Showing papers by "University of Missouri published in 2010"

Genome sequence of the palaeopolyploid soybean

Abstract: Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

The Chicxulub Asteroid Impact and Mass Extinction at the Cretaceous-Paleogene Boundary

Abstract: The Cretaceous-Paleogene boundary similar to 65.5 million years ago marks one of the three largest mass extinctions in the past 500 million years. The extinction event coincided with a large asteroid impact at Chicxulub, Mexico, and occurred within the time of Deccan flood basalt volcanism in India. Here, we synthesize records of the global stratigraphy across this boundary to assess the proposed causes of the mass extinction. Notably, a single ejecta-rich deposit compositionally linked to the Chicxulub impact is globally distributed at the Cretaceous-Paleogene boundary. The temporal match between the ejecta layer and the onset of the extinctions and the agreement of ecological patterns in the fossil record with modeled environmental perturbations (for example, darkness and cooling) lead us to conclude that the Chicxulub impact triggered the mass extinction.

The Origins of C4 Grasslands: Integrating Evolutionary and Ecosystem Science

Abstract: The evolution of grasses using C4 photosynthesis and their sudden rise to ecological dominance 3 to 8 million years ago is among the most dramatic examples of biome assembly in the geological record. A growing body of work suggests that the patterns and drivers of C4 grassland expansion were considerably more complex than originally assumed. Previous research has benefited substantially from dialog between geologists and ecologists, but current research must now integrate fully with phylogenetics. A synthesis of grass evolutionary biology with grassland ecosystem science will further our knowledge of the evolution of traits that promote dominance in grassland systems and will provide a new context in which to evaluate the relative importance of C4 photosynthesis in transforming ecosystems across large regions of Earth.

The Magical Mystery Four How Is Working Memory Capacity Limited, and Why?

Abstract: Working memory storage capacity is important because cognitive tasks can be completed only with sufficient ability to hold information as it is processed. The ability to repeat information depends on task demands but can be distinguished from a more constant, underlying mechanism: a central memory store limited to 3 to 5 meaningful items in young adults. I will discuss why this central limit is important, how it can be observed, how it differs among individuals, and why it may occur.

Diagnostic performance of body mass index to identify obesity as defined by body adiposity: a systematic review and meta-analysis.

Abstract: We performed a systematic review and meta-analysis of studies that assessed the performance of body mass index (BMI) to detect body adiposity. Data sources were MEDLINE, EMBASE, Cochrane, Database of Systematic Reviews, Cochrane CENTRAL, Web of Science, and SCOPUS. To be included, studies must have assessed the performance of BMI to measure body adiposity, provided standard values of diagnostic performance, and used a body composition technique as the reference standard for body fat percent (BF%) measurement. We obtained pooled summary statistics for sensitivity, specificity, positive and negative likelihood ratios (LRs), and diagnostic odds ratio (DOR). The inconsistency statistic (I2) assessed potential heterogeneity. The search strategy yielded 3341 potentially relevant abstracts, and 25 articles met our predefined inclusion criteria. These studies evaluated 32 different samples totaling 31 968 patients. Commonly used BMI cutoffs to diagnose obesity showed a pooled sensitivity to detect high adiposity of 0.50 (95% confidence interval (CI): 0.43–0.57) and a pooled specificity of 0.90 (CI: 0.86–0.94). Positive LR was 5.88 (CI: 4.24–8.15), I2=97.8%; the negative LR was 0.43 (CI: 0.37–0.50), I2=98.5%; and the DOR was 17.91 (CI: 12.56–25.53), I2=91.7%. Analysis of studies that used BMI cutoffs ⩾30 had a pooled sensitivity of 0.42 (CI: 0.31–0.43) and a pooled specificity of 0.97 (CI: 0.96–0.97). Cutoff values and regional origin of the studies can only partially explain the heterogeneity seen in pooled DOR estimates. Commonly used BMI cutoff values to diagnose obesity have high specificity, but low sensitivity to identify adiposity, as they fail to identify half of the people with excess BF%.

