow are more feasible. By contrast, the new field of landscape genetics of adaptive genetic variation, establishing the relationship between adaptive genomic regions and environmental factors in natural populations, is prominent in plant studies. Landscape genetics is ideally suited to study processes such as migration and adaptation under global change.
• Plant phenotypic plasticity in a changing climate
  - Trends Plant Sci 15(12):684-692 (2010)
  Climate change is altering the availability of resources and the conditions that are crucial to plant performance. One way plants will respond to these changes is through environmentally induced shifts in phenotype (phenotypic plasticity). Understanding plastic responses is crucial for predicting and managing the effects of climate change on native species as well as crop plants. Here, we provide a toolbox with definitions of key theoretical elements and a synthesis of the current understanding of the molecular and genetic mechanisms underlying plasticity relevant to climate change. By bringing ecological, evolutionary, physiological and molecular perspectives together, we hope to provide clear directives for future research and stimulate cross-disciplinary dialogue on the relevance of phenotypic plasticity under climate change.
• Patatin-related phospholipase A: nomenclature, subfamilies and functions in plants
  - Trends Plant Sci 15(12):693-700 (2010)
  The release of fatty acids from membrane glycerolipids has been implicated in a variety of cellular processes, but the enzymes involved and their regulation are poorly understood in plants. One large group of acyl-hydrolyzing enzymes is structurally related to patatins. Patatins are potato tuber proteins with acyl-hydrolyzing activity, and the patatin catalytic domain is widely spread in bacterial, yeast, plant and animal enzymes. Recent results have indicated that patatin-related enzymes are involved in different cellular functions, including plant responses to auxin, elicitors or pathogens, and abiotic stresses and lipid mobilization during seed germination. In this review, we highlight recent developments regarding these enzymes and propose the nomenclature pPLA for the patatin-related phospholipase A enzyme.
• Virus-derived small interfering RNAs at the core of plant–virus interactions
  - Trends Plant Sci 15(12):701-707 (2010)
  Once a virus enters a cell, viral double-stranded RNA (dsRNA) is targeted by the RNA silencing machinery to initiate a cascade of regulatory events directed by viral small interfering RNAs (vsiRNAs). Recent genetic and functional studies along with the high-throughput sequencing of vsiRNAs have shed light on the genetic and structural requirements for virus targeting, the origins and compositions of vsiRNAs and their potential for controlling gene expression. The precise nature of the triggering molecules of virus-induced RNA silencing or the targeting constraints for viral genome recognition and processing represent outstanding questions that will be discussed in this review. The contribution of vsiRNAs to antiviral defense and host genome modifications has profound implications for our understanding of viral pathogenicity and host specificity in plants.

Hot off the presses! Aug 01 Trends Genet

The Aug 01 issue of the Trends Genet is now up on Pubget (About Trends Genet): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends Genet 25(8):i (2009)
  
