Influence of historical landscapes, drainage evolution and ecological traits on patterns of genetic diversity in Southeast Asian freshwater snakehead fishes

Snakehead fishes in the family Channidae are obligate freshwater fishes represented by two extant genera, the African Parachannna and the Asian Channa. These species prefer still or slow flowing water bodies, where they are top predators that exercise high levels of parental care, have the ability to breathe air, can tolerate poor water quality, and interestingly, can aestivate or traverse terrestrial habitat in response to seasonal changes in freshwater habitat availability. These attributes suggest that snakehead fishes may possess high dispersal potential, irrespective of the terrestrial barriers that would otherwise constrain the distribution of most freshwater fishes. A number of biogeographical hypotheses have been developed to account for the modern distributions of snakehead fishes across two continents, including ancient vicariance during Gondwanan break-up, or recent colonisation tracking the formation of suitable climatic conditions. Taxonomic uncertainty also surrounds some members of the Channa genus, as geographical distributions for some taxa across southern and Southeast (SE) Asia are very large, and in one case is highly disjunct. The current study adopted a molecular genetics approach to gain an understanding of the evolution of this group of fishes, and in particular how the phylogeography of two Asian species may have been influenced by contemporary versus historical levels of dispersal and vicariance. First, a molecular phylogeny was constructed based on multiple DNA loci and calibrated with fossil evidence to provide a dated chronology of divergence events among extant species, and also within species with widespread geographical distributions. The data provide strong evidence that trans-continental distribution of the Channidae arose as a result of dispersal out of Asia and into Africa in the mid–Eocene. Among Asian Channa, deep divergence among lineages indicates that the Oligocene-Miocene boundary was a time of significant species radiation, potentially associated with historical changes in climate and drainage geomorphology. Mid-Miocene divergence among lineages suggests that a taxonomic revision is warranted for two taxa. Deep intra-specific divergence (~8Mya) was also detected between C. striata lineages that occur sympatrically in the Mekong River Basin. The study then examined the phylogeography and population structure of two major taxa, Channa striata (the chevron snakehead) and the C. micropeltes (the giant snakehead), across SE Asia. Species specific microsatellite loci were developed and used in addition to a mitochondrial DNA marker (Cyt b) to screen neutral genetic variation within and among wild populations. C. striata individuals were sampled across SE Asia (n=988), with the major focus being the Mekong Basin, which is the largest drainage basin in the region. The distributions of two divergent lineages were identified and admixture analysis showed that where they co-occur they are interbreeding, indicating that after long periods of evolution in isolation, divergence has not resulted in reproductive isolation. One lineage is predominantly confined to upland areas of northern Lao PDR to the north of the Khorat Plateau, while the other, which is more closely related to individuals from southern India, has a widespread distribution across mainland SE Asian and Sumatra. The phylogeographical pattern recovered is associated with past river networks, and high diversity and divergence among all populations sampled reveal that contemporary dispersal is very low for this taxon, even where populations occur in contiguous freshwater habitats. C. micropeltes (n=280) were also sampled from across the Mekong River Basin, focusing on the lower basin where it constitutes an important wild fishery resource. In comparison with C. striata, allelic diversity and genetic divergence among populations were extremely low, suggesting very recent colonisation of the greater Mekong region. Populations were significantly structured into at least three discrete populations in the lower Mekong. Results of this study have implications for establishing effective conservation plans for managing both species, that represent economically important wild fishery resources for the region. For C. micropeltes, it is likely that a single fisheries stock in the Tonle Sap Great Lake is being exploited by multiple fisheries operations, and future management initiatives for this species in this region will need to account for this. For C. striata, conservation of natural levels of genetic variation will require management initiatives designed to promote population persistence at very localised spatial scales, as the high level of population structuring uncovered for this species indicates that significant unique diversity is present at this fine spatial scale.