Peritoneal dialysis-related infections recommendations: 2010 update

Abstract: Department of Medicine and Therapeutics,1 Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong; University of Pittsburgh School of Medicine,2 Pittsburgh, PA, USA; Faculdade de Enfermagem, Nutrição e Fisioterapia,3 Pontifícia Universidade Católica do Rio Grande do Sul, Brazil; Sanjay Gandhi Postgraduate Institute of Medical Sciences,4 Lucknow, India; Department of Nephrology,5 Princess Alexandra Hospital, and School of Medicine, University of Queensland, Brisbane, Australia; Department of Medical Microbiology,6 Leiden University Medical Center, Leiden, The Netherlands; Centre for Kidney Diseases,7 Mount Elizabeth Medical Centre, Singapore; Section of Infectious Disease,8 Department of Internal Medicine, University of Missouri-Columbia School of Medicine, Columbia, MO, USA; Pediatric Nephrology Division,9 University Children’s Hospital, Heidelberg, Germany; Dianet Dialysis Centers,10 Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands

Understanding the construct of impulsivity and its relationship to alcohol use disorders.

Abstract: There are well-established links between impulsivity and alcohol use in humans and other model organisms; however, the etiological nature of these associations remains unclear. This is likely due, in part, to the heterogeneous nature of the construct of impulsivity. Many different measures of impulsivity have been employed in human studies, using both questionnaire and laboratory-based tasks. Animal studies also use multiple tasks to assess the construct of impulsivity. In both human and animal studies, different measures of impulsivity often show little correlation and are differentially related to outcome, suggesting that the impulsivity construct may actually consist of a number of more homogeneous (and potentially more meaningful) subfacets. Here, we provide an overview of the different measures of impulsivity used across human and animal studies, evidence that the construct of impulsivity may be better studied in the context of more meaningful subfacets, and recommendations for how research in this direction may provide for better consilience between human and animal studies of the connection between impulsivity and alcohol use.

Tissue engineering by self-assembly and bio-printing of living cells.

Abstract: Biofabrication of living structures with desired topology and functionality requires the interdisciplinary effort of practitioners of the physical, life and engineering sciences. Such efforts are being undertaken in many laboratories around the world. Numerous approaches are pursued, such as those based on the use of natural or artificial scaffolds, decellularized cadaveric extracellular matrices and, most lately, bioprinting. To be successful in this endeavor, it is crucial to provide in vitro micro-environmental clues for the cells resembling those in the organism. Therefore, scaffolds, populated with differentiated cells or stem cells, of increasing complexity and sophistication are being fabricated. However, no matter how sophisticated scaffolds are, they can cause problems stemming from their degradation, eliciting immunogenic reactions and other a priori unforeseen complications. It is also being realized that ultimately the best approach might be to rely on the self-assembly and self-organizing properties of cells and tissues and the innate regenerative capability of the organism itself, not just simply prepare tissue and organ structures in vitro followed by their implantation. Here we briefly review the different strategies for the fabrication of three-dimensional biological structures, in particular bioprinting. We detail a fully biological, scaffoldless, print-based engineering approach that uses self-assembling multicellular units as bio-ink particles and employs early developmental morphogenetic principles, such as cell sorting and tissue fusion.

Penetration of lipid membranes by gold nanoparticles: insights into cellular uptake, cytotoxicity, and their relationship.

Abstract: Nanoparticle penetration into cell membranes is an interesting phenomenon that may have crucial implications on the nanoparticles’ biomedical applications. In this paper, a coarse-grained model for gold nanoparticles (AuNPs) is developed (verified against experimental data available) to simulate their interactions with model lipid membranes. Simulations reveal that AuNPs with different signs and densities of surface charges spontaneously adhere to the bilayer surface or penetrate into the bilayer interior. The potential of mean force calculations show that the energy gains upon adhesion or penetration is significant. In the case of penetration, it is found that defective areas are induced across the entire surface of the upper leaflet of the bilayer and a hydrophilic pore that transports water molecules was formed with its surrounding lipids highly disordered. Penetration and its concomitant membrane disruptions can be a possible mechanism of the two observed phenomena in experiments: AuNPs bypass endocyt...

A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay

Abstract: We report the identification of a recurrent, 520-kb 16p12.1 microdeletion associated with childhood developmental delay. The microdeletion was detected in 20 of 11,873 cases compared with 2 of 8,540 controls (P = 0.0009, OR = 7.2) and replicated in a second series of 22 of 9,254 cases compared with 6 of 6,299 controls (P = 0.028, OR = 2.5). Most deletions were inherited, with carrier parents likely to manifest neuropsychiatric phenotypes compared to non-carrier parents (P = 0.037, OR = 6). Probands were more likely to carry an additional large copy-number variant when compared to matched controls (10 of 42 cases, P = 5.7 x 10(-5), OR = 6.6). The clinical features of individuals with two mutations were distinct from and/or more severe than those of individuals carrying only the co-occurring mutation. Our data support a two-hit model in which the 16p12.1 microdeletion both predisposes to neuropsychiatric phenotypes as a single event and exacerbates neurodevelopmental phenotypes in association with other large deletions or duplications. Analysis of other microdeletions with variable expressivity indicates that this two-hit model might be more generally applicable to neuropsychiatric disease.

