High Levels of Genetic Diversity within Nilo-Saharan Populations: Implications for Human Adaptation

Africa contains more human genetic variation than any other continent, but the majority of the population-scale analyses of the African peoples have focused on just two of the four major linguistic groups, the Niger-Congo and Afro-Asiatic, leaving the Nilo-Saharan and Khoisan populations under-represented. In order to assess genetic variation and signatures of selection within a Nilo-Saharan population and between the Nilo-Saharan and Niger-Congo and Afro-Asiatic, we sequenced 50 genomes from the Nilo-Saharan Lugbara population of North-West Uganda and 250 genomes from 6 previously unsequenced Niger-Congo populations. We compared these data to data from a further 16 Eurasian and African populations including the Gumuz, another putative Nilo-Saharan population from Ethiopia. Of the 21 million variants identified in the Nilo-Saharan population, 3.57 million (17%) were not represented in dbSNP and included predicted non-synonymous mutations with possible phenotypic effects. We found greater genetic differentiation between the Nilo-Saharan Lugbara and Gumuz populations than between any two Afro-Asiatic or Niger-Congo populations. F3 tests showed that Gumuz contributed a genetic component to most Niger-Congo B populations whereas Lugabara did not. We scanned the genomes of the Lugbara for evidence of selective sweeps. We found selective sweeps at four loci (SLC24A5, SNX13, TYRP1, and UVRAG) associated with skin pigmentation, three of which already have been reported to be under selection. These selective sweeps point toward adaptations to the intense UV radiation of the Sahel.

Stathmin and EGFR correlates to HPV status and clinical outcome in sinonasal inverted papilloma

BACKGROUND

Inverted papilloma (IP) is a locally destructive benign tumour of the sinonasal mucosa with a tendency for malignant transformation. Stathmin and epidermal growth factor receptor (EGFR) are important markers in cancer prognosis. Here we investigate if expression of stathmin and EGFR correlate to dysplasia, recurrence and HPV in IP.

METHODS

98 patients with IP diagnosed 2000-2010 were analyzed for stathmin and EGFR by immunohistochemistry (IHC) and HPV by polymerase chain reaction assay (PCR).

RESULTS

All IPs expressed stathmin while its expression was absent or weak in normal mucosa. Dysplasia was present in 26,7% of IPs with high stathmin expression while only 7.4% of IPs with low stathmin expression showed dysplasia. Stathmin positive IPs showed a trend towards earlier recurrences. 57.1% of IP expressed EGFR but no significant association was seen between EGFR-positivity and recurrence or dysplasia. EGFR was expressed by 91.7% of the HPV-positive IPs compared to 52,3% of the HPV negative IPs.

CONCLUSIONS

EGFR expression is significantly higher in HPV positive IP. Stathmin is expressed by all IP tumour cells. Stathmin was also associated with dysplasia and a trend towards a correlation between stathmin positivity and recurrence was found. Stathmin and EGFR might therefore be considered therapeutic targets.

Convergence in disability policies in the welfare states Denmark, Sweden, the UK and Australia?

Background

A state’s relation to citizens who are not able to support themselves due to illness is one of the cornerstones of welfare states. However, rising numbers of people on disability benefits is a challenge in many welfare states. The first aim is to investigate how policies around eligibility to disability benefits articulate a concept of ’incapacity to work’ across social democratic (Denmark and Sweden) and liberal welfare states (Australia and the UK). Secondly, we wish to explore how the conceptualisation of capacity and incapacity to work shapes prevailing constructions of disability.

Methods

In this study, we analyse official policy documents from governments, legislation, scientific and grey literature on disability benefit reforms in the selected countries. The analytical framework introduces the notion of decommodification of labour for people with disability and the ’social model of disability’ in relation to the constructions of disability in current disability benefit reforms.

Results (preliminary)

Restricting access to disability benefits has been a key feature of the recent reforms across all different types of welfare states. Liberal welfare states are more pervasive in reassessment of previously granted benefits compared to social democratic welfare states. The construction of disability in recent reforms is at odds with the social model of disability.

Conclusions (preliminary)

Across both liberal and social democratic welfare states eligibility for disability benefits is articulated around notions of incapacity to work. Retrenchment of benefits is, overall, most pervasive in liberal welfare states.

Key messages

The convergence in social policies across both social democratic and liberal welfare states speaks to the pervasiveness of neo-liberal notions in current social policy. The tightening of eligibility criteria for disability benefits poses great financial and health risks to people with illness struggling to support themselves.

