Cystic fibrosis screening, evaluation, and management of hepatobiliary disease consensus recommendations.

Cystic fibrosis (CF) may cause a spectrum of hepatobiliary complications, including portal hypertension, multilobular cirrhosis, and liver failure. Current guidelines on the detection and monitoring of hepatobiliary complications in CF were published in 1999. The CF Foundation assembled a committee to evaluate research advances and formulate revised guidelines for CF-associated liver disease. A committee of hepatologists, gastroenterologists, pulmonologists, pharmacists, nurses, dietitians, individuals with CF, and the parents of a child with CF devised "population, intervention, comparison, and outcome" questions regarding hepatobiliary disease in CF. PubMed literature searches were performed for each population, intervention, comparison, and outcome question. Recommendations were voted on with 80% agreement required to approve a recommendation. Public comment on initial recommendations was solicited prior to the formulation of final recommendations. Thirty-one population, intervention, comparison, and outcome questions were assembled, 6401 manuscripts were title screened for relevance, with 1053 manuscripts undergoing detailed full-text review. Seven recommendations were approved for screening, 13 for monitoring of existing disease, and 14 for treatment of CF-associated hepatobiliary involvement or advanced liver disease. One recommendation on liver biopsy did not meet the 80% threshold. One recommendation on screening ultrasound was revised and re-voted on. Through a multidisciplinary committee and public engagement, we have assembled updated recommendations and guidance on screening, monitoring, and treatment of CF-associated hepatobiliary involvement and advanced liver disease. While research gaps remain, we anticipate that these recommendations will lead to improvements in CF outcomes through earlier detection and increased evidence-based approaches to monitoring and treatment.

Effect of Metal Nanoparticle Aggregate Structure on the Thermodynamics of Oxidative Dissolution.

Here, we compare the electrochemical oxidation potential of 15 nm diameter citrate-stabilized Au NPs aggregated by acid (low pH) to those aggregated by tetrakis(hydroxymethyl) phosphonium chloride (THPC). For acid-induced aggregation, the solution changes to a blue-violet color, the localized surface plasmon resonance (LSPR) band of Au NPs at 520 nm decreases along with an increase in absorbance at higher wavelengths (600-800 nm), and the peak oxidation potential (Ep) in anodic stripping voltammetry (ASV) obtained in bromide has a positive shift by as large as 200 mV. For THPC-induced aggregation (Au/THPC mole ratio = 62.5), the solution changes to a blue color as the LSPR band at 520 nm decreases and a new distinct peak at 700 nm appears, but the Ep does not exhibit a positive shift. Scanning transmission electron microscopy (STEM) images reveal that acid-induced aggregates are three-dimensional with strongly fused Au NP-Au NP contacts, while THPC-induced aggregates are linear or two-dimensional with ∼1 nm separation between Au NPs. The surface area-to-volume ratio (SA/V) decreases for acid-aggregated Au NPs due to strong Au NP-Au NP contacts, which leads to lower surface free energy and a higher Ep. The SA/V does not change for THPC-aggregated Au NPs since space remains between them and their SA is fully accessible. These findings show that metal NP oxidative stability, as determined by ASV, is highly sensitive to the details of the aggregate structure.

Integrated metabolomics identifies CYP72A67 and CYP72A68 oxidases in the biosynthesis of Medicago truncatula oleanate sapogenins.

