Spectral karyotyping refines cytogenetic diagnostics of constitutional chromosomal abnormalities

Karyotype analysis by chromosome banding is the standard method for identifying numerical and structural chromosomal aberrations in pre- and postnatal cytogenetics laboratories. However, the chromosomal origins of markers, subtle translocations, or complex chromosomal rearrangements are often difficult to identify with certainty. We have developed a novel karyotyping technique, termed spectral karyotyping (SKY), which is based on the simultaneous hybridization of 24 chromosome-specific painting probes labeled with different fluorochromes or fluorochrome combinations. The measurement of defined emission spectra by means of interferometer-based spectral imaging allows for the definitive discernment of all human chromosomes in different colors. Here, we report the comprehensive karyotype analysis of 16 samples from different cytogenetic laboratories by merging conventional cytogenetic methodology and spectral karyotyping. This approach could become a powerful tool for the cytogeneticists, because it results in a considerable improvement of karyotype analysis by identifying chromosomal aberrations not previously detected by G-banding alone. Advantages, limitations, and future directions of spectral karyotyping are discussed. Received: 4 August 1997 / Accepted: 8 September 1997     

Long-Term Miscanthus Yields Influenced by Location,Genotype, Row Distance,Fertilization and Harvest Season

Long-term yield studies in perennial crops like miscanthus are important to determine mean annual energy yield and the farmer’s economy. In two Danish field trials, annual yield of two miscanthus genotypes was followed over a 20-year period. The trials were established in 1993 on loamy sand in Foulum and on coarse sand in Jyndevad. Effects of genotype, row distance and fertilization were investigated. In both trials, yield development over time was characterized by an increase during the first years, optimum yields after 7–8 years and a decrease to a lower level which remained relatively constant from year 11 to 20. Spring harvest reduced the yield by 34–42 % compared to autumn harvest. In Foulum annual fertilization with 75 kg ha^?1 N increased the yield of the genotype Goliath (Miscanthus sinensis) by 26 %. Additional N fertilization only increased the yield of Goliath little, and the genotype Giganteus (Miscanthus?×?giganteus) did not respond to fertilization at all. The highest mean yield in Foulum for the period 1997–2012 was obtained with the shortest row distance (～18,000 rather than ～12,000 plants ha^?1) and harvested in late autumn, namely 13.1 and 12.0 Mg ha^?1 DM annually for Giganteus and Goliath, respectively. In Jyndevad, where only Goliath was studied, the highest yield during 1995–2001 was obtained by short row distance, autumn harvest and annual fertilization with 75 kg ha^?1 N, with yield increasing up to 116 % in response to fertilization. A mean yield of 14.4 Mg ha^?1 DM was achieved over the period 1995–2012.     

Identification of determinants that confer ligand specificity on the insulin receptor.

We have previously shown, using truncated soluble recombinant receptors, that substituting the 62 N-terminal amino acids of the alpha subunit from the insulin-like growth factor I receptor (IGFIR) with the corresponding 68 amino acids from the insulin receptor (IR) results in a chimeric receptor with an approximately 200-fold increase in affinity for insulin and only a 5-fold decrease in insulin-like growth factor I (IGFI) affinity (Kjeldsen, T., Andersen, A. S., Wiberg, F. C., Rasmussen, J. S., Sch?ffer, L., Balschmidt, P., M?ller, K. B., and M?ller, N. P. H. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 4404-4408). We demonstrate that these 68 N-terminal amino acids of the IR also confer insulin affinity on the intact IGFI holoreceptor both in the membrane-bound state and when solubilized by Triton X-100. Furthermore, this domain can be subdivided into two regions (amino acids 1-27 and 28-68 of the IR alpha subunit) that, when replacing the corresponding IGFIR sequences, increases the insulin affinity of truncated soluble receptor chimeras 8- and 20-fold, respectively, with only minor effects on the IGFI affinity. Within the latter of these two regions, we found that amino acids 38-68 of the IR, representing 13 amino acid differences from IGFIR, confer the same 20-fold increase in insulin affinity on the IGFIR. Finally, the amino acids from position 42 to 50 are not responsible for this increase in insulin affinity. We thus propose that at least two determinants within the 68 N-terminal amino acids of the insulin receptor are involved in defining the ligand specificity of the insulin receptor, and that one or a combination of the remaining seven amino acid differences between position 38 and 68 are involved in conferring insulin affinity on the insulin receptor.     

