Sequence analysis of sub-genotype D hepatitis B surface antigens isolated from Jeddah,Saudi Arabia

Little is known about the prevalence of HBV genotypes/sub-genotypes in Jeddah province, although the hepatitis B virus (HBV) was identified as the most predominant type of hepatitis in Saudi Arabia. To characterize HBV genotypes/sub-genotypes, serum samples from 15 patients with chronic HBV were collected and subjected to HBsAg gene amplification and sequence analysis. Phylogenetic analysis of the HBsAg gene sequences revealed that 11 (48%) isolates belonged to HBV/D while 4 (18%) were associated with HBV/C. Notably, a HBV/D sub-genotype phylogenetic tree identified that eight current isolates (72%) belonged to HBV/D1, whereas three isolates (28%) appeared to be more closely related to HBV/D5, although they formed a novel cluster supported by a branch with 99% bootstrap value. Isolates belonging to D1 were grouped in one branch and seemed to be more closely related to various strains isolated from different countries. For further determination of whether the three current isolates belonged to HBV/D5 or represented a novel sub-genotype, HBV/DA, whole HBV genome sequences would be required. In the present study, we verified that HBV/D1 is the most prevalent HBV sub-genotype in Jeddah, and identified novel variant mutations suggesting that an additional sub-genotype designated HBV/DA should be proposed. Overall, the results of the present HBsAg sequence analyses provide us with insights regarding the nucleotide differences between the present HBsAg/D isolates identified in the populace of Jeddah, Saudi Arabia and those previously isolated worldwide. Additional studies with large numbers of subjects in other areas might lead to the discovery of the specific HBV strain genotypes or even additional new sub-genotypes that are circulating in Saudi Arabia.     

Consequences of pH measurement errors

SUMMARY. 1. The pH range over which the effects of acidification on freshwater organisms become apparent may be quite narrow, in some cases less than half a pH unit. Therefore, accurate measurement is important, particularly in dilute surface waters near the biologically critical threshold of hydrogen ion activity.
2. A hypothetical example based on data from two species of fish illustrates the potential errors in predicting mean mortality when pH is measured by probes of varying accuracies, placing our results into an ecosystem management perspective. For a given error, there will be greater uncertainty in predicting mean mortality for species sensitive to increased hydrogen ion activity than for more tolerant species.
3. We review field pH measurement errors, and present unique laboratory (measurements at 1°C and under argon) and field comparisons of current instruments used for continuous, in situ pH monitoring, including the only instrument comparison in low conductivity waters during snow melt. Four operator or sampler-caused measurement errors and three electrode-caused pH measurement errors are illustrated with data from four common types of pH probes and meters.
4. Studies providing no confidence intervals for a set of pH measurements due to the lack of rigorous quality control and assurance procedures are of limited quantitative value to future investigators attempting to analyse temporal trends of surface water acidification. Management and policy decision attempts will remain seriously hampered until more interpretable results are routinely generated.     

Hydrologic versus geomorphic limitation on CPOM storage in stream ecosystems

1. Stream ecosystems are the products of interactions between hydrology, geomorphology and ecology, but examining all three components simultaneously is difficult and rarely attempted. Frequently, either geomorphology or hydrology is treated as invariable or static. 2. To examine the validity of treating either hydrology or geomorphology as static, we studied the individual and combined effects of hydrology and channel geomorphology on coarse particulate organic matter (CPOM) storage. Using data from an experimental leaf release in a hydrologically regulated stream we created a simple numerical model. This allowed us to quantify the relative influence of CPOM trapping and CPOM retention on total long‐term CPOM storage under variable regimes of flood frequency and geomorphic structure. 3. CPOM storage is a function of supply, flood frequency and the type and frequency of in‐stream structures. In‐stream structures perform two distinct functions, trapping and retention, whose relative importance in leaf storage changes with stream hydrology. Trapping is more important for CPOM storage in streams with few floods, while retention is more important in streams with frequent floods. Different structures (e.g. boulders, large wood, small wood) perform these functions at different efficiencies. We found that large wood trapped two to three times more leaves than the bank, but that the bank retained leaves two to three times more efficiently. 4. A modelled channel with five times the amount of large wood as the study channel (a ‘wood restoration’) initially stored 14% more leaves than the modelled ‘natural’ channel. After six floods, however, the modelled wood restoration channel stored 50% less CPOM than the natural channel as the large wood had high trapping but poor retention. The modelled natural channel contained structures that could both trap and retain. Thus, as different structures performed different functions, the structural complexity buffered the stream allochthonous energy base against changes in hydrology through its balance of trapping and retention. 5. As the frequency of floods increased, the spatial distribution of CPOM became increasingly patchy as storage was driven entirely by structures with high retention. Thus, the coupling of flood frequency and geomorphic structure influenced CPOM availability, which in turn has ramifications for the entire stream food web.     

