bluuebunny/crossref_metadata_2025 huggingface dataset:
New Perspectives on Statistical Decisions Under Ambiguity
Authors: Stoye Jörg
Published: June 2012

This review summarizes and connects recent work on the foundations and applications of statistical decision theory. Minimax models of decisions making under ambiguity are identified as a thread running through several literatures. In axiomatic decision theory, these models motivated a large literature on modeling ambiguity aversion. Some findings of this literature are reported in a way that should be directly accessible to statisticians and econometricians. In statistical decision theory, the models inform a rich theory of estimation and treatment choice, which was recently extended to account for partial identification and thereby ambiguity that does not vanish with sample size. This literature is illustrated by discussing global, finite-sample admissible, and minimax decision rules for a number of stylized decision problems with point and partial identification.
The Distribution of Teacher Quality and Implications for Policy
Authors: Hanushek Eric A. , Rivkin Steven G.
Published: June 2012

It has become commonplace to measure teacher quality in terms of teacher value-added. Operationally, this means evaluating teachers according to the learning gains of students on various achievement tests. Existing research consistently shows large variations in teacher effectiveness, much of which is within schools as opposed to between schools. The policy implications of these variations are dramatic. But the underlying statistical modeling has become the subject of intense research, in part because of this direct use of value-added measures in policy discussions.
Natural Resource Wealth: The Challenge of Managing a Windfall
Authors: van der Ploeg Frederick , Venables Anthony J.
Published: June 2012

Many countries have failed to use natural resource wealth to promote growth and development. They have been damaged by the volatility of revenues and have failed to save a sufficiently high proportion of their resource revenues and failed to make high-return investments to support diversification of their economies. This review explores the reasons for these failures and discusses policies to improve performance.
The Theory of Clubs and Competitive Coalitions
Authors: Wooders Myrna
Published: June 2012

This review discusses research demonstrating that club economies and coalition economies with many participants and relatively small effective groups (clubs, jurisdictions, or coalitions) are competitive. Small groups are effective if all or almost all gains to collective activities can be realized by cooperation restricted to them. At this point, there are many papers in the literature demonstrating the competitiveness of club and coalition economies in a variety of contexts. To facilitate the exposition, I treat economies with quasi-linear utilities and games with side payments. The main concepts and results for this framework are discussed. Additionally, relationships are established with regard to broader models of club and coalition economies, including very recent contributions to the literature.
Recent Research on the Economics of Patents
Authors: Hall Bronwyn H. , Harhoff Dietmar
Published: June 2012

This review surveys recent research on the economics of patents. The topics covered include theoretical and empirical evidence on patents as incentives for innovation, the effectiveness of patents for invention disclosure, patent valuation, and the design of patent systems. We also look at some current policy areas, including software and business method patents, university patenting, and the growth in patent litigation.
Life-Cycle Wage Growth and Heterogeneous Human Capital
Authors: Sanders Carl , Taber Christopher
Published: June 2012

Wages grow rapidly for young workers, and the human capital investment model is the classic framework to explain this growth. While estimation and the theory of human capital have traditionally focused on general human capital, both have evolved toward models of heterogeneous human capital. In this article, we review and evaluate the current state of this literature. We exposit the classic model of general human capital investment and extend it to show how a model of heterogeneous human capital can nest previous models. We then summarize the empirical literature on firm-specific human capital, industry- and occupation-specific human capital, and task-specific human capital and discuss how these concepts can explain a wide variety of labor market phenomena that traditional models cannot.
Recent Developments in the Economics of Time Use
Authors: Aguiar Mark , Hurst Erik , Karabarbounis Loukas
Published: June 2012

The proliferation of new data sets and their harmonization with the older data sets have allowed researchers to make significant progress in our understanding of how individuals allocate their time away from market work. We highlight how these new data can be used to test theories of time use and we review recent developments in long-run trends in time use, life-cycle patterns of expenditures and labor supply, and the allocation of time over the business cycle.
Population Identification Using Genetic Data
Authors: Lawson Daniel John , Falush Daniel
Published: June 2012

A large number of algorithms have been developed to classify individuals into discrete populations using genetic data. Recent results show that the information used by both model-based clustering methods and principal components analysis can be summarized by a matrix of pairwise similarity measures between individuals. Similarity matrices have been constructed in a number of ways, usually treating markers as independent but differing in the weighting given to polymorphisms of different frequencies. Additionally, methods are now being developed that take linkage into account. We review several such matrices and evaluate their information content. A two-stage approach for population identification is to first construct a similarity matrix and then perform clustering. We review a range of common clustering algorithms and evaluate their performance through a simulation study. The clustering step can be performed either on the matrix or by first using a dimension-reduction technique; we find that the latter approach substantially improves the performance of most algorithms. Based on these results, we describe the population structure signal contained in each similarity matrix and find that accounting for linkage leads to significant improvements for sequence data. We also perform a comparison on real data, where we find that population genetics models outperform generic clustering approaches, particularly with regard to robustness for features such as relatedness between individuals.
Characterization of Enhancer Function from Genome-Wide Analyses
Authors: Maston Glenn A. , Landt Stephen G. , Snyder Michael , Green Michael R.
Published: June 2012

