Systems Biology: The Next Frontier for Bioinformatics

Biochemical systems biology augments more traditional disciplines, such as genomics, biochemistry and molecular biology, by championing (i) mathematical and computational modeling; (ii) the application of traditional engineering practices in the analysis of biochemical systems; and in the past decade increasingly (iii) the use of near-comprehensive data sets derived from ‘omics platform technologies, in particular “downstream” technologies relative to genome sequencing, including transcriptomics, proteomics and metabolomics. The future progress in understanding biological principles will increasingly depend on the development of temporal and spatial analytical techniques that will provide high-resolution data for systems analyses. To date, particularly successful were strategies involving (a) quantitative measurements of cellular components at the mRNA, protein and metabolite levels, as well as in vivo metabolic reaction rates, (b) development of mathematical models that integrate biochemical knowledge with the information generated by high-throughput experiments, and (c) applications to microbial organisms. The inevitable role bioinformatics plays in modern systems biology puts mathematical and computational sciences as an equal partner to analytical and experimental biology. Furthermore, mathematical and computational models are expected to become increasingly prevalent representations of our knowledge about specific biochemical systems

Mass spectrometry imaging for plant biology: A review

Mass spectrometry imaging (MSI) is a developing technique to measure the spatio-temporal distribution of many biomolecules in tissues. Over the preceding decade, MSI has been adopted by plant biologists and applied in a broad range of areas, including primary metabolism, natural products, plant defense, plant responses to abiotic and biotic stress, plant lipids and the developing field of spatial metabolomics. This review covers recent advances in plant-based MSI, general aspects of instrumentation, analytical approaches, sample preparation and the current trends in respective plant research

De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure

Plant roots are the first organs sensing and responding to salinity stress, manifested differentially between different root types, and also at the individual tissue and cellular level. High genetic diversity and the current lack of an assembled map-based sequence of the barley genome severely limit barley research potential. We used over 580 and 600 million paired-end reads, respectively, to create two de novo assemblies of a barley landrace (Sahara) and a malting cultivar (Clipper) with known contrasting responses to salinity. Generalized linear models were used to statistically access spatial, treatment-related, and genotype-specific responses. This revealed a spatial gene expression gradient along the barley root, with more differentially expressed transcripts detected between different root zones than between treatments. The root transcriptome also showed a gradual transition from transcripts related to sugar-mediated signaling at the root meristematic zone to those involved in cell wall metabolism in the elongation zone, and defense response-related pathways toward the maturation zone, with significant differences between the two genotypes. The availability of these additional transcriptome reference sets will serve as a valuable resource to the cereal research community, and may identify valuable traits to assist in breeding programmes

A Fasciclin-Like Arabinogalactan-Protein (FLA) Mutant of Arabidopsis thaliana, fla1, Shows Defects in Shoot Regeneration

Extent: 11p.BACKGROUND: The fasciclin-like arabinogalactan-proteins (FLAs) are an enigmatic class of 21 members within the larger family of arabinogalactan-proteins (AGPs) in Arabidopsis thaliana. Located at the cell surface, in the cell wall/plasma membrane, they are implicated in many developmental roles yet their function remains largely undefined. Fasciclin (FAS) domains are putative cell-adhesion domains found in extracellular matrix proteins of organisms from all kingdoms, but the juxtaposition of FAS domains with highly glycosylated AGP domains is unique to plants. Recent studies have started to elucidate the role of FLAs in Arabidopsis development. FLAs containing a single FAS domain are important for the integrity and elasticity of the plant cell wall matrix (FLA11 and FLA12) and FLA3 is involved in microspore development. FLA4/SOS5 with two FAS domains and two AGP domains has a role in maintaining proper cell expansion under salt stressed conditions. The role of other FLAs remains to be uncovered. METHOD/PRINCIPAL FINDINGS: Here we describe the characterisation of a T-DNA insertion mutant in the FLA1 gene (At5g55730). Under standard growth conditions fla1-1 mutants have no obvious phenotype. Based on gene expression studies, a putative role for FLA1 in callus induction was investigated and revealed that fla1-1 has a reduced ability to regenerate shoots in an in vitro shoot-induction assay. Analysis of FLA1p:GUS reporter lines show that FLA1 is expressed in several tissues including stomata, trichomes, the vasculature of leaves, the primary root tip and in lateral roots near the junction of the primary root. CONCLUSION: The results of the developmental expression of FLA1 and characterisation of the fla1 mutant support a role for FLA1 in the early events of lateral root development and shoot development in tissue culture, prior to cell-type specification.Kim L. Johnson, Natalie A. J. Kibble, Antony Bacic and Carolyn J. Schult