INTRODUCTION: Triterpene saponins are important bioactive plant natural products found in many plant families including the Leguminosae. OBJECTIVES: We characterize two Medicago truncatula cytochrome P450 enzymes, MtCYP72A67 and MtCYP72A68, involved in saponin biosynthesis including both in vitro and in planta evidence. METHODS: UHPLC-(-)ESI-QToF-MS was used to profile saponin accumulation across a collection of 106 M. truncatula ecotypes. The profiling results identified numerous ecotypes with high and low saponin accumulation in root and aerial tissues. Four ecotypes with significant differential saponin content in the root and/or aerial tissues were selected, and correlated gene expression profiling was performed. RESULTS: Correlation analyses between gene expression and saponin accumulation revealed high correlations between saponin content with gene expression of ß-amyrin synthase, MtCYP716A12, and two cytochromes P450 genes, MtCYP72A67 and MtCYP72A68. In vivo and in vitro biochemical assays using yeast microsomes containing MtCYP72A67 revealed hydroxylase activity for carbon 2 of oleanolic acid and hederagenin. This finding was supported by functional characterization of MtCYP72A67 using RNAi-mediated gene silencing in M. truncatula hairy roots, which revealed a significant reduction of 2ß-hydroxylated sapogenins. In vivo and in vitro assays with MtCYP72A68 produced in yeast showed multifunctional oxidase activity for carbon 23 of oleanolic acid and hederagenin. These findings were supported by overexpression of MtCYP72A68 in M. truncatula hairy roots, which revealed significant increases of oleanolic acid, 2ß-hydroxyoleanolic acid, hederagenin and total saponin levels. CONCLUSIONS: The cumulative data support that MtCYP72A68 is a multisubstrate, multifunctional oxidase and MtCYP72A67 is a 2ß-hydroxylase, both of which function during the early steps of triterpene-oleanate sapogenin biosynthesis.

Size-Selective Electrophoretic Deposition of Gold Nanoparticles Mediated by Hydroquinone Oxidation.

Here we describe the size-selective, hydroquinone (HQ)-mediated electrophoretic deposition of 4 and 15 nm diameter citrate-stabilized Au nanoparticles (NPs) onto a glass/indium-tin-oxide (ITO) electrode. Protons liberated from HQ during electrochemical oxidation at the Au NP surface during collisions with the glass/ITO electrode lead to Au NP deposition through neutralization of the citrate stabilizer surrounding the Au NPs, protonation of the glass/ITO electrode, or some combination of the two. Interestingly, the 4 nm Au NPs deposit at about 300-400 mV more negative potential than that of 15 nm diameter Au NPs because of faster HQ oxidation kinetics at the 4 nm NPs, leading to lower overpotentials. This allows for selective deposition of the 4 nm Au NPs over 15 nm Au NPs in a solution containing a mixture of the two by controlling the electrode potential. Controlled pH experiments indicate that significant NP deposition occurs on glass/ITO at a pH of ∼3, giving insight into the local pH needed from HQ oxidation in order to deposit the Au NPs. Experiments performed at different ionic strengths confirm that migration is a major mode of mass transport of the NPs to the glass/ITO. Long deposition times lead to films of densely packed Au NPs that are mostly free from NP-NP contact, indicating that some electrostatic repulsion between the NPs remains during the deposition. This simple method of Au NP deposition may find use for separation of Au NPs and electrode device preparation for a variety of sensor and electrocatalysis applications.

Aggregation-Dependent Oxidation of Metal Nanoparticles.

Here we describe the effect of aggregation on the oxidation of citrate-stabilized Au nanoparticles (NPs) attached electrostatically to amine-functionalized glass/ITO electrodes. When the Au NPs are attached to the electrode from a solution with pH greater than ∼3.0, they are well-separated on the electrode and oxidize in bromide-containing electrolyte at 0.698, 0.757, and 0.943 V (vs Ag/AgCl) for 4, 15, and 50 nm diameter Au NPs, respectively, in line with their size-dependent oxidation behavior. In solutions below pH 3.0, the Au NPs aggregate in solution and attach to the electrode in the aggregated form. The solution UV-vis spectra and scanning electron microscopy images of the electrodes show clear evidence of aggregation. The oxidation potential for aggregated 4 and 15 nm diameter Au NPs shifts positive by a maximum of 230 and 180 mV, respectively. The magnitude of the shift depends on the extent of aggregation, which was controlled by the solution pH and time. NP aggregation leads to a significant reduction in the surface area-to-volume ratio, which is likely responsible for the positive shift in the oxidation potential. The oxidation potential does not shift at all for aggregated 50 nm diameter Au NPs.