There has been a recent surge in the use of genome-wide methodologies to identify and annotate the transcriptional regulatory elements in the human genome. Here we review some of these methodologies and the conceptual insights about transcription regulation that have been gained from the use of genome-wide studies. It has become clear that the binding of transcription factors is itself a highly regulated process, and binding does not always appear to have functional consequences. Numerous properties have now been associated with regulatory elements that may be useful in their identification. Several aspects of enhancer function have been shown to be more widespread than was previously appreciated, including the highly combinatorial nature of transcription factor binding, the postinitiation regulation of many target genes, and the binding of enhancers at early stages to maintain their competence during development. Going forward, the integration of multiple genome-wide data sets should become a standard approach to elucidate higher-order regulatory interactions.
The Evolution of Human Genetic Studies of Cleft Lip and Cleft Palate
Authors: Marazita Mary L.
Published: June 2012

Orofacial clefts (OFCs)—primarily cleft lip and cleft palate—are among the most common birth defects in all populations worldwide, and have notable population, ethnicity, and gender differences in birth prevalence. Interest in these birth defects goes back centuries, as does formal scientific interest; scientists often used OFCs as examples or evidence during paradigm shifts in human genetics, and have also used virtually every new method of human genetic analysis to deepen our understanding of OFC. This review traces the evolution of human genetic investigations of OFC, highlights the specific insights gained about OFC through the years, and culminates in a review of recent key OFC genetic findings resulting from the powerful tools of the genomics era. Notably, OFC represents a major success for genome-wide approaches, and the field is poised for further breakthroughs in the near future.
Ethical Issues with Newborn Screening in the Genomics Era
Authors: Tarini Beth A. , Goldenberg Aaron J.
Published: June 2012

Continued technological advances have made the prospect of routine whole-genome sequencing (WGS) imminent. To date, much of the discussion about WGS has focused on its application and use in clinical medicine. Relatively little attention has been paid to the potential integration of WGS into newborn screening programs. Given the structure and scope of these programs, it is possible that the early applications of WGS will occur in state-run newborn screening programs. Assessment of the pressing ethical issues currently facing the newborn screening community will provide insight into the challenges that lie ahead in the genomics era.
Evolution of the Egg: New Findings and Challenges
Authors: Claw Katrina G. , Swanson Willie J.
Published: June 2012

The evolution of the egg is dynamic, and eggs have numerous species-specific properties across vertebrates and invertebrates. Interestingly, although the structure and function of the egg have remained relatively conserved over time, some constituents of the egg's extracellular barriers are undergoing rapid evolution. In this article, we review current ideas regarding sperm-egg interactions, discuss genetic approaches used to elucidate egg gene functions, and highlight the interesting differences that have evolved across taxa. We suggest that the rapid evolution of egg components and the mechanisms behind sperm-egg interactions are integrally connected, and delve in depth into each component of the egg's extracellular matrices. Finally, we discuss the promising future of reproductive research and how high-throughput genomics and proteomics have the potential to revolutionize the field and provide new evidence that will challenge previously held views about the fertilization process.
Evolution of the Immune System in the Lower Vertebrates
Authors: Boehm Thomas , Iwanami Norimasa , Hess Isabell
Published: June 2012

The evolutionary emergence of vertebrates was accompanied by the invention of adaptive immunity. This is characterized by extraordinarily diverse repertoires of somatically assembled antigen receptors and the facility of antigen-specific memory, leading to more rapid and efficient secondary immune responses. Adaptive immunity emerged twice during early vertebrate evolution, once in the lineage leading to jawless fishes (such as lamprey and hagfish) and, independently, in the lineage leading to jawed vertebrates (comprising the overwhelming majority of extant vertebrates, from cartilaginous fishes to mammals). Recent findings on the immune systems of jawless and jawed fishes (here referred to as lower vertebrates) impact on the identification of general principles governing the structure and function of adaptive immunity and its coevolution with innate defenses. The discovery of conserved features of adaptive immunity will guide attempts to generate synthetic immunological functionalities and thus provide new avenues for intervening with faulty immune functions in humans.
Evolution-Centered Teaching of Biology
Authors: Burke da Silva Karen
Published: June 2012

