A conserved peptide in West Nile virus NS4A protein contributes to proteolytic processing and is essential for replication

The West Nile virus strain Kunjin virus (WNV(KUN)) NS4A protein is a multifunctional protein involved in membrane proliferation, stimulation of cellular pathways, and evasion of host defense and is a major component of the WNV(KUN) RNA replication complex. We identified a highly conserved region ((120)P-E-P-E(123)) upstream of the viral protease dibasic cleavage site and investigated whether this motif was required for WNV(KUN) replication. Single point mutations to alanine and a PEPE deletion mutation were created in a full-length infectious WNV(KUN) molecular clone. All mutations drastically impaired viral replication and virion production, except that of the P122A mutant, which was slightly attenuated. These mutations were subsequently transferred to a WNV(KUN) replicon to specifically assess effects on RNA replication alone. Again, all mutants, except P122A, showed severely reduced negative-sense RNA production as well as decreased viral protein production. Correspondingly, immunofluorescence analyses showed a lack of double-stranded RNA (dsRNA) labeling and a dispersed localization of the WNV(KUN) proteins, suggesting that replication complex formation was additionally impaired. Attempts to rescue replication via conservative mutants largely failed except for substitution of Asp at E121, suggesting that a negative charge at this residue is equally important. Analysis of viral protein processing suggested that cleavage of the 2K peptide from NS4A did not occur with the mutant constructs. These observations imply that the combined effects of proline and negatively charged residues within the PEPE peptide are essential to promote the cleavage of 2K from NS4A, which is a prerequisite for efficient WNV replication.     

Broadening horizons: holistic viewpoints from the Biology of Genomes

A report on the Cold Spring Harbor Laboratory 27th annual meeting on the Biology of Genomes, held in Cold Spring Harbor, New York, USA, 6-10 May 2014.     

Evaluating regional resiliency of coastal wetlands to sea level rise through hypsometry‐based modeling

Sea level rise (SLR) threatens coastal wetlands worldwide, yet the fate of individual wetlands will vary based on local topography, wetland morphology, sediment dynamics, hydrologic processes, and plant‐mediated feedbacks. Local variability in these factors makes it difficult to predict SLR effects across wetlands or to develop a holistic regional perspective on SLR response for a diversity of wetland types. To improve regional predictions of SLR impacts to coastal wetlands, we developed a model that addresses the scale‐dependent factors controlling SLR response and accommodates different levels of data availability. The model quantifies SLR‐driven habitat conversion within wetlands across a region by predicting changes in individual wetland hypsometry. This standardized approach can be applied to all wetlands in a region regardless of data availability, making it ideal for modeling SLR response across a range of scales. Our model was applied to 105 wetlands in southern California that spanned a broad range of typology and data availability. Our findings suggest that if wetlands are confined to their current extents, the region will lose 12% of marsh habitats (vegetated marsh and unvegetated flats) with 0.6 m of SLR (projected for 2050) and 48% with 1.7 m of SLR (projected for 2100). Habitat conversion was more drastic in wetlands with larger proportions of marsh habitats relative to subtidal habitats and occurred more rapidly in small lagoons relative to larger sites. Our assessment can inform management of coastal wetland vulnerability, improve understanding of the SLR drivers relevant to individual wetlands, and highlight significant data gaps that impede SLR response modeling across spatial scales. This approach augments regional SLR assessments by considering spatial variability in SLR response drivers, addressing data gaps, and accommodating wetland diversity, which will provide greater insights into regional SLR response that are relevant to coastal management and restoration efforts.     

Population impacts of collecting sea anemones and anemonefish for the marine aquarium trade in the Philippines

Tropical marine ornamentals comprise an increasingly important fishery worldwide. Although the potential for overexploitation of marine ornamentals is great, few studies have addressed the population-level impacts of ornamental exploitation and few ornamental fisheries are managed. Analysis of catch records obtained from collectors over a four-month period in the vicinity of Cebu, Philippines, showed that anemonefish and anemones comprised close to 60% of the total catch. Underwater visual census surveys revealed that both anemone and anemonefish densities were significantly lower in exploited areas than in protected areas. The low density of anemones on exploited reefs accounted for over 80% of the reduced density of anemonefish at those sites. There were similar numbers of anemonefish per unit area of anemone in protected and exploited sites; however, biomass of anemonefish per unit area of anemone was lower in exploited areas. Reduction of anemone removals is recommended to support the sustainable harvest of anemonefish from this region.     