A multiplex set of microsatellite markers for the scarlet rosefinch (Carpodacus erythrinus)

Cardueline finches have become important models in studies of sexual selection and evolution of carotenoid‐based ornamentation. Here, we describe eight new polymorphic microsatellites isolated from the Scarlet rosefinch (Carpodacus erythrinus) and four from the House finch (Carpodacus mexicanus). Together with the cross‐species amplification of additional loci, originally published for two species of songbirds, we optimized a multiplex panel for C. erythrinus allowing genotyping of 22 polymorphic loci. Number of alleles and heterozygosity per locus in a sample of 34 individuals ranged from three to 38 and from 0.27 to 0.94, respectively.     

Very-broad-scale assessment of human impacts on river condition

1. Management of whole rivers and river catchments requires a comprehensive set of information about river condition and use, both existing and historical, and the links between them at regional, state or national scales. This paper outlines a new approach to the assessment of river condition, using a small team was able to assess 210 000 km of rivers across more than 3 million km² of Australia in little more than a year. 2. The approach was driven by a hierarchical model of river function, which assumed that broad‐scale catchment characteristics affect local hydrology, habitat features, water quality and, ultimately, aquatic biota. The model provided the basis for selecting important ecologically relevant features that indices should represent. For each reach of each river we derived a biological index and an environmental index based on measures quantifying catchment and hydrological condition, and habitat and water quality condition. Data came from existing state and national databases, satellite images, site measurements and process models. 3. All indices were calculated as deviation from a reference condition, were range‐standardised and were divided into equivalent bands of condition. Amalgamation of index components and of sub‐indices was determined by consideration of their ecological effects; for example, general degradation might be additive, but toxic effects of one component would override all others. 4. Several internal and external validation methods were employed, with the all‐important validation of the final assessments undertaken by comparison with a similar index based on locally measured data. 5. The environmental assessment classified 14% of reaches as largely unmodified, 67% as moderately modified and 19% as substantially modified by human impacts. The biological assessment based on site assessments and modelled data using invertebrates indicated that 70% of reaches were equivalent to reference condition and that 30% were significantly impaired. Catchment disturbance, elevated sediment and nutrient loads, and habitat degradation all contributed to these results. These impacts have all occurred during the last 200 years (post‐European settlement). 6. Partly as a result of the assessments of this study the Australian Government has begun to adopt a more environmentally sustainable approach to broad‐scale water management.     

Male-limited evolution suggests no extant intralocus sexual conflict over the sexually dimorphic cuticular hydrocarbons of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis>

Sexually dimorphic traits are likely to have evolved through sexually antagonistic selection. However, recent empirical data suggest that intralocus sexual conflict often persists, even when traits have diverged between males and females. This implies that evolved dimorphism is often incomplete in resolving intralocus conflict, providing a mechanism for the maintenance of genetic variance in fitness-related traits. We used experimental evolution in Drosophila melanogaster to directly test for ongoing conflict over a suite of sexually dimorphic cuticular hydrocarbons (CHCs) that are likely targets of sex-specific selection. Using a set of experimental populations in which the transmission of genetic material had been restricted to males for 82 generations, we show that CHCs did not evolve, providing experimental evidence for the absence of current intralocus sexual conflict over these traits. The absence of ongoing conflict could indicate that CHCs have never been the target of sexually antagonistic selection, although this would require the existing dimorphism to have evolved via completely sexlinked mutations or as a result of former, but now absent, pleiotropic effects of the underlying loci on another trait under sexually antagonistic selection. An alternative interpretation, and which we believe to be more likely, is that the extensive CHC sexual dimorphism is the result of past intralocus sexual conflict that has been fully resolved, implying that these traits have evolved genetic independence between the sexes and that genetic variation in them is therefore maintained by alternative mechanisms. This latter interpretation is consistent with the known roles of CHCs in sexual communication in this species and with previous studies suggesting the genetic independence of CHCs between males and females. Nevertheless, direct estimates of sexually antagonistic selection will be important to fully resolve these alternatives.     