University teaching remains an area of concern, and perhaps the most difficult discipline for both teaching and learning is evolution. The concepts that underpin evolution, although complex, have been shown to be fairly straightforward, yet students arrive at and leave university with serious misconceptions, misunderstandings related to language, and often a reluctance to learn the subject because of cultural or societal pressures. Because of the unifying power of the theory, however, it is necessary not only for biology students to have a thorough understanding of evolution, but also for them to learn it in their first year so that this knowledge can then be taken into further years of study. Rather than teaching evolution at the end of a degree program, embedding it as a semester-long first-year course will ensure that a far larger number of students are made aware of misconceptions that they have brought with them from high school. Teaching through traditional passive lectures makes learning difficult conceptual material more difficult, and needs to be replaced with more interactive lectures coupled with inquiry-based practicals and small group-learning sessions to increase student engagement and interest in the subject. A new approach in pedagogy, curriculum design, and academic staff professional development is essential, especially at this time, when enrollments across science courses in many countries around the world are in decline.
Functional Genomic Studies: Insights into the Pathogenesis of Liver Cancer
Authors: Han Ze-Guang
Published: June 2012

Liver cancer is the sixth-most-common cancer overall but the third-most-frequent cause of cancer death. Among primary liver cancers, hepatocellular carcinoma (HCC), the major histological subtype, is associated with multiple risk factors, including hepatitis B and C virus infection, alcohol consumption, obesity, and diet contamination. Although previous studies have revealed that certain genetic and epigenetic changes, such as TP53 and β-catenin mutations, occur in HCC cells, the pathogenesis of this cancer remains obscure. Functional genomic approaches—including genome-wide association studies, whole-genome and whole-exome sequencing, array-based comparative genomic hybridization, global DNA methylome mapping, and gene or noncoding RNA expression profiling—have recently been applied to HCC patients with different clinical features to uncover the genetic risk factors and underlying molecular mechanisms involved in this cancer's initiation and progression. The genome-wide analysis of germline and somatic genetic and epigenetic events facilitates understanding of the pathogenesis and molecular classification of liver cancer as well as the identification of novel diagnostic biomarkers and therapeutic targets for cancer.
Genetic Discrimination: International Perspectives
Authors: Otlowski M. , Taylor S. , Bombard Y.
Published: June 2012

Genetic discrimination (GD) is a complex, multifaceted ethical, psychosocial, and legal phenomenon. It is defined as the differential treatment of asymptomatic individuals or their relatives on the basis of their real or assumed genetic characteristics. This article presents an overview of GD within the contemporary international context. It describes the concept of GD and its contextual features, reviews research evidence regarding people's experiences of GD and the impact of GD within a range of domains, and provides an overview of legal and policy responses to GD that have emerged globally. We argue that GD is a significant and internationally established phenomenon that requires multilevel responses to ensure social justice and equitable outcomes for all citizens. Future research should monitor GD and its impacts within the community as well as institutions and should evaluate the effectiveness of legislative, policy, community education, and systemic responses.
Genomic Analysis of Fetal Nucleic Acids in Maternal Blood
Authors: Lo Yuk Ming Dennis , Chiu Rossa Wai Kwun
Published: June 2012

The 15 years since the discovery of fetal DNA in maternal plasma have witnessed remarkable developments in noninvasive prenatal diagnosis. An understanding of biological parameters governing this phenomenon, such as the concentration and molecular size of circulating fetal DNA, has guided its diagnostic applications. Early efforts focused on the detection of paternally inherited sequences, which were absent in the maternal genome, in maternal plasma. Recent developments in precise measurement technologies such as digital polymerase chain reaction (PCR) have allowed the detection of minute allelic imbalances in plasma and have catalyzed analysis of single-gene disorders such as the hemoglobinopathies and hemophilia. The advent of massively parallel sequencing has enabled the robust detection of fetal trisomies in maternal plasma. Recent proof-of-concept studies have detected a chromosomal translocation and a microdeletion and have deduced a genome-wide genetic map of a fetus from maternal plasma. Understanding the ethical, legal, and social aspects in light of such rapid developments is thus a priority for future research.
The Human Microbiome: Our Second Genome
Authors: Grice Elizabeth A. , Segre Julia A.
Published: June 2012

The human genome has been referred to as the blueprint of human biology. In this review we consider an essential but largely ignored overlay to that blueprint, the human microbiome, which is composed of those microbes that live in and on our bodies. The human microbiome is a source of genetic diversity, a modifier of disease, an essential component of immunity, and a functional entity that influences metabolism and modulates drug interactions. Characterization and analysis of the human microbiome have been greatly catalyzed by advances in genomic technologies. We discuss how these technologies have shaped this emerging field of study and advanced our understanding of the human microbiome. We also identify future challenges, many of which are common to human genetic studies, and predict that in the future, analyzing genetic variation and risk of human disease will sometimes necessitate the integration of human and microbial genomic data sets.
Methods for Identifying Higher-Order Chromatin Structure
Authors: Sajan Samin A. , Hawkins R. David
Published: June 2012

