Mature reverse transcriptase (p66/p51) is responsible for low levels of viral DNA found in human immunodeficiency virus type 1 (HIV-1)

Reverse transcription of the HIV RNA genome is thought to occur in the host cell cytoplasm after viral adsorption. However, viral DNA has been isolated in cell-free virus particles. We have quantitated by polymerase chain reaction (PCR) amplification the amount of viral DNA in virions as compared to RNA. Virus produced by proviral DNA transfections of cos-7 cells or by chronically-infected H9 cells; neither of which express the cell surface CD4 receptor, contained at least 1000 times more viral RNA than DNA. In contrast, only 60 times more RNA than DNA was present in virus particles produced by transfection of Jurkat cells, which were CD4-positive and thus potentially susceptible to superinfection. Protease-defective virus, carrying only the precursor of reverse transcriptase (RT) p160gag-pol, contained virtually no detectable DNA. These results indicate that only mature RT (p66/p51) and not its precursor (p160gag-pol) is responsible for the presence of viral DNA in HIV.

Spatial patterns, landscape genetics and post virus recovery of blacklip abalone, Haliotis rubra (Leach), in the western commercial fishing zone of Victoria

Historically, collecting nearshore habitat information has been problematic. Existing methods, such as aerial and satellite image interpretation are limited due to the attenuation of light in the water column obscuring the seabed structure. The advent of airborne bathymetric LiDAR (Light Detection and Ranging) systems (laser scanning of the seabed) now provides high-resolution seabed ‘images’ in areas that were previously difficult to survey. LiDAR imagery is available for the entire coastline of Victoria, Australia to depths of around 25 m, after being initially collected for climate change modelling by the Future Coasts Program (http://www.climatechange.vic.gov.au/adapting-to-climate-change/future-coasts). This dataset has provided the opportunity to test its applicability to inform fisheries management. Detailed geophysical information combined with spatially explicit AbTrack GPS located fisheries records and targeted genetic sampling is used in this study to provide a better understanding of the extent of available fishing grounds, direction of fishing effort and stock population structure within the Victorian western zone abalone fishery.
The species distribution modelling technique MaxEnt was used to produce a potential habitat suitability map for abalone in an attempt to capture the effective footprint of the  fishery. Also, by interrogating the spatially defined effort localities, we demonstrate an approach that may be used to identify areas where fishing effort is concentrated, and how this parameter changes temporally.
Despite barriers to adult dispersal (soft sediment barriers between reef patches), the genetic study indicates that larval movement is able to homogenize the gene pool over  large geographic distances. The western, central and eastern zone abalone stocks in Victoria were found to be a single large panmictic unit. This indicates high levels of stock connectivity and no obvious impacts of Abalone Viral Ganglioneuritis (AVG) on the genetic health of western zone stocks. We used detailed seafloor structure information interpreted from LiDAR to inform a replicated hierarchical fine scale genetic sampling design. We demonstrated that there may be extensive migration among abalone stocks across the Victorian abalone fishery.
This is contrary to previous studies that suggest recruitment is highly localised. In combination, these findings provide a valuable insight into the biology of H. rubra and immediate benefits for fisheries management. We discuss these results in the context of predicting resilience and adaptive potential of H. rubra stocks to environmental pressures and the spread of heritable diseases.
Adoption pathways are also provided to benefit future stock augmentation activities to catalyse the recovery of AVG affected reef codes. As larval dispersal is likely to be spatially and temporally variable, some AVG affected stocks are likely to recover through natural recruitment, while others will benefit from augmentation activities to ‘kick-start’ stock recovery. Evidence of neutral genetic homogeneity across Victorian reef codes suggests that the relocation of animals is unlikely to have significant genetic risks; however the potential for locally adaptive genetic differences may exist, and should be taken into consideration in future stock augmentation planning.
When combined, the spatial and genetic analyses provide valuable insights into stock productivity within the western zone fishery. Reefs appear to be expansive and support much available habitat, and the movement of larvae among reef structures is likely to be extensive in this region. Consequently, we propose that colonisation success and productivity is likely to be driven by ecological factors such as resources and/or competition, or physical factors such as wave exposure.

