The Wavelet-Based Cluster Analysis for Temporal Gene Expression Data

A variety of high-throughput methods have made it possible to generate detailed temporal expression data for a single gene or large numbers of genes. Common methods for analysis of these large data sets can be problematic. One challenge is the comparison of temporal expression data obtained from different growth conditions where the patterns of expression may be shifted in time. We propose the use of wavelet analysis to transform the data obtained under different growth conditions to permit comparison of expression patterns from experiments that have time shifts or delays. We demonstrate this approach using detailed temporal data for a single bacterial gene obtained under 72 different growth conditions. This general strategy can be applied in the analysis of data sets of thousands of genes under different conditions.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29]     

The impact of freezing during maturation on storage products in canola seeds

Mature canoia ( Brassica napus cv. Westar) seeds contain large quantities of the storage proteins cruciferin and napin and storage lipids rich in C18: 1 and C18:2 fatty acids. Both the quantity and quality of these products are altered by freezing during development. Further, the response to freezing changes during seed development. The effects include decreased fatty acid chain elongation, altered fatty acid unsaturation, higher lipid levels and lower protein levels. In addition, seeds in the pivotal moisture range (55%) may be predisposed to precocious germination, which is then inhibited by a lack of adequate seed moisture. The results indicate that freezing imparts its effect in two ways. Initially, there is a freezing (low temperature) component and this is followed by rapid desiccation of the seeds. Although most responses probably result from a combination of the stresses, it appears that inhibition of fatty acid chain elongation is caused by the freezing component and the gradual inhibition of storage protein accumulation is a result of accelerated seed desiccation.     

Southeastern U.S.A. continental shelf respiratory rates revisited

Respiratory rates on the U. S. southeastern continental shelf have been estimated several times by different investigators, most recently by Jiang et al. (Biogeochemistry 98:101–113, 2010) who report lower mean rates than were found in earlier work and attribute the differences to analytical error in all methods used in earlier studies. The differences are, instead, attributable to the differences in the geographical scope of the studies. The lower estimates of regional organic carbon flux of Jiang et al. (Biogeochemistry 98:101–113, 2010) are a consequence of their extrapolation of data from a small portion of the shelf to the entire South Atlantic Bight. This comment examines the methodologies used as well as the variability of respiratory rates in this region over space and time.     

Caffeine promotes in vitro fertilization of mouse ova within 15 minutes

Epididymal sperm were collected from C57Bl6/J X DBA2/J (B6D2) males and allowed to capacitate for 2 hr. When cumulus-free oocytes were exposed to sperm for 15 min in either the presence (6.0 mM) or absence of caffeine, fertilization did not occur. However, when cumulus cells were left intact, 23% of oocytes were fertilized in caffeine-free medium and 62% in caffeine-containing medium. When cumulus-free oocytes were incubated with sperm for 30 min, none was fertilized in the absence of caffeine, but 33% were fertilized when 6.0 mM caffeine was present (P less than .02). These effects of caffeine were on the sperm, as sperm exposed to caffeine and then coincubated with oocytes for 15 min in essentially caffeine-free media fertilized a similar percent of oocytes (93%) as when sperm and oocytes were exposed to caffeine during the fertilization period (86%). When sperm were capacitated in caffeine-containing medium, the percentage of ova fertilized was similar to capacitation without caffeine. We conclude that both cumulus cells and caffeine speed up the fertilization process with mouse gametes and that the effect of caffeine is on the sperm, but not due to more rapid capacitation.     

Staphylococcus aureus bacteriophages mediating the simultaneous lysogenic conversion of beta-lysin, staphylokinase and enterotoxin A: molecular mechanism of triple conversion

A new group of serotype F bacteriophages of Staphylococcus aureus has been found which mediates the simultaneous triple-lysogenic conversion of enterotoxin A, staphylokinase and beta-lysin. The phages were recovered fro methicillin-resistant strains of S. aureus isolated in Irish hospitals between 1971 and 1988 and from strain PS42-D, which has been used as the propagating strain for the S. aureus typing phage 42D since before 1965. The molecular mechanism of triple conversion mediated by three of these phages was determined by molecular cloning, restriction endonuclease site mapping and hybridization analysis, and compared with the mechanism of beta-lysin and staphylokinase conversion mediated by the serotype F, double-converting phase phi 13. THe genetic determinants mediating expression of enterotoxin A (entA) and staphylokinase (sak) were cloned from the DNA of the triple-converting phage and expression of the cloned determinants detected in Escherichia coli and S. aureus. The entA and sak determinants were closely linked in the phage DNA adjacent to the phage attachment site (attP) in each case and furthermore, the sak determinant of phage phi 13 was also located near its attP. The restriction maps of the entA-, sak- and attP-containing DNA regions of the three triple-converting phages were very similar to each other and to the corresponding sak- and attP- containing DNA region of phage phi 13. Hybridization analysis using a cloned beta-lysin determinant (hlb) and cloned attP-containing DNA fragments as probes demonstrated that beta-lysin conversion mediated by the triple-converting phages and phage phi 13 was caused by insertional inactivation of the chromosomally encoded hlb determinant by orientation-specific integration of phage DNA following lysogenization.     

