Hybridisation, paternal leakage and mitochondrial DNA linearization in three anomalous fish (Scombridae)

Using mitochondrial DNA for species identification and population studies assumes that the genome is maternally inherited, circular, located in the cytoplasm and lacks recombination. This study explores the mitochondrial genomes of three anomalous mackerel. Complete mitochondrial genome sequencing plus nuclear microsatellite genotyping of these fish identified them as Scomberomorus munroi (spotted mackerel). Unlike normal S. munroi, these three fish also contained different linear, mitochondrial genomes of Scomberomorus semifasciatus (grey mackerel). The results are best explained by hybridisation, paternal leakage and mitochondrial DNA linearization. This unusual observation may provide an explanation for mtDNA outliers in animal population studies. © 2013.

Stretching single DNA-molecules with temperature-stabilized optical tweezers

This thesis consists of two parts; in the first part we performed a single-molecule force extension measurement with 10kb long DNA-molecules from phage-λ to validate the calibration and single-molecule capability of our optical tweezers instrument. Fitting the worm-like chain interpolation formula to the data revealed that ca. 71% of the DNA tethers featured a contour length within ±15% of the expected value (3.38 µm). Only 25% of the found DNA had a persistence length between 30 and 60 nm. The correct value should be within 40 to 60 nm. In the second part we designed and built a precise temperature controller to remove thermal fluctuations that cause drifting of the optical trap. The controller uses feed-forward and PID (proportional-integral-derivative) feedback to achieve 1.58 mK precision and 0.3 K absolute accuracy. During a 5 min test run it reduced drifting of the trap from 1.4 nm/min in open-loop to 0.6 nm/min in closed-loop.

Modelling end-of-life care practices: Factors associated with critical care nurse engagement in care provision

Objective To identify factors associated with critical care nurses’ engagement in end-of-life care practices. Methods Multivariable regression modelling was undertaken on 392 responses to an online self-report survey of end-of-life care practices and factors influencing practice by Australian critical care nurses’. Univariate general linear models were built for six end-of-life care practice areas. Results Six statistically significant (p < 0.001) models were developed: Information sharing F(3, 377) = 40.53, adjusted R2 23.8%; Environmental modification F(5, 380) = 19.55, adjusted R2 19.4%; Emotional support F(10, 366) = 12.10, adjusted R2 22.8%; Patient and family centred decision making F(8, 362) = 17.61 adjusted R2 26.4%; Symptom management F(8, 376) = 7.10, adjusted R2 11.3%; and Spiritual support F(9, 367) = 14.66, adjusted R2 24.6%. Stronger agreement with values consistent with a palliative approach, and greater support for patient and family preferences were associated with higher levels of engagement in end-of-life care practices. Higher levels of preparedness and access to opportunities for knowledge acquisition were associated with engagement in the interpersonal practices of patient and family centred decision making and emotional support. Conclusion This study provides evidence for interventions to address factors associated with nurse engagement to increase participation in all end-of-life care practice areas.

Rapid assessment of genotype-by-environment interactions and heritability for growth rate in aquaculture species using in vitro fertilisation and DNA tagging

Commercial environments may receive only a fraction of expected genetic gains for growth rate as predicted from the selection environment. This fraction is result of undesirable genotype-by-environment interactions (GxE) and measured by the genetic correlation (rg) of growth between environments. Rapid estimates of genetic correlation achieved in one generation are notoriously difficult to estimate with precision. A new design is proposed where genetic correlations can be estimated by utilising artificial mating from cryopreserved semen and unfertilised eggs stripped from a single female. We compare a traditional phenotype analysis of growth to a threshold model where only the largest fish are genotyped for sire identification. The threshold model was robust to differences in family mortality differing up to 30%. The design is unique as it negates potential re-ranking of families caused by an interaction between common maternal environmental effects and growing environment. The design is suitable for rapid assessment of GxE over one generation with a true 0.70 genetic correlation yielding standard errors as low as 0.07. Different design scenarios were tested for bias and accuracy with a range of heritability values, number of half-sib families created, number of progeny within each full-sib family, number of fish genotyped, number of fish stocked, differing family survival rates and at various simulated genetic correlation levels.

David Jones seeks to exploit top end gap in Australian grocery

While Australia’s supermarkets continue to battle on price, the South African owner of David Jones, Woolworths Holdings, has found a gap in the Australian grocery market and is preparing to exploit it. Reports that the group has appointed Pieter de Wet to overhaul the David Jones food business signals once again the ever-changing face of the Australian food and grocery landscape. A re-energised David Jones food offer will provide positive outcomes for both shoppers and suppliers, while potentially becoming another headache for Coles and Woolworths.