• Are transposable elements simply silenced or are they under house arrest?
  - Trends Genet 25(8):333-334 (2009)
  Despite their role as key players in evolution, it is commonly thought that transposable elements are selected against and silenced. However, their importance in chromosomal biology and, therefore, cell division suggests that their presence in many eukaryote genomes is the result of their having been selected as major components of heterochromatin.
• What controls nucleosome positions?
  - Trends Genet 25(8):335-343 (2009)
  The DNA of eukaryotic genomes is wrapped in nucleosomes, which strongly distort and occlude the DNA from access to most DNA-binding proteins. An understanding of the mechanisms that control nucleosome positioning along the DNA is thus essential to understanding the binding and action of proteins that carry out essential genetic functions. New genome-wide data on in vivo and in vitro nucleosome positioning greatly advance our understanding of several factors that can influence nucleosome positioning, including DNA sequence preferences, DNA methylation, histone variants and post-translational modifications, higher order chromatin structure, and the actions of transcription factors, chromatin remodelers and other DNA-binding proteins. We discuss how these factors function and ways in which they might be integrated into a unified framework that accounts for both the preservation of nucleosome positioning and the dynamic nucleosome repositioning that occur across biological! conditions, cell types, developmental processes and disease.
• Developmental genome rearrangements in ciliates: a natural genomic subtraction mediated by non-coding transcripts
  - Trends Genet 25(8):344-350 (2009)
  Several classes of non-protein-coding RNAs have recently been identified as epigenetic regulators of developmental genome rearrangements in ciliates, providing an interesting insight into the role of genome-wide transcription. In these unicellular eukaryotes, extensive rearrangements of the germline genome occur during the development of a new somatic macronucleus from the germline micronucleus. Rearrangement patterns are not dictated by the germline sequence, but reproduce the pre-existing rearrangements of the maternal somatic genome, implying a homology-dependent global comparison of germline and somatic genomes. We review recent evidence showing that this is achieved by a natural genomic subtraction, computed by pairing interactions between meiosis-specific, germline scnRNAs (small RNAs that resemble metazoan piRNAs) and longer non-coding transcripts from the somatic genome. We focus on current models for the RNA-based mechanisms enabling the cell to recognize the ! germline sequences to be eliminated from the somatic genome and to maintain an epigenetic memory of rearrangement patterns across sexual generations.
• What's in a name? Y chromosomes, surnames and the genetic genealogy revolution
  - Trends Genet 25(8):351-360 (2009)
  Heritable surnames are highly diverse cultural markers of coancestry in human populations. A patrilineal surname is inherited in the same way as the non-recombining region of the Y chromosome and there should, therefore, be a correlation between the two. Studies of Y haplotypes within surnames, mostly of the British Isles, reveal high levels of coancestry among surname cohorts and the influence of confounding factors, including multiple founders for names, non-paternities and genetic drift. Combining molecular genetics and surname analysis illuminates population structure and history, has potential applications in forensic studies and, in the form of 'genetic genealogy', is an area of rapidly growing interest for the public.
• Genetics of complex neurological disease: challenges and opportunities for modeling epilepsy in mice and rats
  - Trends Genet 25(8):361-367 (2009)
  Currently, 20 genetic variants are known to cause Mendelian forms of human epilepsy, leaving a vast heritability undefined. Rodent models for genetically complex epilepsy have been studied for many years, but only recently have strong candidate genes emerged, including Cacna1 g in the GAERS rat model of absence epilepsy and Kcnj10 in the low seizure threshold of DBA/2 mice. In parallel, a growing number of mouse mutations studied on multiple strain backgrounds reveal the impact of genetic modifiers on seizure severity, incidence or form – perhaps mimicking the complexity seen in humans. The field of experimental genetics in rodents is poised to study discrete epilepsy mutations on a diverse choice of strain backgrounds to develop better models and identify modifiers. But, it must find the right balance between embracing the strain diversity available, with the ability to detect and characterize genetic effects. Using alternative strain backgrounds when studying epile! psy mutations will enhance the modeling of epilepsy as a complex genetic disease.
• Understanding synergy in genetic interactions
  - Trends Genet 25(8):368-376 (2009)
  Synergy occurs when the contribution of two mutations to the phenotype of a double mutant exceeds the expectations from the additive effects of the individual mutations. The molecular characterization of genes involved in synergistic interactions has revealed that synergy mainly results from mutations in functionally related genes. Recent research in Arabidopsis thaliana has advanced our understanding of the scenarios resulting in synergistic phenotypes. Those involving homologous loci usually result from various levels of functional redundancy. Some of these loci fail to complement each other or become dose-dependent in certain multiple mutant combinations, suggesting that the effects of haploinsufficiency and redundancy can combine. Synergy involving non-homologous genes probably reflects the topology of the regulatory or metabolic networks and can arise when pathways that converge at a node are disrupted. The Hub genes provide a remarkable example, these genes have ! an extraordinary number of connections and mutations that interact with many unrelated pathways.

Hot off the presses! Jul 01 Trends Plant Sci

The Jul 01 issue of the Trends Plant Sci is now up on Pubget (About Trends Plant Sci): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends Plant Sci 16(7):i (2011)
  