Eukaryotic genomic DNA is combined with histones, nonhistone proteins, and RNA to form chromatin, which is extensively packaged hierarchically to fit inside a cell's nucleus. The nucleosome—comprising a histone octamer with 147 base pairs of DNA wrapped around it—is the initial level and the repeating unit of chromatin packaging, which electron microscopy first made visible to the human eye as “beads on a string” nearly four decades ago. The mechanism and nature of chromatin packaging are still under intense research. Recently, classic methods like chromatin immunoprecipitation and digestion with deoxyribonuclease and micrococcal nuclease have been combined with high-throughput sequencing to provide detailed nucleosome occupancy maps, and chromosome conformation capture and its variants have revealed that higher-order chromatin structure involves long-range loop formation between distant genomic elements. This review discusses the methods for identifying higher-order chromatin structure and the information they have provided on this important topic.
Human Genetic Individuality
Authors: Olson Maynard V.
Published: June 2012

The central preoccupation of human genetics is an effort to understand the genotypic basis of human phenotypic diversity. Although recent progress in identifying the genes that, when mutated, underlie major genetic diseases has been rapid, knowledge of the genetic influences on the vast range of variable, and at least partially heritable, traits that constitute the “normal” range of human phenotypic variation lags. Spectacular advances in our knowledge of human genetic variation have laid the groundwork for a synthesis of insights from medical genetics, population genetics, molecular evolution, and the study of human origins that places basic constraints on models of human genetic individuality. Balancing selection, local adaptation, mutation-selection balance, and founder effects have all extensively shaped contemporary genetic variation. Long-term-balancing selection appears largely to reflect the consequences of host-pathogen arms races. Local adaptation has been widespread—and involved responses to a plethora of selective pressures, some identifiable but most unknown. However, it appears to be a combination of mutation-selection balance and founder effects that largely accounts for genetic individuality. If true, this inference has major implications for future research programs in human genetics.
Sampling Populations of Humans Across the World: ELSI Issues
Authors: Knoppers Bartha Maria , Zawati Ma'n H. , Kirby Emily S.
Published: June 2012

There are an increasing number of population studies collecting data and samples to illuminate gene-environment contributions to disease risk and health. The rising affordability of innovative technologies capable of generating large amounts of data helps achieve statistical power and has paved the way for new international research collaborations. Most data and sample collections can be grouped into longitudinal, disease-specific, or residual tissue biobanks, with accompanying ethical, legal, and social issues (ELSI). Issues pertaining to consent, confidentiality, and oversight cannot be examined using a one-size-fits-all approach—the particularities of each biobank must be taken into account. It remains to be seen whether current governance approaches will be adequate to handle the impact of next-generation sequencing technologies on communication with participants in population biobanking studies.
The Genetics of Sudden Cardiac Death
Authors: Arking Dan E. , Sotoodehnia Nona
Published: June 2012

Sudden cardiac death (SCD), a sudden pulseless condition due to cardiac arrhythmia, remains a major public health problem despite recent progress in the treatment and prevention of overall coronary heart disease. In this review, we examine the evidence for genetic susceptibility to SCD in order to provide biological insight into the pathogenesis of this devastating disease and to explore the potential for genetics to impact clinical management of SCD risk. Both candidate gene approaches and unbiased genome-wide scans have identified novel biological pathways contributing to SCD risk. Although risk stratification in the general population remains an elusive goal, several studies point to the potential utility of these common genetic variants in high-risk individuals. Finally, we highlight novel methodological approaches to deciphering the molecular mechanisms involved in arrhythmogenesis. Although further epidemiological and clinical applications research is needed, it is increasingly clear that genetic approaches are yielding important insights into SCD that may impact the public health burden imposed by SCD and its associated outcomes.
The Genetics of Substance Dependence
Authors: Wang Jen-Chyong , Kapoor Manav , Goate Alison M.
Published: June 2012

A large segment of the population suffers from addiction to alcohol, smoking, or illicit drugs. Not only do substance abuse and addiction pose a threat to health, but the consequences of addiction also impose a social and economic burden on families, communities, and nations. Genome-wide linkage and association studies have been used for addiction research with varying degrees of success. The most well-established genetic factors associated with alcohol dependence are in the genes encoding alcohol dehydrogenase (ADH), which oxidizes alcohol to acetaldehyde, and aldehyde dehydrogenase (ALDH2), which oxidizes acetaldehyde to acetate. Recently emerging genetic studies have linked variants in the genes encoding the α3, α5, and β4 nicotinic acetylcholine receptor subunits to smoking risk. However, the influence of these well-established genetic variants accounts for only a small portion of the heritability of alcohol and nicotine addiction, and it is likely that there are both common and rare risk variants yet to be identified. Newly developed DNA sequencing technologies could potentially advance the detection of rare variants with a larger impact on addiction risk.
A Comparative Genomics Approach to Understanding Transmissible Cancer in Tasmanian Devils
Authors: Deakin Janine E. , Belov Katherine
Published: June 2012

