New insights into the effects of ethylene on ABA catabolism, sweetening and dormancy in stored potato tubers.

Continuous ethylene supplementation suppresses postharvest sprouting, but it can increase reducing sugars, limiting its use as an alternative to chlorpropham for processing potatoes. To elucidate the mechanisms involved, tubers were treated after curing with or without the ethylene binding inhibitor 1-methylcyclopropene (1-MCP at 1 µL L-1 for 24 h), and then stored in air or air supplemented with continuous ethylene (10 µL L-1). Across three consecutive seasons, changes in tuber physiology were assessed alongside transcriptomic and metabolomic analysis. Exogenous ethylene alone consistently induced a respiratory rise and the accumulation of undesirable reducing sugars. The transient respiratory peak was preceded by the strong upregulation of two genes encoding 1-aminocyclopropane-1-carboxylate oxidase (ACO), typical of wound and stress induced ethylene production. Profiles of parenchymatic tissue highlighted that ethylene triggered abscisic acid (ABA) catabolism, evidenced by a steep fall in ABA levels and a transient rise in the catabolite phaseic acid, accompanied by upregulation of transcripts encoding an ABA 8'-hydroxylase. Moreover, analysis of non-structural carbohydrate-related genes revealed that ethylene strongly downregulated the expression of the Kunitz-type invertase inhibitor, already known to be involved in cold-induced sweetening. All these ethylene-induced effects were negated by 1-MCP with one notable exception: 1-MCP enhanced the sprout suppressing effect of ethylene whilst preventing ethylene-induced sweetening. This study supports the conclusions that: i) tubers adapt to ethylene by regulating conserved pathways (e.g. ABA catabolism); ii) ethylene-induced sweetening acts independently from sprout suppression, and is similar to cold-induced sugar accumulation.

Assessment of genetic diversity and population structure in cultured Australian Pacific oysters.

The recent development of Pacific oyster (Crassostrea gigas) SNP genotyping arrays has allowed detailed characterisation of genetic diversity and population structure within and between oyster populations. It also raises the potential of harnessing genomic selection for genetic improvement in oyster breeding programmes. The aim of this study was to characterise a breeding population of Australian oysters through genotyping and analysis of 18 027 SNPs, followed by comparison with genotypes of oyster sampled from Europe and Asia. This revealed that the Australian populations had similar population diversity (HE ) to oysters from New Zealand, the British Isles, France and Japan. Population divergence was assessed using PCA of genetic distance and revealed that Australian oysters were distinct from all other populations tested. Australian Pacific oysters originate from planned introductions sourced from three Japanese populations. Approximately 95% of these introductions were from geographically, and potentially genetically, distinct populations from the Nagasaki oysters assessed in this study. Finally, in preparation for the application of genomic selection in oyster breeding programmes, the strength of LD was evaluated and subsets of loci were tested for their ability to accurately infer relationships. Weak LD was observed on average; however, SNP subsets were shown to accurately reconstitute a genomic relationship matrix constructed using all loci. This suggests that low-density SNP panels may have utility in the Australian population tested, and the findings represent an important first step towards the design and implementation of genomic approaches for applied breeding in Pacific oysters.

Validation of a national hand hygiene proxy measure in NHS Scotland.

The Scottish national hand hygiene proxy measure uses the volume of alcohol-based hand rub (ABHR) purchased by NHS Scotland boards as an indicator of the number of hand hygiene moments being performed per patient-bed-day. The proxy measure calculation is based on the assumption that 3 mL of ABHR is used per hand hygiene moment. This study aimed to validate the volume of ABHR being used per hand hygiene moment. It found that the median volume of ABHR being used in practice is approximately 1 mL per hand hygiene moment, and that using this validated volume in the calculation substantially increases the proxy measure of hand hygiene compliance.

Optimising the use of medicines to reduce acute kidney injury in children and babies.