• Understanding pollen tube growth: the hydrodynamic model versus the cell wall model
  - Trends Plant Sci 16(7):347-352 (2011)
  Scientific progress stimulates the evolution of models used to understand and conceptualize biological behaviors. The widely accepted cell wall model of pollen tube growth explains stochastic growth of the apical pectin wall, but fails to explain the mechanism driving oscillations in growth and cell signaling. Recent advances led to the formulation of a new hydrodynamic model that explains the mechanism that drives both stochastic and oscillatory growth, as well as oscillations in cell signaling and ion fluxes. A critical analysis of evidence that has been used to challenge the validity of the hydrodynamic model yields new information on turgor pressure, cell mechanical properties and nonlinear dynamics in pollen tube growth. These results may have broader significance for plant cell growth.
• Pollen tubes and the physical world
  - Trends Plant Sci 16(7):353-355 (2011)
  The primary goal of our previous opinion paper (Winship, L.J. et al. (2010) Trends Plant Sci. 15, 363–369) [1] was to put two models for the control of pollen tube growth on the same theoretical and biophysical footing, and to then test both for consistency with basic principles and with experimental data. Our central thesis, then and now, is that the biophysical and biochemical mechanisms that enable pollen tubes to grow and to respond to their environment evolved in a physical context constrained by known, inescapable principles. First, pressure is a scalar, not a vector quantity. Second, the water movement in and out of plant cells that generates pressure is passive, not active, and is controlled by differences in water potential. Here we respond to the issues raised by Zonia and Munnik (Trends Plant Sci. 2011; this issue) [2] in the light of new evidence concerning turgor pressure and pollen tube growth rates.
• Successful joint ventures of plants: arbuscular mycorrhiza and beyond
  - Trends Plant Sci 16(7):356-362 (2011)
  Among the oldest symbiotic associations of plants are arbuscular mycorrhiza (AM) with fungi of the phylum Glomeromycota. Although many of the symbiotic signaling components have been identified on the side of the plant, AM fungi have long evaded genetic analysis owing to their strict biotrophy and their exceptional genetics. Recently, the identification of the fungal symbiosis signal (Myc factor) and of a corresponding Myc factor receptor, and new insights into AM fungal genetics, have opened new avenues to address early communication and functional aspects of AM symbiosis. These advances will pave the way for breeding programs towards adapted AM fungi for crop production, and will shed light on the ecology and evolution of this remarkably successful symbiosis.
• Agricultural biotechnology for crop improvement in a variable climate: hope or hype?
  - Trends Plant Sci 16(7):363-371 (2011)
  Developing crops that are better adapted to abiotic stresses is important for food production in many parts of the world today. Anticipated changes in climate and its variability, particularly extreme temperatures and changes in rainfall, are expected to make crop improvement even more crucial for food production. Here, we review two key biotechnology approaches, molecular breeding and genetic engineering, and their integration with conventional breeding to develop crops that are more tolerant of abiotic stresses. In addition to a multidisciplinary approach, we also examine some constraints that need to be overcome to realize the full potential of agricultural biotechnology for sustainable crop production to meet the demands of a projected world population of nine billion in 2050.
• Poly(ADP-ribosyl)ation in plants
  - Trends Plant Sci 16(7):372-380 (2011)