A fatal contagious cancer is driving an entire species to extinction. Comparative genomics will unravel the origin and evolution of devil facial tumor disease (DFTD). The DFTD allograft arose from a Schwann cell in a female Tasmanian devil more than 15 years ago; since then, the tumor has passed through at least 100,000 hosts, evolving and mutating along the way. Tumor genome sequencing and molecular cytogenetic technologies now allow direct comparisons of candidate genes involved in tumorigenesis in human cancers. As a stable transmissible cancer, DFTD provides unique insights into cancer development, progression, and immune evasion and is likely to help increase our understanding of human cancer. In addition, these studies provide hope for discoveries of drug targets or vaccine candidates that will prevent the extinction of this iconic Australian marsupial.
Genomics and Genetics of Human and Primate Y Chromosomes
Authors: Hughes Jennifer F. , Rozen Steve
Published: June 2012

In mammals, the Y chromosome plays the pivotal role in male sex determination and is essential for normal sperm production. Yet only three Y chromosomes have been completely sequenced to date—those of human, chimpanzee, and rhesus macaque. While Y chromosomes are notoriously difficult to sequence owing to their highly repetitive genomic landscapes, these dedicated sequencing efforts have generated tremendous yields in medical, biological, and evolutionary insight. Knowledge of the complex structural organization of the human Y chromosome and a complete catalog of its gene content have provided a deeper understanding of the mechanisms that generate disease-causing mutations and large-scale rearrangements. Variation among human Y-chromosome sequences has been an invaluable tool for understanding relationships among human populations. Comprehensive comparisons of the human Y-chromosome sequence with those of other primates have illuminated aspects of Y-chromosome evolutionary dynamics over much longer timescales (>25 million years compared with 100,000 years). The future sequencing of additional Y chromosomes will provide a basis for a more comprehensive understanding of the evolution of Y chromosomes and their roles in reproductive biology.
Yeast ATP-Binding Cassette Transporters Conferring Multidrug Resistance
Authors: Prasad Rajendra , Goffeau Andre
Published: June 2012

Overexpression of the ATP-binding cassette (ABC) drug transporter P-glycoprotein (P-gp) is often responsible for the failure of chemotherapy as a treatment for human tumors. The presence of proteins homologous to P-gp in organisms ranging from prokaryotes to eukaryotes indicates that drug export is a general mechanism of multidrug resistance. Yeasts are no exception. They have developed a large subfamily of ABC exporters involved in pleiotropic drug resistance (PDR) and in the cellular efflux of a wide variety of drugs. The PDR transporters Pdr5p of Saccharomyces cerevisiae and Cdr1p of Candida albicans are important members of this PDR subfamily, which comprises up to 10 phylogenetic clusters in fungi. Here, we review current achievements concerning the structure, molecular mechanism, and physiological functions of yeast Pdr transporters.
Arthur Kelman: Tribute and Remembrance
Authors: Sequeira Luis
Published: June 2012

With the death of Professor Arthur Kelman at age 90, the plant sciences, and particularly the field of plant pathology, lost one of its most influential and effective leaders. His long career involved important positions in the Departments of Plant Pathology at North Carolina State University (1949–1965) and the University of Wisconsin (1965–1989). Recognized not only for his achievements in research and his charismatic influence on his numerous students, Arthur was, most of all, an extraordinary teacher. He and his students made significant contributions in the fields of virulence, ecology, and control of bacterial plant pathogens. In addition, he was extremely active in service to professional societies, including the American Phytopathological Society, and a major force in the development of the International Society for Plant Pathology. In addition, he was an influential member of the Council of the National Academy of Sciences, and, after retirement from the University of Wisconsin, he served for two years as Chief Scientist of the Competitive Grants Program of the US Department of Agriculture. He received numerous awards as a teacher and researcher, and felt an intense sense of duty to his profession. He was one of the most influential plant pathologists of the twentieth century and will be remembered for his great intellect and his humanity.
Gall Midges (Hessian Flies) as Plant Pathogens
Authors: Stuart Jeff J. , Chen Ming-Shun , Shukle Richard , Harris Marion O.
Published: June 2012

Gall midges constitute an important group of plant-parasitic insects. The Hessian fly (HF; Mayetiola destructor), the most investigated gall midge, was the first insect hypothesized to have a gene-for-gene interaction with its host plant, wheat (Triticum spp.). Recent investigations support that hypothesis. The minute larval mandibles appear to act in a manner that is analogous to nematode stylets and the haustoria of filamentous plant pathogens. Putative effector proteins are encoded by hundreds of genes and expressed in the HF larval salivary gland. Cultivar-specific resistance (R) genes mediate a highly localized plant reaction that prevents the survival of avirulent HF larvae. Fine-scale mapping of HF avirulence (Avr) genes provides further evidence of effector-triggered immunity (ETI) against HF in wheat. Taken together, these discoveries suggest that the HF, and other gall midges, may be considered biotrophic, or hemibiotrophic, plant pathogens, and they demonstrate the potential that the wheat-HF interaction has in the study of insect-induced plant gall formation.
Diversity and Natural Functions of Antibiotics Produced by Beneficial and Plant Pathogenic Bacteria
Authors: Raaijmakers Jos M. , Mazzola Mark
Published: June 2012

