Assessment of the scalability of a microtiter plate system for screening of oleaginous microorganisms

Applied Microbiology and Biotechnology - Recent developments in molecular biology and metabolic engineering have resulted in a large increase in the number of strains that need to be tested,...     

In vivo analysis of the regulatory genes in the nystatin biosynthetic gene cluster of Streptomyces noursei ATCC 11455 reveals their differential control over antibiotic biosynthesis

Six putative regulatory genes are located at the flank of the nystatin biosynthetic gene cluster in Streptomyces noursei ATCC 11455. Gene inactivation and complementation experiments revealed that nysRI, nysRII, nysRIII, and nysRIV are necessary for efficient nystatin production, whereas no significant roles could be demonstrated for the other two regulatory genes. To determine the in vivo targets for the NysR regulators, chromosomal integration vectors with the xylE reporter gene under the control of seven putative promoter regions upstream of the nystatin structural and regulatory genes were constructed. Expression analyses of the resulting vectors in the S. noursei wild-type strain and regulatory mutants revealed that the four regulators differentially affect certain promoters. According to these analyses, genes responsible for initiation of nystatin biosynthesis and antibiotic transport were the major targets for regulation. Data from cross-complementation experiments showed that nysR genes could in some cases substitute for each other, suggesting a functional hierarchy of the regulators and implying a cascade-like mechanism of regulation of nystatin biosynthesis.     

Nitrogen uptake in the Weddell Sea during late winter and spring

Summary Uptake rates of ammonium, nitrate and urea were measured during the EPOS leg 1 cruise to the Weddell Sea in October–November 1988 using the isotope ¹⁵N. Nitrate was the most important nitrogen source both for ice algae (f-ratio 0.88) and for phytoplankton in the water column (f-ratio 0.85). Indications of a gradual decrease in % new production with time were found in the outer marginal ice zone. Nitrogen uptake rates in ice algae from the sub-ice assemblage were light-limited at in situ irradiances. Significant regeneration of ammonium was found in ice algal samples only.Data presented here were collected during the European Polarstern Study (EPOS) sponsored by the European Science Foundation     

Female-biased dispersal, low female recruitment, unpaired males, and the extinction of small and isolated bird populations

Small and isolated populations are usually assumed to be at a high risk of extinction due to environmental or demographic stochasticity, genetic problems, or too little immigration. In birds, natal dispersal is usually female-biased, but the consequences of such a pattern on vulnerability to extinction of isolated populations has not received much attention before. In this paper I derive predictions as to how female-biased natal dispersal may differentially affect the extinction risk of populations and species with contrasting distributions, migratory behaviours, life histories and mating systems. Female-biased dispersal will lead to male-biased sex ratios in small, isolated or fragmented populations, in particular because recent research has shown that females often have a limited ability to search for mates and may therefore effectively be lost from the breeding population if they disperse into areas empty of conspecifics. I reviewed published studies on birds and found that a high proportion of unpaired males is common in isolated populations or populations in small habitat fragments. Dispersal of females may therefore increase the vulnerability to extinction of small or isolated populations, or populations at the periphery of a species' distribution range. I also predict that vulnerability to extinction should be greater for migratory than for resident species and greater for short-lived than for long-lived species because of differences in the time available for females to locate unpaired males. Further, extinction risk may also be greater for birds than for mammals due to differences in which sex disperses and patterns of parental care. Finally, mating system will also affect vulnerability to extinction when natal dispersal leads to biased sex ratios. I review available evidence for these predictions (e.g. songbird declines in North America) and discuss implications for conservation.     

