The probability of electrophoretic idendity of proteins as a function of amino acid divergence

Summary Whenever proteins differ by two or more substitutions involving charged amino acids, there is a possibility of spurious electrophoreiic identity because one difference may cancel another. Probability of spurious identity can be calculated as a function of the total number of site differences between the two proteins. This in turn is a complex function of the number of evolutionary events in the divergence of the proteins from a common ancestor and of the number of sites able to accept evolutionary substitutions during the period of divergence. The probability of electrophoretic identity is a decidedly nonlinear, although monotonic, function of the genetic distance.     

Effect of salinity gradients and heterotrophic microbial activity on biodegradation of nitrilotriacetic acid in laboratory simulations of the estuarine environment

The biodegradation of nitrilotriacetic acid (NTA), a synthetic replacement detergent builder, in the estuarine environment was examined by using a laboratory estuarine simulation. Two interdependent microcosms were used; each of five vessels was equilibrated with a saline gradient between 1.30 and 17.17%, with the final vessel subsequently being increased to a maximum salinity of 31.6%. Each microcosm was seeded simultaneously with heterotrophic bacteria from both fresh and saline sources. Viable counts demonstrated the ability of each microcosm to sustain a mixed heterotrophic bacterial community throughout the range of salinities for 183 days after a stabilization period. Isolation studies demonstrated that both systems contained four bacterial species, representatives of the genera Vibrio and Flavobacterium and members of the coryneform group and the family Enterobacteriaceae. Total bacterial numbers and species diversity decreased with increased salinity. NTA was administered at low and high concentrations, one concentration to each microcosm, initially with the least amount of saline. Removal of both concentrations of NTA occurred and was attributed to biodegradation after a period of bacterial acclimatization. Subsequent dosing of NTA to vessels of higher salinity demonstrated that biodegradation was incomplete at observed mean salinities of greater than 9.18% at low influent NTA concentrations and greater than 5.08% at high influent NTA concentrations. Therefore, acclimatization was dose dependent. It was concluded that NTA acclimatization at the higher salinities ceased because of salinity stress-induced failure of NTA catabolism and not the disappearance of a particular bacterial species.     

Fish distributions along depth gradients of a sea mountain range conform to the mid‐domain effect

Species richness often peaks in the middle of bounded geographic domains (e.g. latitude, altitude or depth). Hump‐shaped richness distributions may be due to deterministic processes, such as adaptations to environmental variation. Alternatively, such distributions might also be due to stochastic process. The mid‐domain effect (MDE) posits that hump‐shaped richness distributions arise when species ranges are randomly arranged within the limits of the domain. We tested whether the MDE could account for the richness of bottom‐associated (demersal) fishes between 200 and 800 m on the Chatham Rise, New Zealand. We quantified the depth distributions of 59 fish species from 1891 research trawl catches made between 1991 and 2007. Results showed a broad plateau of high species richness near the centre of the domain (between 300 and 700 m), which was consistent with expectations of the MDE. Further, empirical species richness was better explained statistically by predictions of the MDE than models incorporating additional abiotic predictor variables. Our results deviated from previous studies that identified a greater richness of fishes in warmer, shallower depths with higher primary production. However, our study was conducted entirely below the euphotic zone, at depths where gradients are relatively weak, suggesting that support for the mid‐domain effect may increase across oceanic domains characterised by weak environmental gradients.     

The apparent establishment and subsequent eradication of the Australian giant bulldog ant Myrmecia brevinoda Forel (Hymenoptera: Formicidae) in New Zealand

Abstract

The Australian giant bulldog ant Myrmecia brevinoda Forel was first observed in New Zealand in 1940 (Keall 1981). Further observations of this species were made at a location in Devonport in 1948 and 1965, and a nest destroyed at this site in 1981. Since this time no further observations have been made, yet the status of this species is commonly listed as “uncertain establishment” on New Zealand faunal lists. We describe the control procedure used in 1981. In addition, to determine its current status we resurveyed ants in the area of earlier infestation using visual searches, pitfall trapping, and a reward for discovery posted to local residents. No evidence of M. brevinoda was found, though several other invasive species were found, including the Argentine ant Linepithema humile (Mayr), Pheidole rugosula Forel, and a recently established Australian cryptic Solenopsis species. Given the results of our survey and the absence of other reports of M. brevinoda over the last 24 years, we consider this species to be extinct or eradicated from New Zealand.     

Structural requirements for efficient prion protein conversion: Cofactors may promote a conversion-competent structure for PrPC

To understand why cross-species infection of prion disease often results in inefficient transmission and reduced protein conversion, most research has focused on defining the effect of variations in PrP primary structures, including sequence compatibility of substrate and seed. By contrast, little research has been aimed at investigating structural differences between different variants of PrP^C and secondary structural requirements for efficient conversion. This is despite a clear role for molecular chaperones in formation of prions in non-mammalian systems, indicating the importance of secondary/tertiary structure during the conversion process. Recent data from our laboratory on the cellular location of disease-specific prion cofactors supports the critical role of specific secondary structural motifs and the stability of these motifs in determining the efficiency of disease-specific prion protein conversion. In this paper we summarize our recent results and build on the hypothesis previously suggested by Wuthrich and colleagues, that stability of certain regions of the prion protein is crucial for protein conversion to abnormal isoforms in vivo. It is suggested that one role for molecular cofactors in the conversion process is to stabilize PrP^C structure in a form that is amenable for conversion to PrP^Sc.Key words: cofactor, structure, cell-free conversion assay, fibrillization, stability, loop region     

A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability

Background  

Large discrepancies in signature composition and outcome concordance have been observed between different microarray breast cancer expression profiling studies. This is often ascribed to differences in array platform as well as biological variability. We conjecture that other reasons for the observed discrepancies are the measurement error associated with each feature and the choice of preprocessing method. Microarray data are known to be subject to technical variation and the confidence intervals around individual point estimates of expression levels can be wide. Furthermore, the estimated expression values also vary depending on the selected preprocessing scheme. In microarray breast cancer classification studies, however, these two forms of feature variability are almost always ignored and hence their exact role is unclear.