Hordein accumulation in developing barley grains

The temporal pattern of accumulation of hordein storage proteins in developing barley grains was studied by enzyme-linked immunosorbent assay (ELISA), western blot and liquid chromatography tandem mass spectrometry (LC-MS/MS). Hordein accumulation was compared to the pattern seen for two abundant control proteins, serpin Z4 (an early accumulator) and lipid transferase protein (LTP1, a late accumulator). Hordeins were detected from 6 days post-anthesis (DPA) and peaked at 30 DPA. Changes in fresh weight indicate that desiccation begins at 20 DPA and by 37 DPA fresh weight had decreased by 35%. ELISA analysis of hordein content, expressed on a protein basis, increased to a maximum at 30 DPA followed by a 17% decrease by 37 DPA. The accumulation of 39 tryptic and 29 chymotryptic hordein peptides representing all classes of hordein was studied by LC-MS/MS. Most peptides increased to a maximum at 30 DPA, and either remained at the maximum or did not decrease significantly. Only five tryptic peptides, members of the related B1- and γ1-hordeins decreased significantly by 21–51% at 37 DPA. Thus, the concentration of some specific peptides was reduced while remaining members of the same family were not affected. The N-terminal signal region was removed by proteolysis during co-translation. In addition to a suite of previously characterized hordeins, two novel barley B-hordein isoforms mapping to wheat low molecular weight glutenins (LMW-GS-like B-hordeins), and two avenin-like proteins (ALPs) sharing homology with wheat ALPs, were identified. These identified isoforms have not previously been mapped in the barley genome. Cereal storage proteins provide significant nutritional content for human consumption and seed germination. In barley, the bulk of the storage proteins comprise the hordein family and the final hordein concentration affects the quality of baked and brewed products. It is therefore important to study the accumulation of hordeins as this knowledge may assist plant breeding for improved health outcomes (by minimizing triggering of detrimental immune responses), nutrition and food processing properties

Differences in glycosyltransferase family 61 accompany variation in seed coat mucilage composition in Plantago spp.

Xylans are the most abundant non-cellulosic polysaccharide found in plant cell walls. A diverse range of xylan structures influence tissue function during growth and development. Despite the abundance of xylans in nature, details of the genes and biochemical pathways controlling their biosynthesis are lacking. In this study we have utilized natural variation within the Plantago genus to examine variation in heteroxylan composition and structure in seed coat mucilage. Compositional assays were combined with analysis of the glycosyltransferase family 61 (GT61) family during seed coat development, with the aim of identifying GT61 sequences participating in xylan backbone substitution. The results reveal natural variation in heteroxylan content and structure, particularly in P. ovata and P. cunninghamii, species which show a similar amount of heteroxylan but different backbone substitution profiles. Analysis of the GT61 family identified specific sequences co-expressed with IRREGULAR XYLEM 10 genes, which encode putative xylan synthases, revealing a close temporal association between xylan synthesis and substitution. Moreover, in P. ovata, several abundant GT61 sequences appear to lack orthologues in P. cunninghamii. Our results indicate that natural variation in Plantago species can be exploited to reveal novel details of seed coat development and polysaccharide biosynthetic pathways.Jana L. Phan, Matthew R. Tucker, Shi Fang Khor, Neil Shirley, Jelle Lahnstein, Cherie Beahan, Antony Bacic and Rachel A. Burto

Supporting employees' work-family needs improves health care quality: Longitudinal evidence from long-term care

We analyzed qualitative and quantitative data from U.S.-based employees in 30 long-term care facilities. Analysis of semi-structured interviews from 154 managers informed quantitative analyses. Quantitative data include 1214 employees' scoring of their supervisors and their organizations on family supportiveness (individual scores and aggregated to facility level), and three outcomes: (1), care quality indicators assessed at facility level (n = 30) and collected monthly for six months after employees' data collection; (2), employees' dichotomous survey response on having additional off-site jobs; and (3), proportion of employees with additional jobs at each facility. Thematic analyses revealed that managers operate within the constraints of an industry that simultaneously: (a) employs low-wage employees with multiple work-family challenges, and (b) has firmly institutionalized goals of prioritizing quality of care and minimizing labor costs. Managers universally described providing work-family support and prioritizing care quality as antithetical to each other. Concerns surfaced that family-supportiveness encouraged employees to work additional jobs off-site, compromising care quality. Multivariable linear regression analysis of facility-level data revealed that higher family-supportive supervision was associated with significant decreases in residents' incidence of all pressure ulcers (−2.62%) and other injuries (−9.79%). Higher family-supportive organizational climate was associated with significant decreases in all falls (−17.94%) and falls with injuries (−7.57%). Managers' concerns about additional jobs were not entirely unwarranted: multivariable logistic regression of employee-level data revealed that among employees with children, having family-supportive supervision was associated with significantly higher likelihood of additional off-site jobs (RR 1.46, 95%CI 1.08–1.99), but family-supportive organizational climate was associated with lower likelihood (RR 0.76, 95%CI 0.59–0.99). However, proportion of workers with additional off-site jobs did not significantly predict care quality at facility levels. Although managers perceived providing work-family support and ensuring high care quality as conflicting goals, results suggest that family-supportiveness is associated with better care quality