  Poly(ADP-ribose) polymerases (PARPs) and poly(ADP-ribose) glycohydrolases (PARGs) are the main enzymes responsible for the post-translational modification known as poly(ADP-ribosyl)ation. These enzymes play important roles in genotoxic stress tolerance and DNA repair, programmed cell death, transcription, and cell cycle control in animals. Similar impacts are being discovered in plants, as well as roles in plant-specific processes. In particular, we review recent work that has revealed significant roles for poly(ADP-ribosyl)ation in plant responses to biotic and abiotic stress, as well as roles for ADP-ribose pyrophosphatases (a subset of the nucleoside diphosphate linked to some moiety-X or NUDX hydrolases). Future challenges include identification of poly(ADP-ribosyl)ation targets and interacting proteins, improved use of inhibitors and plant mutants, and field-based studies with economically valuable plant species.
• The biochemistry of nitrogen mobilization: purine ring catabolism
  - Trends Plant Sci 16(7):381-387 (2011)
  The enzymatic route of purine ring catabolism has recently been completed by the discovery of several novel enzymes identified through comparative genome analyses. Here, we review these recent discoveries and present an overview of purine ring catabolism in plants. Xanthine is oxidized to urate in the cytosol, followed by three enzymatic steps taking place in the peroxisome and four reactions in the endoplasmic reticulum releasing the four ring nitrogen as ammonia. Although the main physiological function of purine degradation might lie in the remobilization of nitrogen resources, it has also emerged that catabolic intermediates, the ureides allantoin and allantoate, are likely to be involved in protecting plants against abiotic stress. Conserved alternative splicing mediating the peroxisomal as well as cytosolic localization of allantoin synthase potentially links purine ring catabolism to brassinosteroid signaling.
• Cytokinins and plant immunity: old foes or new friends?
  - Trends Plant Sci 16(7):388-394 (2011)
  Cytokinins are plant growth promoting hormones involved in the specification of embryonic cells, maintenance of meristematic cells, shoot formation and development of vasculature. Cytokinins have also emerged as a major factor in plant–microbe interactions during nodule organogenesis and pathogenesis. Microbe-originated cytokinins confer abnormal hypersensitivity of cytokinins to plants, augmenting the sink activity of infected regions. However, recent findings have shed light on a distinct role of cytokinins in plant immune responses. Plant-borne cytokinins systemically induce resistance against pathogen infection. This resistance is orchestrated by endogenous cytokinin and salicylic acid signaling. Here, we discuss how plant- and pathogen-derived cytokinins inversely affect the plant defense response. In addition, we consider the molecular mechanisms underlying plant-derived cytokinin action in plant immunity.
• Chloroplastic and mitochondrial metal homeostasis
  - Trends Plant Sci 16(7):395-404 (2011)
  Transition metal deficiency has a strong impact on the growth and survival of an organism. Indeed, transition metals, such as iron, copper, manganese and zinc, constitute essential cofactors for many key cellular functions. Both photosynthesis and respiration rely on metal cofactor-mediated electron transport chains. Chloroplasts and mitochondria are, therefore, organelles with high metal ion demand and represent essential components of the metal homeostasis network in photosynthetic cells. In this review, we describe the metal requirements of chloroplasts and mitochondria, the acclimation of their functions to metal deficiency and recent advances in our understanding of their contributions to cellular metal homeostasis, the control of the cellular redox status and the synthesis of metal cofactors.