A dense linkage map of hybrid cottonwood (Populus fremontii x P. angustifolia) contributes to long-term ecological research and comparison mapping in a model forest tree

Cottonwoods are foundation riparian species, and hybridization among species is known to produce ecological effects at levels higher than the population, including effects on dependent species, communities and ecosystems. Because these patterns result from increased genetic variation in key cottonwood traits, novel applications of genetic tools (for example, QTL mapping) could be used to place broad-scale ecological research into a genomic perspective. In addition, linkage maps have been produced for numerous species within the genus, and, coupled with the recent publication of the Populus genome sequence, these maps present a unique opportunity for genome comparisons in a model system. Here, we conducted linkage analyses in order to (1) create a platform for QTL and candidate gene studies of ecologically important traits, (2) create a framework for chromosomal-scale perspectives of introgression in a natural population, and (3) enhance genome-wide comparisons using two previously unmapped species. We produced 246 backcross mapping (BC(1)) progeny by crossing a naturally occurring F(1) hybrid (Populus fremontii x P. angustifolia) to a pure P. angustifolia from the same population. Linkage analysis resulted in a dense linkage map of 541 AFLP and 111 SSR markers distributed across 19 linkage groups. These results compared favorably with other Populus linkage studies, and addition of SSR loci from the poplar genome project provided coarse alignment with the genome sequence. Preliminary applications of the data suggest that our map represents a useful framework for applying genomic research to ecological questions in a well-studied system, and has enhanced genome-wide comparisons in a model tree.     

Genetic population structure of Euphausia superba DANA in the Atlantic Sector of the Southern Ocean as demonstrated by different electrophoretic techniques

Summary Electrophoretic analyses of allele distributions at nine polymorphic gene loci were conducted in samples of Euphausia superba from the Bransfield Strait, off the South Orkney Islands, and from the south-eastern part of the Weddell Sea. The aim was to determine whether reported phenotypic differences between krill stocks from these areas could be linked to genotypic differences. Despite minor deviations of genotype distributions from Hardy-Weinberg expectations, the data gave no evidence of genetic heterogeneity over the sampled area, and the hypothesis of a single genetically homogeneous krill population could not be rejected. Genetic data for four selected loci were verified by using two different electrophoretic methods. Results from these two techniques yielded no discrepancies in interpretation of the data.     

Sulfation in the Golgi lumen of Madin-Darby canine kidney cells is inhibited by brefeldin A and depends on a factor present in the cytoplasm and on Golgi membranes

Madin-Darby canine kidney cells are more resistant than most other cell types to the classical effects of brefeldin A (BFA) treatment, the induction of retrograde transport of Golgi cisternae components to the endoplasmic reticulum. Here we show that sulfation of heparan sulfate proteoglycans (HSPGs), chondroitin sulfate proteoglycans (CSPGs), and proteins in the Golgi apparatus is dramatically reduced by low concentrations of BFA in which Golgi morphology is unaffected and secretion still takes place. BFA treatment seems to reduce sulfation by inhibition of the uptake of adenosine 3'-phosphate 5'-phosphosulfate (PAPS) into the Golgi lumen, and the inhibitory effect of BFA was similar for HSPGs, CSPGs, and proteins. This was different from the effect of chlorate, a well known inhibitor of PAPS synthesis in the cytoplasm. Low concentrations of chlorate (2-5 mm) inhibited sulfation of CSPGs and proteins only, whereas higher concentrations (15-30 mm) were required to inhibit sulfation of HSPGs. Golgi fractions pretreated with BFA had a reduced capacity for the synthesis of glycosaminoglycans (GAGs), but control level capacity could be restored by the addition of cytosol from various sources. This indicates that the PAPS pathway to the Golgi lumen depends on a BFA-sensitive factor that is present both on Golgi membranes and in the cytoplasm.     