Suppression of bovine viral diarrhea virus replication by small interfering RNA and short hairpin RNA-mediated RNA interference

Bovine viral diarrhea virus (BVDV) is a ubiquitous viral pathogen that affects cattle herds’ worldwide causing significant economic loss. The current strategies to control BVDV infection include vaccination (modified-live or killed) and control of virus spread by enhanced biosecurity management, however, the disease remains prevalent. With the discovery of the sequence-specific method of gene silencing known as RNA interference (RNAi), a new era in antiviral therapies has begun. Here we report the efficient inhibition of BVDV replication by small interfering (siRNA) and short hairpin RNA (shRNA)-mediated gene silencing. siRNAs were generated to target the 5′ non-translated (NTR) region and the regions encoding the C, NS4B and NS5A proteins of the BVDV genome. The siRNAs were first validated using an EGFP/BVDV reporter system and were then shown to suppress BVDV-induced cytopathic effects and viral titers in cell culture with surprisingly different activities compared to the reporter system. Efficient viral suppression was then achieved by bovine 7SK-expressed BVDV-specific shRNAs. Overall, our results demonstrated the use of siRNA and shRNA-mediated gene silencing to achieve efficient inhibition of the  replication of this virus in cell culture.

The cost of community-managed viral respiratory illnesses in a cohort of healthy preschool-aged children

Background : Acute respiratory illnesses (ARIs) during childhood are often caused by respiratory viruses, result in significant morbidity, and have associated costs for families and society. Despite their ubiquity, there is a lack of interdisciplinary epidemiologic and economic research that has collected primary impact data, particularly associated with indirect costs, from families during ARIs in children.
Methods : We conducted a 12-month cohort study in 234 preschool children with impact diary recording and PCR testing of nose-throat swabs for viruses during an ARI. We used applied values to estimate a virus-specific mean cost of ARIs.
Results : Impact diaries were available for 72% (523/725) of community-managed illnesses between January 2003 and January 2004. The mean cost of ARIs was AU$309 (95% confidence interval $263 to $354). Influenza illnesses had a mean cost of $904, compared with RSV, $304, the next most expensive single-virus illness, although confidence intervals overlapped. Mean carer time away from usual activity per day was two hours for influenza ARIs and between 30 and 45 minutes for all other ARI categories.
Conclusion : From a societal perspective, community-managed ARIs are a significant cost burden on families and society. The point estimate of the mean cost of community-managed influenza illnesses in healthy preschool aged children is three times greater than those illnesses caused by RSV and other respiratory viruses. Indirect costs, particularly carer time away from usual activity, are the key cost drivers for ARIs in children. The use of parent-collected specimens may enhance ARI surveillance and reduce any potential Hawthorne effect caused by compliance with study procedures. These findings reinforce the need for further integrated epidemiologic and economic research of ARIs in children to allow for comprehensive cost-effectiveness assessments of preventive and therapeutic options.

The effects of the social structure of digital networks on viral marketing performance

Viral marketing is a form of peer-to-peer communication in which individuals are encouraged to pass on promotional messages within their social networks. Conventional wisdom holds that the viral marketing process is both random and unmanageable. In this paper, we deconstruct the process and investigate the formation of the activated digital network as distinct from the underlying social network. We then consider the impact of the social structure of digital networks (random, scale free, and small world) and of the transmission behavior of individuals on campaign performance. Specifically, we identify alternative social network models to understand the mediating effects of the social structures of these models on viral marketing campaigns. Next, we analyse an actual viral marketing campaign and use the empirical data to develop and validate a computer simulation model for viral marketing. Finally, we conduct a number of simulation experiments to predict the spread of a viral message within different types of social network structures under different assumptions and scenarios. Our findings confirm that the social structure of digital networks play a critical role in the spread of a viral message. Managers seeking to optimize campaign performance should give consideration to these findings before designing and implementing viral marketing campaigns. We also demonstrate how a simulation model is used to quantify the impact of campaign management inputs and how these learnings can support managerial decision making.