Hot off the presses! Jul 01 Trends Genet

The Jul 01 issue of the Trends Genet is now up on Pubget (About Trends Genet): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends Genet 27(7):i (2011)
  
• Demography, kinship, and the evolving theory of genomic imprinting
  - Trends Genet 27(7):251-257 (2011)
  Genomic imprinting is the differential expression of an allele based on the parent of origin. Recent transcriptome-wide evaluations of the number of imprinted genes reveal complex patterns of imprinted expression among developmental stages and cell types. Such data demand a comprehensive evolutionary framework in which to understand the effect of natural selection on imprinted gene expression. We present such a framework for how asymmetries in demographic parameters and fitness effects can lead to the evolution of genomic imprinting and place recent theoretical advances in this framework. This represents a modern interpretation of the kinship theory, is well suited to studying populations with complex social interactions, and provides predictions which can be tested with forthcoming transcriptomic data. To understand the intricate phenotypic patterns that are emerging from the recent deluge of data, future investigations of genomic imprinting will require integrating e! volutionary theory, transcriptomic data, developmental and functional genetics, and natural history.
• Evolutionary genetics of plant adaptation
  - Trends Genet 27(7):258-266 (2011)
  Plants provide unique opportunities to study the mechanistic basis and evolutionary processes of adaptation to diverse environmental conditions. Complementary laboratory and field experiments are important for testing hypotheses reflecting long-term ecological and evolutionary history. For example, these approaches can infer whether local adaptation results from genetic tradeoffs (antagonistic pleiotropy), where native alleles are best adapted to local conditions, or if local adaptation is caused by conditional neutrality at many loci, where alleles show fitness differences in one environment, but not in a contrasting environment. Ecological genetics in natural populations of perennial or outcrossing plants can also differ substantially from model systems. In this review of the evolutionary genetics of plant adaptation, we emphasize the importance of field studies for understanding the evolutionary dynamics of model and nonmodel systems, highlight a key life history tr! ait (flowering time) and discuss emerging conservation issues.
• Functional consequences of bidirectional promoters
  - Trends Genet 27(7):267-276 (2011)
  Several studies have shown that promoters of protein-coding genes are origins of pervasive non-coding RNA transcription and can initiate transcription in both directions. However, only recently have researchers begun to elucidate the functional implications of this bidirectionality and non-coding RNA production. Increasing evidence indicates that non-coding transcription at promoters influences the expression of protein-coding genes, revealing a new layer of transcriptional regulation. This regulation acts at multiple levels, from modifying local chromatin to enabling regional signal spreading and more distal regulation. Moreover, the bidirectional activity of a promoter is regulated at multiple points during transcription, giving rise to diverse types of transcripts.
• Constitutive gene expression and the specification of tissue identity in adult planarian biology
  - Trends Genet 27(7):277-285 (2011)
  Planarians are flatworms that constitutively maintain adult tissues through cell turnover and can regenerate entire organisms from tiny body fragments. In addition to requiring new cells (from neoblasts), these feats require mechanisms that specify tissue identity in the adult. Crucial roles for Wnt and BMP signaling in the regeneration and maintenance of the body axes have been uncovered, among other regulatory factors. Available data indicate that genes involved in positional identity regulation at key embryonic stages in other animals display persisting regionalized expression in adult planarians. These expression patterns suggest that a constitutively active gene expression map exists for the maintenance of the planarian body. Planarians thus present a fertile ground for the identification of factors regulating the regionalization of the metazoan body plan and for the study of the attributes of these factors that can lead to the maintenance and regeneration of adul! t tissues.
• Strategies for viral RNA stability: live long and prosper
  - Trends Genet 27(7):286-293 (2011)
  Eukaryotic cells have a powerful RNA decay machinery that plays an important and diverse role in regulating both the quantity and the quality of gene expression. Viral RNAs need to successfully navigate around this cellular machinery to initiate and maintain a highly productive infection. Recent work has shown that viruses have developed a variety of strategies to accomplish this, including inherent RNA shields, hijacking host RNA stability factors, incapacitating the host decay machinery and changing the entire landscape of RNA stability in cells using virally encoded nucleases. In addition to maintaining the stability of viral transcripts, these strategies can also contribute to the regulation and complexity of viral gene expression as well as to viral RNA evolution.

