Genetic organization of the mau gene cluster in Methylobacterium extorquens AM1: complete nucleotide sequence and generation and characteristics of mau mutants.

The nucleotide sequence of the methylamine utilization (mau) gene region from Methylobacterium extorquens AM1 was determined. Open reading frames for 11 genes (mauFBEDACJGLMN) were found, all transcribed in the same orientation. The mauB, mauA, and mauC genes encode the periplasmic methylamine dehydrogenase (MADH) large and small subunit polypeptides and amicyanin, respectively. The products of mauD, mauG, mauL, and mauM were also predicted to be periplasmic. The products of mauF, mauE, and mauN were predicted to be membrane associated. The mauJ product is the only polypeptide encoded by the mau gene cluster which is predicted to be cytoplasmic. Computer analysis showed that the MauG polypeptide contains two putative heme binding sites and that the MauM and MauN polypeptides have four and two FeS cluster signatures, respectively. Mutants generated by insertions in mauF, mauB, mauE, mauD, mauA, mauG, and mauL were not able to grow on methylamine or any other primary amine as carbon sources, while a mutant generated from an insertion in mauC was not able to utilize methylamine as a source of carbon but utilized C2 to C4 n-alkylamines as carbon sources. Insertion mutations in mauJ, mauM, and mauN did not impair the ability of the mutants to utilize primary n-alkylamines as carbon sources. All mau mutants were able to utilize methylamine as a nitrogen source, implying the existence of an alternative (methyl)amine oxidation system, and a low activity of N-methylglutamate dehydrogenase was detected. The mauD, mauE, and mauF mutants were found to lack the MADH small subunit polypeptide and have a decreased amount of the MADH large subunit polypeptide. In the mauG and mauL mutants, the MADH large and small subunit polypeptides were present at wild-type levels, although the MADHs in these strains were not functional. In addition, MauG has sequence similarity to cytochrome c peroxidase from Pseudomonas sp. The mauA, mauD, and mauE genes from Paracoccus denitrificans and the mauD and mauG genes from Methylophilus methylotrophus W3A1 were able to complement corresponding mutants of M. extorquens AM1, confirming their functional equivalence. Comparison of amino acid sequences of polypeptides encoded by mau genes from M. extorquens AM1, P. denitrificans, and Thiobacillus versutus shows that they have considerable similarity.     

Pre-erythrocytic immunity to Plasmodium falciparum: the case for an LSA-1 vaccine

A vaccine is urgently needed to stem the global resurgence of Plasmodium falciparum malaria. Vaccines targeting the erythrocytic stage are often viewed as an anti-disease strategy. By contrast, infection might be completely averted by a vaccine against the liver stage, a pre-erythrocytic stage during which the parasite multiplies 10000-fold within hepatocytes. Sterilizing immunity can be conferred by inoculating humans with irradiated pre-erythrocytic parasites, and a recombinant pre-erythrocytic vaccine partially protects humans from infection. Liver-stage antigen-1, one of a few proteins known to be expressed by liver-stage parasites, holds particular promise as a vaccine. Studies of naturally exposed populations have consistently related immune responses against this antigen to protection.     

Evidence of spawning by green sturgeon, Acipenser medirostris, in the upper Sacramento River, California

This study reports the only direct evidence of spawning of green sturgeon, Acipenser medirostris, in the upper Sacramento River, CA. Two green sturgeon eggs were collected with substrate mats immediately below Red Bluff Diversion Dam. One green sturgeon larva was collected with a larval net at Bend Bridge. We concluded that green sturgeon spawn in the upper Sacramento River, both above and below RBDD. Temperature ranges in the study area (10–15°C) are similar to conditions used in successful artificial rearing of green sturgeon and do not appear to be a limiting factor to successful spawning of green sturgeon; however, suitable habitat upstream of RBDD is inaccessible when dam gates are lowered.     