Ribosome inactivating proteins (RIPs) from momordica charantia for anti viral therapy

This review describes the nature and applications of ribosome inactivating proteins (RIPs) from Momordica charantia (bitter melon). RIPs from the plant kingdom have received much attention in biomedical research because they target conserved host protein synthesis machinery and show specificity towards human and animal cell targets. Recent studies aimed at unravelling the enzymatic activities of the M charantia RIPs provide a structural basis for their activities. It has been reported that RIPs are member of the single chain ribosome inactivating protein (SCRIP) family which act irreversibly on ribosome by removing adenine residue from eukaryotic ribosomal RNA. Various activities of RIPs include anti-tumor, broad anti-viral, ribonuclease and deoxyribonuclease. MAP30 (Momordica Anti-HIV Protein), alpha- and beta-momorcharins inhibit HIV replication in acutely and chronically infected cells and thus are considered potential therapeutic agent in HIV infection and AIDS. Further, MAP30 improved the efficacy of anti-HIV therapy when used in combination with other anti-viral drugs. MAP30 holds therapeutic promise over other RIPs because not only it is active against infection and replication of both HSV and HIV but is non toxic to normal cells. Here we review the nature, action, structure function relationship and applications of RIPs from Momordica charantia and evaluate their potential for anti-cancer and anti-viral therapy.

Virulence determinants of infectious bursal disease virus

The very virulent (vv) pathotype of infectious bursal disease virus (IBDV) has spread rapidly throughout Europe, Asia, and the Middle East. Although Australia is currently unaffected, there remains the potential for incursion of an exotic isolate. The aim of this study was to identify putative virulence determinants of IBDV to facilitate the development of improved diagnostic assays for detection and characterisation of vvIBDV isolates. Sequencing of Indonesian vvIBDV Tasik94 revealed a unique substitution [ A�¨S222] in the hypervariable region (HVR) of viral protein (VP) VP2, which did not appear to impinge on virulence or antigenicity. Phylogenetic analyses indicated that Tasik94 was closely related to Asian and European vvIBDV strains. Extensive alignment of deduced protein sequences across the HVR of VP2 identified residuesI242 I256 and I294 as putative markers of the vv phcnotype. Comparison of the pathology induced by mildly-virulent Australian IBDV 002/73 and Indonesian vvIBDV Tasik94, revealed that histological lesions in the spleen, thymus and bone marrow were restricted to Tasik94-infected birds, suggesting the enhanced pathogenicity of vvIBDV might be attributed to replication in non-bursal lymphoid organs. The biological significance of the VP2 HVR in virulence was assessed using recombinant viruses generated by reverse genetics. Both genomic segments of Australian IBDV 002/73, and recombinant segment A constructs in which the HVR of 002/73 was replaced with the corresponding region of either tissue culture-adapted virus or vvIBDV (Tasik94), were cloned behind T7 RNA polymerase promoter sequences. In vitro transcription/translation of each construct resulted in expression of viral proteins. Co-transfection of synthetic RNA transcripts initiated replication of both tissue culture-adapted parental and recombinant viruses, however attempts to rescue non-adapted viruses in specific-pathogen-free (SPF) chickens were unsuccessful. Nucleotide sequence variation in the HVR of VP2 was exploited for the development of a new diagnostic assay to rapidly detect exotic IBDV isolates, including vvIBDV, using reverse transcription polymerase chain reaction (RT-PCR) amplification and Bmrl restriction enzyme digestion. The assay was capable of differentiating between endemic and exotic IBDV in 96% of 105 isolates sequenced to date.

Conservation genetics of the New Holland mouse Pseudomys novaehollandiae, Waterhouse, 1843 (Rodentia: Muridae) : an analysis of mitochondrial DNA control region variation

An investigation of the genetic diversity of New Holland mouse populations using DNA. Ten distinct restriction enzyme fragment patterns or haplotypes were detected. From the fragment patterns, estimates of genetic divergence between the haplotypes revealed a degree of genetic structuring within New Holland mouse with four population assemblages apparent.