Growth line deposition and variability in growth of two circumpolar bivalves (Serripes groenlandicus, and Clinocardium ciliatum)

Growth patterns of two common circumpolar bivalves, the Greenland cockle (Serripes groenlandicus), and the hairy cockle (Clinocardium ciliatum) have been used in previous studies to reconstruct environmental conditions in the arctic. To date, there has been no direct determination that growth lines in either species are deposited periodically, and there has been no examination of factors affecting growth. We placed calcein-marked individuals of both species on oceanographic moorings in two fjords (Rijpfjord and Kongsfjord) in the Svalbard archipelago for one and two (Kongsfjord only) years. Growth patterns were compared with concurrent in situ temperature and fluorescence data in order to assess environmental controls on growth. Dark growth lines are evident on the outer shell surface and internally in shell cross section in both S. groenlandicus and C. ciliatum, and both species deposited only one line per year, unequivocally confirming that internal lines are deposited annually. Growth line deposition in both species began in late summer to early fall, before the seasonal decline in temperature. There was no difference in growth of S. groenlandicus between the two fjords despite differences in water temperature (3°C), fluorescence (nearly threefold) and the onset and duration of the winter season. C. ciliatum, however, grew approximately 2.8 times faster in the warmer, more food-rich Kongsfjord than in Rijpfjord. Subannual lines were counted in two individuals of each species from each fjord, but deposition of these lines was not clearly related to number of growing days estimated by temperature and fluorescence.     

Dietary and environmental reconstruction with stable isotope analyses of herbivore tooth enamel from the Miocene locality of Fort Ternan, Kenya

Tooth enamel of nine Middle Miocene mammalian herbivores from Fort Ternan, Kenya, was analyzed for δ¹³C and δ¹⁸O. The δ¹⁸O values of the tooth enamel compared with pedogenic and diagenetic carbonate confirm the use of stable isotope analysis of fossil tooth enamel as a paleoenvironmental indicator. Furthermore, the δ¹⁸O of tooth enamel indicates differences in water sources between some of the mammals. The δ¹³C values of tooth enamel ranged from −8·6–−13·0‰ which is compatible with a pure C₃diet, though the possibility of a small C₄fraction in the diet of a few of the specimens sampled is not precluded. The carbon isotopic data do not support environmental reconstructions of a Serengeti-typed wooded grassland with a significant proportion of C₄grasses. This study does not preclude the presence of C₃grasses at Fort Ternan; it is possible that C₃grasses could have had a wider geographic range if atmospheric CO₂levels were higher than the present values.     

Invasion of Cryptococcus neoformans into human brain microvascular endothelial cells requires protein kinase C-alpha activation

Pathogenic fungus Cryptococcus neoformans has a predilection for the central nervous system causing devastating meningoencephalitis. Traversal of C. neoformans across the blood–brain barrier (BBB) is a crucial step in the pathogenesis of C. neoformans . Our previous studies have shown that the CPS1 gene is required for C. neoformans adherence to the surface protein CD44 of human brain microvascular endothelial cells (HBMEC), which constitute the BBB. In this report, we demonstrated that C. neoformans invasion of HBMEC was blocked in the presence of G109203X, a protein kinase C (PKC) inhibitor, and by overexpression of a dominant-negative form of PKCα in HBMEC. During C. neoformans infection, phosphorylation of PKCα was induced and the PKC enzymatic activity was detected in the HBMEC membrane fraction. Our results suggested that the PKCα isoform might play a crucial role during C. neoformans invasion. Immunofluorescence microscopic images showed that induced phospho-PKCα colocalized with β-actin on the membrane of HBMEC. In addition, cytochalasin D (an F-filament-disrupting agent) inhibited fungus invasion into HBMEC in a dose-dependent manner. Furthermore, blockage of PKCα function attenuated actin filament activity during C. neoformans invasion. These results suggest a significant role of PKCα and downstream actin filament activity during the fungal invasion into HBMEC.     

