Biologically relevant effects of mRNA amplification on gene expression profiles

Background  

Gene expression microarray technology permits the analysis of global gene expression profiles. The amount of sample needed limits the use of small excision biopsies and/or needle biopsies from human or animal tissues. Linear amplification techniques have been developed to increase the amount of sample derived cDNA. These amplified samples can be hybridised on microarrays. However, little information is available whether microarrays based on amplified and unamplified material yield comparable results.     

HeatMapper: powerful combined visualization of gene expression profile correlations, genotypes, phenotypes and sample characteristics

Background  

Accurate interpretation of data obtained by unsupervised analysis of large scale expression profiling studies is currently frequently performed by visually combining sample-gene heatmaps and sample characteristics. This method is not optimal for comparing individual samples or groups of samples. Here, we describe an approach to visually integrate the results of unsupervised and supervised cluster analysis using a correlation plot and additional sample metadata.     

The challenge for genetic epidemiologists: how to analyze large numbers of SNPs in relation to complex diseases

Background

Molecular genetic approaches have much to offer population biology. Despite recent advances, convenient techniques to develop and screen highly-resolving markers can be limiting for some applications and taxa. We describe an improved PCR-based, cloning-free, nuclear marker development procedure, in which single-stranded conformation polymorphism (SSCP) plays a central role. Sequence-variable alleles at putative nuclear loci are simultaneously identified and isolated from diploid tissues. Based on a multiple allele alignment, locus-specific primers are designed in conserved regions, minimizing 'null' alleles. Using two undescribed endemic Australian Collembola as exemplars, we outline a comprehensive approach to generating and validating suites of codominant, sequence-yielding nuclear loci for previously unstudied invertebrates.

Results

Six markers per species were developed without any baseline genetic information. After evaluating the characteristics of each new locus via SSCP pre-screening, population samples were genotyped on the basis of either DNA sequence, restriction site, or insertion/deletion variation, depending on which assay was deemed most appropriate. Polymorphism was generally high (mean of nine alleles per locus), and the markers were capable of resolving population structuring over very fine spatial scales (<100 km). SSCP coupled with targeted DNA sequencing was used to obtain genotypic, genic and genealogical information from six loci (three per species). Phylogeographic analysis identified introns as being most informative.

Conclusion

The comprehensive approach presented here feasibly overcomes technical hurdles of (i) developing suitably polymorphic nuclear loci for non-model organisms, (ii) physically isolating nuclear allele haplotypes from diploid tissues without cloning, and (iii) genotyping population samples on the basis of nuclear DNA sequence variation.     

Do distribution volumes and clearances relate to tissue volumes and blood flows? A computer simulation

Background

Thoracotomy is associated with severe pain that may persist for years. Acupuncture is a complementary therapy with a proven role in pain control. A randomized trial showed that acupuncture was effective in controlling pain after abdominal surgery, but the efficacy of this technique for the treatment of thoracotomy pain has not been established. We developed a novel technique for convenient application of acupuncture to patients undergoing thoracotomy, and in a Phase II trial evaluated the safety of this intervention and the feasibility of doing a randomized trial.

Methods

Adult patients scheduled for unilateral thoracotomy with preoperative epidural catheter placement received acupuncture immediately prior to surgery. Eighteen semi-permanent intradermal needles were inserted on either side of the spine, and four were inserted in the legs and auricles. Needles were removed after four weeks. Using a numerical rating scale, pain was measured on the first five postoperative days. After discharge, pain was assessed using the Brief Pain Inventory at 7, 30, 60 and 90 days.

Results

Thirty-six patients were treated with acupuncture. Of these, 25, 23, and 22 patients provided data at 30, 60, and 90 days, respectively. The intervention was well tolerated by patients with only one minor and transient adverse event of skin ulceration.

Conclusion

The rate of data completion met our predefined criterion for determining a randomized trial to be feasible (at least 75% of patients tolerated the intervention and provided evaluable data). This novel intervention is acceptable to patients undergoing thoracotomy and does not interfere with standard preoperative care. There was no evidence of important adverse events. We are now testing the hypothesis that acupuncture significantly adds to standard perioperative pain management in a randomized trial.     

