Computer programs for the analysis and the management of DNA sequences

A program package is described for the management and the analysis of DNA sequence data. The programs - with the exception of a few Fortran routines - are written in the programming language APL. They are best used interactively although batch processing is possible. The package has been in constant use for about 3 years and contains programs for most of the routine problems presently found in a DNA sequencing laboratory.

Computer support of DNA sequence analysis

The paper describes a package of APL-programs suited for the management and the analysis of DNA sequence data. Most of the application programs are related to experimental work in a DNA sequencing laboratory: Search for overlapping DNA fragments to construct complete DNA sequences; search for restriction sites; computing fragment patterns when cutting a DNA with restriction enzymes; plotting physical and genetic maps of a DNA; search for homologies as well as various counting procedures. More sophisticated programs are concerned with the prediction of RNA secondary structure and its graphical representation.

[Routine serum digoxin determination on hospital admission (author's transl)]

The purpose of the present study was the collection of data concerning digitalis treatment of patients outside hospital. The investigation was carried out on 200 patients over 60 years of age, consecutively admitted to a 750-bed general hospital (35% ot a medical ward, 65% to other specialities). An ECG and serum creatinine and digoxin determinations were performed on the day of admission and a careful history taken of the drugs administered before admission. 30 patients reported the use of digoxin or other digitalis drugs, whilst another 48 patients reported taking cardiac drugs in general. The prevalence of digoxin levels exceeding 2 ng/ml was 11.5% in the group of patients known to have taken digitalis preparations, 18% among the 92 patients with positive serum digoxin levels and highest (30%) in the subgroup admitted due to cardiac failure. In patients with digoxin levels above 2 ng/ml the prevalence of elevated serum creatinine values (greater than 1.2 mg%) was markedly increased. Among patients with normal serum creatinine levels the mean age of patients with digoxin levels above 2 ng/ml was significantly higher than of those with digoxin levels below 2 ng/ml. A clear correlation between digoxin levels and ECG changes was not demonstrable; simultaneous administration of diuretics promotes the appearance of electrocardiographic signs of digitalis toxicity.

Sequence of a ribosomal RNA gene intron from Tetrahymena

Recently, several genes coding for messenger RNA, transfer RNA and ribosomal RNA in eukaryotes have been found to be interrupted in their coding regions by DNA sequences which are not represented in the mature RNA transcripts (see ref. 1 for review). Many of these intervening sequences, or introns, are now known to be transcribed in the precursor RNA, from which they are subsequently processed out to form the mature RNA. As the intron-exon junctions must in some way be recognised for accurate splicing, the nucleotide sequences of these regions from a number of protein-coding and tRNA genes have been analysed. Sequence homologies were found at the splice points of the protein-coding gene introns from diverse organisms, but the tRNA intron boundaries were not similar to these. This has led to the speculation that different splicing activities are necessary for the processing of introns in mRNA and tRNA precursors. We report here the sequence of a ribosomal RNA gene intron from Tetrahymena in which intron-exon junctions differ from those analysed to date.

[Anticonvulsive combined therapy (author's transl)]

19 patients were treated with valproic acid (VPR) in combination with classical anticonvulsants (phenytoin, phenobarbitone, primidone, carbamazepine). Patients with a mean serum concentration of 340 micron moles/l showed a marked improvement as to the frequency of seizures or were even completely free from seizures, provided that the other anticonvulsants were also given in the therapeutic range. Cases showing only a slight reduction in seizure frequency or no improvement had a mean serum level of 229 micron moles/l. This investigation shows that in severe cases of epilepsy treated by combined therapy all given anticonvulsants must reach therapeutic levels to achieve effective control of seizures in most patients.

Determination of renal clearances of amylase/creatinine with chromogenic and enzymatic methods

Urinary amylase was estimated by chromogenic (amylochrome Roche) as well as enzymatic methods (SKI and Beckman: substrate starch and substrate maltotetraose respectively). Random and timed urines (24 hour collections) were analysed. Clearances of amylase gave different results dependent upon the amylase-test used and the glomerular filtration rate. Correlation between chromogenic and enzymatic methods (starch as substrate) was poor. The ratio of amylase and creatinine clearance was used to test different methods. Reference values for this ratio for the amylochrome method (N = 106) were 2.85 +/- 0.99% and for the Beckman-DS method (N = 60) 2.82 +/- 0.87%.