Effect of nanoparticle surface charge at the plasma membrane and beyond

Abstract: Herein, we demonstrate that the surface charge of gold nanoparticles (AuNPs) plays a critical role in modulating membrane potential of different malignant and nonmalignant cell types and subsequent downstream intracellular events. The findings presented here describe a novel mechanism for cell-nanoparticle interactions and AuNP uptake: modulation of membrane potential and its effect on intracellular events. These studies will help understand the biology of cell-nanoparticle interactions and facilitate the engineering of nanoparticles for specific intracellular targets.

Halstead‐Reitan Neuropsychological Test Battery

Abstract: The Halstead-Reitan Neuropsychological Test Battery consists of a series of individual neuropsychological measures that, in combination, permit a skilled examiner to make detailed inferences about the integrity of the cerebral hemispheres. Because the brain is the organ of adaptive behavior, brain dysfunction is typically observable in some behavioral aberrations. The tests included in the Halstead-Reitan Battery are designed to sample behavior across every possible sphere and assess all major cognitive, sensory, expressive, and motor functions. Keywords: halstead-reitan neuropsychological test battery; brain damage; neuropsychological impairment; brain-behavior relationships

Revised NESARC personality disorder diagnoses: gender, prevalence, and comorbidity with substance dependence disorders.

Abstract: We applied different diagnostic rules for diagnosing personality disorders to the NESARC epidemiological study of over 40,000 individuals. Specifically, unlike previous NESARC publications, we required that each personality disorder criterion be associated with significant distress or impairment in order to be counted toward a personality disorder (PD) diagnosis. Results demonstrated significant reductions in prevalence rates for PDs (9.1% versus 21.5% using original NESARC algorithms), and these revised prevalence rates were much more consistent with recent epidemiological studies in the U.S. and Great Britain. We also found gender differences in the prevalence rate for most PDs. Comorbidity analyses revealed strong associations between PDs and alcohol dependence, drug dependence, and tobacco dependence. PD diagnoses were also associated with scores on dysfunction and impairment, perceived stress and less social support, lifetime history of suicide attempts, interpersonal difficulties, and problems with legal authorities.

The Questionnaire for Eudaimonic Well-Being: Psychometric properties, demographic comparisons, and evidence of validity

Abstract: The Questionnaire for Eudaimonic Well-Being (QEWB) was developed to measure well-being in a manner consistent with how it is conceptualized in eudaimonist philosophy. Aspects of eudaimonic well-being assessed by the QEWB include self-discovery, perceived development of one's best potentials, a sense of purpose and meaning in life, intense involvement in activities, investment of significant effort, and enjoyment of activities as personally expressive. The QEWB was administered to two large, ethnically diverse samples of college students drawn from multiple sites across the United States. A three-part evaluation of the instrument was conducted: (1) evaluating psychometric properties, (2) comparing QEWB scores across gender, age, ethnicity, family income, and family structure, and (3) assessing the convergent, discriminant, construct, and incremental validity of the QEWB. Six hypotheses relating QEWB scores to identity formation, personality traits, and positive and negative psychological functioning were evaluated. The internal consistency of the scale was high and results of independent CFAs indicated that the QEWB items patterned onto a common factor. The distribution of scores approximated a normal curve. Demographic variables were found to predict only small proportions of QEWB score variability. Support for the hypotheses tested provides evidence for the validity of the QEWB as an instrument for assessing eudaimonic well-being. Implications for theory and future research directions are discussed.

Cystic Fibrosis Pigs Develop Lung Disease and Exhibit Defective Bacterial Eradication at Birth

Abstract: Lung disease causes most of the morbidity and mortality in cystic fibrosis (CF). Understanding the pathogenesis of this disease has been hindered, however, by the lack of an animal model with characteristic features of CF. To overcome this problem, we recently generated pigs with mutated CFTR genes. We now report that, within months of birth, CF pigs spontaneously developed hallmark features of CF lung disease, including airway inflammation, remodeling, mucus accumulation, and infection. Their lungs contained multiple bacterial species, suggesting that the lungs of CF pigs have a host defense defect against a wide spectrum of bacteria. In humans, the temporal and causal relations between inflammation and infection have remained uncertain. To investigate these processes, we studied newborn pigs. Their lungs showed no inflammation but were less often sterile than controls. Moreover, after introduction of bacteria into their lungs, pigs with CF failed to eradicate bacteria as effectively as wild-type pigs. These results suggest that impaired bacterial elimination is the pathogenic event that initiates a cascade of inflammation and pathology in CF lungs. Our finding that pigs with CF have a host defense defect against bacteria within hours of birth provides an opportunity to further investigate CF pathogenesis and to test therapeutic and preventive strategies that could be deployed before secondary consequences develop.