Numerical investigation of aerosol particle transport and deposition in realistic lung airway

Different human activities like combustion of fossil fuels, biomass burning, industrial and agricultural activities, emit a large amount of particulates into the atmosphere. As a consequence, the air we inhale contains significant amount of suspended particles, including organic and inorganic solids and liquids, as well as various microorganism, which are solely responsible for a number of pulmonary diseases. Developing a numerical model for transport and deposition of foreign particles in realistic lung geometry is very challenging due to the complex geometrical structure of the human lung. In this study, we have numerically investigated the airborne particle transport and its deposition in human lung surface. In order to obtain the appropriate results of particle transport and deposition in human lung, we have generated realistic lung geometry from the CT scan obtained from a local hospital. For a more accurate approach, we have also created a mucus layer inside the geometry, adjacent to the lung surface and added all apposite mucus layer properties to the wall surface. The Lagrangian particle tracking technique is employed by using ANSYS FLUENT solver to simulate the steady-state inspiratory flow. Various injection techniques have been introduced to release the foreign particles through the inlet of the geometry. In order to investigate the effects of particle size on deposition, numerical calculations are carried out for different sizes of particles ranging from 1 micron to 10 micron. The numerical results show that particle deposition pattern is completely dependent on its initial position and in case of realistic geometry; most of the particles are deposited on the rough wall surface of the lung geometry instead of carinal region.

3D lung and rib cage reconstruction using low dose CT scans of adolescent idiopathic scoliosis pre and post anterior thoracoscopic correction

Adolescent Idiopathic Scoliosis (AIS) has been associated with reduced pulmonary function believed to be due to a restriction of lung volume by the deformed thoracic cavity. A recent study by our group examined the changes in lung volume pre and post anterior thoracoscopic scoliosis correction using pulmonary function testing (1), however the anatomical changes in ribcage shape and left/right lung volume after thoracoscopic surgery which govern overall respiratory capacity are unknown. The aim of this study was to use 3D rendering from CT scan data to compare lung and ribcage anatomical changes from pre to two years post thoracoscopic anterior scoliosis correction. The study concluded that 3D volumetric reconstruction from CT scans is a powerful means of evaluating changes in pulmonary and thoracic anatomy following surgical AIS correction. Most likely, lung volume changes following thoracoscopic scoliosis correction are multifactorial and affected by changes in height (due to residual growth), ribcage shape, diaphragm positioning, Cobb angle correction in the thoracic spine. Further analysis of the 3D reconstructions will be performed to assess how each of these factors affect lung volume in this patient cohort.

Image acquisition and manipulation protocols for CT-PET fusion to improve the accuracy of gross tumour volume localisation for 3D conformal radiotherapy for lung cancer

Aims: To develop clinical protocols for acquiring PET images, performing CT-PET registration and tumour volume definition based on the PET image data, for radiotherapy for lung cancer patients and then to test these protocols with respect to levels of accuracy and reproducibility. Method: A phantom-based quality assurance study of the processes associated with using registered CT and PET scans for tumour volume definition was conducted to: (1) investigate image acquisition and manipulation techniques for registering and contouring CT and PET images in a radiotherapy treatment planning system, and (2) determine technology-based errors in the registration and contouring processes. The outcomes of the phantom image based quality assurance study were used to determine clinical protocols. Protocols were developed for (1) acquiring patient PET image data for incorporation into the 3DCRT process, particularly for ensuring that the patient is positioned in their treatment position; (2) CT-PET image registration techniques and (3) GTV definition using the PET image data. The developed clinical protocols were tested using retrospective clinical trials to assess levels of inter-user variability which may be attributed to the use of these protocols. A Siemens Somatom Open Sensation 20 slice CT scanner and a Philips Allegro stand-alone PET scanner were used to acquire the images for this research. The Philips Pinnacle3 treatment planning system was used to perform the image registration and contouring of the CT and PET images. Results: Both the attenuation-corrected and transmission images obtained from standard whole-body PET staging clinical scanning protocols were acquired and imported into the treatment planning system for the phantom-based quality assurance study. Protocols for manipulating the PET images in the treatment planning system, particularly for quantifying uptake in volumes of interest and window levels for accurate geometric visualisation were determined. The automatic registration algorithms were found to have sub-voxel levels of accuracy, with transmission scan-based CT-PET registration more accurate than emission scan-based registration of the phantom images. Respiration induced image artifacts were not found to influence registration accuracy while inadequate pre-registration over-lap of the CT and PET images was found to result in large registration errors. A threshold value based on a percentage of the maximum uptake within a volume of interest was found to accurately contour the different features of the phantom despite the lower spatial resolution of the PET images. Appropriate selection of the threshold value is dependant on target-to-background ratios and the presence of respiratory motion. The results from the phantom-based study were used to design, implement and test clinical CT-PET fusion protocols. The patient PET image acquisition protocols enabled patients to be successfully identified and positioned in their radiotherapy treatment position during the acquisition of their whole-body PET staging scan. While automatic registration techniques were found to reduce inter-user variation compared to manual techniques, there was no significant difference in the registration outcomes for transmission or emission scan-based registration of the patient images, using the protocol. Tumour volumes contoured on registered patient CT-PET images using the tested threshold values and viewing windows determined from the phantom study, demonstrated less inter-user variation for the primary tumour volume contours than those contoured using only the patient’s planning CT scans. Conclusions: The developed clinical protocols allow a patient’s whole-body PET staging scan to be incorporated, manipulated and quantified in the treatment planning process to improve the accuracy of gross tumour volume localisation in 3D conformal radiotherapy for lung cancer. Image registration protocols which factor in potential software-based errors combined with adequate user training are recommended to increase the accuracy and reproducibility of registration outcomes. A semi-automated adaptive threshold contouring technique incorporating a PET windowing protocol, accurately defines the geometric edge of a tumour volume using PET image data from a stand alone PET scanner, including 4D target volumes.