On the use of Timed Species Counts to estimate avian abundance indices in species-rich communities

Timed Species Counts (TSCs) have been found to provide useful data for assessing the relative abundances of birds in conservation studies, particularly in species‐rich areas, such as many tropical habitats. An index is conventionally based upon the mean TSC from a number of counts. In this paper, we develop a new statistic, λ, which is based upon the assumption that the number of encounters with a species in unit time has a Poisson distribution. Using the same assumptions on detectability that underlie earlier analyses of TSC data, values of λ, unlike the simple mean TSC, are directly proportional to abundance. However, TSC data are affected by detectability, so that comparisons of relative abundance for the same species between similar sites have greater validity than those between different species. Explicit formulae for calculating an estimate of λ and its SE from sample data are described. Although λ can be estimated from either TSC data or the simple proportion of counts in which the species was encountered, for the commonest species a simulation study shows that only data in full TSC form provide accurate estimates. The difference becomes negligible for scarcer species. The use of λ in preference to mean TSC scores is recommended where it is important to compare values of relative abundance.     

Where have all the fathers gone? An extensive microsatellite analysis of paternity in the grey seal (Halichoerus grypus)

Microsatellites were used to conduct an extensive analysis of paternity of grey seals from two Scottish breeding colonies at North Rona (n = 1189) and the Isle of May (n = 694), spanning more than a decade. A maximum of 46% of pups at North Rona and 29% of pups at the Isle of May could be allocated a father, even though the majority of candidate males for specific study sites within each colony were believed to have been sampled. Based on the paternities which could be assigned, both colonies showed evidence of reproductive skew, apparently due to the presence of approximately five males who were exceptionally successful. Some males were assigned paternities at least 10 years before, and colleagues 10 years after, being sampled, implying a reproductive lifespan of at least 10 years, and there are indications that the real maximum lies in the range 15-20 years. Male grey seals appear to have at least two breeding strategies they can adopt. On land, some males benefit from a traditionally polygynous system. However, between 50 and 70% of grey seal pups born at a particular colony are not fathered by males who are likely to be sampled by us, implying that these males seldom venture ashore here. We conclude that aquatic mating may play a much larger role in the grey seal than has previously been thought.     

Miles to go (mtgo) encodes FNDC3 proteins that interact with the chaperonin subunit CCT3 and are required for NMJ branching and growth in Drosophila

Analysis of mutants that affect formation and function of the Drosophila larval neuromuscular junction (NMJ) has provided valuable insight into genes required for neuronal branching and synaptic growth. We report that NMJ development in Drosophila requires both the Drosophila ortholog of FNDC3 genes; CG42389 (herein referred to as miles to go; mtgo), and CCT3, which encodes a chaperonin complex subunit. Loss of mtgo function causes late pupal lethality with most animals unable to escape the pupal case, while rare escapers exhibit an ataxic gait and reduced lifespan. NMJs in mtgo mutant larvae have dramatically reduced branching and growth and fewer synaptic boutons compared with control animals. Mutant larvae show normal locomotion but display an abnormal self-righting response and chemosensory deficits that suggest additional functions of mtgo within the nervous system. The pharate lethality in mtgo mutants can be rescued by both low-level pan- and neuronal-, but not muscle-specific expression of a mtgo transgene, supporting a neuronal-intrinsic requirement for mtgo in NMJ development. Mtgo encodes three similar proteins whose domain structure is most closely related to the vertebrate intracellular cytosolic membrane-anchored fibronectin type-III domain-containing protein 3 (FNDC3) protein family. Mtgo physically and genetically interacts with Drosophila CCT3, which encodes a subunit of the TRiC/CCT chaperonin complex required for maturation of actin, tubulin and other substrates. Drosophila larvae heterozygous for a mutation in CCT3 that reduces binding between CCT3 and MTGO also show abnormal NMJ development similar to that observed in mtgo null mutants. Hence, the intracellular FNDC3-ortholog MTGO and CCT3 can form a macromolecular complex, and are both required for NMJ development in Drosophila.