Variability of kokanee and rainbow trout food habits,distribution, and population dynamics,in an ultraoligotrophic lake with no manipulative management

Crater Lake is a unique environment to evaluate the ecology of introduced kokanee and rainbow trout because of its otherwise pristine state, low productivity, absence of manipulative management, and lack of lotic systems for fish spawning. Between 1986 and 2004, kokanee displayed a great deal of variation in population demographics with a pattern that reoccurred in about 10 years. We believe that the reoccurring pattern resulted from density dependent growth, and associated changes in reproduction and abundance, driven by prey resource limitation that resulted from low lake productivity exacerbated by prey consumption when kokanee were abundant. Kokanee fed primarily on small-bodied prey from the mid-water column; whereas rainbow trout fed on large-bodied prey from the benthos and lake surface. Cladoceran zooplankton abundance may be regulated by kokanee. And kokanee growth and reproductive success may be influenced by the availability of Daphnia pulicaria, which was absent in zooplankton samples collected annually from 1990 to 1995, and after 1999. Distribution and diel migration of kokanee varied over the duration of the study and appeared to be most closely associated with prey availability, maximization of bioenergetic efficiency, and fish density. Rainbow trout were less abundant than were kokanee and exhibited less variation in population demographics, distribution, and food habits. There is some evidence that the population dynamics of rainbow trout were in-part related to the availability of kokanee as prey.     

Can spatial and temporal food variability explain the winter foraging movements of a threatened saltmarsh insectivore?

The white‐fronted chat (Epthianura albifrons) is a small, insectivorous passerine that is threatened with extinction in the north‐eastern part of its range, partially due to loss and degradation of its saltmarsh habitat. Food availability is a potential limiting factor for the disjunct populations that survive in saltmarsh refugia, surrounded by urbanized land, because the anthropogenic matrix reduces the capacity of birds to commute to alternative grassland habitat to exploit temporary insect outbreaks. This limitation is likely to be exacerbated during the winter months when local arthropod abundance in saltmarsh is reduced. This study measured temporal and spatial variation in the abundance of saltmarsh arthropods to determine whether patch switching by foraging flocks can be explained by variation in food availability. Arthropods in the size range known to be important in the diet of white‐fronted chats were vacuum‐sampled from six patches within a continuous area of Sarcocornia‐dominated saltmarsh over a four‐month period. The location of foraging birds was recorded during the same period. Despite superficial similarity in vegetation composition and structure, there was significant variation in arthropod biomass among sites through time, such that the patches with the highest food abundance changed from month to month. There was little evidence, however, to suggest that white‐fronted chats foraged in saltmarsh patches with the highest overall food abundance. During the course of the study, birds were discovered flying 2 km from the saltmarsh to a development site where they foraged in weedy grassland. Arthropod samples collected from this site contained an extremely high abundance of Hemiptera and Neuroptera larvae, supporting previous research indicating that white‐fronted chats forage on irruptions of particular arthropod taxa. These findings indicate that food abundance is unlikely to be the main determinant of foraging site selection within saltmarsh, but highlights the potential importance of alternative foraging habitat types for this species.     

Distribution and abundance of zooplankton populations in Crater Lake,Oregon

The zooplankton assemblages in Crater Lake exhibited consistency in species richness and general taxonomic composition, but varied in density and biomass during the period between 1988 and 2000. Collectively, the assemblages included 2 cladoceran taxa and 10 rotifer taxa (excluding rare taxa). Vertical habitat partitioning of the water column to a depth of 200 m was observed for most species with similar food habits and/or feeding mechanisms. No congeneric replacement was observed. The dominant species in the assemblages were variable, switching primarily between periods of dominance of Polyarthra-Keratella cochlearis and Daphnia. The unexpected occurrence and dominance of Asplanchna in 1991 and 1992 resulted in a major change in this typical temporal shift between Polyarthra-K. cochlearis and Daphnia. Following a collapse of the zooplankton biomass in 1993 that was probably caused by predation from Asplanchna, Kellicottia dominated the zooplankton assemblage biomass between 1994 and 1997. The decline in biomass of Kellicottia by 1998 coincided with a dramatic increase in Daphnia biomass. When Daphnia biomass declined by 2000, Keratella biomass increased again. Thus, by 1998 the assemblage returned to the typical shift between Keratella-Polyarthra and Daphnia. Although these observations provided considerable insight about the interannual variability of the zooplankton assemblages in Crater Lake, little was discovered about mechanisms behind the variability. When abundant, kokanee salmon may have played an important role in the disappearance of Daphnia in 1990 and 2000 either through predation, inducing diapause, or both. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Thermal,chemical, and optical properties of Crater Lake,Oregon