Soil- and plant-associated environments harbor numerous bacteria that produce antibiotic metabolites with specific or broad-spectrum activities against coexisting microorganisms. The function and ecological importance of antibiotics have long been assumed to yield a survival advantage to the producing bacteria in the highly competitive but resource-limited soil environments through direct suppression. Although specific antibiotics may enhance producer persistence when challenged by competitors or predators in soil habitats, at subinhibitory concentrations antibiotics exhibit a diversity of other roles in the life history of the producing bacteria. Many processes modulated by antibiotics may be inherently critical to the producing bacterium, such as the acquisition of substrates or initiation of developmental changes that will ensure survival under stressful conditions. Antibiotics may also have roles in more complex interactions, including in virulence on host plants or in shaping the outcomes of multitrophic interactions. The innate functions of antibiotics to producing bacteria in their native ecosystem are just beginning to emerge, but current knowledge already reveals a breadth of activities well beyond the historical perspective of antibiotics as weaponry in microbial conflicts.
Fire Blight: Applied Genomic Insights of the Pathogen and Host
Authors: Malnoy Mickael , Martens Stefan , Norelli John L. , Barny Marie-Anne , Sundin George W. , Smits Theo H.M. , Duffy Brion
Published: June 2012

The enterobacterial phytopathogen Erwinia amylovora causes fire blight, an invasive disease that threatens a wide range of commercial and ornamental Rosaceae host plants. The response elicited by E. amylovora in its host during disease development is similar to the hypersensitive reaction that typically leads to resistance in an incompatible host-pathogen interaction, yet no gene-for-gene resistance has been described for this host-pathogen system. Comparative genomic analysis has found an unprecedented degree of genetic uniformity among strains of E. amylovora, suggesting that the pathogen has undergone a recent genetic bottleneck. The genome of apple, an important host of E. amylovora, has been sequenced, creating new opportunities for the study of interactions between host and pathogen during fire blight development and for the identification of resistance genes. This review includes recent advances in the genomics of both host and pathogen.
Interrelationships of Food Safety and Plant Pathology: The Life Cycle of Human Pathogens on Plants
Authors: Barak Jeri D. , Schroeder Brenda K.
Published: June 2012

Bacterial food-borne pathogens use plants as vectors between animal hosts, all the while following the life cycle script of plant-associated bacteria. Similar to phytobacteria, Salmonella, pathogenic Escherichia coli, and cross-domain pathogens have a foothold in agricultural production areas. The commonality of environmental contamination translates to contact with plants. Because of the chronic absence of kill steps against human pathogens for fresh produce, arrival on plants leads to persistence and the risk of human illness. Significant research progress is revealing mechanisms used by human pathogens to colonize plants and important biological interactions between and among bacteria in planta. These findings articulate the difficulty of eliminating or reducing the pathogen from plants. The plant itself may be an untapped key to clean produce. This review highlights the life of human pathogens outside an animal host, focusing on the role of plants, and illustrates areas that are ripe for future investigation.
Landscape Epidemiology of Emerging Infectious Diseases in Natural and Human-Altered Ecosystems
Authors: Meentemeyer Ross K. , Haas Sarah E. , Václavík Tomáš
Published: June 2012

A central challenge to studying emerging infectious diseases (EIDs) is a landscape dilemma: Our best empirical understanding of disease dynamics occurs at local scales, whereas pathogen invasions and management occur over broad spatial extents. The burgeoning field of landscape epidemiology integrates concepts and approaches from disease ecology with the macroscale lens of landscape ecology, enabling examination of disease across spatiotemporal scales in complex environmental settings. We review the state of the field and describe analytical frontiers that show promise for advancement, focusing on natural and human-altered ecosystems. Concepts fundamental to practicing landscape epidemiology are discussed, including spatial scale, static versus dynamic modeling, spatially implicit versus explicit approaches, selection of ecologically meaningful variables, and inference versus prediction. We highlight studies that have advanced the field by incorporating multiscale analyses, landscape connectivity, and dynamic modeling. Future research directions include understanding disease as a component of interacting ecological disturbances, scaling up the ecological impacts of disease, and examining disease dynamics as a coupled human-natural system.
New Grower-Friendly Methods for Plant Pathogen Monitoring
Authors: De Boer Solke H. , López María M.
Published: June 2012

