Unlocking the barley genome by chromosomal and comparative genomics

We used a novel approach that incorporated chromosome sorting, next-generation sequencing, array hybridization, and systematic exploitation of conserved synteny with model grasses to assign ~86% of the estimated ~32,000 barley (Hordeum vulgare) genes to individual chromosome arms. Using a series of bioinformatically constructed genome zippers that integrate gene indices of rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium distachyon in a conserved synteny model, we were able to assemble 21,766 barley genes in a putative linear order. We show that the barley (H) genome displays a mosaic of structural similarity to hexaploid bread wheat (Triticum aestivum) A, B, and D subgenomes and that orthologous genes in different grasses exhibit signatures of positive selection in different lineages. We present an ordered, information-rich scaffold of the barley genome that provides a valuable and robust framework for the development of novel strategies in cereal breeding.     

Influenza virus H1N1pdm09 infections in the young and old: evidence of greater antibody diversity and affinity for the hemagglutinin globular head domain (HA1 Domain) in the elderly than in young adults and children

The H1N1 2009 influenza virus (H1N1pdm09) pandemic had several unexpected features, including low morbidity and mortality in older populations. We performed in-depth evaluation of antibody responses generated following H1N1pdm09 infection of naïve ferrets and of 130 humans ranging from the very young (0 to 9 years old) to the very old (70 to 89 years old). In addition to hemagglutination inhibition (HI) titers, we used H1N1pdm09 whole-genome-fragment phage display libraries (GFPDL) to evaluate the antibody repertoires against internal genes, hemagglutinin (HA), and neuraminidase (NA) and also measured antibody affinity for antigenic domains within HA. GFPDL analyses of H1N1pdm09-infected ferrets demonstrated gradual development of antibody repertoires with a focus on M1 and HA1 by day 21 postinfection. In humans, H1N1pdm09 infection in the elderly (>70 years old) induced antibodies with broader epitope recognition in both the internal genes and the HA1 receptor binding domain (RBD) than for the younger age groups (0 to 69 years). Importantly, post-H1N1 infection serum antibodies from the elderly demonstrated substantially higher avidity for recombinant HA1 (rHA1) (but not HA2) than those from younger subjects (50% versus <22% 7 M urea resistance, respectively) and lower antibody dissociation rates using surface plasmon resonance. This is the first study in humans that provides evidence for a qualitatively superior antibody response in the elderly following H1N1pdm09 infection, indicative of recall of long-term memory B cells or long-lived plasma cells. These findings may help explain the age-related morbidity and mortality pattern observed during the H1N1pdm09 pandemic.     

Genetic,morphological, and niche variation in the widely hybridizing Rhus integrifolia-Rhus ovata species complex

Hybridization and introgression are common processes among numerous plant species that present both challenges and opportunities for studies of species delimitation, phylogenetics, taxonomy and adaptation. Rhus integrifolia and R. ovata are two ecologically important shrubs native to the southwestern USA and Mexico, and are known to hybridize frequently, but the morphological, genetic and ecological implications of hybridization in these species are poorly studied on a broad geographic scale. Analyses were conducted using leaf morphology, genetic variation of plastid and nuclear loci, and species distribution models for both species and their putative hybrid introgressants across 19 localities in California and Arizona, USA. These analyses revealed evidence for morphological and genetic distinction among localities comprising putative parental species, but a high degree of morpho-genetic intermediacy among localities with putative hybrids. Comparison of morphological and genetic population structure among localities revealed evidence for putative local adaptation or widespread phenotypic plasticity. Multiple regression models identified a weak but statistically significant negative association between leaf area and precipitation. Finally, species distribution modeling inferred northward range shifts over time, with both species predicted to occupy more coastal regions in the future, possibly increasing the frequency of hybridization among them. These findings underscore the importance of integrative assessment of multiple data sources in the study of hybridizing species and highlight the R. integrifolia-ovata complex as a powerful model for investigating the adaptive implications of hybridization.     

The comparison of vanadyl(IV) and insulin-induced hyperpolarization of the mammalian muscle cell

Extracellularly applied vanadyl(IV) hyperpolarized the membrane potential of mouse diaphragm muscle from about −74.0 mV up to −81.7 mV. The hyperpolarizing effect of 10⁻⁴ mol·l⁻¹ vanadyl(IV) is comparable with hyperpolarization induced by 100 mU·ml⁻¹ insulin. Both compounds increased the intracellular K⁺ concentration, the hyperpolarizing effect of vanadyl(IV) and insulin is blocked by ouabain and is unaffected by removal of K⁺ from the external medium. Triggering of the release of intracellular K⁺ associated with cellular proteins is proposed as the mechanism of vanadyl(IV) and insulin-induced hyperpolarization.     

