Rapid genome walking: a simplified oligo-cassette mediated polymerase chain reaction using a single genome-specific primer

In the present report we show that unknown DNA fragments are easily amplified in a single PCR reaction from an oligo-cassette library with a single genome-specific primer in combination with a cassette-specific primer. The novelty of the system, in comparison to the vectorette PCR method, lies in the use of unphosphorylated in contrast with phosphorylated oligo-cassettes in the ligation to the chromosomal DNA fragments. After denaturation of the DNA library, all chromosomal fragments carry a single-stranded linker attached to the 5′-end only. Therefore, the presence of the vectorette mismatched region is not required when unphosphorylated cassettes are used. As an example we report the amplification of the era gene from Lactococcus lactis.     

Ice nucleation and antinucleation in nature

Plants and ectothermic animals use a variety of substances and mechanisms to survive exposure to subfreezing temperatures. Proteinaceous ice nucleators trigger freezing at high subzero temperatures, either to provide cold protection from released heat of fusion or to establish a protective extracellular freezing in freeze-tolerant species. Freeze-avoiding species increase their supercooling potential by removing ice nucleators and accumulating polyols. Terrestrial invertebrates and polar marine fish stabilize their supercooled state by means of noncolligatively acting antifreeze proteins. Some organisms also depress their body fluid melting point to ambient temperature by evaporation and/or solute accumulation.     

A description of Mallomonas marsupialis nov. sp. (Synurophyceae), a new chrysophyte from Australia, with comments on the endemicity of Australian freshwater algae

Mallomonas marsupialis is described and illustrated by TEM and SEM micrographs, being found in Australia on sub-tropical Fraser Island and in cool-temperate Tasmania. Its taxonomic location within the genus Mallomonas (sect. Mallomonopsis, ser. Marsupiales) is discussed, together with its inclusion in a suite of unusual endemic algae which have been described from Australian sites largely protected from human interference.     

Nitrogen uptake in the infiltration community, an ice algal community in Antarctic pack-ice

An infiltration community was the dominating ice algal community in pack-ice off Queen Maud Land, Southern Ocean, in January 1993. The community was dominated by autotrophic processes, and the most common species were the prymnesiophyte Phaeocystis antarctica and the diatoms Chaetoceros neglectus and Fragilariopsis cylindrus. The concentration of chlorophyll a was 1.3–47.9 μg l⁻¹, and the inner part of the community was nitrate depleted. Uptake rates of nitrate, nitrite, ammonium, urea and amino acids were measured using ¹⁵N. Nitrate was the major nitrogen source for ice algal growth (67 ± 6% nitrate uptake). It is suggested that % nitrate uptake in the infiltration community decreases during the growth season, from 92% during spring (literature data) to 67% during summer. Scalar irradiance in the infiltration community was high and variable. It reached ca. 2000 μmol m⁻² s⁻¹ at some locations, and nitrate uptake rate was potentially photoinhibited at irradiances >500 μmol m⁻² s⁻¹. Nitrate uptake rate in an average infiltration community (0.6 m of snow cover) was lowered by 13% over a 2-week period due to photoinhibition. Received: 16 December 1996 / Accepted: 5 January 1998     

Dietary and microtopographical selectivity of Greenland white-fronted geese feeding on Icelandic hayfields

The feeding ecology of Greenland white-fronted geese Anser albifrons flavirostris was studied during .spring staging in Iceland 1997. Geese feeding on Poa pratense dominated hayfields (> 80% cover) were highly selective, selecting for Deschampsia caespitosa which comprised only 10% of the sward. Geese fed most on the south-facing fringes of Deschampsia tussocks. Subsequent analysis showed that the southern fringes of Deschampsia tussocks supported significantly greater biomass (27% greater mass of green material) and that leaves growing on the southern faces had significantly higher protein content than those on the northern faces (33.9% vs 30.5%)_- It appears that the geese maximise their nutritional intake in spring by selecting the grass species of highest quality and taking the most nutritious parts of the plants.     

Citric acid production and morphology of Aspergillus niger as functions of the mixing intensity in a stirred tank and a tubular loop bioreactor

The relationship between Aspergillus niger morphology and citric acid production was investigated in two reactor systems with different configurations, a tubular loop and a stirred tank bioreactor, with operating volumes of 6 and 8 dm³, respectively. Morphology was quantified by image analysis. In each system, morphology, characterized by the parameter P (mean convex perimeter of clumps), and citric acid production, were agitation-dependent and closely linked. Increased agitation caused a reduction of clump sizes and results when both reactors demonstrate that the parameter P should not exceed a threshold value in order to achieve increased productivities. The results obtained from the two reactors were in agreement, both qualitatively and quantitatively. Reducing the fundamentally different mixing conditions of the two bioreactors to the order of the dimensionless mixing parameter relative mixing time (τ_m), results showed that the loop simulated the stirred tank. Also, relationships valid for one system accurately described the results obtained from the other system, demonstrating the validity of the relationship between morphology and productivity for the particular fermentation, regardless of the reactor type. Previous attempts to evaluate the use of loop configurations as scale-up tools and their performance as bioreactors, neglected the morphology of the producer micro-organisms. This study demonstrated the close link between morphology and productivity for citric acid production by A. niger, and identified a morphology parameter that was used successfully to characterize the process performance.     

Systems‐wide analysis of BCR signalosomes and downstream phosphorylation and ubiquitylation

B‐cell receptor (BCR) signaling is essential for the development and function of B cells; however, the spectrum of proteins involved in BCR signaling is not fully known. Here we used quantitative mass spectrometry‐based proteomics to monitor the dynamics of BCR signaling complexes (signalosomes) and to investigate the dynamics of downstream phosphorylation and ubiquitylation signaling. We identify most of the previously known components of BCR signaling, as well as many proteins that have not yet been implicated in this system. BCR activation leads to rapid tyrosine phosphorylation and ubiquitylation of the receptor‐proximal signaling components, many of which are co‐regulated by both the modifications. We illustrate the power of multilayered proteomic analyses for discovering novel BCR signaling components by demonstrating that BCR‐induced phosphorylation of RAB7A at S72 prevents its association with effector proteins and with endo‐lysosomal compartments. In addition, we show that BCL10 is modified by LUBAC‐mediated linear ubiquitylation, and demonstrate an important function of LUBAC in BCR‐induced NF‐κB signaling. Our results offer a global and integrated view of BCR signaling, and the provided datasets can serve as a valuable resource for further understanding BCR signaling networks.