Philip Slomovitz South End collection 1969-1974

Contains 1969 and 1971-73 issues of The South End, Wayne State University student paper, as well as correspondence, public statements, petitions and a tape-recording relating to controversies generated by the printing of alleged anti-Zionist/anti-Semitic articles in the newspaper. The correspondence consists for the most part of an exchange of letters between university officials, Jewish community leaders and Leonard N. Simons, a Detroit advertising executive, during the 1969 controversy, and correspondence with Philip Slomovitz, editor of the Detroit Jewish news, in 1972-73. The tape recording is of a February 2, 1969 interview with John Watson, editor of the South end.

Development of type I genetic markers from expressed sequence tags in highly polymorphic species

Expressed sequence tag (EST) databases provide a primary source of nuclear DNA sequences for genetic marker development in non-model organisms. To date, the process has been relatively inefficient for several reasons: - 1) priming site polymorphism in the template leads to inferior or erratic amplification; - 2) introns in the target amplicon are too large and/or numerous to allow effective amplification under standard screening conditions, and; - 3) at least occasionally, a PCR primer straddles an exon–intron junction and is unable to bind to genomic DNA template. The first is only a minor issue for species or strains with low heterozygosity but becomes a significant problem for species with high genomic variation, such as marine organisms with extremely large effective population sizes. Problems arising from unanticipated introns are unavoidable but are most pronounced in intron-rich species, such as vertebrates and lophotrochozoans. We present an approach to marker development in the Pacific oyster Crassostrea gigas, a highly polymorphic and intron-rich species, which minimizes these problems, and should be applicable to other non-model species for which EST databases are available. Placement of PCR primers in the 3′ end of coding sequence and 3′ UTR improved PCR success rate from 51% to 97%. Almost all (37 of 39) markers developed for the Pacific oyster were polymorphic in a small test panel of wild and domesticated oysters.

Studies on CNTs/DNA composite

The electrical and optical properties of MWCNTs/DNA composite were studied. Electrical conductivity studies reveal that, the increase in CNTs concentration in DNA increases the conductivity. Fourier transformed Infrared (FTIR) spectrum shows that the CNTs are bonded to DNA covalently at the ends and defects sites and the wrapping of DNA on the CNTs is due to van der Waals force.

Characterization of Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease, reveals a unique mode of DNA-binding, helical distortion and cleavage, compared to a canonical LAGLIDADG homing endonuclease

Mycobacterium leprae, which has undergone reductive evolution leaving behind a minimal set of essential genes, has retained intervening sequences in four of its genes implicating a vital role for them in the survival of the leprosy bacillus. A single in-frame intervening sequence has been found embedded within its recA gene. Comparison of M. leprae recA intervening sequence with the known intervening sequences indicated that it has the consensus amino acid sequence necessary for being a LAGLIDADG-type homing endonuclease. In light of massive gene decay and function loss in the leprosy bacillus, we sought to investigate whether its recA intervening sequence encodes a catalytically active homing endonuclease. Here we show that the purified M. leprae RecA intein (PI-MleI) binds to cognate DNA and displays endonuclease activity in the presence of alternative divalent cations, Mg2+ or Mn2+. A combination of approaches including four complementary footprinting assays such as DNase I, Cu/phenanthroline, methylation protection and KMnO4, enhancement of 2-aminopurine fluorescence and mapping of the cleavage site revealed that PI-MleI binds to cognate DNA flanking its insertion site, induces helical distortion at the cleavage site and generates two staggered double-strand breaks. Taken together, these results implicate that PI-MleI possess a modular structure with separate domains for DNA target recognition and cleavage, each with distinct sequence preferences. From a biological standpoint, it is tempting to speculate that our findings have implications for understanding the evolution of LAGLIDADG family of homing endonucleases

Influence of site, storage and steaming on Eucalyptus nitens log-end splitting

Key message Log-end splitting is one of the single most important defects in veneer logs. We show that log-end splitting in the temperate plantation species Eucalyptus nitens varies across sites and within-tree log position and increases with time in storage. Context Log-end splitting is one of the single most important defects in veneer logs because it can substantially reduce the recovery of veneer sheets. Eucalyptus nitens can develop log-end splits, but factors affecting log-end splitting in this species are not well understood. Aims The present study aims to describe the effect of log storage and steaming on the development of log-end splitting in logs from different plantations and log positions within the tree. Methods The study was conducted on upper and lower logs from each of 41 trees from three 20–22-year-old Tasmanian E. nitens plantations. Log-end splitting was assessed immediately after felling, after transport and storage in a log-yard, and just before peeling. A pre-peeling steam treatment was applied to half the logs. Results Site had a significant effect on splitting, and upper logs split more than lower logs with storage. Splitting increased with tree diameter breast height (DBH), but this relationship varied with site. The most rapidly growing site had more splitting even after accounting for DBH. No significant effect of steaming was detected. Conclusion Log-end splitting varied across sites and within-tree log position and increased with time in storage.