Size-Dependent Electrophoretic Deposition of Catalytic Gold Nanoparticles.

Here we describe size-dependent electrophoretic deposition (EPD) of citrate-stabilized Au nanoparticles (NPs) onto indium-tin-oxide-coated glass (glass/ITO) electrodes as studied by linear sweep stripping voltammetry (LSSV) and scanning electron microscopy (SEM). LSSV allows both the determination of the Au NP coverage and NP size from the peak area and the peak potential, respectively. Two-electrode EPD in aqueous solutions of Au NPs plus H2O2 reveal that a minimum potential of 1.5 V is needed for significant deposition of 4 nm diameter Au NPs as opposed to 2.0 V for 33 nm diameter Au NPs. EPD at 0.4 V in a solution of Au NPs prepared with a short 5 min reaction time led to the successful capture of 1-2 nm diameter Au NPs with appreciable coverage. In all cases, deposition did not occur in the absence of H2O2. Three-electrode experiments with a real reference electrode revealed the same size selective deposition with potential and that the amount of Au deposited depends on the deposition time and H2O2 concentration. The deposition occurs indirectly by oxidation of H2O2, which liberates protons and neutralizes the citrate stabilizer, leading to precipitation of the Au NPs onto the glass/ITO electrode. Studies on pH stability show that larger Au NPs aggregate at lower pH compared to smaller Au NPs. More importantly, though, 4 nm diameter Au NPs are much more catalytic for H2O2 oxidation, which is the main reason for the size selective deposition.

Integrated metabolomics and transcriptomics reveal enhanced specialized metabolism in Medicago truncatula root border cells.

Integrated metabolomics and transcriptomics of Medicago truncatula seedling border cells and root tips revealed substantial metabolic differences between these distinct and spatially segregated root regions. Large differential increases in oxylipin-pathway lipoxygenases and auxin-responsive transcript levels in border cells corresponded to differences in phytohormone and volatile levels compared with adjacent root tips. Morphological examinations of border cells revealed the presence of significant starch deposits that serve as critical energy and carbon reserves, as documented through increased ß-amylase transcript levels and associated starch hydrolysis metabolites. A substantial proportion of primary metabolism transcripts were decreased in border cells, while many flavonoid- and triterpenoid-related metabolite and transcript levels were increased dramatically. The cumulative data provide compounding evidence that primary and secondary metabolism are differentially programmed in border cells relative to root tips. Metabolic resources normally destined for growth and development are redirected toward elevated accumulation of specialized metabolites in border cells, resulting in constitutively elevated defense and signaling compounds needed to protect the delicate root cap and signal motile rhizobia required for symbiotic nitrogen fixation. Elevated levels of 7,4'-dihydroxyflavone were further increased in border cells of roots exposed to cotton root rot (Phymatotrichopsis omnivora), and the value of 7,4'-dihydroxyflavone as an antimicrobial compound was demonstrated using in vitro growth inhibition assays. The cumulative and pathway-specific data provide key insights into the metabolic programming of border cells that strongly implicate a more prominent mechanistic role for border cells in plant-microbe signaling, defense, and interactions than envisioned previously.

A structure-guided mutation in the major capsid protein retargets BK polyomavirus.

Viruses within a family often vary in their cellular tropism and pathogenicity. In many cases, these variations are due to viruses switching their specificity from one cell surface receptor to another. The structural requirements that underlie such receptor switching are not well understood especially for carbohydrate-binding viruses, as methods capable of structure-specificity studies are only relatively recently being developed for carbohydrates. We have characterized the receptor specificity, structure and infectivity of the human polyomavirus BKPyV, the causative agent of polyomavirus-associated nephropathy, and uncover a molecular switch for binding different carbohydrate receptors. We show that the b-series gangliosides GD3, GD2, GD1b and GT1b all can serve as receptors for BKPyV. The crystal structure of the BKPyV capsid protein VP1 in complex with GD3 reveals contacts with two sialic acid moieties in the receptor, providing a basis for the observed specificity. Comparison with the structure of simian virus 40 (SV40) VP1 bound to ganglioside GM1 identifies the amino acid at position 68 as a determinant of specificity. Mutation of this residue from lysine in BKPyV to serine in SV40 switches the receptor specificity of BKPyV from GD3 to GM1 both in vitro and in cell culture. Our findings highlight the plasticity of viral receptor binding sites and form a template to retarget viruses to different receptors and cell types.