Molecular genetics and comparative genomics reveal RNAi is not functional in malaria parasites

Techniques for targeted genetic disruption in Plasmodium, the causative agent of malaria, are currently intractable for those genes that are essential for blood stage development. The ability to use RNA interference (RNAi) to silence gene expression
would provide a powerful means to gain valuable insight into the pathogenic blood stages but its functionality in Plasmodium remains controversial. Here we have used various RNA-based gene silencing approaches to test the utility of RNAi in malaria
parasites and have undertaken an extensive comparative genomics search using profile hidden Markov models to clarify whether RNAi machinery
exists in malaria. These investigative approaches revealed that Plasmodium lacks the enzymology required for RNAi-based ablation of gene expression
and indeed no experimental evidence for RNAi was observed. In its absence, the most likely explanations for previously reported RNAi-mediated knockdown are either the general toxicity of introduced RNA (with global down-regulation of gene expression) or a specific antisense effect mechanistically distinct from RNAi, which will need systematic
analysis if it is to be of use as a molecular genetic tool for malaria parasites.

Viral RNA silencing suppressors (RSS) : novel strategy of viruses to ablate the host RNA interference (RNAi) defense system

Pathogenic viruses have developed a molecular defense arsenal for their survival by counteracting the host anti-viral system known as RNA interference (RNAi). Cellular RNAi, in addition to regulating gene expression through microRNAs, also serves as a barrier against invasive foreign nucleic acids. RNAi is conserved across the biological species, including plants, animals and invertebrates. Viruses in turn, have evolved mechanisms that can counteract this anti-viral defense of the host. Recent studies of mammalian viruses exhibiting RNA silencing suppressor (RSS) activity have further advanced our understanding of RNAi in terms of host–virus interactions. Viral proteins and non-coding viral RNAs can inhibit the RNAi (miRNA/siRNA) pathway through different mechanisms. Mammalian viruses having dsRNA-binding regions and GW/WG motifs appear to have a high chance of conferring RSS activity. Although, RSSs of plant and invertebrate viruses have been well characterized, mammalian viral RSSs still need in-depth investigations to present the concrete evidences supporting their RNAi ablation characteristics. The information presented in this review together with any perspective research should help to predict and identify the RSS activity-endowed new viral proteins that could be the potential targets for designing novel anti-viral therapeutics.

Population genetics of the spotted seahorse (Hippocampus kuda) in Thai waters : implications for conservation

A population genetics approach was used to investigate the genetic diversity of the spotted seahorse (Hippocampus kuda) in Thai waters; specifically, the degree of genetic differentiation and species evolution was inferred from sequence analysis of 353 bp of the mitochondrial (mt)DNA control region. The data were then used to identify discrete populations in Thai waters for effective conservation and management. Spotted seahorses were collected from 4 regions on the east and west coasts of the Gulf of Thailand and a geographically separated region in the Andaman Sea. Of the 101 mtDNA sequences analyzed, 7 haplotypes were identified, 5 of which were shared among individuals from the east and west coasts of the Gulf of Thailand. The remaining haplotypes were restricted to individuals from the Andaman Sea. Nucleotide and haplotype diversities were similar within the Gulf of Thailand samples, whereas diversity was lower in the Andaman Sea sample. Genetic differentiation appeared between pairs of samples from the Gulf of Thailand and Andaman Sea (FST, p < 0.0001). A large genetic variance appeared among the 2 population groups (94.46%, ΦCT = 0.94464, p < 0.01). A Neighbor-joining tree indicated that individuals from the Gulf of Thailand and Andaman Sea formed 2 phylogenetically distinct groups, which were segregated into different population-based clades. While results reported here indicate that populations from the Gulf of Thailand and Andaman Sea should be treated as separate conservation units, a larger sample size from the Andaman Sea is required to confirm this genetic partitioning and low level of diversity observed in the present study.

Genetics and public health - evolution, or revolution?

During the 19th and early 20th century, public health and genetics shared common ground through similar approaches to health promotion in the population. By the mid-20th century there was a division between public health and genetics, with eugenicists estranged and clinical genetics focused on single gene disorders, usually only relevant to small numbers of people. Now through a common interest in the aetiology of complex diseases such as heart disease and cancer, there is a need for people working in public health and genetics to collaborate. This is not a comfortable convergence for many, particularly those in public health. Nine main concerns are reviewed: fear of eugenics; genetic reductionism; predictive power of genes; non-modifiable risk factors; rights of individuals compared with populations; resource allocation; commercial imperative; discrimination; and understanding and education. This paper aims to contribute to the thinking and discussion about an evolutionary, multidisciplinary approach to understanding, preventing, and treating complex diseases.