The majority of medications in children are administered in an unlicensed or off-label manner. Paediatricians are obliged to prescribe using the limited evidence available. The 2007 EU regulation on the use of paediatric drugs means pharmaceutical companies are now obliged to (and receive incentives for) contributing to paediatric drug data and carrying out paediatric clinical trials. This is important, as the efficacy and adverse effect profiles of medicines vary across childhood. Additionally, there are significant age-related changes in the pharmacodynamic and pharmacokinetic activity of many drugs. This may be related to physiological (differential expressions of cytochrome P450 enzymes or variable glomerular filtration rates at different ages for example) and psychological (increasing autonomy and risk perception in teenage years) changes. Increasing numbers of children are surviving life-threatening childhood conditions due to medical advances. This means there is an increasing population who are at risk of the consequences of the long-term, early exposure to nephrotoxic agents. The kidney is an organ that is particularly vulnerable to damage as a consequence of drugs. Drug-induced acute kidney injury (AKI) episodes in children and babies are principally due to non-steroidal anti-inflammatory drugs, antibiotics or chemotherapeutic agents. The renal tubules are vulnerable to injury because of their concentrating ability and high-energy hypoxic environment. This review focuses on drug-induced AKI and the methods to minimise its effect, including general management plus the role of child-specific pharmacokinetic data, the use of pharmacogenomics and early detection of AKI using urinary biomarkers and electronic triggers.

Genomic architecture of histone 3 lysine 27 trimethylation during late ovine skeletal muscle development.

The ruminant developmental transition from late foetus to lamb is associated with marked changes in skeletal muscle structure and function that reflect programming for new physiological demands following birth. To determine whether epigenetic changes are involved in this transition, we investigated the genomic architecture of the chromatin modification, histone 3 lysine 27 trimethylation (H3K27me3), which typically regulates early life developmental processes; however, its role in later life processes is unclear. Chromatin immunoprecipitation coupled with next-generation sequencing was used to map H3K27me3 nucleosomes in ovine longissimus lumborum skeletal muscle at 100 days of gestation and 12 weeks post-partum. In both states, H3K27me3 modification was associated with genes, transcription start sites and CpG islands and with transcriptional silencing. The H3K27me3 peaks consisted of two major categories, promoter specific and regional, with the latter the dominant feature. Genes encoding homeobox transcription factors regulating early life development and genes involved in neural functions, particularly gated ion channels, were strongly modified by H3K27me3. Gene promoters differentially modified by H3K27me3 in the foetus and lamb were enriched for gated ion channels, which may reflect changes in neuromuscular function. However, most modified genes showed no changes, indicating that H3K27me3 does not have a large role in late muscle maturation. Notably, promyogenic transcription factors were strongly modified with H3K27me3 but showed no differences between the late gestation foetus and lamb, likely reflecting their lack of involvement in the myofibre fusion process occurring in this transition. H3K27me3 is a major architectural feature of the epigenetic landscape of ruminant skeletal muscle, and it comments on gene transcription and gene function in the context of late skeletal muscle development.

How to use: C-reactive protein.

C-reactive protein (CRP) is an acute-phase protein that increases 4-6 h after an inflammatory trigger and peaks at 36-50 h. Levels decrease rapidly with the resolution of inflammation. CRP is generally highly elevated in invasive bacterial infections and is often used as a marker of inflammation. A single CRP level is neither sensitive nor specific enough to identify all children with serious bacterial infection. However, a raised CRP does suggest serious bacterial infection and should suggest further assessment is needed. CRP levels that fail to decrease, or continue to rise, after 48 h of antibiotic therapy suggest treatment failure. In infants with suspected neonatal sepsis, two CRP measurements 24 h apart that are <10 mg/l are useful in excluding sepsis.

A radiation hybrid comparative map of ovine chromosome 1 aligned to the virtual sheep genome.

Ovis aries chromosome one (OAR1) is the largest submetacentric chromosome in the sheep genome and is homologous to regions on human chromosomes 1, 2, 3 and 21. Using the USUoRH5000 ovine whole-genome radiation hybrid (RH) panel, we have constructed a RH map of OAR1 comprising 102 framework and 75 placed/binned markers across five linkage groups spanning 3759.43 cR5000, with an average marker density of 21.2 cR5000/marker. The alignment of our OAR1 RH map shows good concordance with the recently developed virtual sheep genome, with fewer than 1.86% discrepancies. A comparative map of OAR1 was constructed by examining the location of RH-mapped orthologues in sheep within the genomes of cow, human, horse and dog. Analysis of the comparative map indicates that conserved syntenies within the five ovine RH linkage groups underwent internal chromosomal rearrangements which, in general, reflect the evolutionary distances between sheep and each of these four species. The ovine RH map presented here integrates all available mapping data and includes new genomic information for ovine chromosome 1.

