Parser for protein folding units

General patterns of protein structural organization have emerged from studies of hundreds of structures elucidated by X-ray crystallography and nuclear magnetic resonance. Structural units are commonly identified by visual inspection of molecular models using qualitative criteria. Here, we propose an algorithm for identification of structural units by objective, quantitative criteria based on atomic interactions. The underlying physical concept is maximal interactions within each unit and minimal interaction between units (domains). In a simple harmonic approximation, interdomain dynamics is determined by the strength of the interface and the distribution of masses. The most likely domain decomposition involves units with the most correlated motion, or largest interdomain fluctuation time. The decomposition of a convoluted 3-D structure is complicated by the possibility that the chain can cross over several times between units. Grouping the residues by solving an eigenvalue problem for the contact matrix reduces the problem to a one-dimensional search for all reasonable trial bisections. Recursive bisection yields a tree of putative folding units. Simple physical criteria are used to identify units that could exist by themselves. The units so defined closely correspond to crystallographers' notion of structural domains. The results are useful for the analysis of folding principles, for modular protein design and for protein engineering. © 1994 Wiley-Liss, Inc.     

Organogenesis and fine structure in megagametophyte callus lines of Picea abies

Differentiation and fine structure were studied in 63 callus lines originating from the haploid megagametophyte of Picea abies (L.) Karst. Developing cones were collected from 27 trees growing in 13 localities in Finland. Vernalization of cones for 12–42 days at 4°C was optimal for callus initiation from the immature megagametophyte (primary endosperm). Five combinations of media based on the macronutrient elements of Chu et al. (1975; Sci. Sin. 18: 659–668) and the micronutrient elements and vitamins of Murashige and Skoog were tested for callus induction, growth and differentiation. Only about 1.5% of the megagametophytes produced subculturable callus (which may be partly due to the high frequency of lethal genes), although in certain mother trees callus production was as high as 20%. In most of the trees sampled, polyamines could not replace casein hydrolysate and glutamine in induction of megagametophyte callus. About half of the originally haploid, diploid and mixoploid callus lines were able to differentiate. A combination of three polyamines (putrescine 0.25, spermidine 0.1 and spermine 0.025 m M ) favoured development of roots. In five callus lines shoots and roots developed in the same piece of callus, but these organs usually had no connection with each other. The fine structure of the callus cells was normal, but their starch stores were rather abundant. Mesophyll cells of needles differentiated from originally haploid callus had chloroplasts with fairly well-developed grana. Secondary metabolites were observed in the vacuoles of some callus cells and in organ initials. Plasmodesmata were very rare in callus cells but they were characteristic of those of the needles. The electron microscope observations showed that the poor capacity for differentiation of P. abies callus cultures was not due to cytological instability.     

Fossil remains of an unknown Alona species (Chydoridae, Aloninae) from a high arctic lake in Nordaustlandet (Svalbard) in relation to glaciation and Holocene environmental history

We analyzed a lacustrine sediment core covering the Holocene from Lake Einstaken, Nordaustlandet, for its fossil Cladocera (Crustacea) with an aim to reconstruct past aquatic communities in this environmentally extreme and unexplored region. In the analysis, we encountered remains (carapaces, ephippia, headshields, and postabdomens) of an unknown chydorid (Chydoridae, Aloninae) species during two separate periods in the early Holocene. The remains had some comparable morphological characters with the European Alona guttata s.str. Sars, 1862 and with the glacial relict Alona werestschagini Sinev, 1999, but they differed clearly from the previous species; the headshield had broadly rounded rostrum and narrow fornices, the ephippium was heavily pigmented and reticulated, and the postabdomen had convex dorsal and ventral margins. The postabdomen had evidently similar morphology with Alona bergi R?en, 1992, which has been described, although inadequately, from arctic Canada and northern Greenland. We conclude, based on the morphology of the postabdomen, that the unknown remains belong to species closely resembling A. bergi, named here Alona cf. bergi, and assume that the species, whether the true A. bergi or some other cryptic species of the A. guttata group, is a postglacial relict of the high arctic adapted to cold climate. Herewith, we emphasize the need for extensive biogeographical investigations into both fossil and intact specimens of chydorids in the arctic.     