First record of Stegomyia albopicta (= Aedes albopictus) in Morocco: a major threat to public health in North Africa?

The Asian tiger mosquito Stegomyia albopicta (= Aedes albopictus) (Diptera: Culicidae), native to Asian forests, is a nuisance mosquito and is responsible for the transmission of arboviruses of public health importance, such as dengue, chikungunya and Zika viruses. It has colonized parts of all continents, except Antarctica, over the past 30–40 years. However, to date, the only records of S. albopicta in North Africa refer to occasional collections in 2010 and 2014 in Algeria. In early September 2015, S. albopicta larvae and adults were collected in a district of Rabat, Morocco. Morphological identification was confirmed by molecular analysis. This is the first record of this invasive mosquito in Morocco. A national surveillance programme will be implemented in 2016 to establish its geographical distribution in Morocco and to instigate control measures to prevent the establishment of new populations and the transmission of arboviruses.     

Monitoring the persistence of Laccaria bicolor as an ectomycorrhizal symbiont of nursery-grown Douglas fir by PCR of the rDNA intergenic spacer

The large-scale inoculation of selected beneficial ectomycorrhizal fungi in forest nurseries has generated renewed interest in the ecology of these symbiotic fungi. However, information on the dissemination and persistence of introduced symbionts is scarce due to the limitation of the current identification methods. To identify ectomycorrhizal fungi on single root tips, we investigated the polymorphism of the PCR-amplified ribosomal DNA intergenic spacer (IGS) from a wide range of ectomycorrhizal fungi. To investigate the reliability of this molecular approach in large-scale surveys, the dissemination and persistence on Douglas fir seedlings of the introduced Laccaria bicolor S238N were assessed in a forest nursery in the Massif Central (France). Several hundred ectomycorrhizas and fruiting bodies were sampled from plots where control and L. bicolor inoculated-Douglas fir seedlings were grown for 1.5 years. PCR typing of mycorrhizas indicated that trees inoculated with L. bicolor S238N remained exclusively colonized by that isolate (or sexually derived isolates) for the entire test period. In contrast, control seedlings were infected by indigenous isolates of Laccaria laccata and Thelephora terrestris. The molecular evidence for the persistence of the introduced mycobiont despite the competition from indigenous isolates of the same species provides further illustration of the potential of exotic species for large-scale microbial application.     

CURRICULUM GUIDE FOR RESEARCH ETHICS WORKSHOPS FOR COUNTRIES IN THE MIDDLE EAST

To help ensure the ethical conduct of research, many have recommended educational efforts in research ethics to investigators and members of research ethics committees (RECs). One type of education activity involves multi‐day workshops in research ethics. To be effective, such workshops should contain the appropriate content and teaching techniques geared towards the learning styles of the targeted audiences. To ensure consistency in content and quality, we describe the development of a curriculum guide, core competencies and associated learning objectives and activities to help educators organize research ethics workshops in their respective institutions. The curriculum guide is divided into modular units to enable planners to develop workshops of different lengths and choose content materials that match the needs, abilities, and prior experiences of the target audiences. The content material in the curriculum guide is relevant for audiences in the Middle East, because individuals from the Middle East who participated in a Certificate Program in research ethics selected and developed the training materials (e.g., articles, powerpoint slides, case studies, protocols). Also, many of the activities incorporate active‐learning methods, consisting of group work activities analyzing case studies and reviewing protocols. The development of such a workshop training curriculum guide represents a sustainable educational resource to enhance research ethics capacity in the Middle East.