Transcriptional response of Arabidopsis seedlings during spaceflight reveals peroxidase and cell wall remodeling genes associated with root hair development.

UNLABELLED: • PREMISE OF THE STUDY: Plants will be an important component of advanced life support systems during space exploration missions. Therefore, understanding their biology in the spacecraft environment will be essential before they can be used for such systems.• METHODS: Seedlings of Arabidopsis thaliana were grown for 2 wk in the Biological Research in Canisters (BRIC) hardware on board the second to the last mission of the space shuttle Discovery (STS-131). Transcript profiles between ground controls and space-grown seedlings were compared using stringent selection criteria.• KEY RESULTS: Expression of transcripts associated with oxidative stress and cell wall remodeling was repressed in microgravity. These downregulated genes were previously shown to be enriched in root hairs consistent with seedling phenotypes observed in space. Mutations in genes that were downregulated in microgravity, including two uncharacterized root hair-expressed class III peroxidase genes (PRX44 and PRX57), led to defective polar root hair growth on Earth. PRX44 and PRX57 mutants had ruptured root hairs, which is a typical phenotype of tip-growing cells with defective cell walls and those subjected to stress.• CONCLUSIONS: Long-term exposure to microgravity negatively impacts tip growth by repressing expression of genes essential for normal root hair development. Whereas changes in peroxidase gene expression leading to reduced root hair growth in space are actin-independent, root hair development modulated by phosphoinositides could be dependent on the actin cytoskeleton. These results have profound implications for plant adaptation to microgravity given the importance of tip growing cells such as root hairs for efficient nutrient capture.

Establishment of the Lotus japonicus Gene Expression Atlas (LjGEA) and its use to explore legume seed maturation.

Lotus japonicus is a model species for legume genomics. To accelerate legume functional genomics, we developed a Lotus japonicus Gene Expression Atlas (LjGEA), which provides a global view of gene expression in all organ systems of this species, including roots, nodules, stems, petioles, leaves, flowers, pods and seeds. Time-series data covering multiple stages of developing pod and seed are included in the LjGEA. In addition, previously published L. japonicus Affymetrix data are included in the database, making it a 'one-stop shop' for transcriptome analysis of this species. The LjGEA web server (http://ljgea.noble.org/) enables flexible, multi-faceted analyses of the transcriptome. Transcript data may be accessed using the Affymetrix probe identification number, DNA sequence, gene name, functional description in natural language, and GO and KEGG annotation terms. Genes may be discovered through co-expression or differential expression analysis. Users may select a subset of experiments and visualize and compare expression profiles of multiple genes simultaneously. Data may be downloaded in a tabular form compatible with common analytical and visualization software. To illustrate the power of LjGEA, we explored the transcriptome of developing seeds. Genes represented by 36 474 probe sets were expressed at some stage during seed development, and almost half of these genes displayed differential expression during development. Among the latter were 624 transcription factor genes, some of which are orthologs of transcription factor genes that are known to regulate seed development in other species, while most are novel and represent attractive targets for reverse genetics approaches to determine their roles in this important organ.

Global reprogramming of transcription and metabolism in Medicago truncatula during progressive drought and after rewatering.

