In Vivo Quantification Reveals Extensive Natural Variation in Mitochondrial Form and Function in Caenorhabditis briggsae

We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5Δ) that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial phenotypes including reactive oxygen species level, membrane potential, and aspects of organelle morphology, and observed significant among-isolate variation in 18 traits. Although several mitochondrial phenotypes were non-linearly associated with nad5Δ levels, most of the among-isolate phenotypic variation could be accounted for by phylogeographic clade membership. In particular, isolate-specific mitochondrial membrane potential was an excellent predictor of clade membership. We interpret this result in light of recent evidence for local adaptation to temperature in C. briggsae. Analysis of mitochondrial-nuclear hybrid strains provided support for both mtDNA and nuclear genetic variation as drivers of natural mitochondrial phenotype variation. This study demonstrates that multicellular eukaryotic species are capable of extensive natural variation in organellar phenotypes and highlights the potential of integrating evolutionary and cell biology perspectives.     

Genotyping of Bacillus cereus strains by microarray-based resequencing

The ability to distinguish microbial pathogens from closely related but nonpathogenic strains is key to understanding the population biology of these organisms. In this regard, Bacillus anthracis, the bacterium that causes inhalational anthrax, is of interest because it is closely related and often difficult to distinguish from other members of the B. cereus group that can cause diverse diseases. We employed custom-designed resequencing arrays (RAs) based on the genome sequence of Bacillus anthracis to generate 422 kb of genomic sequence from a panel of 41 Bacillus cereus sensu lato strains. Here we show that RAs represent a "one reaction" genotyping technology with the ability to discriminate between highly similar B. anthracis isolates and more divergent strains of the B. cereus s.l. Clade 1. Our data show that RAs can be an efficient genotyping technology for pre-screening the genetic diversity of large strain collections to selected the best candidates for whole genome sequencing.     

Replication of Measles Virus: Distinct Species of Short Nucleocapsids in Cytoplasmic Extracts of Infected Cells

Cytoplasmic extracts of Vero cells infected with wild-strain Edmonston measles virus were found to contain two and probably three distinct species of nucleocapsids. Species sedimenting at 200 and 110S contained RNA which sedimented at 50 and 16 to 18S, respectively. The third nucleocapsid species which sedimented at 170S was not present in all experiments and was not characterized in detail. Essentially all 200 and 170S, as well as a portion of the 110S, nucleocapsids were membrane associated and probably present in part in cell-associated virions. Five of six plaque purified strains derived from wild-type Edmonston virus produced only 200S nucleocapsids. One of these five plaque-purified strains subsequently produced both 200 and 110S nucleocapsids after being passaged by using undiluted inocula. These results suggest that measles virus may produce distinct classes of defective virus containing short nucleocapsids and subgenomic viral RNA.     

Replication of Measles Virus: Continued Synthesis of Nucleocapsid RNA and Increased Synthesis of mRNA in the Presence of Cycloheximide

The effect of cycloheximide on virus specific RNA synthesis in Vero cells infected with either wild-strain (Edmonston) or subacute sclerosing panencephalitis strain measles virus was investigated. At 3 days postinfection, cells treated with cycloheximide (2.6 x 10(-4) M) and then exposed to [(3)H]uridine showed a marked increase in labeled virus-specific RNA. A major portion of this incremental labeled RNA was putative viral mRNA which sedimented at 16, 22, and 30S. Five distinct classes of polyribosomes, which were not evident in untreated cells, were found in cycloheximide-treated cells and each contained similar species of virus-specific RNA. Viral nucleocapsid RNA, 50 and 18S, was synthesized and encapsidated in the presence of cycloheximide. The latter observation is in apparent contrast to reports that cycloheximide inhibits replication of RNA of classical paramyxoviruses, and may indicate that mechanisms for replicating RNA of measles virus are different from those for replicating RNA of paramyxoviruses.     