Physiotherapy for cystic fibrosis in Australia and New Zealand: A clinical practice guideline

Physiotherapy management is a key element of care for people with cystic fibrosis (CF) throughout the lifespan. Although considerable evidence exists to support physiotherapy management of CF, there is documented variation in practice. The aim of this guideline is to optimize the physiotherapy management of people with CF in Australia and New Zealand. A systematic review of the literature in key areas of physiotherapy practice for CF was undertaken. Recommendations were formulated based on National Health and Medical Research Council (Australia) guidelines and considered the quality, quantity and level of the evidence; the consistency of the body of evidence; the likely clinical impact; and applicability to physiotherapy practice in Australia and New Zealand. A total of 30 recommendations were made for airway clearance therapy, inhalation therapy, exercise assessment and training, musculoskeletal management, management of urinary incontinence, managing the newly diagnosed patient with CF, delivery of non-invasive ventilation, and physiotherapy management before and after lung transplantation. These recommendations can be used to underpin the provision of evidence-based physiotherapy care to people with CF in Australia and New Zealand.

Identification of Anisakis species (Nematoda: Anisakidae) in marine fish hosts from Papua New Guinea

The third-stage larvae of several genera of anisakid nematodes are important etiological agents for zoonotic human anisakiasis. The present study investigated the prevalence of potentially zoonotic anisakid larvae in fish collected on the coastal shelves off Madang and Rabaul in Papua New Guinea (PNG) where fish represents a major component of the diet. Nematodes were found in seven fish species including Decapterus macarellus, Gerres oblongus, Pinjalo lewisi, Pinjalo pinjalo, Selar crumenophthalmus, Scomberomorus maculatus and Thunnus albacares. They were identified by both light and scanning electron microscopy as Anisakis Type I larvae. Sequencing and phylogenetic analysis of the ribosomal internal transcribed spacer (ITS) and the mitochondrial cytochrome C oxidase subunit II (cox2) gene identified all nematodes as Anisakis typica. This study represents the first in-depth characterisation of Anisakis larvae from seven new fish hosts in PNG. The overall prevalence of larvae was low (7.6%) and no recognised zoonotic Anisakis species were identified, suggesting a very low threat of anisakiasis in PNG.

Aneurysm of the inferior vena cava: case report

Venous aneurysms are uncommon. Despite their infrequency, venous aneurysms can present with significant clinical complications such as thrombosis, pulmonary embolism, and death. In this report, we present the case of a thrombosed inferior vena cava aneurysm discovered in a 16-year-old male who had deep vein thrombosis of the right lower extremity. Thrombosis of the inferior vena cava is uncommon in the pediatric population. Therefore, congenital abnormalities such as an inferior vena cava aneurysm should be considered when evaluating pediatric patients who present with deep vein thrombosis.

Scientific lessons from the first influenza pandemic of the 20th century

Re-analysis of the influenza pandemic of 1918 has given reassurance about a rather low reproductive number (R(o)), a prolonged herald wave of virus and that the skewed mortality towards the young adult could be a singularly unique event dependent upon previous infection history, perhaps not to be repeated in a future pandemic. Over 99% of those who contracted the virus survived, in spite of the absence of antivirals, vaccine and antibiotics for the secondary bacteria infections which probably accounted for one-third of the 50 million deaths. Therefore, in spite of a three-fold population increase since 1918 and 100 thousand plane journeys daily, judicious and careful planning together with a stockpile of antiviral drugs, oseltamivir, zanamivir and M2 blockers and a generic H5N1 vaccine, and application of hygiene would be expected to reduce mortality in a new pandemic, to figures significantly less than 1918.

A hypothesis: the conjunction of soldiers, gas, pigs, ducks, geese and horses in Northern France during the Great War provided the conditions for the emergence of the “Spanish” influenza pandemic of 1918–1919

The Great Influenza Pandemic of 1918-1919 was a cataclysmic outbreak of infection wherein over 50 million people died worldwide within 18 months. The question of the origin is important because most influenza surveillance at present is focussed on S.E. Asia. Two later pandemic viruses in 1957 and 1968 arose in this region. However we present evidence that early outbreaks of a new disease with rapid onset and spreadability, high mortality in young soldiers in the British base camp at Etaples in Northern France in the winter of 1917 is, at least to date, the most likely focus of origin of the pandemic. Pathologists working at Etaples and Aldershot barracks later agreed that these early outbreaks in army camps were the same disease as the infection wave of influenza in 1918. The Etaples camp had the necessary mixture of factors for emergence of pandemic influenza including overcrowding (with 100,000 soldiers daily changing), live pigs, and nearby live geese, duck and chicken markets, horses and an additional factor 24 gases (some of them mutagenic) used in large 100 ton quantities to contaminate soldiers and the landscape. The final trigger for the ensuing pandemic was the return of millions of soldiers to their homelands around the entire world in the autumn of 1918.