Estructuras espaciales para la representación de mapas

Unos pocos años atrás la información geográfica se representaba en mapas de papel y la manipulación de esta información estaba limitada a un proceso manual no interactivo. El rápido desarrollo de la digitalización de la información geográfica junto con una demanda creciente de manipulación y análisis de estos datos ha generado la necesidad de software dedicado. La información geográfica está constituida por grandes volúmenes de información espacial y se hace necesario contar con métodos eficientes para almacenarla y recuperar datos relevantes. Los datos espaciales consisten de objetos espaciales basados en puntos, líneas, superficies, volúmenes y otros datos de mayor dimensión. Ejemplo de datos espaciales son ciudades, rutas, ríos, etc. En un mapa, estos objetos espaciales combinados con ciertos atributos no espaciales tales como nombres de ciudades, nombres de calles, numeración de rutas, etc. conforman la información geográfica. Las bases de datos espaciales facilitan el almacenamiento y el procesamiento eficiente de información espacial y no espacial, idealmente sin favorecer una sobre otra. Una propuesta para la representación de datos espaciales es separar estructuralmente los datos no espaciales de los espaciales manteniendo apropiadamente la relación entre ambos. Esto nos permite agilizar las consultas sobre los datos espaciales (las operaciones espaciales son realizadas directamente sobre la estructura de datos espaciales) y nos da la libertad de elegir una estructura de datos espacial más apropiada de las que nos impone la estructura no espacial. Existen muchos estudios teóricos dedicados al tratamiento de información espacial; no obstante, la mayoría de los trabajos de alcance público se basan en la utilización de bases de datos relacionales las cuales no resultan adecuadas debido a la naturaleza de la información subyacente. En este contexto, se están estudiando distintas técnicas que permitan representar y manejar adecuadamente datos espaciales, restringiendo la atención a objetos cuyas componentes estén definidas en el plano 2D. Como parte de este estudio se está desarrollando un prototipo para la recuperación y visualización de información espacial que sirva de base para el diseño de distintas aplicaciones de planeamiento urbano.Eje: Computación gráfica. VisualizaciónRed de Universidades con Carreras en Informática (RedUNCI

Estructuras espaciales para la representación de mapas

Unos pocos años atrás la información geográfica se representaba en mapas de papel y la manipulación de esta información estaba limitada a un proceso manual no interactivo. El rápido desarrollo de la digitalización de la información geográfica junto con una demanda creciente de manipulación y análisis de estos datos ha generado la necesidad de software dedicado. La información geográfica está constituida por grandes volúmenes de información espacial y se hace necesario contar con métodos eficientes para almacenarla y recuperar datos relevantes. Los datos espaciales consisten de objetos espaciales basados en puntos, líneas, superficies, volúmenes y otros datos de mayor dimensión. Ejemplo de datos espaciales son ciudades, rutas, ríos, etc. En un mapa, estos objetos espaciales combinados con ciertos atributos no espaciales tales como nombres de ciudades, nombres de calles, numeración de rutas, etc. conforman la información geográfica. Las bases de datos espaciales facilitan el almacenamiento y el procesamiento eficiente de información espacial y no espacial, idealmente sin favorecer una sobre otra. Una propuesta para la representación de datos espaciales es separar estructuralmente los datos no espaciales de los espaciales manteniendo apropiadamente la relación entre ambos. Esto nos permite agilizar las consultas sobre los datos espaciales (las operaciones espaciales son realizadas directamente sobre la estructura de datos espaciales) y nos da la libertad de elegir una estructura de datos espacial más apropiada de las que nos impone la estructura no espacial. Existen muchos estudios teóricos dedicados al tratamiento de información espacial; no obstante, la mayoría de los trabajos de alcance público se basan en la utilización de bases de datos relacionales las cuales no resultan adecuadas debido a la naturaleza de la información subyacente. En este contexto, se están estudiando distintas técnicas que permitan representar y manejar adecuadamente datos espaciales, restringiendo la atención a objetos cuyas componentes estén definidas en el plano 2D. Como parte de este estudio se está desarrollando un prototipo para la recuperación y visualización de información espacial que sirva de base para el diseño de distintas aplicaciones de planeamiento urbano.Eje: Computación gráfica. VisualizaciónRed de Universidades con Carreras en Informática (RedUNCI