The Statistical Analysis of Interval-censored Failure Time Data

Abstract: Inference for Parametric Models and Imputation Approaches.- Nonparametric Maximum Likelihood Estimation.- Comparison of Survival Functions.- Regression Analysis of Current Status Data.- Regression Analysis of Case II Interval-censored Data.- Analysis of Bivariate Interval-censored Data.- Analysis of Doubly Censored Data.- Analysis of Panel Count Data.- Other Topics.

A Simple Genetic Architecture Underlies Morphological Variation in Dogs

Abstract: Domestic dogs exhibit tremendous phenotypic diversity, including a greater variation in body size than any other terrestrial mammal. Here, we generate a high density map of canine genetic variation by genotyping 915 dogs from 80 domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across 60,968 single-nucleotide polymorphisms (SNPs). Coupling this genomic resource with external measurements from breed standards and individuals as well as skeletal measurements from museum specimens, we identify 51 regions of the dog genome associated with phenotypic variation among breeds in 57 traits. The complex traits include average breed body size and external body dimensions and cranial, dental, and long bone shape and size with and without allometric scaling. In contrast to the results from association mapping of quantitative traits in humans and domesticated plants, we find that across dog breeds, a small number of quantitative trait loci (≤3) explain the majority of phenotypic variation for most of the traits we studied. In addition, many genomic regions show signatures of recent selection, with most of the highly differentiated regions being associated with breed-defining traits such as body size, coat characteristics, and ear floppiness. Our results demonstrate the efficacy of mapping multiple traits in the domestic dog using a database of genotyped individuals and highlight the important role human-directed selection has played in altering the genetic architecture of key traits in this important species.

Advances and Challenges in Protein-Ligand Docking

Abstract: Molecular docking is a widely-used computational tool for the study of molecular recognition, which aims to predict the binding mode and binding affinity of a complex formed by two or more constituent molecules with known structures. An important type of molecular docking is protein-ligand docking because of its therapeutic applications in modern structure-based drug design. Here, we review the recent advances of protein flexibility, ligand sampling, and scoring functions—the three important aspects in protein-ligand docking. Challenges and possible future directions are discussed in the Conclusion.

Invasion, Competition, and Biodiversity Loss in Urban Ecosystems

Abstract: The global decline in biodiversity as a result of urbanization remains poorly understood. Whereas habitat destruction accounts for losses at the species level, it may not explain diversity loss at the community level, because urban centers also attract synanthropic species that do not necessarily exist in wildlands. Here we suggest an alternative framework for understanding this phenomenon: the competitive exclusion of native, nonsynanthropic species by invasive species. We use data from two urban centers (Phoenix and Baltimore) and two taxa (birds and spiders) to link diversity loss with reduced community evenness among species in urban communities. This reduction in evenness may be caused by a minority of invasive species dominating the majority of the resources, consequently excluding nonsynanthropic species that could otherwise adapt to urban conditions. We use foraging efficiency as a mechanism to explain the loss of diversity. Thus, to understand the effects of habitat conversion on biodiversity, and to sustain species-rich communities, future research should give more attention to interspecific interactions in urban settings.

Ethylene-Induced Stabilization of ETHYLENE INSENSITIVE3 and EIN3-LIKE1 Is Mediated by Proteasomal Degradation of EIN3 Binding F-Box 1 and 2 That Requires EIN2 in Arabidopsis