Ureaplasma colonization of amniotic fluid and efficacy of antenatal corticosteroids for preterm lung maturation in sheep

Objective: To assess the efficacy of maternal betamethasone for improving preterm lung function, in the presence of inflammation induced by amniotic fluid ureaplasma colonization. ----- ----- Study design: Ewes bearing single fetuses were randomized to receive an intra-amniotic injection of Ureaplasma parvum (serovar 6; 2×107 colony forming units) or vehicle at 86±2 days of pregnancy (mean±SD: term is 150d), followed by maternal intramuscular betamethasone (0.5mg/kg) or saline, either 2 or 7 days before delivery of lambs at 123±1d. ----- ----- Results: Amniotic fluid IL-8 was elevated by ureaplasmas (p=0.049) but unaffected by betamethasone. Lung inflammation induced by ureaplasmas was not affected by betamethasone. Lung compliance was increased by ureaplasma colonization (p=0.009) and betamethasone (p=0.042), and effects were additive. Lung surfactant was increased by ureaplasma colonization (p<0.001) and betamethasone 7 days (p=0.001), but not 2 days, before delivery. ----- ----- Conclusion: Inflammation improves preterm lung function due to increases in surfactant. Antenatal corticosteroids further augment lung function, through an apparently independent mechanism.

The effect of endotracheal suction on regional tidal ventilation and end-expiratory lung volume

Purpose: To examine the impact of different endotracheal tube (ETT) suction techniques on regional end-expiratory lung volume (EELV) and tidal volume (VT) in an animal model of surfactant-deficient lung injury. Methods: Six 2-week old piglets were intubated (4.0 mm ETT), muscle-relaxed and ventilated, and lung injury was induced with repeated saline lavage. In each animal, open suction (OS) and two methods of closed suction (CS) were performed in random order using both 5 and 8 French gauge (FG) catheters. The pre-suction volume state of the lung was standardised on the inflation limb of the pressure-volume relationship. Regional EELV and VT expressed as a proportion of the impedance change at vital capacity (%ZVCroi) within the anterior and posterior halves of the chest were measured during and for 60 s after suction using electrical impedance tomography. Results: During suction, 5 FG CS resulted in preservation of EELV in the anterior (nondependent) and posterior(dependent) lung compared to the other permutations, but these only reached significance in the anterior regions (p\0.001 repeated-measures ANOVA). VT within the anterior, but not posterior lung was significantly greater during 5FG CS compared to 8 FG CS; the mean difference was 15.1 [95% CI 5.1, 25.1]%ZVCroi. Neither catheter size nor suction technique influenced post-suction regional EELV or VT compared to pre-suction values (repeated-measures ANOVA). Conclusions: ETT suction causes transient loss of EELV and VT throughout the lung. Catheter size exerts a greater influence than suction method, with CS only protecting against derecruitment when a small catheter is used, especially in the non-dependent lung.

A Bayesian approach to assess interaction between known risk factors: The risk of lung cancer from exposure to asbestos and smoking

We review the literature on the combined effect of asbestos exposure and smoking on lung cancer, and explore a Bayesian approach to assess evidence of interaction. Previous approaches have focussed on separate tests for an additive or multiplicative relation. We extend these approaches by exploring the strength of evidence for either relation using approaches which allow the data to choose between both models. We then compare the different approaches.