DNA sequences and austral taxa indicate generic synonymy of Paratrichocladius Santos-Abreu with Cricotopus Wulp (Diptera: Chironomidae)

In the century since the description of the orthoclad genus Paratrichocladius Santos-Abreu (Diptera: Chironomidae), separation in any life stage from the cosmopolitan, diverse Cricotopus Wulp has been problematic. Molecular analysis reveals the presence of two species in Australia that conform in morphology to Paratrichocladius and which form a well-supported clade including Paratrichocladius micans (Kieffer) from Africa and a distinct southern African larva. This clade clusters with taxa allied with Cricotopus albitibia (Walker), in turn nested within all other sampled Australian Cricotopus. Relevant nodes strongly support Cricotopus as nonmonophyletic without inclusion of Paratrichocladius. We synonymize Paratrichocladius with Cricotopus syn.n, treating Paratrichocladius as a subgenus. Cricotopus (Paratrichocladius) australiensis Cranston sp.n. is described for Trichocladius pluriserialis Freeman from Australia, which is not the same species under that name in New Zealand. Cricotopus (Paratrichocladius) bifenestrus Cranston sp.n. from Australia is described, also in all life stages. The many new combinations, listed in an Appendix, include three replacement names for new secondary homonyms, namely: Cricotopus (Paratrichocladius) sinobicinctus Cranston & Krosch nom.n. for Paratrichocladius bicinctus Fu, Sæther & Wang, Cricotopus draysoni Cranston & Krosch nom.n. for Cricotopus brevicornis Drayson, Krosch & Cranston, and Cricotopus (Paratrichocladius) sikhotealinus Makarchenko & Makarchenko nom.n. for Cricotopus orientalis Kieffer. We conclude with comments on wider issues in the taxonomy of Paratrichocladius, especially concerning New Zealand species.

End-of-life care pathways for improving outcomes in caring for the dying

This is an updated version of a Cochrane review published in Issue 11, 2013 in the Cochrane Library. In many clinical areas, integrated care pathways are utilised as structured multidisciplinary care plans that detail essential steps in caring for patients with specific clinical problems. In particular, care pathways for the dying have been developed as a model to improve care of patients who are in the last days of life. The care pathways were designed with an aim of ensuring that the most appropriate management occurs at the most appropriate time, and that it is provided by the most appropriate health professional. Since the last update, there have been sustained concerns about the safety of implementing end-of-life care pathways, particularly in the United Kingdom (UK). Therefore, there is a significant need for clinicians and policy makers to be informed about the effects of end-of-life care pathways via a systematic review.

Computational Methods for Locating and Analyzing Conserved Gene Regulatory DNA Elements

This thesis presents methods for locating and analyzing cis-regulatory DNA elements involved with the regulation of gene expression in multicellular organisms. The regulation of gene expression is carried out by the combined effort of several transcription factor proteins collectively binding the DNA on the cis-regulatory elements. Only sparse knowledge of the 'genetic code' of these elements exists today. An automatic tool for discovery of putative cis-regulatory elements could help their experimental analysis, which would result in a more detailed view of the cis-regulatory element structure and function. We have developed a computational model for the evolutionary conservation of cis-regulatory elements. The elements are modeled as evolutionarily conserved clusters of sequence-specific transcription factor binding sites. We give an efficient dynamic programming algorithm that locates the putative cis-regulatory elements and scores them according to the conservation model. A notable proportion of the high-scoring DNA sequences show transcriptional enhancer activity in transgenic mouse embryos. The conservation model includes four parameters whose optimal values are estimated with simulated annealing. With good parameter values the model discriminates well between the DNA sequences with evolutionarily conserved cis-regulatory elements and the DNA sequences that have evolved neutrally. In further inquiry, the set of highest scoring putative cis-regulatory elements were found to be sensitive to small variations in the parameter values. The statistical significance of the putative cis-regulatory elements is estimated with the Two Component Extreme Value Distribution. The p-values grade the conservation of the cis-regulatory elements above the neutral expectation. The parameter values for the distribution are estimated by simulating the neutral DNA evolution. The conservation of the transcription factor binding sites can be used in the upstream analysis of regulatory interactions. This approach may provide mechanistic insight to the transcription level data from, e.g., microarray experiments. Here we give a method to predict shared transcriptional regulators for a set of co-expressed genes. The EEL (Enhancer Element Locator) software implements the method for locating putative cis-regulatory elements. The software facilitates both interactive use and distributed batch processing. We have used it to analyze the non-coding regions around all human genes with respect to the orthologous regions in various other species including mouse. The data from these genome-wide analyzes is stored in a relational database which is used in the publicly available web services for upstream analysis and visualization of the putative cis-regulatory elements in the human genome.

Macromolecular synthesis in mycobacteriophage I3 infected cells

DNA-, RNA- and protein synthesis have been studied inMycobacterium smegmatis cells infected with phage 13. The macromolecular synthesis continued until the end of latent period. Early RNA and protein synthesis were necessary prior to the commencement of DNA replication. The infecting phage DNA sedimented as larger than unit length of genome, after initiation of DNA synthesis. Although the host DNA was not degraded, 90 percent of the RNA synthesized after phage infection hybridized to phage DNA.