Geographic variation of the storing behaviour in the Coal tit Parus ater: role of winter residency and environmental conditions

Foraging and hoarding behaviour of the Coal Tit Parus ater were studied in two widely separated populations, in the Pyrenees and in Norway. The two populations differed in their degree of winter residence and environmental pressures. Location of foraging and hoarding sites were described in the Pyrenees during winter, and during autumn in Norway where no hoarding takes place during winter. Significant differences in the hoarding behaviour of Coal Tits between these areas were observed. In the Pyrenees, birds hoarded on inner and lower parts of the trees, using trunks and thick branches as caching sites, which are the substrates most heavily used in conditions of winter environmental stress. In Norway, birds hoarded items on outer and higher parts of the trees, mainly among needled twigs, which were the substrates used in normal foraging. Animal food was hoarded more frequently by the Norwegian population. Our results show that hoarding behaviour varies among populations and suggest that the differences recorded may be related to differences in competitive pressures and the prevailing environmental conditions. Furthermore, the absence of a safe long-term hoarding niche in the Norwegian population, due to interspecific competition, would make a strong sedentary habit difficult, offering a functional explanation for the differences observed in the degree of winter residence between Norwegian and Pyrenean Coal Tits.     

Elemental Composition (C, N, P) and Cell Volume of Exponentially Growing and Nutrient-Limited Bacterioplankton

Marine bacterioplankton were isolated and grown in batch cultures until their growth became limited by organic carbon (C), nitrogen (N), or phosphorus (P). Samples were taken from the cultures at both the exponential and stationary phases. The elemental composition of individual bacterial cells was analyzed by X-ray microanalysis with an electron microscope. The cell size was also measured. The elemental content was highest in exponentially growing cells (149 ± 8 fg of C cell⁻¹, 35 ± 2 fg of N cell⁻¹, and 12 ± 1 fg of P cell⁻¹; average of all isolates ± standard error). The lowest C content was found in C-limited cells (39 ± 3 fg of C cell⁻¹), the lowest N content in C- and P-limited cells (12 ± 1 and 12 ± 2 fg of N cell⁻¹, respectively), and the lowest P content in P-limited cells (2.3 ± 0.6 fg of P cell⁻¹). The atomic C:N ratios varied among treatments between 3.8 ± 0.1 and 9.5 ± 1.0 (average ± standard error), the C:P ratios between 35 ± 2 and 178 ± 28, and the N:P ratios between 6.7 ± 0.3 and 18 ± 3. The carbon-volume ratios showed large variation among isolates due to different types of nutrient limitation (from 51± 4 to 241 ± 38 fg of C μm⁻¹; average of individual isolates and treatments ± standard error). The results show that different growth conditions and differences in the bacterial community may explain some of the variability of previously reported elemental and carbon-volume ratios.     

Lumican is a major small leucine-rich proteoglycan (SLRP) in Atlantic cod (Gadus morhua L.) skeletal muscle

Knowledge on fish matrix biology is important to ensure optimal fish -quality, -growth and -health in aquaculture. The aquaculture industry face major challenges related to matrix biology, such as inflammations and malformations. Atlantic cod skeletal muscle was investigated for collagen I, decorin, biglycan, and lumican expression and distribution by real-time PCR, immunohistochemical staining and Western blotting. Immunohistochemical staining and Western immunoblotting were also performed using antibodies against glycosaminoglycan side chains of these proteoglycans, in addition to fibromodulin. Real-time PCR showed highest mRNA expression of lumican and collagen I. Collagen I and proteoglycan immunohistochemical staining revealed distinct thread-like structures in the myocommata, with the exception of fibromodulin, which stained in dense structures embedded in the myocommata. Chondroitinase AC-generated epitopes stained more limited than cABC-generated epitopes, indicating a stronger presence of dermatan sulfate than chondroitin sulfate in cod muscle. Lumican and keratan sulfate distribution patterns were strong and ubiquitous in endomysia and myocommata. Western blots revealed similar SLRPs sizes in cod as are known from mammals. Staining of chondroitin/dermatan sulfate epitopes in Western blots were similar in molecular size to those of decorin and biglycan, whereas staining of keratan sulfate epitopes coincided with expected molecular sizes of lumican and fibromodulin. In conclusion, lumican was a major proteoglycan in cod muscle with ubiquitous distribution overlapping with keratan sulfate. Other leucine-rich proteoglycans were also present in cod muscle, and Western blot using antibodies developed for mammalian species showed cross reactivity with fish, demonstrating similar structures and molecular weights as in mammals.