Accurate plant disease diagnoses and rapid detection and identification of plant pathogens are of utmost importance for controlling plant diseases and mitigating the economic losses they incur. Technological advances have increasingly simplified the tools available for the identification of pathogens to the extent that, in some cases, this can be done directly by growers and producers themselves. Commercially available immunoprinting kits and lateral flow devices (LFDs) for detection of selected plant pathogens are among the first tools of what can be considered grower-friendly pathogen monitoring methods. Research efforts, spurned on by point-of-care needs in the medical field, are paving the way for the further development of on-the-spot diagnostics and multiplex technologies in plant pathology. Grower-friendly methods need to be practical, robust, readily available, and cost-effective. Such methods are not restricted to on-the-spot testing but extend to laboratory services, which are sometimes more practicable for growers, extension agents, regulators, and other users of diagnostic tests.
PhytophthoraBeyond Agriculture
Authors: Hansen Everett M. , Reeser Paul W. , Sutton Wendy
Published: June 2012

Little is known about indigenous Phytophthora species in natural ecosystems. Increasing evidence, however, suggests that a diverse, trophically complex Phytophthora community is important in many forests. The number of described species has steadily increased, with a dramatic spike in recent years as new species have been split from old and new species have been discovered through exploration of new habitats. Forest soil, streams, and the upper canopies of trees are now being explored for Phytophthora diversity, and a new appreciation for the ecological amplitude of the genus is emerging. Ten to twenty species are regularly identified in temperate forest surveys. Half or more of this Phytophthora diversity comes from species described since 2000. Taxa in internal transcribed spacer (ITS) Clade 6 are especially numerous in forest streams and may be saprophytic in this habitat. Three ecological assemblages of forest Phytophthora species are hypothesized: aquatic opportunists, foliar pathogens, and soilborne fine-root and canker pathogens. Aggressive invasive species are associated with all three groups.
An Ideal Job
Authors: Leonard Kurt J.
Published: June 2012

A brief personal history illustrates how fortunate I was to have stumbled into a career in plant pathology, which turned out to be the ideal job for me. Several of the people who steered me or facilitated my development in research on plant diseases are mentioned. Starting with my PhD research, I have had the good fortune to indulge a career-long fascination with epidemiology and genetics of disease resistance in plants, particularly coevolution of gene-for-gene host-pathogen systems. I hope that my example may inspire others of like minds to consider a research career in plant pathology.
Pathogenomics of theRalstonia solanacearumSpecies Complex
Authors: Genin Stéphane , Denny Timothy P.
Published: June 2012

Ralstonia solanacearum is a major phytopathogen that attacks many crops and other plants over a broad geographical range. The extensive genetic diversity of strains responsible for the various bacterial wilt diseases has in recent years led to the concept of an R. solanacearum species complex. Genome sequencing of more than 10 strains representative of the main phylogenetic groups has broadened our knowledge of the evolution and speciation of this pathogen and led to the identification of novel virulence-associated functions. Comparative genomic analyses are now opening the way for refined functional studies. The many molecular determinants involved in pathogenicity and host-range specificity are described, and we also summarize current understanding of their roles in pathogenesis and how their expression is tightly controlled by an intricate virulence regulatory network.
Apple Replant Disease: Role of Microbial Ecology in Cause and Control
Authors: Mazzola Mark , Manici Luisa M.
Published: June 2012

Replant disease of apple is common to all major apple growing regions of the world. Difficulties in defining disease etiology, which can be exacerbated by abiotic factors, have limited progress toward developing alternatives to soil fumigation for disease control. However, the preponderance of data derived from studies of orchard soil biology employing multidisciplinary approaches has defined a complex of pathogens/parasites as causal agents of the disease. Approaches to manipulate microbial resources endemic to the orchard soil system have been proposed to induce a state of general soil suppressiveness to replant disease. Such a long-term strategy may benefit the existing orchard through extending the period of economic viability and reduce overall disease pressure to which young trees are exposed during establishment of successive plantings on the site. Alternatively, more near-term methods have been devised to achieve specific quantitative and qualitative changes in soil biology during the period of orchard renovation that may lead to effective disease suppression.
Role of Nematode Peptides and Other Small Molecules in Plant Parasitism
Authors: Mitchum Melissa G. , Wang Xiaohong , Wang Jianying , Davis Eric L.
Published: June 2012