Abstract: Plant responses to ethylene are mediated by regulation of EBF1/2-dependent degradation of the ETHYLENE INSENSITIVE3 (EIN3) transcription factor. Here, we report that the level of EIL1 protein is upregulated by ethylene through an EBF1/2-dependent pathway. Genetic analysis revealed that EIL1 and EIN3 cooperatively but differentially regulate a wide array of ethylene responses, with EIL1 mainly inhibiting leaf expansion and stem elongation in adult plants and EIN3 largely regulating a multitude of ethylene responses in seedlings. When EBF1 and EBF2 are disrupted, EIL1 and EIN3 constitutively accumulate in the nucleus and remain unresponsive to exogenous ethylene application. Further study revealed that the levels of EBF1 and EBF2 proteins are downregulated by ethylene and upregulated by silver ion and MG132, suggesting that ethylene stabilizes EIN3/EIL1 by promoting EBF1 and EBF2 proteasomal degradation. Also, we found that EIN2 is indispensable for mediating ethylene-induced EIN3/EIL1 accumulation and EBF1/2 degradation, whereas MKK9 is not required for ethylene signal transduction, contrary to a previous report. Together, our studies demonstrate that ethylene similarly regulates EIN3 and EIL1, the two master transcription factors coordinating myriad ethylene responses, and clarify that EIN2 but not MKK9 is required for ethylene-induced EIN3/EIL1 stabilization. Our results also reveal that EBF1 and EBF2 act as essential ethylene signal transducers that by themselves are subject to proteasomal degradation.

A Terror Management Analysis of the Psychological Functions of Religion

Abstract: From a terror management theory (TMT) perspective, religion serves to manage the potential terror engendered by the uniquely human awareness of death by affording a sense of psychological security and hope of immortality. Although secular beliefs can also serve a terror management function, religious beliefs are particularly well suited to mitigate death anxiety because they are all encompassing, rely on concepts that are not easily disconfirmed, and promise literal immortality. Research is reviewed demonstrating that mortality salience produces increased belief in afterlife, supernatural agency, human ascension from nature, and spiritual distinctions between mind and body. The social costs and benefits of religious beliefs are considered and compared to those of secular worldviews. The terror management functions of, and benefits and costs associated with, different types of religious orientation, such as intrinsic religiosity, quest, and religious fundamentalism, are then examined. Finally, the TMT analysis is compared to other accounts of religion.

Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions.

Abstract: The scoring function is one of the most important components in structure-based drug design. Despite considerable success, accurate and rapid prediction of protein–ligand interactions is still a challenge in molecular docking. In this perspective, we have reviewed three basic types of scoring functions (force-field, empirical, and knowledge-based) and the consensus scoring technique that are used for protein–ligand docking. The commonly-used assessment criteria and publicly available protein–ligand databases for performance evaluation of the scoring functions have also been presented and discussed. We end with a discussion of the challenges faced by existing scoring functions and possible future directions for developing improved scoring functions.

Lymphedema beyond breast cancer

Abstract: BACKGROUND: Secondary lymphedema is a debilitating, chronic, progressive condition that commonly occurs after the treatment of breast cancer. The purpose of the current study was to perform a systematic review and meta-analysis of the oncology-related literature excluding breast cancer to derive estimates of lymphedema incidence and to identify potential risk factors among various malignancies. METHODS: The authors systematically reviewed 3 major medical indices (MEDLINE, Cochrane Library databases, and Scopus) to identify studies (1972-2008) that included a prospective assessment of lymphedema after cancer treatment. Studies were categorized according to malignancy, and data included treatment, complications, lymphedema measurement criteria, lymphedema incidence, and follow-up interval. A quality assessment of individual studies was performed using established criteria for systematic reviews. Bayesian meta-analytic techniques were applied to derive summary estimates when sufficient data were available. RESULTS: A total of 47 studies (7779 cancer survivors) met inclusion criteria: melanoma (n = 15), gynecologic malignancies (n = 22), genitourinary cancers (n = 8), head/neck cancers (n = 1), and sarcomas (n = 1). The overall incidence of lymphedema was 15.5% and varied by malignancy (P < .001): melanoma, 16% (upper extremity, 5%; lower extremity, 28%); gynecologic, 20%; genitourinary, 10%; head/neck, 4%; and sarcoma, 30%. Increased lymphedema risk was also noted for patients undergoing pelvic dissections (22%) and radiation therapy (31%). Objective measurement methods and longer follow-up were both associated with increased lymphedema incidence. CONCLUSIONS: Lymphedema is a common condition affecting cancer survivors with various malignancies. The incidence of lymphedema is related to the type and extent of treatment, anatomic location, heterogeneity of assessment methods, and length of follow-up. Cancer 2010. © 2010 American Cancer Society.