The Structure and Receptor Binding Properties of the 1918 Influenza Hemagglutinin

The 1918 influenza pandemic resulted in about 20 million deaths. This enormous impact, coupled with renewed interest in emerging infections, makes characterization of the virus involved a priority. Receptor binding, the initial event in virus infection, is a major determinant of virus transmissibility that, for influenza viruses, is mediated by the hemagglutinin (HA) membrane glycoprotein. We have determined the crystal structures of the HA from the 1918 virus and two closely related HAs in complex with receptor analogs. They explain how the 1918 HA, while retaining receptor binding site amino acids characteristic of an avian precursor HA, is able to bind human receptors and how, as a consequence, the virus was able to spread in the human population.

Cryptosporidium muris infection in bilbies (Macrotis lagotis)

Cryptosporidiosis is an enteric disease of animals and humans that can be fatal in immunocompromised individuals. There is no known effective treatment for cryptosporidiosis. Bilbies are threatened marsupials and are bred in captivity as part of a recovery program to re-introduce this species to the southwest of Western Australia. Cryptosporidium muris infection was detected in the faeces of bilbies at a captive breeding colony. Stress associated with a high density of bilbies in enclosures may have predisposed some of the bilbies to infection with C. muris. C. muris has been described in mice and was found in the faeces of one mouse trapped in the breeding enclosures. It is likely the bilbies acquired the infection from mice by faecal contamination of food and water. The infection cleared within 2 months from some bilbies, however others remained infected for 6 months and treatment was attempted with dimetridazole. Subsequently the parasite was no longer be detectable in the faeces.

Prevalence of obstructive lung diseases and respiratory symptoms in relation to living environment and socio-economic group

We wanted to test whether living environment, occupation and social position are risk factors for asthma and chronic bronchitis/emphysema (CBE). The prevalence of bronchial asthma, CBE, respiratory symptoms and smoking habits in a random sample of 12,071 adults aged 20-59 years was assessed in a postal survey with a slightly modified questionnaire previously used in central and northern Sweden (The OLIN studies). Occupation was coded according to a socio-economic classification system. Six different living environment areas were defined; city-countryside, seaside-not seaside and living close to heavy traffic-not living close to heavy traffic. Multiple logistic regression analysis (forward conditional) was applied to estimate the association between the proposed set of risk factors and self-reported obstructive lung diseases and lower respiratory symptoms controlling for age, gender and smoking. After two reminders, the response rate was 70.1% (n=8469); 33.8% of the responders were smokers. In all, 469 subjects (5.5%) stated that they had asthma and 4.6% reported CBE. Besides smoking, which was a risk for both asthma and CBE, there were different risk patterns for self-reported asthma and CBE. In the economically active population there was a tendency that CBE was more common among 'unskilled and semi-skilled workers'. This fact was further emphasized when the population was merged into the two groups 'low social position' and 'middle/high social position', with 'low social position' as a risk for CBE (OR=1.35, 95% CI=1.06-1.72). No social risk factors were identified for asthma. Living close to heavy traffic was a risk factor for asthma (OR=1.29, 95% CI=1.02-1.62) but not for CBE. Apart from this no living environmental risk factors for obstructive pulmonary diseases were identified. Asthma symptoms and long-standing cough were more common among those subjects living close to heavy traffic compared to those not living close to heavy traffic. To conclude, low social position was a risk factor for CBE and living close to heavy traffic was a risk factor for asthma.

Molecular and phylogenetic analysis of Cryptosporidium muris from various hosts

Isolates of Cryptosporidium muris and C. serpentis were characterized from different hosts using nucleotide sequence analysis of the rDNA 18S and ITS1 regions, and the heat-shock (HSP-70) gene. Phylogenetic analysis confirmed preliminary evidence that C. muris is not a uniform species. Two distinct genotypes were identified within C. muris; (1) C. muris genotype A; comprising bovine and camel isolates of C. muris from different geographical locations, and (2) C. muris genotype B comprising C. muris isolates from mice, a hamster, a rock hyrax and a camel from the same enclosure. These 2 genotypes may represent separate species but further biological and molecular studies are required for confirmation.