[The serum concentration of anticonvulsants -- pharmacokinetic findings and practical therapeutic applications (author's transl)]

Routine determination of the blood serum concentration of most of the usual anticonvulsants is possible by means of an immunoenzymatic method (EMIT). Determination of the total concentration permits conclusions as to the amount of available, unbound and, thus, effective amount of the substance. Regular determination of serum values provides insight into the relevant pharmacokinetics. Metabolism of anticonvulsants differs greatly among individuals and therefore considerable individual variation exists in the relation between the applied dose and the attained serum level. The metabolic rate of the various substances is unequal and, accordingly, the time necessary to reach a steady state and the half life is very variable. Metabolism may be altered by various biological adaptations, diseases or other drugs, causing alterations in the serum level of the anticonvulsant. Results obtained to date indicate a therapeutic threshold concentration range. In a certain percentage of patients seizures are abolished or diminish in frequency only on attaining such a serum level. In more benign cases an adequate therapeutic effect may be obtained with lower ("subtherapeutic") concentrations, while on the other hand, in malignant cases, no efficient control of seizure activity can be attained even at a high serum concentration. The method should be used in all problematic patients. Up to 50% of patients with insufficient control of seizures show improvement or, even, absence of seizures if this method is included in the therapeutic concept.

[Determination of alpha-amylase by an enzymatic kinetic method on the ABA-100 (author's transl)]

The enzymatic method of H. W. Schiwara (1972) Z. Klim. Chem. Klin. Biochem. 10,12--16 (reagents by Smith Kline Instruments), using the enzymatic reaction sequence alpha-amylase -- alpha-glucosidase -- hexokinase/glucose 6-phosphate dehydrogenase for the determination of alpha-amylase was evaluated on the ABA-100. The coefficient of variation for control sera and human pooled serum was 0.9--4.2% within series, and 1.4--6.6% day to day. Reference values for a healthy population (212 blood donors) in sera were 13--79 U/1 (+/- 2 SD), mean 46 U/1. In catch urines the values did not show a normal distribution; the minimal and maximal range for men was 58--385 U/1, for women 7--318 U/1. The kinetic curve of the enzymatic test was measured and the influence of glucose and linearity studied. In comparison with the enzymatic test, the chromogenic method Amlyochrom Roche was tested on the sera and urine of patients. The coefficient of correlation in sera was r = 0.975, in urine r = 0.965.

Nucleotide sequence of the recognition site of the B-specific restriction modification system in E. coli

Two sB mutations in the genome of bacteriophage fd were located by sequence analysis in the fd sequence at positions 971 and 6341. Base changes at or close to these positions in phage M13 and in phage fl am 124 also correlate with a loss of sensitivity to B restriction. From the sequence homology between the sequences at the two sB sites the recognition signal for the E. coli B restriction/modification enzzyme is predicted to be: 5' TGA---8N---TGCT 3' 3' ACT---8N---ACGA 5'.

Nucleotide sequence of bacteriophage fd DNA

The sequence of the 6,408 nucleotides of bacteriophage fd DNA has been determined. This allows to deduce the exact organisation of the filamentous phage genome and provides easy access to DNA segments of known structure and function.

[A simple and quick method for measuring low blood-glucose concentrations (author's transl)]

A new method of measuring glucose concentrations (Reflotest-Hypoglycemie) was tested on 141 serum samples and 119 capillary blood samples and compared with the hexokinase-glucose-6-phosphate dehydrogenase method. The Reflotest (reflectance meter) compared well with the reference test. Comparison of results with three sera measured by the method in six different laboratories indicated the accuracy of the test. Endogenous bilirubin, uric acid, and haematocrit values did not influence the result. The test is therefore suitable for quantitative measurements.