Medicago truncatula is a model legume forage crop native to the arid and semi-arid environments of the Mediterranean. Given its drought-adapted nature, it is an ideal candidate to study the molecular and biochemical mechanisms conferring drought resistance in plants. Medicago plants were subjected to a progressive drought stress over 14 d of water withholding followed by rewatering under controlled environmental conditions. Based on physiological measurements of plant water status and changes in morphology, plants experienced mild, moderate and severe water stress before rehydration. Transcriptome analysis of roots and shoots from control, mildly, moderately and severely stressed, and rewatered plants, identified many thousands of genes that were altered in expression in response to drought. Many genes with expression tightly coupled to the plant water potential (i.e. drought intensity) were identified suggesting an involvement in Medicago drought adaptation responses. Metabolite profiling of drought-stressed plants revealed the presence of 135 polar and 165 non-polar compounds in roots and shoots. Combining Medicago metabolomic data with transcriptomic data yielded insight into the regulation of metabolic pathways operating under drought stress. Among the metabolites detected in drought-stressed Medicago plants, myo-inositol and proline had striking regulatory profiles indicating involvement in Medicago drought tolerance.

Vapyrin, a gene essential for intracellular progression of arbuscular mycorrhizal symbiosis, is also essential for infection by rhizobia in the nodule symbiosis of Medicago truncatula.

Intracellular invasion of root cells is required for the establishment of successful endosymbioses in legumes of both arbuscular mycorrhizal (AM) fungi and rhizobial bacteria. In both interactions a requirement for successful entry is the activation of a common signalling pathway that includes five genes required to generate calcium oscillations and two genes required for the perception of the calcium response. Recently, it has been discovered that in Medicago truncatula, the Vapyrin (VPY) gene is essential for the establishment of the arbuscular mycorrhizal symbiosis. Here, we show by analyses of mutants that the same gene is also required for rhizobial colonization and nodulation. VPY encodes a protein featuring a Major Sperm Protein domain, typically featured on proteins involved in membrane trafficking and biogenesis, and a series of ankyrin repeats. Plants mutated in this gene have abnormal rhizobial infection threads and fewer nodules, and in the case of interactions with AM fungi, epidermal penetration defects and aborted arbuscule formation. Calcium spiking in root hairs in response to supplied Nod factors is intact in the vpy-1 mutant. This, and the elevation of VPY transcripts upon application of Nod factors which we show to be dependent on NFP, DMI1, and DMI3, indicates that VPY acts downstream of the common signalling pathway.

A WD40 repeat protein from Medicago truncatula is necessary for tissue-specific anthocyanin and proanthocyanidin biosynthesis but not for trichome development.

WD40 repeat proteins regulate biosynthesis of anthocyanins, proanthocyanidins (PAs), and mucilage in the seed and the development of trichomes and root hairs. We have cloned and characterized a WD40 repeat protein gene from Medicago truncatula (MtWD40-1) via a retrotransposon-tagging approach. Deficiency of MtWD40-1 expression blocks accumulation of mucilage and a range of phenolic compounds, including PAs, epicatechin, other flavonoids, and benzoic acids, in the seed, reduces epicatechin levels without corresponding effects on other flavonoids in flowers, reduces isoflavone levels in roots, but does not impair trichome or root hair development. MtWD40-1 is expressed constitutively, with highest expression in the seed coat, where its transcript profile temporally parallels those of PA biosynthetic genes. Transcript profile analysis revealed that many genes of flavonoid biosynthesis were down-regulated in a tissue-specific manner in M. truncatula lines harboring retrotransposon insertions in the MtWD40-1 gene. MtWD40-1 complemented the anthocyanin, PA, and trichome phenotypes of the Arabidopsis (Arabidopsis thaliana) transparent testa glabrous1 mutant. We discuss the function of MtWD40-1 in natural product formation in M. truncatula and the potential use of the gene for engineering PAs in the forage legume alfalfa (Medicago sativa).

A gene expression atlas of the model legume Medicago truncatula.