Immunoglobulin constant kappa gene alleles in twelve strains of mice

Genomic DNA for the immunoglobulin (Ig) constant kappa Igk-C gene region was amplified by the polymerase chain reaction (PCR) method and sequenced from twelve commonly used inbred mouse strains. PCR products were used directly as templates in dideoxy-DNA-sequencing, a method which avoids the sequencing errors caused by Taq polymerase, since no cloning step is required. In restriction fragment length polymorphism (RFLP) studies the SJL mouse strain has been shown to belong to a Igk-C allogroup different from other common inbred mouse strains. The BALB/c Igk-C region was sequenced earlier, but our Igk-C sequences clarify the situation and confirm the existence of three Igk-C alleles in inbred mice (Mus musculus domesticus). Mice belonging to the kappa (Igk) haplotype e (SJL) have allele c of the Igk-C gene. The strains belonging to the kappa haplotype [a albino strain, K subline (AKR), PL and d (C58)] have allele a, and all other eight strains belonging to three different Igk haplotypes (b, c, and f) use allele b of the gene. Allele b has at least one (possibly two) nucleotide differences from allele a in the Igk-C region, but five compared to allele c. The allelic sequences also predict two allotypic kappa polypeptide chains among twelve inbred strains. Alleles a and b encode identical polypetides, but allele c (SJL) has a conserved lysine to arginine substitution in residue 142.The nucleotide sequence data reported in this paper have been submitted to the EMBL nucleotide sequence database and have been assigned the accession numbers X67002-X67012.     

Searching protein structure databases has come of age

The number of protein structures known in atomic detail has increased from one in 1960 (Kendrew, J. C., Strandberg, B. E., Hart, R. G., Davies, D. R., Phillips, D. C., Shore, V. C. Nature (London) 185:422–427, 1960) to more than 1000 in 1994. The rate at which new structures are being published exceeds one a day as a result of recent advances in protein engineering, crystallography, and spectroscopy. More and more frequently, a newly determined structure is similar in fold to a known one, even when no sequence similarity is detectable. A new generation of computer algorithms has now been developed that allows routine comparison of a protein structure with the database of all known structures. Such structure database searches are already used daily and they are beginning to rival sequence database searches as a tool for discovering biologically interesting relationships. © 1994 Wiley-Liss, Inc.     

Individual variation in immune function in the ant Formica exsecta; effects of the nest, body size and sex

It has been generally thought that sex differences in the immune system are the result of the differing life history strategies of the sexes, although the available data are not entirely consistent with the hypothesis. In this study, we studied the variation in the immune function in the mound-building wood ant Formica exsecta. F. exsecta has two forms of males, distinguished by size: the small males (micraners) and the large males (macraners), which die after the mating period, whereas females live tens of years laying their eggs. We found that in general males have a lower encapsulation response against nylon monofilament (i.e. lower immune function) than queens. Among males, the micraners had a lower encapsulation rate than the macraners. However, in queens, there was no correlation between size and encapsulation rate. The origin nest had an effect on the encapsulation rate of males: males from the large nests had a stronger encapsulation rate than males from small nests. However, in queens, nest size did not have any effect on encapsulation response. The observed variation between sexes and individuals in the encapsulation rate is discussed in the context of reproductive strategies and parasite-mediated sexual selection.     

β-Carotene extraction from Dunaliella salina by supercritical CO2

This paper reports the results of supercritical carbon dioxide (scCO₂) extraction of β-carotene from Dunaliella salina as potential alternative to conventional organic solvent extraction. In pilot-scale scCO₂ experiments, the pressure, temperature, and co-solvent concentration were varied. The supercritical extraction at 500 bar, 70 °C, and 10 wt% ethanol as co-solvent yielded in the highly efficient pigment recovery of over 90%. Techno-economic assessment demonstrated higher energy consumption for the scCO₂ extraction that was compensated by lower solvent costs. Thus, comparable pigment production costs to the reference extraction with n-hexane were estimated for the scCO₂ process. Due to the green solvent properties of scCO₂ and ethanol, this approach is highly promising for extraction of algal biomass in industrial scale.

     

Sometimes hidden but always there: the assumptions underlying genetic inference of demographic histories

Demographic processes directly affect patterns of genetic variation within contemporary populations as well as future generations, allowing for demographic inference from patterns of both present-day and past genetic variation. Advances in laboratory procedures, sequencing and genotyping technologies in the past decades have resulted in massive increases in high-quality genome-wide genetic data from present-day populations and allowed retrieval of genetic data from archaeological material, also known as ancient DNA. This has resulted in an explosion of work exploring past changes in population size, structure, continuity and movement. However, as genetic processes are highly stochastic, patterns of genetic variation only indirectly reflect demographic histories. As a result, past demographic processes need to be reconstructed using an inferential approach. This usually involves comparing observed patterns of variation with model expectations from theoretical population genetics. A large number of approaches have been developed based on different population genetic models that each come with assumptions about the data and underlying demography. In this article I review some of the key models and assumptions underlying the most commonly used approaches for past demographic inference and their consequences for our ability to link the inferred demographic processes to the archaeological and climate records.This article is part of the theme issue ‘Cross-disciplinary approaches to prehistoric demography’.