Hot off the presses! Jan 01 Trends Plant Sci

The Jan 01 issue of the Trends Plant Sci is now up on Pubget (About Trends Plant Sci): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends Plant Sci 16(1):i (2011)
  
• Transcription strength and halophytic lifestyle
  - Trends Plant Sci 16(1):1-3 (2011)
  
• Reconnecting plants and pollinators: challenges in the restoration of pollination mutualisms
  - Trends Plant Sci 16(1):4-12 (2011)
  Ecological restoration of plant–pollinator interactions has received surprisingly little attention, despite animal-mediated pollination underpinning reproduction of the majority of higher plants. Here, we offer a conceptual and practical framework for the ecological restoration of pollination mutualisms. Through the use of targeted restoration plantings to attract and sustain pollinators and increased knowledge of the ecological requirements of pollinators, we propose that pollination could be successfully restored in degraded ecosystems. The challenge for pollination biologists is to integrate their findings with those of plant restoration ecologists to ensure sustainable pollination in restored ecosystems.
• Taking a tree's perspective on forest fragmentation genetics
  - Trends Plant Sci 16(1):13-18 (2011)
  Despite longstanding research, how anthropogenic disturbance affects the genetics of tree populations remains poorly understood. Although empirical evidence often conflicts with theoretical expectations, little progress has been made in refining experimental design or in reformulating theoretical hypotheses. Such progress is, however, essential to understand how forest tree species can tolerate anthropogenic disturbance. Further advances in forest fragmentation genetics research will require that processes driving reproduction and recruitment in fragmented populations are assessed from a tree's perspective instead of experimental convenience, using a multidisciplinary approach to explain the spatiotemporal dynamics of gene dispersal. In this opinion article we aim to inspire a new perspective in forest fragmentation genetics research.
• PIFs: pivotal components in a cellular signaling hub
  - Trends Plant Sci 16(1):19-28 (2011)
  A small subset of basic helix–loop–helix transcription factors called PIFs (phytochrome-interacting factors) act to repress seed germination, promote seedling skotomorphogenesis and promote shade-avoidance through regulated expression of over a thousand genes. Light-activated phytochrome molecules directly reverse these activities by inducing rapid degradation of the PIF proteins. Here, we review recent advances in dissecting this signaling pathway and examine emerging evidence that indicates that other pathways also converge to regulate PIF activity, including the gibberellin pathway, the circadian clock and high temperature. Thus PIFs have broader roles than previously appreciated, functioning as a cellular signaling hub that integrates multiple signals to orchestrate regulation of the transcriptional network that drives multiple facets of downstream morphogenesis. The relative contributions of the individual PIFs to this spectrum of regulatory functions ranges f! rom quantitatively redundant to qualitatively distinct.
• Porphyra: a marine crop shaped by stress
  - Trends Plant Sci 16(1):29-37 (2011)
  The marine red alga Porphyra is an important marine crop, worth US$1.3 billion per year. Cultivation research now includes farm ecology, breeding, strain conservation and new net-seeding technologies. The success of cultivation is due, in part, to the high stress tolerance of Porphyra. Many species of Porphyra lose 85–95% of their cellular water during the daytime low tide, when they are also exposed to high light and temperature stress. Antioxidant and mycosporine-like amino acid activities have been partially characterized in Porphyra, but, as we discuss here, the Porphyra umbilicalis genome project will further elucidate proteins associated with stress tolerance. Furthermore, phylogenomic and transcriptomic investigations of Porphyra sensu lato could elucidate tradeoffs made during physiological acclimation and factors associated with life-history evolution in this ancient lineage.
• WD40 and CUL4-based E3 ligases: lubricating all aspects of life
  - Trends Plant Sci 16(1):38-46 (2011)
  The ubiquitin proteasome pathway is one of the major regulatory tools used by eukaryotic cells. E3 ligases, which allow controlled modification of proteins with ubiquitin, are crucial for the specificity of the pathway. Recently, an additional plant cullin-based E3 ligase complex was described which contains cullin 4 (CUL4) and DAMAGED DNA BINDING 1 protein as core subunits. Our knowledge of this E3 ligase has increased tremendously since its first description, and it seems to be involved in many developmental and physiological processes. Here, we review the most recent studies on CUL4 E3 complexes, with a focus on their substrate recognition and the plethora of processes that they regulate in plants, such as photomorphogenesis, flowering and abiotic stress response.
• Defining the boundaries: structure and function of LOB domain proteins
  - Trends Plant Sci 16(1):47-52 (2011)
  The plant-specific LBD (Lateral Organ Boundaries Domain) gene family is essential in the regulation of plant lateral organ development and is involved in the regulation of anthocyanin and nitrogen metabolism. LBD proteins contain a characteristic LOB domain composed of a C-motif required for DNA-binding, a conserved glycine residue, and a leucine-zipper-like sequence required for protein–protein interactions. Recently, several LBD genes associated with mutant phenotypes related to almost all aspects of plant development, including embryo, root, leaf, and inflorescence development have been functionally characterized. These novel insights contribute to a better understanding of the molecular definition of boundaries between organs or boundaries between organs and meristems and the regulation of these processes by environmental cues and phytohormones.
• Photoprotection in plants: a new light on photosystem II damage
  - Trends Plant Sci 16(1):53-60 (2011)
  Sunlight damages photosynthetic machinery, primarily photosystem II (PSII), and causes photoinhibition that can limit plant photosynthetic activity, growth and productivity. The extent of photoinhibition is associated with a balance between the rate of photodamage and its repair. Recent studies have shown that light absorption by the manganese cluster in the oxygen-evolving complex of PSII causes primary photodamage, whereas excess light absorbed by light-harvesting complexes acts to cause inhibition of the PSII repair process chiefly through the generation of reactive oxygen species. As we review here, PSII photodamage and the inhibition of repair are therefore alleviated by photoprotection mechanisms associated with avoiding light absorption by the manganese cluster and successfully consuming or dissipating the light energy absorbed by photosynthetic pigments, respectively.

Hot off the presses! May 01 Trends Pl Sci

The May 01 issue of the Trends Pl Sci is now up on Pubget (About Trends Pl Sci): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

• Editorial Board
  - Trends Pl Sci 16(5):i (2011)
  
• Combining phenotypic data from ordinal rating scales in multiple plant experiments
  - Trends Pl Sci 16(5):235-237 (2011)
  