Gene expression patterns during intramuscular fat development in cattle.

Deposition of intramuscular fat, or "marbling," in beef cattle contributes significantly to meat quality variables, including juiciness, flavor, and tenderness. The accumulation of intramuscular fat is largely influenced by the genetic background of cattle, as well as their age and nutrition. To identify genes that can be used as early biomarkers for the prediction of marbling capacity, we studied the muscle transcriptome of 2 cattle crossbreeds with contrasting intramuscular fat content. The transcriptomes of marbling LM tissue of heifers from Wagyu x Hereford (WxH; n = 6) and Piedmontese x Hereford (PxH; n = 7) crosses were profiled by using a combination of complementary DNA microarray and quantitative reverse transcription-PCR. Five biopsies of LM were taken from each animal at approximately 3, 7, 12, 20, and 25 mo from birth. Tissue was also collected from the LM of each animal at slaughter (approximately 30 mo). Microarray experiments, conducted on the first 3 biopsies of 2 animals from each crossbreed, identified 97 differentially expressed genes. The gene expression results indicated that the LM transcriptome of animals with high marbling potential (WxH) could be reliably distinguished from less marbled animals (PxH) when the animals were as young as 7 mo of age. At this early age, one cannot reliably determine meaningful differences in intramuscular fat deposition. We observed greater expression of a set of adipogenesis- and lipogenesis-related genes in the LM of young WxH animals compared with their PxH contemporaries. In contrast, genes highly expressed in PxH animals were associated with mitochondrial oxidative activity. Further quantitative reverse transcription-PCR experiments revealed that the messenger RNA of 6 of the lipogenesis-related genes also peaked at the age of 20 to 25 mo in WxH animals. The messenger RNA expression of ADIPOQ, SCD, and THRSP was highly correlated with intramuscular fat content of an individual in WxH animals. Our study provides clear evidence of early molecular changes associated with marbling and also identifies specific time frames when intramuscular fat development in cattle muscle can be detected by using gene expression. This information could be used by animal scientists to design optimal nutrition for high marbling potential. In addition, the genes found to be highly expressed during development of marbling could be used to develop genetic markers or biomarkers to assist with beef production strategies.

A high-resolution comparative radiation hybrid map of ovine chromosomal regions that are homologous to human chromosome 6 (HSA6).

In this study, we constructed high-resolution radiation hybrid (RH) and comparative maps of ovine chromosomes or chromosomal segments that are homologous to human chromosome 6 (HSA6). A total of 251 markers were successfully genotyped across the recently developed USUoRH5000 whole-genome panel; 208 of these markers were assigned to five RH linkage groups distributed on three ovine chromosomes (OAR8, 9 and 20). The RH maps have good correspondence with previous chromosome painting data, although a small centromeric region on OAR9 that is homologous to HSA6 had not been previously detected using human chromosome paints on ovine chromosomal spreads. High percentages of the ovine markers were identified as orthologues in the bovine (86.3%), dog (85.8%), horse (69.3%) and human (88.7%) genomes. These maps contribute to investigations in mammalian chromosome evolution and the search for economic trait loci in sheep.

A rapid method for computationally inferring transcriptome coverage and microarray sensitivity.

MOTIVATION: There are many different gene expression technologies, including cDNA and oligo-based microarrays, SAGE and MPSS. For each organism of interest, coverage of the transcriptome and the genome will be different. We address the question of what level of coverage is required to exploit the sensitivity of the different technologies, and what is the sensitivity of the different approaches in the experimental study. RESULTS: We estimate the transcriptome coverage by randomly sampling transcripts from a pre-defined tag-to-gene mapping function. For a given microarray experiment, we locate the thresholds in intensities that define the distribution of transcript abundance. These values are compared against the distribution obtained by applying the same thresholds to the intensities from differentially expressed genes. The ratio of these two distributions meets at the equilibrium defining sensitivity. We conclude that a collection of approximately 340,000 sequences is adequate for microarrays, but not large enough for maximum utilization of tag-based technologies. In the absence of large-scale sequencing, the majority of the tags detected by the latter approaches will remain unidentified until the genome sequence is available.

