Fast Acquisition of (13)C NMR Spectra using the Steady-state Free Precession Sequence

In this paper, we show that the steady-state free precession sequence can be used to acquire (13)C high-resolution nuclear magnetic resonance spectra and applied to qualitative analysis. The analysis of brucine sample using this sequence with 60 degrees flip angle and time interval between pulses equal to 300 ms (acquisition time, 299.7 ms; recycle delay, 300 ms) resulted in spectrum with twofold enhancement in signal-to-noise ratio, when compared to standard (13)C sequence. This gain was better when a much shorter time interval between pulses (100 ms) was applied. The result obtained was more than fivefold enhancement in signal-to-noise ratio, equivalent to more than 20-fold reduction in total data recording time. However, this short time interval between pulses produces a spectrum with severe phase and truncation anomalies. We demonstrated that these anomalies can be minimized by applying an appropriate apodization function and plotting the spectrum in the magnitude mode.

Reworked Devonian (Givetian-Frasnian) spores from a Permian glacially-derived sequence at Bacchus Marsh, Victoria

Emphanisporites rotatus McGregor emend. McGregor 1973 is a distinctive Devonian spore with a known primary source age range in Australia spanning the upper Givetian to early Frasnian (Middle to Late Devonian). This is the first record of the species from Victoria. It occurs as a reworked element in an Early Permian assemblage belonging to the Granularisporites confluens Zone derived from glacigene diamictite in the Bacchus Marsh area. As the predominant direction of Permian ice movement recorded in the Bacchus Marsh district was south-west to north-east, it is possible that the reworked spores were transported from Antarctica.

A preliminary study of 16S rRNA sequence variation in Australia Macrobrachium shrimps (Palaemonidae: Decapoda) reveals inconsistencies in their current classification

The systematic relationships among Australian palaemonid shrimps have been the subject of speculation for some time. A preliminary phylogenetic study was undertaken to clarify the relationships of five species, Macrobrachium intermedium (Stimpson), M. australiense (Holthuis), M. atactum (Riek), M. rosenbergii (de Man) and Palaemon serenus (Heller), using 16S rRNA mitochondrial gene sequences. Phylogenetic analyses indicated inconsistencies with the current classification in two respects. First, M. intermedium formed a very well-supported clade with P. serenus distinct from M. australiense, M. atactum and M. rosenbergii. Second, the two species from inland Australia, M. australiense and M. atactum, showed a high level of genetic similarity over a substantial geographic range, suggesting that they may represent conspecific populations. The taxonomic and biogeographic implications of these findings for Macrobrachium in Australia are discussed.

Large-scale biological sequence assembly and alignment by using computing grid

Large-scale sequence assembly and alignment are fundamental parts of biological computing. However, most of the large-scale sequence assembly and alignment require intensive computing power and normally take very long time to complete. To speedup the assembly and alignment process, this paper parallelizes the Euler sequence assembly and pair-wise/multiple sequence assembly, two important sequence assembly methods, and takes advantage of Computing Grid which has a colossal computing capacity to meet the large-scale biological computing demand.

Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapoda: Parastacidae): a novel gene order revealed

The complete mitochondrial DNA sequence was determined for the Australian freshwater crayfish Cherax destructor (Crustacea: Decapoda: Parastacidae). The 15,895-bp genome is circular with the same gene composition as that found in other metazoans. However, we report a novel gene arrangement with respect to the putative arthropod ancestral gene order and all other arthropod mitochondrial genomes sequenced to date. It is apparent that 11 genes have been translocated (ND1, ND4, ND4L, Cyt b, srRNA, and tRNAs Ser(UGA), Leu(CUN), Ile, Cys, Pro, and Val), two of which have also undergone inversions (tRNAs Pro and Val). The ‘duplication/random loss’ mechanism is a plausible model for the observed translocations, while ‘intramitochondrial recombination’ may account for the gene inversions. In addition, the arrangement of rRNA genes is incompatible with current mitochondrial transcription models, and suggests that a different transcription mechanism may operate in C. destructor.

Mitochondrial DNA sequence and gene organization in the Australian Blacklip Abalone Haliotis rubra (Leach)

The complete mitochondrial DNA of the blacklip abalone Haliotis rubra (Gastropoda: Mollusca) was cloned and 16,907 base pairs were sequenced. The sequence represents an estimated 99.85% of the mitochondrial genome, and contains 2 ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes found in other metazoan mtDNA. An AT tandem repeat and a possible C-rich domain within the putative control region could not be fully sequenced. The H. rubra mtDNA gene order is novel for mollusks, separated from the black chiton Katharina tunicata by the individual translocations of 3 tRNAs. Compared with other mtDNA regions, sequences from the ATP8, NAD2, NAD4L, NAD6, and 12S rRNA genes, as well as the control region, are the most variable among representatives from Mollusca, Arthropoda, and Rhynchonelliformea, with similar mtDNA arrangements to H. rubra. These sequences are being evaluated as genetic markers within commercially important Haliotis species, and some applications and considerations for their use are discussed.

All maximal-pairs in step-leap representation of melodic sequence

This paper proposes an efficient pattern extraction algorithm that can be applied on melodic sequences that are represented as strings of abstract intervallic symbols; the melodic representation introduces special “binary don’t care” symbols for intervals that may belong to two partially overlapping intervallic categories. As a special case the well established “step–leap” representation is examined. In the step–leap representation, each melodic diatonic interval is classified as a step (±s), a leap (±l) or a unison (u). Binary don’t care symbols are used to represent the possible overlapping between the various abstract categories e.g. *=s, *=l and #=-s, #=-l. We propose an O(n+d(n-d)+z)-time algorithm for computing all maximal-pairs in a given sequence x=x[1..n], where x contains d occurrences of binary don’t cares and z is the number of reported maximal-pairs.

All maximal-pairs in step-leap representation of melodic sequence

This paper proposes an efficient pattern extraction algorithm that can be applied on melodic sequences that are represented as strings of abstract intervallic symbols; the melodic representation introduces special “binary don’t care” symbols for intervals that may belong to two partially overlapping intervallic categories. As a special case the well established “step–leap” representation is examined. In the step–leap representation, each melodic diatonic interval is classified as a step (±s), a leap (±l) or a unison (u). Binary don’t care symbols are used to represent the possible overlapping between the various abstract categories e.g. *=s, *=l and #=-s, #=-l. We propose an O(n+d(n-d)+z)-time algorithm for computing all maximal-pairs in a given sequence x=x[1..n], where x contains d occurrences of binary don’t cares and z is the number of reported maximal-pairs.