Sequence diversity in the coat protein coding region of the genome RNA of Johnsongrass mosaic virus in Australia

Sequence diversity in the coat protein coding region of Australian strains of Johnsongrass mosaic virus (JGMV) was investigated. Field isolates were sampled during a seven year period from Johnsongrass, sorghum and corn across the northern grain growing region. The 23 isolates were found to have greater than 94% nucleotide and amino acid sequence identity. The Australian isolates and two strains from the U.S.A. had about 90% nucleotide sequence identity and were between 19 and 30% different in the N-terminus of the coat protein. Two amino acid residues were found in the core region of the coat protein in isolates obtained from sorghum having the Krish gene for JGMV resistance that differed from those found in isolates from other hosts which did not have this single dominant resistance gene. These amino acid changes may have been responsible for overcoming the resistance conferred by the Krish gene for JGMV resistance in sorghum. The identification of these variable regions was essential for the development of durable pathogen-derived resistance to JGMV in sorghum.

Completion of the genome sequence of Lettuce necrotic yellows virus, type species of the genus Cytorhabdovirus

We completed the genome sequence of Lettuce necrotic yellows virus (LNYV) by determining the nucleotide sequences of the 4a (putative phosphoprotein), 4b, M (matrix protein), G (glycoprotein) and L (polymerase) genes. The genome consists of 12,807 nucleotides and encodes six genes in the order 3' leader-N-4a(P)-4b-M-G-L-5' trailer. Sequences were derived from clones of a cDNA library from LNYV genomic RNA and from fragments amplified using reverse transcription-polymerase chain reaction. The 4a protein has a low isoelectric point characteristic for rhabdovirus phosphoproteins. The 4b protein has significant sequence similarities with the movement proteins of capillo- and trichoviruses and may be involved in cell-to-cell movement. The putative G protein sequence contains a predicted 25 amino acids signal peptide and endopeptidase cleavage site, three predicted glycosylation sites and a putative transmembrane domain. The deduced L protein sequence shows similarities with the L proteins of other plant rhabdoviruses and contains polymerase module motifs characteristic for RNA-dependent RNA polymerases of negative-strand RNA viruses. Phylogenetic analysis of this motif among rhabdoviruses placed LNYV in a group with other sequenced cytorhabdoviruses, most closely related to Strawberry crinkle virus. (c) 2005 Elsevier B.V. All rights reserved.

Optimal preventive maintenance of leased equipment with corrective minimal repairs

For leased equipment, the lessor carries out the maintenance of the equipment. Usually, the contract of lease specifies the penalty for equipment failures and for repairs not being carried out within specified time limits. This implies that optimal preventive maintenance policies must take these penalty costs into account and properly traded against the cost of preventive maintenance actions. The costs associated with failures are high as unplanned corrective maintenance actions are costly and the resulting penalties due to lease contract terms being violated. The paper develops a model to determine the optimal parameters of a preventive maintenance policy that takes into account all these costs to minimize the total expected cost to the lessor for new item lease. The parameters of the policy are (i) the number of preventive maintenance actions to be carried out over the lease period, (ii) the time instants for such actions, and (iii) the level of action. (c) 2005 Elsevier B.V. All rights reserved.

Origin and diversity of the Sox transcription factor gene family: genome-wide analysis in Fugu rubripes

The SOX family of transcription factors are found throughout the animal kingdom and are important in a variety of developmental contexts. Genome analysis has identified 20 Sox genes in human and mouse, which can be subdivided into 8 groups, based on sequence comparison and intron-exon structure. Most of the SOX groups identified in mammals are represented by a single SOX sequence in invertebrate model organisms, suggesting a duplication and divergence mechanism has operated during vertebrate evolution. We have now analysed the Sox gene complement in the pufferfish, Fugu rubripes, in order to shed further light on the diversity and origins of the Sox gene family. Major differences were found between the Sox family in Fugu and those in humans and mice. In particular, Fugu does not have orthologues of Sry, Sox,15 and Sox30, which appear to be specific to mammals, while Sox19, found in Fugu and zebrafish but absent in mammals, seems to be specific to fishes. Six mammalian Sox genes are represented by two copies each in Fugu, indicating a large-scale gene duplication in the fish lineage. These findings point to recent Sox gene loss, duplication and divergence occurring during the evolution of tetrapod and teleost lineages, and provide further evidence for large-scale segmental or a whole-genome duplication occurring early in the radiation of teleosts. (C) 2004 Elsevier B.V. All rights reserved.

Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome

Recent large-scale analyses of mainly full-length cDNA libraries generated from a variety of mouse tissues indicated that almost half of all representative cloned sequences did flat contain ail apparent protein-coding sequence, and were putatively derived from non-protein-coding RNA (ncRNA) genes. However, many of these clones were singletons and the majority were unspliced, raising the possibility that they may be derived from genomic DNA or unprocessed pre-rnRNA contamination during library construction, or alternatively represent nonspecific transcriptional noise. Here we Show, using reverse transcriptase-dependent PCR, microarray, and Northern blot analyses, that many of these clones were derived from genuine transcripts Of unknown function whose expression appears to be regulated. The ncRNA transcripts have larger exons and fewer introns than protein-coding transcripts. Analysis of the genomic landscape around these sequences indicates that some cDNA clones were produced not from terminal poly(A) tracts but internal priming sites within longer transcripts, only a minority of which is encompassed by known genes. A significant proportion of these transcripts exhibit tissue-specific expression patterns, as well as dynamic changes in their expression in macrophages following lipopolysaccharide Stimulation. Taken together, the data provide strong support for the conclusion that ncRNAs are an important, regulated component of the mammalian transcriptome.

Retroviral invasion of the koala genome

Endogenous retroviruses are a common ancestral feature of mammalian genomes with most having been inactivated over time through mutation and deletion(1). A group of more intact endogenous retroviruses are considered to have entered the genomes of some species more recently, through infection by exogenous viruses(2), but this event has never been directly proved. We have previously reported koala retrovirus (KoRV) to be a functional virus that is associated with neoplasia(3). Here we show that KoRV also shows features of a recently inserted endogenous retrovirus that is vertically transmitted. The finding that some isolated koala populations have not yet incorporated KoRV into their genomes, combined with its high level of activity and variability in individual koalas, suggests that KoRV is a virus in transition between an exogenous and endogenous element. This ongoing dynamic interaction with a wild species provides an exciting opportunity to study the process and consequences of retroviral endogenization in action, and is an attractive model for studying the evolutionary event in which a retrovirus invades a mammalian genome.

Safety behaviors and dysfunctional beliefs about sleep: Testing a cognitive model of the maintenance of insomnia

Objective: Our aim was to determine if insomnia severity, dysfunctional beliefs about sleep, and depression predicted sleep-related safety behaviors. Method: Standard sleep-related measures (such as the Insomnia Severity Index; the Dysfunctional Beliefs About Sleep scale; the Depression, Anxiety, and Stress Scale; and the Sleep-Related Behaviors Questionnaire) were administered. Additionally, 14 days of sleep diary (Pittsburg Sleep Diary) data and actual use of sleep-related behaviors were collected. Results: Regression analysis revealed that dysfunctional beliefs about sleep predicted sleep-related safety behaviors. Insomnia severity did not predict sleep-related safety behaviors. Depression accounted for the greatest amount of unique variance in the prediction of safety behaviors, followed by dysfunctional beliefs. Exploratory analysis revealed that participants with higher levels of depression used more sleep-related behaviors and reported greater dysfunctional beliefs about their sleep. Conclusion: The findings underlie the significant influence that dysfunctional beliefs have on individuals' behaviors. Moreover, the results suggest that depression may need to be considered as an explicit component of cognitive-behavioral models of insomnia. (c) 2006 Elsevier Inc. All rights reserved.

Community center-based resistance training for the maintenance of glycemic control in adults with type 2 diabetes

OBJECTIVE - The purpose of this study was to determine whether beneficial effects on glycemic control of an initial laboratory-supervised resistance training program could be sustained through a community center-based maintenance program. RESEARCH DESIGN AND METHODS - We studied 57 overweight (BMI >= 27 kg/m(2)) sedentary men and women aged 40-80 years with established (> 6 months) type 2 diabetes. initially, all participants attended a twice-weekly 2-month supervised resistance training program conducted in the exercise laboratory. Thereafter, participants undertook a resistance training maintenance program (2 times/week) for 12 months and were randomly assigned to carry this out either in a community fitness and recreation center (center) or in their domestic environment (home). Glycemic control (HbA(1c) [A1C]) was assessed at 0, 2, and 14 months. RESULTS - Pooling data from the two groups for the 2-month supervised resistance training program showed that compared with baseline, mean A1C fell by -0.4% [95% CI -0.6 to -0.2]. Within-group comparisons showed that A I C remained lower than baseline values at 14 months in the center group (- 0.4% [-0.7 to -0.03]) but not in the home group (-0.1% [-0.4 to 0.3]). However, no between-group differences were observed at each time point. Changes in AIC during the maintenance period were positively associated with exercise adherence in the center group only. CONCLUSIONS - Center-based but not home-based resistance training was associated with the maintenance of modestly improved glycemic control from baseline, which was proportional to program adherence. Our findings emphasize the need to develop and test behavioral methods to promote healthy lifestyles including increased physical activity in adults with type 2 diabetes.