Gene expression profiling of muscle tissue in Brahman steers during nutritional restriction.

Expression profiling using microarrays allows for the detailed characterization of the gene networks that regulate an animal's response to environmental stresses. During nutritional restriction, processes such as protein turnover, connective tissue remodeling, and muscle atrophy take place in the skeletal muscle of the animal. These processes and their regulation are of interest in the context of managing livestock for optimal production efficiency and product quality. Here we expand on recent research applying complementary DNA (cDNA) microarray technology to the study of the effect of nutritional restriction on bovine skeletal muscle. Using a custom cDNA microarray of 9,274 probes from cattle muscle and s.c. fat libraries, we examined the differential gene expression profile of the LM from 10 Brahman steers under three different dietary treatments. The statistical approach was based on mixed-model ANOVA and model-based clustering of the BLUP solutions for the gene x diet interaction effect. From the results, we defined a transcript profile of 156 differentially expressed array elements between the weight loss and weight gain diet substrates. After sequence and annotation analyses, the 57 upregulated elements represented 29 unique genes, and the 99 downregulated elements represented 28 unique genes. Most of these co-regulated genes cluster into groups with distinct biological function related to protein turnover and cytoskeletal metabolism and contribute to our mechanistic understanding of the processes associated with remodeling of muscle tissue in response to nutritional stress.

Mapping of 12 bovine ribosomal protein genes using a bovine radiation hybrid panel.

Twelve bovine ribosomal protein genes, for which sequence data had been acquired from complementary deoxyribonucleic acid (cDNA) clones isolated from a cattle skin cDNA library, were mapped. As ribosomal protein genes are a group of highly conserved house keeping genes, specific primers were designed to span the intron-exon splice sites and to amplify intronic sequences, in order to obtain bovine-specific polymerase chain reaction (PCR) products. Two of 12 ribosomal protein genes were genotyped in this way and the remaining 10 were mapped using additional primers designed from within the intron. Eleven previously unmapped ribosomal protein genes were localized and one previously reported ribosomal protein gene localization was confirmed. The 12 ribosomal protein genes mapped in this study are spread over 10 chromosomes, including the X chromosome. The locations show conservation of comparative map position in cattle and human.

Hydrogen bonding in C-methylated nitroanilines: a room-temperature monoclinic polymorph of 4-methyl-3-nitroaniline with Z' = 2.

The title compound, C(7)H(8)N(2)O(2), is monoclinic (space group P2(1)/n) at 295 (2) K with Z' = 2. The two types of molecule form independent C(7) chains, and the structure is related to that of the low-temperature triclinic polymorph, where Z' = 4 in P1, by a simple displacive transformation.

Hydrogen bonding in nitroaniline analogues: a three-dimensional framework in 2-amino-6-nitro-1,3-benzothiazole.

In the title compound, C(7)H(5)N(3)O(2)S, the molecules are linked into a three-dimensional framework by a combination of a three-centre N-H...(O)(2) hydrogen bond, and two-centre N-H...N and C-H...O hydrogen bonds.

4-Iodo-2-methyl-5-nitroaniline exhibits neither strong hydrogen bonding nor intermolecular I...nitro interactions.

In the title compound, C(7)H(7)IN(2)O(2), the O atoms of the nitro group are disordered over two sets of sites and there is evidence that the intramolecular I...nitro interaction is repulsive. In the crystal structure, there are neither strong hydrogen bonds, nor intermolecular I...nitro interactions, nor aromatic pi-pi-stacking interactions.

Triclinic and orthorhombic polymorphs of 2-iodo-4-nitroaniline: interplay of hydrogen bonds, nitro...I interactions and aromatic pi-pi-stacking interactions.