Molecular, genetic, and biochemical studies are demonstrating an increasingly important role of peptide signaling in nematode parasitism of plants. To date, the majority of nematode-secreted peptides identified share similarity with plant CLAVATA3/ESR (CLE) peptides, but bioinformatics analyses of nematode genomes have revealed sequences homologous to other classes of plant peptide hormones that may be utilized by these pests. Extracellular host receptors for secreted nematode peptides are beginning to be identified and their roles in parasitism elucidated. Here, we outline recent advances from studies of biologically active nematode-secreted peptides that function as molecular mimics of endogenous plant peptides to promote parasitism. Several strategies are being used to exploit this information to provide new targets for engineering nematode resistance.
The Role of Secretion Systems and Small Molecules in Soft-Rot Enterobacteriaceae Pathogenicity
Authors: Charkowski Amy , Blanco Carlos , Condemine Guy , Expert Dominique , Franza Thierry , Hayes Christopher , Hugouvieux-Cotte-Pattat Nicole , Solanilla Emilia López , Low David , Moleleki Lucy , Pirhonen Minna , Pitman Andrew , Perna Nicole , Reverchon Sylvie , Rodríguez Palenzuela Pablo , San Francisco Michael , Toth Ian , Tsuyumu Shinji , van der Waals Jacquie , van der Wolf Jan , Van Gijsegem Frédérique , Yang Ching-Hong , Yedidia Iris
Published: June 2012

Soft-rot Enterobacteriaceae (SRE), which belong to the genera Pectobacterium and Dickeya, consist mainly of broad host-range pathogens that cause wilt, rot, and blackleg diseases on a wide range of plants. They are found in plants, insects, soil, and water in agricultural regions worldwide. SRE encode all six known protein secretion systems present in gram-negative bacteria, and these systems are involved in attacking host plants and competing bacteria. They also produce and detect multiple types of small molecules to coordinate pathogenesis, modify the plant environment, attack competing microbes, and perhaps to attract insect vectors. This review integrates new information about the role protein secretion and detection and production of ions and small molecules play in soft-rot pathogenicity.
Stagonospora nodorum: From Pathology to Genomics and Host Resistance
Authors: Oliver Richard P. , Friesen Timothy L. , Faris Justin D. , Solomon Peter S.
Published: June 2012

Stagonospora nodorum is a major necrotrophic pathogen of wheat that causes the diseases S. nodorum leaf and glume blotch. A series of tools and resources, including functional genomics, a genome sequence, proteomics and metabolomics, host-mapping populations, and a worldwide collection of isolates, have enabled the dissection of pathogenicity mechanisms. Metabolic and signaling genes required for pathogenicity have been defined. Interaction with the host is dominated by interplay of fungal effectors that induce necrosis on wheat lines carrying specific sensitivity loci. As such, the pathogen has emerged as a model for the Pleosporales group of pathogens.
Genome-Enabled Perspectives on the Composition, Evolution, and Expression of Virulence Determinants in Bacterial Plant Pathogens
Authors: Lindeberg Magdalen
Published: June 2012

Genome sequence analyses of bacterial plant pathogens are revealing important insights into the molecular determinants of pathogenicity and, through transcript characterization, responses to environmental conditions, evidence for small RNAs, and validation of uncharacterized genes. Genome comparison sheds further light on the processes impacting pathogen evolution and differences in gene repertoire among isolates contributing to niche specialization. Information derived from pathogen genome analysis is providing tools for use in diagnosis and interference with host-pathogen interactions for the purpose of disease control. However, the existing information infrastructure fails to adequately integrate the increasing numbers of sequence data sets, bioinformatic analyses, and experimental characterization, as required for effective systems-level analysis. Enhanced standardization of data formats at the point of publication is proposed as a possible solution.
The Genomics of Obligate (and Nonobligate) Biotrophs
Authors: Spanu Pietro D.
Published: June 2012

Biotrophy is a pervasive trait that evolved independently in plant pathogenic fungi and oomycetes. Comparative genomics of the first sequenced biotrophic pathogens highlight remarkable convergences, including gene losses in the metabolism of inorganic nitrogen, inorganic sulfur, and thiamine, and genes encoding carbohydrate active enzymes and secondary metabolism enzymes. Some biotrophs, but not all, display marked increases in overall genome size because of a proliferation of retrotransposons. I argue here that the release of constraints on transposon activity is driven by the advantages conferred by the genetic variability that results from transposition, in particular by the creation and diversification of broad palettes of effector genes. Increases in genome size and gene losses are the consequences of this trade-off. Genes that are not necessary for growth on a plant disappeared, but we still do not know what lost functions make some of these pathogens obligate.
Variation and Selection of Quantitative Traits in Plant Pathogens
Authors: Lannou Christian
Published: June 2012

The first section presents the quantitative traits of pathogenicity that are most commonly measured by plant pathologists, how the expression of those traits is influenced by environmental factors, and why the traits must be taken into account for understanding pathogen evolution in agricultural systems. Particular attention is given to the shared genetic control of these traits by the host and the pathogen. Next, the review discusses how quantitative traits account for epidemic development and how they can be related to pathogen fitness. The main constraints that influence the evolution of quantitative traits in pathogen populations are detailed. Finally, possible directions for research on the management of pathogen virulence (as defined by evolutionists) and host quantitative resistance are presented. The review evaluates how the theoretical corpus developed by epidemiologists and evolutionists may apply to plant pathogens in the context of agriculture. The review also analyzes theoretical papers and compares the modeling hypotheses to the biological characteristics of plant pathogens.