Cryptosporidium meleagridis in an Indian ring-necked parrot (Psittacula krameri)

OBJECTIVE

To perform a morphological and genetic characterisation of a Cryptosporidium infection in an Indian ring-necked parrot (Psittacula krameri) and to compare this with C meleagridis from a turkey.

DESIGN

Tissue and intestinal sections from an Indian ring-necked parrot were examined microscopically for Cryptosporidium. The organism was also purified from the crop and intestine, the DNA extracted and a portion of the 18S rDNA gene amplified, sequenced and compared with sequence and biological information obtained for C meleagridis from a turkey as well as sequence information for other species of Cryptosporidium.

RESULTS

Morphological examination of tissue sections from an Indian ring-necked parrot revealed large numbers of Cryptosporidium oocysts attached to the apical border of enterocytes lining the intestinal tract. Purified Cryptosporidium oocysts measured about 5.1 x 4.5 microns, which conformed morphologically to C meleagridis. The sequence obtained from this isolate was identical to sequence information obtained from a C meleagridis isolate from a turkey.

CONCLUSION

Cryptosporidium meleagridis was detected in an Indian ring-necked parrot using morphological and molecular methods. This is the first time that this species of Cryptosporidium has been reported in a non-galliform host and extends the known host range of C meleagridis.

Sequence and PCR-RFLP analysis of the internal transcribed spacers of the rDNA repeat unit in isolates of Cryptosporidium from different hosts

The Cryptosporidium ITS1, 5.8S and ITS2 rDNA regions from a number of Cryptosporidium isolates from different hosts and geographical areas were cloned and sequenced in order to investigate the extent of sequence heterogeneity between human and cattle-derived isolates from different geographical locations and also between isolates of Cryptosporidium from different hosts such as cats, pigs, mice and a koala. Calf-derived isolates from different continents were virtually identical as were human-derived isolates from the UK and Australia. Genetic differences between Cryptosporidium isolates were extensive and were in fact greater than the level of nucleotide divergence between Toxoplasma gondii and Neospora caninum rDNA sequences. Based on the sequence information derived from this study, PCR-RFLP of the ITS1 region was undertaken in order to directly amplify and genotype Cryptosporidium isolates from different hosts. This PCR-RFLP approach can now be used for molecular epidemiology studies, circumventing the need for costly sequencing and allowing a wider range of genetically different isolates to be examined.

Molecular and biological characterisation of Cryptosporidium in pigs

OBJECTIVE

Genetic and biological characterisation of 12 isolates of Cryptosporidium from pigs and comparing them with Cryptosporidium isolates from humans and cattle.

DESIGN

Cryptosporidium isolates from pigs were compared with those obtained from human and cattle using rDNA sequence analysis. The infectivity of two of the porcine isolates was determined in neonatal mice and the clinical history of the infected pigs recorded.

RESULTS

Pig-derived isolates of Cryptosporidium exhibited two distinct genotypes; a porcine genotype and a bovine genotype, which is common to cattle and other livestock. The porcine genotype did not produce any infection in neonatal mice whereas the bovine genotype did.

CONCLUSION

Two distinct genetically and biologically differing strains of Cryptosporidium appeared to be associated with acute diarrhoea in pigs. Whether Cryptosporidium was a primary or secondary pathogen is unclear but warrants further investigation. As the bovine genotype is known to infect humans, the results suggest that pigs can act as reservoirs of cryptosporidial infections for humans and other live-stock. The zoonotic potential of the pig-adapted genotype is uncertain and requires further study.

Molecular characterization of Cryptosporidium from various hosts

A 298 bp region of the Cryptosporidium parvum 18S rDNA and a 390 bp region of the acetyl-CoA synthetase gene were sequenced for a range of human and animal isolates of Cryptosporidium from different geographical areas. A distinct genotype is common to isolates from cattle, sheep and goats and also an alpaca from Peru and is referred to here as the 'calf'-derived Cryptosporidium genotype. Another genotype of 'human'-derived isolates also appears to be conserved amongst human isolates although humans are also susceptible to infection with the 'calf' Cryptosporidium genotype. Mice and pigs carry genetically distinct genotypes of Cryptosporidium. Three snake isolates were also analysed, 2 of which exhibited C. muris genotypes and the third snake isolate carried a distinct 'mouse' genotype.