• Self-incompatibility: Smi silences through a novel sRNA pathway
  - Trends Pl Sci 16(5):238-241 (2011)
  Self-incompatibility in Brassicaceae is determined by the interaction between S-Locus Protein 11 (SP11) on the pollen and S-receptor kinase (SRK) in the stigma. Pollen from heterozygotes generally displays products of both SP11 alleles, but in some heterozygotes SP11 expression is monoallelic, with one allele (SP11R) being silenced by promoter methylation. An exciting development in understanding the mechanism behind monoallelic silencing came recently when Y. Tarutani et al. [Nature 2010;466:983–986] identified a 24-nucleotide sRNA (termed Smi) derived from a non-coding gene within the dominant S-haplotype, and suggested that Smi directs promoter methylation. We propose that rather than having a direct effect on DNA methylation, Smi is the first step in a novel cis-acting siRNA pathway that directs widespread monoallelic SP11R promoter methylation.
• MicroRNA misregulation: an overlooked factor generating somaclonal variation?
  - Trends Pl Sci 16(5):242-248 (2011)
  Somaclonal variation is an important phenomenon that can be observed at high levels in plant tissue culture. Although known to science since plant cell culture techniques were first developed, its origins remain mysterious. Here, we propose that misregulation of microRNAs and small RNA pathways can make a significant contribution to the phenomenon. For many reasons, microRNAs and related small RNAs appear ideal candidates. Their mode of action gives them disproportionate influence over the transcriptome, proteome and epigenome. They regulate important developmental and physiological events such as meristem formation, phase changes and hormone responses. However, the genomic locations of microRNA genes and their unique biogenesis might make them unusually susceptible to aberrant regulation in vitro.
• Jasmonate-induced defenses: a tale of intelligence, collaborators and rascals
  - Trends Pl Sci 16(5):249-257 (2011)
  Plants have sophisticated defense systems to protect their tissues against the attack of herbivorous organisms. Many of these defenses are orchestrated by the oxylipin jasmonate. A growing body of evidence indicates that the expression of jasmonate-induced responses is tightly regulated by the ecological context of the plant. Ecological information is provided by molecular signals that indicate the nature of the attacker, the value of the attacked organs, phytochrome status and thereby proximity of competing plants, association with beneficial organisms and history of plant interactions with pathogens and herbivores. This review discusses recent advances in this field and highlights the need to map the activities of informational modulators to specific control points within our emerging model of jasmonate signaling.
• MicroRNA networks and developmental plasticity in plants
  - Trends Pl Sci 16(5):258-264 (2011)
  Plant microRNAs (miRNAs) are embedded in regulatory networks that coordinate different gene expression programs in support of developmental plasticity. Modification of miRNA-target nodes during evolution might in turn underlie morphological and physiological diversity. A survey of the literature indicates that miRNA-target nodes themselves are organized in networks, and here we discuss some of the developmental traits they control along with possible interactions between miRNA and their targets. Because miRNAs and their interactions are not only at the heart of regulating many aspects of developmental plasticity, but because they also have an inherently quantitative mode of action, they present important targets for biotechnology applications.
• Viral suppressors of RNA silencing
  - Trends Pl Sci 16(5):265-272 (2011)
  The infection and replication of viruses in the host induce diverse mechanisms for combating viral infection. One of the best-studied antiviral defence mechanisms is based on RNA silencing. Consistently, several viral suppressors of RNA silencing (VSRs) have been identified from almost all plant virus genera, which are surprisingly diverse within and across kingdoms, exhibiting no obvious sequence similarities. VSRs efficiently inhibit host antiviral responses by interacting with the key components of cellular silencing machinery, often mimicking their normal cellular functions. Recent findings have revealed that the impact of VSRs on endogenous pathways is more complex and profound than had been estimated thus far. This review highlights the current understanding of and new insights into the mechanisms and functions of plant VSRs.
• Organization and dynamics of plant interphase chromosomes
  - Trends Pl Sci 16(5):273-281 (2011)
  Eukaryotic chromosomes occupy distinct territories within interphase nuclei. The arrangement of chromosome territories (CTs) is important for replication, transcription, repair and recombination processes. Our knowledge about interphase chromatin arrangement is mainly based on results from in situ labeling approaches. The phylogenetic affiliation of a species, cell cycle, differentiation status and environmental factors are all likely to influence interphase nuclear architecture. In this review we survey current data about relative positioning of CTs, somatic pairing of homologs, and sister chromatid alignment in meristematic and differentiated tissues, using data derived mainly from Arabidopsis thaliana, wheat (Triticum aestivum) and their relatives. We discuss morphological constraints and epigenetic impacts on nuclear architecture, the evolutionary stability of CT arrangements, and alterations of nuclear architecture during transcription and repair.
• Fast-forward genetics enabled by new sequencing technologies
  - Trends Pl Sci 16(5):282-288 (2011)
  New sequencing technologies are dramatically accelerating progress in forward genetics, and the use of such methods for the rapid identification of mutant alleles will be soon routine in many laboratories. A straightforward extension will be the cloning of major-effect genetic variants in crop species. In the near future, it can be expected that mapping by sequencing will become a centerpiece in efforts to discover the genes responsible for quantitative trait loci. The largest impact, however, might come from the use of these strategies to extract genes from non-model, non-crop plants that exhibit heritable variation in important traits. Deployment of such genes to improve crops or engineer microbes that produce valuable compounds heralds a potential paradigm shift for plant biology.