Circadian rhythm of glycoprotein secretion in the vas deferens of the moth, Spodoptera littoralis

Background  

Reproductive systems of male moths contain circadian clocks, which time the release of sperm bundles from the testis to the upper vas deferens (UVD) and their subsequent transfer from the UVD to the seminal vesicles. Sperm bundles are released from the testis in the evening and are retained in the vas deferens lumen overnight before being transferred to the seminal vesicles. The biological significance of periodic sperm retention in the UVD lumen is not understood. In this study we asked whether there are circadian rhythms in the UVD that are correlated with sperm retention.     

Evolution of extreme ontogenetic allometric diversity and heterochrony in pythons,a clade of giant and dwarf snakes

Ontogenetic allometry, how species change with size through their lives, and heterochony, a decoupling between shape, size, and age, are major contributors to biological diversity. However, macroevolutionary allometric and heterochronic trends remain poorly understood because previous studies have focused on small groups of closely related species. Here, we focus on testing hypotheses about the evolution of allometry and how allometry and heterochrony drive morphological diversification at the level of an entire species‐rich and diverse clade. Pythons are a useful system due to their remarkably diverse and well‐adapted phenotypes and extreme size disparity. We collected detailed phenotype data on 40 of the 44 species of python from 1191 specimens. We used a suite of analyses to test for shifts in allometric trajectories that modify morphological diversity. Heterochrony is the main driver of initial divergence within python clades, and shifts in the slopes of allometric trajectories make exploration of novel phenotypes possible later in divergence history. We found that allometric coefficients are highly evolvable and there is an association between ontogenetic allometry and ecology, suggesting that allometry is both labile and adaptive rather than a constraint on possible phenotypes.     

Modelling the longitudinal distribution,abundance, and habitat use of the giant freshwater shrimp (Macrobrachium spinipes) in a large intermittent,tropical Australian river to inform water resource policy

1. Water development threatens rivers and their biodiversity. Amphidromous shrimp are particularly vulnerable as they require migration between freshwater and estuaries to complete their life cycle. The Fitzroy River is a large tropical intermittent river undergoing water development that is home to the amphidromous shrimp Macrobrachium spinipes (cherabin), yet little is known about its habitat use and flow-ecology making it difficult to inform sustainable water-take.
2. We investigated habitat associations, distributional patterns suggestive of amphidromy, and the influence of water availability by sampling main channel and floodplain pools along a 350-km river length during 2 contrasting flow years. Applying a size-specific abundance model, we estimated abundance per size class, site, and year. We then predicted abundance at the landscape scale with remotely sensed water to reveal the impact of water availability on the meta-population.
3. Our model revealed that juveniles were in greatest abundance in downstream main channel pools, whereas adults were in greatest abundance in upstream floodplain pools. Abundance varied by year with lower numbers predicted in the low-flow year. Longitudinal and habitat patterns remained when our pool-level results were scaled to the landscape, and the positive relationship of abundance to wet-season flow was strengthened. The predominance of smaller cherabin in the lower reaches of the river provides indirect support for an estuarine nursery and amphidromous life history; however, small individuals observed in landlocked pools, during late dry season suggests possible within-river recruitment.
4. The importance of water development policies that protect wet-season flow and passage along the Fitzroy River is supported by this work. These types of policies are likely to be important for this and other amphidromous shrimp species across Australia, Southeast Asia and further afield. Further research detailing the species life history and describing flow–recruitment relationships will be important contributions to understanding this important taxonomic group and refining policies for current and future water resource development.

     

Structure of the β-orcinol depsidones,connorstictic and consalazinic acids

The structures of connorstictic acid from Pertusaria pseudocorallina and consalazinic acid from Parmotrema subisidiosum were determined.     

New β-orcinol depsidones from Xanthoparmelia quintaria and a Thelotrema species

A new depsidone isolated from a new species of Thelotrema was identified as hyopstictic acid. Xanthoparmelia quintaria contains hypostictic and hyposalazinic acids.