Significance of nucleotide sequence alignments: a method for random sequence permutation that preserves dinucleotide and codon usage

The similarity of two nucleotide sequences is often expressed in terms of evolutionary distance, a measure of the amount of change needed to transform one sequence into the other. Given two sequences with a small distance between them, can their similarity be explained by their base composition alone? The nucleotide order of these sequences contributes to their similarity if the distance is much smaller than their average permutation distance, which is obtained by calculating the distances for many random permutations of these sequences. To determine whether their similarity can be explained by their dinucleotide and codon usage, random sequences must be chosen from the set of permuted sequences that preserve dinucleotide and codon usage. The problem of choosing random dinucleotide and codon-preserving permutations can be expressed in the language of graph theory as the problem of generating random Eulerian walks on a directed multigraph. An efficient algorithm for generating such walks is described. This algorithm can be used to choose random sequence permutations that preserve (1) dinucleotide usage, (2) dinucleotide and trinucleotide usage, or (3) dinucleotide and codon usage. For example, the similarity of two 60-nucleotide DNA segments from the human beta-1 interferon gene (nucleotides 196-255 and 499-558) is not just the result of their nonrandom dinucleotide and codon usage.      

Three-year study of benthic algal spring bloom development in a small, Danish lowland stream

Seasonal development of benthic algae was studied over a three-year period in a small, nutrient-rich lowland stream to investigate inter-annual variation in the algal spring bloom and differences in algal biomass regulation on two different substrata: fine-grained sediments and stones. The algal spring bloom was initiated when irradiance at the sediment surface exceeded 7 mol photons m^-2 d^-1 and mean water velocity was concomitantly below the threshold for bed load transport in the stream. Large inter-annual and substratum-dependent differences in peak algal biomass were observed, thus suggesting that different parameters regulate algal biomass development on the two substrata. On fine-grained sediments algal biomass development was predominantly coupled to light availability, while on stony substrata algal composition and peak biomass might be affected by invertebrate grazing.     

Association between Atherosclerotic Diseases and Carboxyhaemoglobin Levels in Tobacco Smokers

In a cross-sectional study carboxyhaemoglobin (COHb) levels in tobacco smokers were found to provide a better indication of a person''s risk of having developed certain atherosclerotic diseases, including ischaemic heart disease, than the smoking history. In the age group 30-69 years a person with a COHb level of 5% or more was found to be 21 times (lower 95% confidence limit 3·3 times) as likely to be affected by these diseases as another person of the same age and sex with similar smoking history and current smoking habits but with a COHb level of less than 3%.     

The fluorescent protein iLOV as a reporter for screening of high-yield production of antimicrobial peptides in Pichia pastoris

The methylotrophic yeast Pichia pastoris is commonly used for the production of recombinant proteins at scale. The identification of an optimally overexpressing strain following transformation can be time and reagent consuming. Fluorescent reporters like GFP have been used to assist identification of superior producers, but their relatively big size, maturation requirements and narrow temperature range restrict their applications. Here, we introduce the use of iLOV, a flavin-based fluorescent protein, as a fluorescent marker to identify P. pastoris high-yielding strains easily and rapidly. The use of this fluorescent protein as a fusion partner is exemplified by the production of the antimicrobial peptide NI01, a difficult target to overexpress in its native form. iLOV fluorescence correlated well with protein expression level and copy number of the chromosomally integrated gene. An easy and simple medium-throughput plate-based screen directly following transformation is demonstrated for low complexity screening, while a high-throughput method using fluorescence-activated cell sorting (FACS) allowed for comprehensive library screening. Both codon optimization of the iLOV_NI01 fusion cassettes and different integration strategies into the P. pastoris genome were tested to produce and isolate a high-yielding strain. Checking the genetic stability, process reproducibility and following the purification of the active native peptide are eased by visualization of and efficient cleavage from the iLOV reporter. We show that this system can be used for expression and screening of several different antimicrobial peptides recombinantly produced in P. pastoris.     

The road to the first,fully active and more stable human insulin variant with an additional disulfide bond

Insulin, a small peptide hormone, is crucial in maintaining blood glucose homeostasis. The stability and activity of the protein is directed by an intricate system involving disulfide bonds to stabilize the active monomeric species and by their non‐covalent oligomerization. All known insulin variants in vertebrates consist of two peptide chains and have six cysteine residues, which form three disulfide bonds, two of them link the two chains and a third is an intra‐chain bond in the A‐chain. This classical insulin fold appears to have been conserved over half a billion years of evolution. We addressed the question whether a human insulin variant with four disulfide bonds could exist and be fully functional. In this review, we give an overview of the road to engineering four‐disulfide bonded insulin analogs. During our journey, we discovered several active four disulfide bonded insulin analogs with markedly improved stability and gained insights into the instability of analogs with seven cysteine residues, importance of dimerization for stability, insulin fibril formation process, and the conformation of insulin binding to its receptor. Our results also open the way for new strategies in the development of insulin biopharmaceuticals. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.