Legumes played central roles in the development of agriculture and civilization, and today account for approximately one-third of the world's primary crop production. Unfortunately, most cultivated legumes are poor model systems for genomic research. Therefore, Medicago truncatula, which has a relatively small diploid genome, has been adopted as a model species for legume genomics. To enhance its value as a model, we have generated a gene expression atlas that provides a global view of gene expression in all major organ systems of this species, with special emphasis on nodule and seed development. The atlas reveals massive differences in gene expression between organs that are accompanied by changes in the expression of key regulatory genes, such as transcription factor genes, which presumably orchestrate genetic reprogramming during development and differentiation. Interestingly, many legume-specific genes are preferentially expressed in nitrogen-fixing nodules, indicating that evolution endowed them with special roles in this unique and important organ. Comparative transcriptome analysis of Medicago versus Arabidopsis revealed significant divergence in developmental expression profiles of orthologous genes, which indicates that phylogenetic analysis alone is insufficient to predict the function of orthologs in different species. The data presented here represent an unparalleled resource for legume functional genomics, which will accelerate discoveries in legume biology.

Analysis of cDNA libraries from developing seeds of guar (Cyamopsis tetragonoloba (L.) Taub).

BACKGROUND: Guar, Cyamopsis tetragonoloba (L.) Taub, is a member of the Leguminosae (Fabaceae) family and is economically the most important of the four species in the genus. The endosperm of guar seed is a rich source of mucilage or gum, which forms a viscous gel in cold water, and is used as an emulsifier, thickener and stabilizer in a wide range of foods and industrial applications. Guar gum is a galactomannan, consisting of a linear (1-->4)-beta-linked D-mannan backbone with single-unit, (1-->6)-linked, alpha-D-galactopyranosyl side chains. To better understand regulation of guar seed development and galactomannan metabolism we created cDNA libraries and a resulting EST dataset from different developmental stages of guar seeds. RESULTS: A database of 16,476 guar seed ESTs was constructed, with 8,163 and 8,313 ESTs derived from cDNA libraries I and II, respectively. Library I was constructed from seeds at an early developmental stage (15-25 days after flowering, DAF), and library II from seeds at 30-40 DAF. Quite different sets of genes were represented in these two libraries. Approximately 27% of the clones were not similar to known sequences, suggesting that these ESTs represent novel genes or may represent non-coding RNA. The high flux of energy into carbohydrate and storage protein synthesis in guar seeds was reflected by a high representation of genes annotated as involved in signal transduction, carbohydrate metabolism, chaperone and proteolytic processes, and translation and ribosome structure. Guar unigenes involved in galactomannan metabolism were identified. Among the seed storage proteins, the most abundant contig represented a conglutin accounting for 3.7% of the total ESTs from both libraries. CONCLUSION: The present EST collection and its annotation provide a resource for understanding guar seed biology and galactomannan metabolism.

Salicylic acid and systemic acquired resistance play a role in attenuating crown gall disease caused by Agrobacterium tumefaciens.

We investigated the effects of salicylic acid (SA) and systemic acquired resistance (SAR) on crown gall disease caused by Agrobacterium tumefaciens. Nicotiana benthamiana plants treated with SA showed decreased susceptibility to Agrobacterium infection. Exogenous application of SA to Agrobacterium cultures decreased its growth, virulence, and attachment to plant cells. Using Agrobacterium whole-genome microarrays, we characterized the direct effects of SA on bacterial gene expression and showed that SA inhibits induction of virulence (vir) genes and the repABC operon, and differentially regulates the expression of many other sets of genes. Using virus-induced gene silencing, we further demonstrate that plant genes involved in SA biosynthesis and signaling are important determinants for Agrobacterium infectivity on plants. Silencing of ICS (isochorismate synthase), NPR1 (nonexpresser of pathogenesis-related gene 1), and SABP2 (SA-binding protein 2) in N. benthamiana enhanced Agrobacterium infection. Moreover, plants treated with benzo-(1,2,3)-thiadiazole-7-carbothioic acid, a potent inducer of SAR, showed reduced disease symptoms. Our data suggest that SA and SAR both play a major role in retarding Agrobacterium infectivity.