Morphological and genetic characterisation of Cryptosporidium oocysts from domestic cats

Faecal samples were collected from domestic cats in the metropolitan area of the city of Perth, Western Australia, and screened for the presence of Cryptosporidium by both microscopy and PCR. Of 162 samples screened, two were positive for Cryptosporidium (a prevalence of 1.2%). Sample Ct33 was from an 18-month-old female and sample Ct131 from a 12-month-old female. Morphological studies revealed oocysts with an average size of 4.6 x 4.0 microm, smaller in size than isolates typically seen in humans (5.0 x 4.5 microm). Sequence analysis of PCR products showed sequences from cat isolates to be different to previously sequenced human and calf isolates, with cat isolates exhibiting 8.1% sequence divergence from these isolates. Phylogenetic analysis grouped the cat isolates into a distinct group, separate from other C. parvum isolates and Cryptosporidium species. These results lend support to the existence of a cat-adapted Cryptosporidium strain or species.

The relation between cognitive ability and psychological readiness of semi-skilled employees in the South African mining industry

Political change has, especially in the South African mining industry, created the need for the application of culturefair tests with the view of affirmative action. These tests are especially applied to measure cognitive ability, which is widely accepted to be positively correlated with work performance. The question arose whether cognitive tests are able to predict psychological readiness to perform as implicated by Hemstein and Murray's (1994) work on the "Bell Curve". In this study, no meaningful relation between cognitive ability and psychological readiness was found. This reflects some support for a multi-dimensional approach to the study of intelligence. Opsomming Politieke verandering het veral in die Suid-Afrikaanse mynbedryf, gelei tot 'n behoefte aan die toepassing van kultuurbillike toetse vir die doeleindes van regstellende aksie. Hierdie toetse word toegepas om kognitiewe vermoe te meet en daar word wyd aanvaar dat dit positief met werksprestasie korreleer. Die vraag het ontstaan of hierdie toetse daartoe in staat is om sielkundige gereedheid om te presteer, voorspel soos geimpliseer deur Hemstein en Murray (1994) se werk oor die "Bell Curve". In hierdie studie is geen betekenisvolle verband tussen kognitiewe vermoe en sielkundige gereedheid om te presteer, gevind nie. Daar word dus steun vir 'n multi-dimensionele benadering tot die bestudering van intelligensie, gevind.

X-ray surface dose measurements using TLD extrapolation

Surface dose measurements in therapeutic x-ray beams are of importance in determining the dose to the skin of patients undergoing radiotherapy. Measurements were performed in the 6-MV beam of a medical linear accelerator with LiF thermoluminescence dosimeters (TLD) using a solid water phantom. TLD chips (surface area 3.17 x 3.17 cm2) of three different thicknesses (0.230, 0.099, and 0.038 g/cm2) were used to extrapolate dose readings to an infinitesimally thin layer of LiF. This surface dose was measured for field sizes ranging from 1 x 1 cm2 to 40 x 40 cm2. The surface dose relative to maximum dose was found to be 10.0% for a field size of 5 x 5 cm2, 16.3% for 10 x 10 cm2, and 26.9% for 20 x 20 cm2. Using a 6-mm Perspex block tray in the beam increased the surface dose in these fields to 10.7%, 17.7%, and 34.2% respectively. Due to the small size of the TLD chips, TLD extrapolation is applicable also for intracavity and exit dose determinations. The technique used for in vivo dosimetry could provide clinicians information about the build up of dose up to 1-mm depth in addition to an extrapolated surface dose measurement.

The prognosis of tunnel preparations in treatment of class III furcations. A follow-up study

The present study evaluated the long-term prognosis of tunnel preparations performed in a large number of teeth with advanced periodontal furcation defects. One hundred seven (107) patients, in which 156 teeth had been treated by tunnel preparations, were recalled for an evaluation, which was based on a questionnaire, a clinical examination, and radiographs; 102 patients attended (149 teeth = 95%). The mean observation time per tooth was 37.5 months (range 10 to 107 months). The results showed that 10 teeth (6.7%) had been extracted and 7 teeth (4.7%) hemisected. The indication for 12 of these extractions or hemisections was root caries. Among the remaining 132 teeth, 23 (15.4%) showed initial or established caries. There was no relationship between caries development and length of the observation time. Thus, approximately 75% of the teeth were still caries-free and in function. The findings demonstrated that tunnel preparations have a considerably better prognosis than previously reported and should be considered a valid treatment alternative.

Virus specific antigens in mammalian cells infected with herpes simplex virus

Antisera to specific proteins in herpes simplex infected cells were produced by immunization of rabbits with infected rabbit kidney cells. These antisera were highly virus specific and produced up to twelve lines in immunodiffusion tests against infected cell extracts. Acrylamide electrophoresis and immunoelectrophoresis revealed up to ten virus specific proteins of varying size.