Comparative Studies of Wild-Type and “Cold-Mutant” (Temperature-Sensitive) Influenza Viruses: Polypeptide Synthesis by an Asian (H2N2) Strain and Its Cold-Adapted Variant

The structure and replication of a cold-adapted, temperature-sensitive (TS) mutant of an Asian (H2N2) influenza virus was compared with that of its wild-type (WT) parent. Viruses were grown in a chicken kidney cell system, and at the nonpermissive temperature of 40 C, production of infectious TS virus was about 100,000-fold less than at 35 C, in contrast to WT virus. Major structural polypeptides of each virus grown at 35 C were similar, except that the hemagglutinin glycopolypeptide (HA) of the TS virions was slightly more heterogenous than that of WT virions. Synthesis of viral polypeptides was examined by sodium dodecyl sulfate acrylamide gel electrophoresis of pulse-labeled infected cells. This revealed a defect in the synthesis of TS viral hemagglutinin that was most pronounced at the nonpermissive temperature. Other TS viral polypeptides appeared to be synthesized normally at 40 C. A defect in the TS virus hemagglutinin was also indicated by serological studies that demonstrated that TS virus hemagglutinin had lost antigenic sites present on the WT virus. Thus, it is concluded that the virus mutant examined contains lesions in the hemagglutinin gene, although the possibility of additional unrecognized lesions is not excluded.     

Differential modification of seawater carbonate chemistry by major coral reef benthic communities

Ocean acidification (OA) resulting from uptake of anthropogenic CO₂ may negatively affect coral reefs by causing decreased rates of biogenic calcification and increased rates of CaCO₃ dissolution and bioerosion. However, in addition to the gradual decrease in seawater pH and Ω _a resulting from anthropogenic activities, seawater carbonate chemistry in these coastal ecosystems is also strongly influenced by the benthic metabolism which can either exacerbate or alleviate OA through net community calcification (NCC = calcification – CaCO₃ dissolution) and net community organic carbon production (NCP = primary production ? respiration). Therefore, to project OA on coral reefs, it is necessary to understand how different benthic communities modify the reef seawater carbonate chemistry. In this study, we used flow-through mesocosms to investigate the modification of seawater carbonate chemistry by benthic metabolism of five distinct reef communities [carbonate sand, crustose coralline algae (CCA), corals, fleshy algae, and a mixed community] under ambient and acidified conditions during summer and winter. The results showed that different communities had distinct influences on carbonate chemistry related to the relative importance of NCC and NCP. Sand, CCA, and corals exerted relatively small influences on seawater pH and Ω _a over diel cycles due to closely balanced NCC and NCP rates, whereas fleshy algae and mixed communities strongly elevated daytime pH and Ω _a due to high NCP rates. Interestingly, the influence on seawater pH at night was relatively small and quite similar across communities. NCC and NCP rates were not significantly affected by short-term acidification, but larger diel variability in pH was observed due to decreased seawater buffering capacity. Except for corals, increased net dissolution was observed at night for all communities under OA, partially buffering against nighttime acidification. Thus, algal-dominated areas of coral reefs and increased net CaCO₃ dissolution may partially counteract reductions in seawater pH associated with anthropogenic OA at the local scale.     

Riparian roots through time, space and disturbance

Riparian zones are landscape features adjacent to streams and are widely recognized as important in reducing erosion and filtering groundwater. Few studies directly investigate rooting dynamics of riparian areas, and little information exists concerning riparian root densities, biomass, depth profiles, changes through time, or vulnerability to disturbance. This study examined spatial and temporal patterns in root systems in streamsides influenced by season, hydrologic regime, vegetative composition, and ice storm disturbance in the eastern Adirondacks, New York. Sequential root cores and in-growth cores were collected from June 2000 through August 2001 in a riparian area with minimal ice storm damage adjacent to a third-order stream. Data were used to assess seasonal trends in root biomass and to provide a reference for spatial comparisons. The biomass and surface area of roots collected in the reference site cores were compared with cores collected at nine additional riparian sites differing in degree of canopy damage from the January 1998 ice storm. Average root biomass at the reference site was 1330 g/m², comparable to or greater than values reported for terrestrial and other riparian systems. Root biomass varied seasonally with a maximum root biomass in August, 2000; this result was not repeated the following year after the water table inundated much of the rooting zone in mid-June. Root biomass was spatially variable on a range of scales. Although the maximum root surface area occurred in the upper 10 cm, root biomass peaked at 20–30 cm belowground, unlike observations from most other root studies where the maximum root biomass has been found in the top 10 cm. Areas severely damaged by the ice storm had significantly less root biomass and surface area than areas with low damage. This study demonstrates that root biomass in riparian areas is highly dynamic over time, space, and across disturbance sites. Our findings suggest that the spatial variability in root densities has direct implications for riparian vulnerability to erosion.