Analysis of synonymous codon usage in Hepatitis A virus

<p>Abstract</p> <p>Background</p> <p>Hepatitis A virus is the causative agent of type A viral hepatitis, which causes occasional acute hepatitis. Nevertheless, little information about synonymous codon usage pattern of HAV genome in the process of its evolution is available. In this study, the key genetic determinants of codon usage in HAV were examined.</p> <p>Results</p> <p>The overall extent of codon usage bias in HAV is high in <it>Picornaviridae</it>. And the patterns of synonymous codon usage are quite different in HAV genomes from different location. The base composition is closely correlated with codon usage bias. Furthermore, the most important determinant that results in such a high codon bias in HAV is mutation pressure rather than natural selection.</p> <p>Conclusions</p> <p>HAV presents a higher codon usage bias than other members of <it>Picornaviridae</it>. Compositional constraint is a significant element that influences the variation of synonymous codon usage in HAV genome. Besides, mutation pressure is supposed to be the major factor shaping the hyperendemic codon usage pattern of HAV.</p

Predator-Induced Demographic Shifts in Coral Reef Fish Assemblages

In recent years, it has become apparent that human impacts have altered community structure in coastal and marine ecosystems worldwide. Of these, fishing is one of the most pervasive, and a growing body of work suggests that fishing can have strong effects on the ecology of target species, especially top predators. However, the effects of removing top predators on lower trophic groups of prey fishes are less clear, particularly in highly diverse and trophically complex coral reef ecosystems. We examined patterns of abundance, size structure, and age-based demography through surveys and collection-based studies of five fish species from a variety of trophic levels at Kiritimati and Palmyra, two nearby atolls in the Northern Line Islands. These islands have similar biogeography and oceanography, and yet Kiritimati has ∼10,000 people with extensive local fishing while Palmyra is a US National Wildlife Refuge with no permanent human population, no fishing, and an intact predator fauna. Surveys indicated that top predators were relatively larger and more abundant at unfished Palmyra, while prey functional groups were relatively smaller but showed no clear trends in abundance as would be expected from classic trophic cascades. Through detailed analyses of focal species, we found that size and longevity of a top predator were lower at fished Kiritimati than at unfished Palmyra. Demographic patterns also shifted dramatically for 4 of 5 fish species in lower trophic groups, opposite in direction to the top predator, including decreases in average size and longevity at Palmyra relative to Kiritimati. Overall, these results suggest that fishing may alter community structure in complex and non-intuitive ways, and that indirect demographic effects should be considered more broadly in ecosystem-based management

VIRUSES AND VIRUS-LIKE PARTICLES IN THE FECES OF DOGS WITH AND WITHOUT DIARRHEA

Negative staining electron microscopy was used to identify viruses in 157 normal and 29 diarrhoeal faecal samples collected from 156 dogs admitted to an animal shelter during an 8 month period (March to October) in 1982. Seven distinct viral types were detected: 21-26 nm parvovirus-like particles, 28-31 nm astrovirus-like particles, a previously undescribed 34-35 nm "round" virus particle, coronavirus, coronavirus-like particles ( CVLP ), rotavirus and papova-like virus. Parvovirus-like particles alone were detected in 14 diarrhoeal and 50 normal faeces, astrovirus-like particles in 3 normal faeces, "round" viruses in 4 normal faeces, coronavirus in 2 diarrhoeal and 5 normal faeces, CVLP in one diarrhoeal and one normal faeces, rotavirus in 2 normal faeces, papova-like virus in one normal faeces, both parvovirus-like particles and coronavirus in 2 diarrhoeal and 2 normal faeces, parvovirus-like particles and rotavirus in one normal faeces and parvovirus-like and papova-like virus in one normal faeces. The significance of these findings in canine and human disease is discussed