Meningitic Escherichia coli K1 penetration and neutrophil transmigration across the blood-brain barrier are modulated by alpha7 nicotinic receptor

Alpha7 nicotinic acetylcholine receptor (nAChR), an essential regulator of inflammation, is abundantly expressed in hippocampal neurons, which are vulnerable to bacterial meningitis. However, it is unknown whether α7 nAChR contributes to the regulation of these events. In this report, an aggravating role of α7 nAChR in host defense against meningitic E. coli infection was demonstrated by using α7-deficient (α7(-/-)) mouse brain microvascular endothelial cells (BMEC) and animal model systems. As shown in our in vitro and in vivo studies, E. coli K1 invasion and polymorphonuclear neutrophil (PMN) transmigration across the blood-brain barrier (BBB) were significantly reduced in α7(-/-) BMEC and α7(-/-) mice. Stimulation by nicotine was abolished in the α7(-/-) cells and animals. The same blocking effect was achieved by methyllycaconitine (α7 antagonist). The tight junction molecules occludin and ZO-1 were significantly reduced in the brain cortex of wildtype mice infected with E. coli and treated with nicotine, compared to α7(-/-) cells and animals. Decreased neuronal injury in the hippocampal dentate gyrus was observed in α7(-/-) mice with meningitis. Proinflammatory cytokines (IL-1β, IL-6, TNFα, MCP-1, MIP-1alpha, and RANTES) and adhesion molecules (CD44 and ICAM-1) were significantly reduced in the cerebrospinal fluids of the α7(-/-) mice with E. coli meningitis. Furthermore, α7 nAChR is the major calcium channel for nicotine- and E. coli K1-increased intracellular calcium concentrations of mouse BMEC. Taken together, our data suggest that α7 nAChR plays a detrimental role in the host defense against meningitic infection by modulation of pathogen invasion, PMN recruitment, calcium signaling and neuronal inflammation.     

Ecological Theory and Community Restoration Ecology

Community ecological theory may play an important role in the development of a science of restoration ecology. Not only will the practice of restoration benefit from an increased focus on theory, but basic research in community ecology will also benefit. We pose several major thematic questions that are relevant to restoration from the perspective of community ecological theory and, for each, identify specific areas that are in critical need of further research to advance the science of restoration ecology. We ask, what are appropriate restoration endpoints from a community ecology perspective? The problem of measuring restoration at the community level, particularly given the high amount of variability inherent in most natural communities, is not easy, and may require a focus on restoration of community function (e.g., trophic structure) rather than a focus on the restoration of particular species. We ask, what are the benefits and limitations of using species composition or biodiversity measures as endpoints in restoration ecology? Since reestablishing all native species may rarely be possible, research is needed on the relationship between species richness and community stability of restored sites and on functional redundancy among species in regional colonist “pools.” Efforts targeted at restoring system function must take into account the role of individual species, particularly if some species play a disproportionate role in processing material or are strong interactors. We ask, is restoration of habitat a sufficient approach to reestablish species and function? Many untested assumptions concerning the relationship between physical habitat structure and restoration ecology are being made in practical restoration efforts. We need rigorous testing of these assumptions, particularly to determine how generally they apply to different taxa and habitats. We ask, to what extent can empirical and theoretical work on community succession and dispersal contribute to restoration ecology? We distinguish systems in which succession theory may be broadly applicable from those in which it is probably not. If community development is highly predictable, it may be feasible to manipulate natural succession processes to accelerate restoration. We close by stressing that the science of restoration ecology is so intertwined with basic ecological theory that practical restoration efforts should rely heavily on what is known from theoretical and empirical research on how communities develop and are structured over time.