In the triclinic polymorph of 2-iodo-4-nitroaniline, C(6)H(5)IN(2)O(2), space group P-1, the molecules are linked by paired N-H...O hydrogen bonds into C(8)[R(2)(2)(6)] chains of rings. These chains are linked into sheets by nitro...I interactions, and the sheets are pairwise linked by aromatic pi-pi-stacking interactions. In the orthorhombic polymorph, space group Pbca, the molecules are linked by single N-H...O hydrogen bonds into spiral C(8) chains; the chains are linked by nitro...O interactions into sheets, each of which is linked to its two immediate neighbours by aromatic pi-pi-stacking interactions, so producing a continuous three-dimensional structure.

Hydrogen-bonded chains in N-(2-nitrophenyl)phenylamine.

Molecules of the title compound, C(12)H(10)N(2)O(2), are markedly non-planar. There is an intramolecular N-H...O hydrogen bond, and the molecules are linked into zigzag chains by a single C-H...O hydrogen bond. Comparisons are made with the supramolecular aggregation in isomeric amino-nitro derivatives, and in some N-methylnitroanilines.

Soft C-H.O hydrogen bonds in methyl 2,4-dinitrobenzenesulfenate: sheets built from R22(10) and R66(42) rings.

Molecules of the title compound, C(7)H(6)N(2)O(5)S, are linked into sheets containing R(2)(2)(10) and R(6)(6)(42) rings by C-H.O hydrogen bonds [C.O 3.405 (3) and 3.511 (2) A; C-H.O 159 and 169 degrees ], in which both acceptors are in the same nitro group. Comparisons are made with the hydrogen bonding in other nitrobenzenesulfenate esters.

Hydrogen bonding in substituted nitroanilines: isolated nets in 1,3-diamino-4-nitrobenzene and continuously interwoven nets in 3,5-dinitroaniline.

Molecules of 1,3-diamino-4-nitrobenzene, C(6)H(7)N(3)O(2), are linked by N-H.O hydrogen bonds [N.O 2.964 (2) and 3.021 (2) A; N-H.O 155 and 149 degrees] into (4,4) nets. In 3,5-dinitroaniline, C(6)H(5)N(3)O(4), where Z' = 2, the molecules are linked by three N-H.O hydrogen bonds [N.O 3.344 (2)-3.433 (2) A and N-H.O 150-167 degrees] into deeply puckered nets, each of which is interwoven with its two immediate neighbours.

Genome organization and transcription strategy in the complex GNS-L intergenic region of bovine ephemeral fever rhabdovirus.

A 1622 nucleotide region of the bovine ephemeral fever virus (BEFV) genome, located between the second glycoprotein (GNS) gene and the polymerase (L) gene, has been cloned and sequenced in Australian (BB7721) and Chinese (Beijing-1) isolates of the virus. In the Australian isolate, the region contains five long open reading frames (ORFs) organized into three coding regions (alpha, beta and gamma), each of which are bound by a consensus transcription initiation and transcription termination-polyadenylation-like sequences. The alpha coding region contains three long ORFs (alpha 1, alpha 2 and alpha 3). The alpha 1 ORF encodes a 10.6 kDa polypeptide which contains hydrophobic and highly basic regions characteristic of a viroporin. The alpha 2 ORF encodes a 13.7 kDa polypeptide and overlaps the alpha 3 ORF which encodes a 5.7 kDa polypeptide. The beta coding region contains a single long ORF encoding a polypeptide of 12.2 kDa. The gamma coding region, which does not occur in Adelaide River virus (ARV), contains a single long ORF encoding a polypeptide of 13.4 kDa. The Chinese isolate shares 91% nucleotide sequence identity with the Australian isolate. The organization of the alpha, beta and gamma coding regions is preserved and the sequences of the encoded polypeptides are similar to those of BB7721. The major transcription products of the region were identified in BB7721 as polycistronic alpha (alpha 1-alpha 2-alpha 3) and beta-gamma mRNAs. Sequence similarities in the BEFV alpha-beta and beta-gamma gene junctions, and the gamma-L and beta-L gene junctions of BEFV and ARV, suggest that the gamma gene may have evolved from the beta-gene by sequence duplication.