Enhanced levels of free and protein-bound threonine in transgenic alfalfa (Medicago sativa L.) expressing a bacterial feedback-insensitive aspartate kinase gene

Threonine, lysine, methionine, and tryptophan are essential amino acids for humans and monogastric animals. Many of the commonly used diet formulations, particularly for pigs and poultry, contain limiting amounts of these amino acids. One approach for raising the level of essential amino acids is based on altering the regulation of their biosynthetic pathways in transgenic plants. Here we describe the first production of a transgenic forage plant, alfalfa (Medicago sativa L.) with modified regulation of the aspartate-family amino acid biosynthetic pathway. This was achieved by over-expressing the Escherichia coli feedback-insensitive aspartate kinase (AK) in transgenic plants. These plants showed enhanced levels of both free and protein-bound threonine. In many transgenic plants the rise in free threonine was accompanied by a significant reduction both in aspartate and in glutamate. Our data suggest that in alfalfa, AK might not be the only limiting factor for threonine biosynthesis, and that the free threonine pool in this plant limits its incorporation into plant proteins.     

Phenotypic profiling of mGlu7 knockout mice reveals new implications for neurodevelopmental disorders

Neurodevelopmental disorders are characterized by deficits in communication, cognition, attention, social behavior and/or motor control. Previous studies have pointed to the involvement of genes that regulate synaptic structure and function in the pathogenesis of these disorders. One such gene, GRM7, encodes the metabotropic glutamate receptor 7 (mGlu₇), a G protein‐coupled receptor that regulates presynaptic neurotransmitter release. Mutations and polymorphisms in GRM7 have been associated with neurodevelopmental disorders in clinical populations; however, limited preclinical studies have evaluated mGlu₇ in the context of this specific disease class. Here, we show that the absence of mGlu₇ in mice is sufficient to alter phenotypes within the domains of social behavior, associative learning, motor function, epilepsy and sleep. Moreover, Grm7 knockout mice exhibit an attenuated response to amphetamine. These findings provide rationale for further investigation of mGlu₇ as a potential therapeutic target for neurodevelopmental disorders such as idiopathic autism, attention deficit hyperactivity disorder and Rett syndrome.     

Habitat requirements, short-term population dynamics and coexistence of native and invasive Impatiens species: a field study

The genus Impatiens (Balsaminaceae) includes three widespread species in the Czech Republic, central Europe: the native I. noli-tangere, and two invasive species, I. parviflora and I. glandulifera, differing in the dynamics of invasion. They all occur in similar habitats and share basic life-history characteristics, which make them a suitable model for studying species traits associated with invasiveness. In this study we investigated differences in habitat requirements of these Impatiens species, their coexistence and short-term population dynamics in the field. We established 84 1 × 1 m permanent plots in five localities where all three species co-occurred. In each plot vascular plant species were determined, their cover estimated and all individuals of Impatiens species counted. Site characteristics including tree canopy cover, soil moisture, nitrogen and carbon content, and slope were measured directly. Nutrients, light, humidity and soil reaction were estimated using Ellenberg indicator values. The presence of I. noli-tangere was strongly correlated with high soil moisture, that of I. parviflora with high tree canopy cover and low soil moisture. Impatiens glandulifera exhibited a unimodal response to tree canopy cover, avoiding both very shaded and fully open sites. The current-year abundances of all species were negatively related to those of congeneric species. These results suggest that the coexistence of Impatiens species in the same habitat is due to microsite differentiation. Further spread of I. glandulifera to new habitats, and reduction of the native I. noli-tangere niche, can be expected in areas where the latter species co-occurs with competitively strong invasive congeners.     

Four Pathogenic Candida Species Differ in Salt Tolerance

The virulence of Candida species depends on many environmental conditions, including extracellular pH and concentration of alkali metal cations. Tests of the tolerance/sensitivity of four pathogenic Candida species (C. albicans, C. dubliniensis, C. glabrata, and C. parapsilosis) to alkali metal cations under various growth conditions revealed significant differences among these species. Though all of them can be classified as rather osmotolerant yeast species, they exhibit different levels of tolerance to different salts. C. parapsilosis and C. albicans are the most salt-tolerant in general; C. dubliniensis is the least tolerant on rich YPD media and C. glabrata on acidic (pH 3.5) minimal YNB medium. C. dubliniensis is relatively salt-sensitive in spite of its ability to maintain as high intracellular K⁺/Na⁺ ratio as its highly salt-tolerant relative C. albicans. On the other hand, C. parapsilosis can grow in the presence of very high external NaCl concentrations in spite of its high intracellular Na⁺ concentrations (and thus lower K⁺/Na⁺ ratio) and thus resembles salt-tolerant (halophilic) Debaryomyces hansenii.