A computational framework for nucleic acid sub-sequence identification

Identification of nucleic acid sub-sequences within larger background sequences is a fundamental need of the biology community. The applicability correlates to research studies looking for homologous regions, diagnostic purposes and many other related activities. This paper serves to detail the approaches taken leading to sub-sequence identification through the use of hidden Markov models and associated scoring optimisations. The investigation of techniques for locating conserved basal promoter elements correlates to promoter thus gene identification techniques. The case study centred on the TATA box basal promoter element, as such the background is a gene sequence with the TATA box the target. Outcomes from the research conducted, highlights generic algorithms for sub-sequence identification, as such these generic processes can be transposed to any case study where identification of a target sequence is required. Paths extending from the work conducted in this investigation have led to the development of a generic framework for the future applicability of hidden Markov models to biological sequence analysis in a computational context.

Molecular depth profiling of organic and biological materials

Atomic depth profiling using secondary ion mass spectrometry, SIMS, is common in the field micro-electronics; however, the generation of molecular information as a function of sample depth is difficult due to the accumulation of damage both on and beneath the sample surface. The introduction of polyatomic ion beams such as SF<sub>5sub> and C<sub>60sub> have raised the possibility of overcoming this problem as they deposit the majority of their energy in the upper surface of the sample resulting in increased sputter yields but with a complimentary reduction in sub-surface damage accumulation. In this paper we report the depth profile analysis of the bio-polymer polycaprolactone, PCL, using the polyatomic ions Au<sub>3sub>⁺ and C<sub>60sub>⁺ and the monoatomic Au+. Results are compared to recent analysis of a similar sample using . depth profiling of cellulose is also demonstrated, an experiment that has been reported as unsuccessful when attempted with implications for biological analysis are discussed.

Biological vulnerability of two exploited sharks of the genus Deania (Centrophoridae)

Life-history parameters of Deania calcea and Deania quadrispinosa suggested that their productivity was very low. Maturity (L<sub>T50sub>) occurs at c. 80% of maximum observed total lengths (L<sub>Tsub>) for both species and sexes. A large proportion of mature females were neither pre-ovulatory nor pregnant, and the reproductive cycle included a distinct resting phase after pregnancy. For D. calcea, mean ovarian fecundity was 12 and maximum observed litter size was 10 (average of six); D. quadrispinosa averaged 17 pups per litter. Birth L<sub>Tsub> was 28-33 cm for D. calcea and 23-25 cm for D. quadrispinosa. The male and female reproductive cycles were aseasonal, and consequently, the length of the reproductive cycle could not be determined. Preliminary ageing data from dorsal-spine growth bands suggested that female D. calcea lived to 31-36 years and males to 24-32 years. The L<sub>Tsub>-at-age data using external bands on the spines showed maturity occurring at 15·5 years (males) and 21·5 years (females), whereas banding on the internal dentine indicated maturity at 10·5 and 17·5 years for males and females. Thus, a female lifetime of 31-36 years allowed for a maximum of 7 litters if a 2 year cycle is assumed or only five litters with a 3 year cycle, resulting in a lifetime fecundity of only 42 pups (2 year cycle) or even lower (3 year cycle).

Electrogenerated chemiluminescence of tris(2,2' bipyridine)ruthenium(ii) using common biological buffers as co-reactant, pH buffer and supporting electrolyte

A series of aliphatic tertiary amines (HEPES, POPSO, EPPS and BIS-TRIS) commonly used to buffer the pH in biological experiments, were examined as alternative, non-toxic co-reactants for the electrogenerated chemiluminescence (ECL) of tris(2,2'-bipyridine)ruthenium(ii) ([Ru(bpy)3](2+)). These were found to be very attractive as "multi-tasking" reagents, serving not only as co-reactants, but also fulfiling the roles of pH buffer and supporting electrolyte within an aqueous environment; thus significantly simplifying the overall ECL analysis. Sub-nanomolar detection limits were obtained for [Ru(bpy)3](2+) in the presence of BIS-TRIS, making this species an valuable option for co-reactant ECL-based bioanalytical applications.