Validation of DNA methylation profiling in formalin-fixed paraffin-embedded samples using the Infinium HumanMethylation450 Microarray

A formalin-fixed paraffin-embedded (FFPE) sample usually yields highly degraded DNA, which limits the use of techniques requiring high-quality DNA, such as Infinium Methylation microarrays. To overcome this restriction, we have applied an FFPE restoration procedure consisting of DNA repair and ligation processes in a set of paired fresh-frozen (FF) and FFPE samples. We validated the FFPE results in comparison with matched FF samples, enabling us to use FFPE samples on the Infinium HumanMethylation450 Methylation array.     

The effect of mobbing vocalizations on risk perception in common mynas (Acridotheres tristis)

Journal of Ethology - Animals emit predator-elicited calls in response to potential predation threats. These vocalizations induce a variety of anti-predator behaviors in conspecific receivers...     

Evaluation of a crown-of-thorns starfish (Acanthaster planci) control program at Grub Reef (central Great Barrier Reef)

A crown-of-thorns starfish control program was conducted at Grub Reef (central Great Barrier Reef) in an area (0.64 km²) which encompassed 53 individual patch reefs. During a two week period, 15 divers injected 3175 starfish with copper sulphate. The program was considered unsuccessful. Although starfish abundance had declined significantly after the control efforts, biological surveys indicated that a relatively large number of starfish remained. The surveys also indicated a general decline in the number of starfish along the reef perimeter, outside the control area. The total cost of the control program was $35 per starfish. These results have important implications for the implementation of future control programs and highlight the need to undertake before and after biological surveys to assess the effectiveness of the control efforts.     

Impact of the Arundo scale Rhizaspidiotus donacis (Hemiptera: Diaspididae) on the weight of Arundo donax (Poaceae: Arundinoideae) rhizomes in Languedoc southern France and Mediterranean Spain

Arundo donax L. (Poaceae) is native to Mediterranean Europe and invasive in the Rio Grande Basin of North America. Rhizomes from nine sites in France and Spain infested with a candidate control agent, the armoured scale Rhizaspidiotus donacis (Hemiptera: Diaspididae) weighed 50% less than those from nine sites without scale.     

Wives and Warriors: Women and the Military in the United States and Canada

Wives and Warriors: Women and the Military in the United States and Canada. Laurie Weinstein and Christie C. White. eds. Westport, CT: Bergin and Garvey, 1997. 252 pp.     

Termite Prey Specialization in the Pitcher Plant Nepenthes albomarginata--Evidence from Stable Isotope Analysis

Old World pitcher plants (Nepenthes spp., Nepenthaceae) trapand digest invertebrate prey to derive nutrients, primarilynitrogen (N). In the majority of lowland Nepenthes species studiedto date, ants (Hymenoptera, Formicidae) are numerically thedominant prey taxon. Nepenthes albomarginata is unusual in showingan apparent bias towards the capture of termites (Isoptera).We tested the hypothesis that N. albomarginata derives N fromtermite capture, by comparison of foliar stable N isotope abundance(     

Different functional domains of the adenovirus E1A gene are involved in regulation of host cell cycle products.

We have analyzed the cell cycle effects that different domains of the adenovirus E1A proteins have on quiescent primary BRK cells. Studies with deletion mutants that in combination removed all but the N-terminal 85 amino acids common to both the 12S and 13S proteins suggest that this region may be sufficient for the induction of synthesis of proliferating cell nuclear antigen and the stimulation of DNA synthesis. A second domain also common to the N-terminal exon of the 12S and 13S proteins was required for the induction of mitosis and stimulation of proliferation of primary BRK cells. A virus containing a mutation in this region was still able to stimulate DNA synthesis efficiently. A third domain, unique to the 13S protein, was required for the accelerated activation of the cellular thymidylate synthase gene in a manner similar to the 13S-dependent stimulation of adenovirus early region genes.     

Nucleotide sequence of the DdeI restriction-modification system and characterization of the methylase protein.

The DdeI restriction-modification system was previously cloned and has been maintained in E. coli on two separate and compatible plasmids (1). The nucleotide sequence of the endonuclease and methylase genes has now been determined; it predicts proteins of 240 amino acids, Mr = 27,808, and 415 amino acids, Mr = 47,081, respectively. Inspection of the DNA sequence shows that the 3' end of the methylase gene had been deleted during cloning. The clone containing the complete methylase gene was made and compared to that containing the truncated gene; only clones containing the truncated form support the endonuclease gene in E. coli. Bal-31 deletion studies show that methylase expression in the Dde clones is also dependent upon orientation of the gene with respect to pBR322. The truncated and complete forms of the methylase protein were purified and compared; the truncated form appears to be more stable and active in vitro. Finally, comparison of the deduced amino acid sequence of M. DdeI with that of other known cytosine methylases shows significant regions of homology.     

The common src homology region 2 domain of cytoplasmic signaling proteins is a positive effector of v-fps tyrosine kinase function.

A conserved noncatalytic domain SH2 (for src homology region 2) is located immediately N terminal to the kinase domains of all cytoplasmic protein-tyrosine kinases. We found that the wild-type v-fps SH2 domain stimulated the enzymatic activity of the adjacent kinase domain 10-fold and functioned as a powerful positive effector of catalytic and transforming activities within the v-fps oncoprotein (P130gag-fps). Partial proteolysis of P130gag-fps and supporting genetic data indicated that the v-fps SH2 domain exerts its effect on catalytic activity through an intramolecular interaction with the kinase domain. Amino acid alterations in the SH2 domain that impaired kinase function interfered with association of the SH2 domain with the kinase domain. Deletion of a conserved octapeptide motif converted the v-fps SH2 domain from an activator to an inhibitor of tyrosine kinase activity. This latent inhibitory activity of v-fps SH2 has functional implications for phospholipase C-gamma and p21ras GTPase-activating protein, both of which have two distinct SH2 domains suggestive of complex regulation. In addition to regulating the specific activity of the kinase domain, the SH2 domain of P130gag-fps was also found to be required for the tyrosine phosphorylation of specific cellular proteins, notably polypeptides of 124 and 62 kilodaltons. The SH2 domain therefore appears to play a dual role in regulation of kinase activity and recognition of cellular substrates.