The Dutch Hunger Winter and the developmental origins of health and disease

Abstract: In the early 1980s, David Barker and others noted a paradox: although overall rates of cardiovascular disease increase with rising national prosperity, the least prosperous residents of a wealthy nation suffer the highest rates. He and others proposed over a series of studies that an adverse fetal environment followed by plentiful food in adulthood may be a recipe for adult chronic disease, a claim referred to as the Barker Hypothesis. These studies generally correlated birth weight and other infant parameters to the incidence of adult disease. Detractors, including an editorial in BMJ in 1995, complained that “[e]arly nutrition is inferred indirectly from fetal and infant growth, and fetal growth especially is a doubtful surrogate measure” (1). Most of the epidemiological studies were also vulnerable to confounding factors, particularly social class, that influence both intrauterine and adult environment, which delayed acceptance of the hypothesis. In PNAS, Rooij et al. (2) present another chapter in the ongoing study of the children of the Dutch Hunger Winter, a key test of the hypothesis (2). They show that, in addition to the previously shown effects of food restriction in utero on metabolism and cardiovascular health, there are effects on age-associated decline of cognitive functions. In the winter and spring of 1944 after a railway strike, the German occupation limited rations such that people, including pregnant women, in the western region of The Netherlands, including Amsterdam, received as little as 400–800 calories/d. The famine affected people of all social classes and was followed by growing prosperity in the postwar period. Thus, the Dutch Hunger Winter study, from which results were first published in 1976, provides an almost perfectly designed, although tragic, human experiment in the effects of intrauterine deprivation on subsequent adult health. This study has provided crucial support and fundamental insights for the growing field of the developmental origins of health and disease (DOHaD).

The Arabidopsis Nitrate Transporter NRT1.8 Functions in Nitrate Removal from the Xylem Sap and Mediates Cadmium Tolerance

Abstract: Long-distance transport of nitrate requires xylem loading and unloading, a successive process that determines nitrate distribution and subsequent assimilation efficiency. Here, we report the functional characterization of NRT1.8, a member of the nitrate transporter (NRT1) family in Arabidopsis thaliana. NRT1.8 is upregulated by nitrate. Histochemical analysis using promoter-beta-glucuronidase fusions, as well as in situ hybridization, showed that NRT1.8 is expressed predominantly in xylem parenchyma cells within the vasculature. Transient expression of the NRT1.8:enhanced green fluorescent protein fusion in onion epidermal cells and Arabidopsis protoplasts indicated that NRT1.8 is plasma membrane localized. Electrophysiological and nitrate uptake analyses using Xenopus laevis oocytes showed that NRT1.8 mediates low-affinity nitrate uptake. Functional disruption of NRT1.8 significantly increased the nitrate concentration in xylem sap. These data together suggest that NRT1.8 functions to remove nitrate from xylem vessels. Interestingly, NRT1.8 was the only nitrate assimilatory pathway gene that was strongly upregulated by cadmium (Cd(2+)) stress in roots, and the nrt1.8-1 mutant showed a nitrate-dependent Cd(2+)-sensitive phenotype. Further analyses showed that Cd(2+) stress increases the proportion of nitrate allocated to wild-type roots compared with the nrt1.8-1 mutant. These data suggest that NRT1.8-regulated nitrate distribution plays an important role in Cd(2+) tolerance.

An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants

Abstract: *SUMMARY Soybean (Glycine max L.) is a major crop providing an important source of protein and oil, which can also be converted into biodiesel. A major milestone in soybean research was the recent sequencing of its genome. The sequence predicts 69 145 putative soybean genes, with 46 430 predicted with high confidence. In order to examine the expression of these genes, we utilized the Illumina Solexa platform to sequence cDNA derived from 14 conditions (tissues). The result is a searchable soybean gene expression atlas accessible through a browser (http://digbio.missouri.edu/soybean_atlas). The data provide experimental support for the transcription of 55 616 annotated genes and also demonstrate that 13 529 annotated soybean genes are putative pseudogenes, and 1736 currently unannotated sequences are transcribed. An analysis of this atlas reveals strong differences in gene expression patterns between different tissues, especially between root and aerial organs, but also reveals similarities between gene expression in other tissues, such as flower and leaf organs. In order to demonstrate the full utility of the atlas, we investigated the expression patterns of genes implicated in nodulation, and also transcription factors, using both the Solexa sequence data and large-scale qRT-PCR. The availability of the soybean gene expression atlas allowed a comparison with gene expression documented in the two model legume species, Medicago truncatula and Lotus japonicus, as well as data available for Arabidopsis thaliana, facilitating both basic and applied aspects of soybean research.