Crater Lake covers the floor of the Mount Mazama caldera that formed 7700 years ago. The lake has a surface area of 53 km² and a maximum depth of 594 m. There is no outlet stream and surface inflow is limited to small streams and springs. Owing to its great volume and heat, the lake is not covered by snow and ice in winter unlike other lakes in the Cascade Range. The lake is isothermal in winter except for a slight increase in temperature in the deep lake from hyperadiabatic processes and inflow of hydrothermal fluids. During winter and spring the water column mixes to a depth of about 200–250 m from wind energy and convection. Circulation of the deep lake occurs periodically in winter and spring when cold, near-surface waters sink to the lake bottom; a process that results in the upwelling of nutrients, especially nitrate-N, into the upper strata of the lake. Thermal stratification occurs in late summer and fall. The maximum thickness of the epilimnion is about 20 m and the metalimnion extends to a depth of about 100 m. Thus, most of the lake volume is a cold hypolimnion. The year-round near-bottom temperature is about 3.5°C. Overall, hydrothermal fluids define and temporally maintain the basic water quality characteristics of the lake (e.g., pH, alkalinity and conductivity). Total phosphorus and orthophosphate-P concentrations are fairly uniform throughout the water column, where as total Kjeldahl-N and ammonia-N are highest in concentration in the upper lake. Concentrations of nitrate-N increase with depth below 200 m. No long-term changes in water quality have been detected. Secchi disk (20-cm) clarity varied seasonally and annually, but was typically highest in June and lowest in August. During the current study, August Secchi disk clarity readings averaged about 30 m. The maximum individual clarity reading was 41.5 m in June 1997. The lowest reading was 18.1 m in July 1995. From 1896 (white-dinner plate) to 2003, the average August Secchi disk reading was about 30 m. No long-term changes in the Secchi disk clarity were observed. Average turbidity of the water column (2–550 m) between June and September from 1991 to 2000 as measured by a transmissometer ranged between 88.8% and 90.7%. The depth of 1% of the incident solar radiation during thermal stratification varied annually between 80 m and 100 m. Both of these measurements provided additional evidence about the exceptional clarity of Crater Lake.     

Imaging of individual biopolymers and supramolecular assemblies using noncontact atomic force microscopy

A variety of biopolymers is imaged using noncontact atomic force microscopy. Samples are prepared by aerosol spray deposition of aqueous solutions on freshly cleaved mica followed by air drying. The distributions of contour lengths and chain or fibril thicknesses normal to the mica substrate can be measured for individual polymer molecules or molecular assemblies. In many cases it is possible to conclude that the structures imaged and quantitatively analyzed are representative of those present in solution and not artifacts of the deposition/dessication process. Imaging of linear and cyclic triple helices of the polysaccharide scleroglucan is demonstrated. Measurements of the triple helix thickness normal to the mica surface are analyzed, and successful measurements of the molecular weight distribution and mean molar mass are described. It is demonstrated that the extent of chain association in the polysaccharide xanthan can be modulated by the addition of low molecular weight salts. The contour length and chain thickness distributions in a xanthan fraction are presented. Increases in the extent of chain association with increasing polymer concentration are documented for the gelling polysaccharide gellan, and the formation of stiff fibrillar gellan aggregates in the presence of added low molecular salt is demonstrated. Images are presented of the polysaccharide κ-carrageenan in its disordered, and presumably single-stranded, state. Biopolymers other than polysaccharides can be imaged by the same technique; this is demonstrated with the fibrous protein collagen. In general it is shown that aerosol spray deposition of biopolymer samples can be used in conjunction with noncontact atomic force microscopy to provide a fast, reliable, and reproducible method for assessing the size and shape distributions of individual biological macromolecules and macromolecular assemblies in solution with a minimum of time and effort devoted to sample preparation. © 1997 John Wiley & Sons, Inc. Biopoly 42: 133–146, 1997     

Role of the membrane concanavalin A binding site in platelet-fibrin interactions

Concanavalin A was employed to study the role of platelet membrane glycoproteins in platelet-fibrin interactions during clot formation. A rheological technique was used to study the interactions, measuring the clot rigidity and platelet contractile force simultaneously during the formation of network structure. Concanavalin A lowered the clot rigidity and contractile force of a platelet-rich plasma clot by a small extent. Plasma glycoproteins probably compete with platelet membranes for concanavalin A binding in platelet-rich plasma. Both native concanavalin A (tetrameric) and succinyl concanavalin A (dimeric) lowered the clot rigidity and contractile force of a washed platelet-fibrin clot dramatically, almost down to those values found for fibrin clots. Inhibition studies with alpha-methyl-D-mannoside indicated that the concanavalin A effects were specific for the concanavalin A binding capacity to platelets. The effects of native concanavalin A on platelet-fibrin clots were only partially reversible, while the succinyl concanavalin A effects were completely reversible. The observed concanavalin A effects are probably mainly due to concanavalin A binding to platelet membrane glycoproteins. The concanavalin A binding site appears to play an important role in the fibrin binding to platelets.