Structure of the orgin of DNA replication of bacteriophage fd

An RNA-polymerase-protected DNA fragment of 125 nucleotides from the origin of single-strand to double-strand replication of bacteriophage fd (ori-DNA) was located on the physical map of the phage genome. A stretch of 187 base pairs of DNA including the ori-DNA was sequenced. This DNA segment contains regions with a highly asymmetric pyrimidine/purine distribution next to regions with 2-fold symmetry that form stable hairpin structures in the viral DNA strand.

[The value of the blood xylose test in children with the malabsorption syndrome (author's transl)]

Blood xylose levels were studied 30, 60 and 90 minutes after oral administration of D-xylose in 121 patients aged 2 months to 12 years with symptoms of malabsorption. The results show that the 60-minute test aline is sufficiently accurate and the dose of 15g xylose/m2 surface area seems perferable to a uniform dosage of 5g xylose. Reference values of blood xylose were determined in children with normal intestinal mucosa and prove a significant difference between babies and elder children. Comparison between the results of the xylose test in normal children and in different conditions of intestinal mucosa showed that the one-hour blood xylose test is of little value in the selection of cases requiring primary diagnostic intestinal biopsy in children with malabsorption. This test, however, might be valuable in the control of patients with diagnosed coeliac disease and as a screening test for other members of those families.

[Quality control of coagulation tests (author's transl)]

The results of quality control of coagulation tests from intralaboratory control programmes are reported and compared with interlaboratory surveys. The test programme includes the following assays: the thromboplastin time (Quick), the partial thromboplastin time and the thrombotest. It can be seen from the results of the thromboplastin time that reliable figures were obtained from intralaboratory quality control examinations only (CV=7% to 13%). In comparison to these results great differences were found in interlaboratory surveys (CV=15% to 30%). The result of interlaboratory surveys of the thrombotest demonstrated a CV of 15% to 20%. The intralaboratory quality control of the partial thromboplastin time showed satisfactory reliability (CV=7.4%). Satisfactory conformity of results was obtained between different laboratories only by using common reagents (CV=8.7%). Possible factors responsible for deviations in laboratory examinations are discussed and proposals for improvement in the realibility of coagulation tests are made.

[Studies on the accuracy and precision of total serum cholesterol in regional interlaboratory trials (author's transl)]

The between-run precision of the Liebermann-Burchard reaction modified by Watson was, in our laboratory, 2-3%, the within-run coefficient of variation was 1-2%. The between-run precision of the enzymatic test was 3-4%, the within-run coefficient of variation was 3%. The regression analysis of 92 serum specimens from patients was y = -17.31 + 1.04 chi, the coefficient of regression was r = 0.996. Interlaboratory trials of serum cholesterol were studied in the normal and pathological range. Lyophilized samples of serum prepared commercially and from fresh specimens from patients were analysed by the method of Liebermann-Burchard as well as by the enzymatic procedure. Acceptable results estimated by Liebermann-Burchard were obtained in the different laboratories after using a common standard of cholesterol. The coefficient of variation of the enzymatic test in the interlaboratory trial was higher in comparison to the Liebermann-Burchard reaction. Methodological difficulties of the Liebermann-Burchard reaction are discussed and compared with the specific, enzymatic assay.

[Blood-sugar determination with the Reflomat (author's transl)]

A total of 710 blood samples was tested with the new Reflomat apparatus. There was a good correlation with the GOD-Perid method (correlation coefficient for serum r = 0.993; for whole blood r = 0.983). In two thirds of the cases deviation from the reference value was less than +/- 7 mg/dl for serum, less than +/- 14 mg/dl in 95%, the corresponding values for whole blood +/- 11 mg/dl and +/- 22 mg/dl, respectively. The percentage deviation from the reference value was below +/- 13% for serum, and under +/- 22% for whole blood in 95% of measurements. In the range under 100 mg/dl variations were much more marked for whole blood than at the higher levels (100-350 mg/dl). The accuracy of the Reflotest¿ system and the accuracy from day to day proved to be exceptionally good. In the range 100-200 mg/dl the variation coefficient was between 1 and 2%.