A new approach in the evaluation of chromosome variants in man

Summary A new approach is proposed for the evaluation of chromosome variants, which uses a scanning microdensitometer in the determination of the area of a variant. Results are assigned into five classes based on the difference from an average in terms of standard deviation. In the first two papers of the present series, results obtained in C variants of 1, 9, and 16 and LBA variants in 12 pairs lacking an established variable site (e.g., nos. 2, 5, 6, etc.) were described.In the present communication, results obtained in pairs with a known Q-variable site are described. When a variable region outside of ±1 SD of the average is defined as a variant, 9, 11, 7, 10, and 10 variants are detected in pairs 13, 14, 15, 21, and 22, respectively, from 12 individuals by means of LBA preparations, in addition to Q variants, which can be detected by the standard QFQ technique.     

A long Y chromosome in man

Summary An unusually long Y chromosome was described in the phenotypically normal father and paternal grandfather of a girl with Down's syndrome, and likewise in a male infant with multiple malformations and his father, normal in phenotype. Measurements revealed that the long Y chromosome corresponded in length to autosomes of group 16–18.Information was obtained to show that the increased length of the Y chromosome was an inheritable character, and that a long Y chromosome was not always associated with an abnormal phenotype (or phenotypes).Contribution No. 585 from the Zoological Institute, Hokkaido University.     

A new disease-specific machine learning approach for the prediction of cancer-causing missense variants

High-throughput genotyping and sequencing techniques are rapidly and inexpensively providing large amounts of human genetic variation data. Single Nucleotide Polymorphisms (SNPs) are an important source of human genome variability and have been implicated in several human diseases, including cancer. Amino acid mutations resulting from non-synonymous SNPs in coding regions may generate protein functional changes that affect cell proliferation. In this study, we developed a machine learning approach to predict cancer-causing missense variants. We present a Support Vector Machine (SVM) classifier trained on a set of 3163 cancer-causing variants and an equal number of neutral polymorphisms. The method achieve 93% overall accuracy, a correlation coefficient of 0.86, and area under ROC curve of 0.98. When compared with other previously developed algorithms such as SIFT and CHASM our method results in higher prediction accuracy and correlation coefficient in identifying cancer-causing variants.     

A new approach to chromosome doubling for haploid rice plants

Summary Rice nodal segments from three flowering haploids were excised and treated for different lengths of time with 0.3% or 0.4% colchicine (dissolved in 2% DMSO) in an attempt to induce fertile seeds. A combination of higher colchicine concentration and longer hours of treatment reduced the survival rate of treated segments, but more fertile plants were transformed. Pooled data showed that of the 842 segments used, 42.2% survived the treatment and sprouted, but only 31.9% were successfully established and grown to maturity. Among the 269 mature plants, 29,4% produced fertile seeds (panicles) with an average of 146.2 seeds per diploidized plant.     

New gene assignments in the baboon and new chromosome homoeologies with man

Eight new gene assignments were demonstrated in the baboon (Papio papio, PPA) by cosegregation analysis of twelve hybrid clones obtained by fusion between PPA fibroblasts and a mouse cell line deficient in thymidine kinase. The following markers and syntenic groups were assigned: SOD1 to PPA3, GLO-ME1 to PPA-4, PGM2 to PPA5, CKBB-SORD to PPA7, LDHB to PPA11 and LDHA to PPA14. These localizations are in agreement wit hthe following homoeologies with the human karyotype: PPA3-HSA21, PPA4-HSA6, PPA5-HSA4, PPA7-HSA14 and 15, PPA11-HSA12, PPA14-HSA11.     

Quantitative differences between variants of A spermatogonia in man

The area of cytoplasm, nucleus, nucleolus and mitochondria, as well as the elongation and irregular outline of the nucleus were determined, on electron micrographs by using an image analyser, for Ap (pale), Ad (dark with intranuclear vacuole), Ad-like (dark without intranuclear vacuole), Ac (cloudy) and Al (long) human spermatogonia. Ap and Ac spermatogonia had larger nucleus, larger nucleolus, and more cytoplasm than did Ad, Ad-like, and Al spermatogonia. In addition, the nuclei of Ap and Ac spermatogonia were more spherical and had a more distinct outline.     

Amylase heterogeneity variants in man

The existence of six amylase heterogeneity variants in serum and urine has been discovered in a group of 111 families with twins, and the frequence of each variant was determined. It had been shown that each of these amylase heterogeneity variants is inherited codominantly, and the mode of inheritance is demonstrated schematically.These amylase heterogeneity variants may be used as an aid to twin zygosity determination and also in paternity problems.     

LBA technique in the detection of chromosome variants

Summary In Part I of this communication, a technique (LBA) was described which used DNA replication in the evaluation of chromosome variants in man. It was shown that the method was very useful in the detection of variants in D-and G-group chromosomes. Results on pairs 3 and 4 were also presented.In Part II, the rest of chromosomes were examined. In the evaluation of qh variants in 1,9 and 16, the LBA technique proved itself to be a very effective implement. It was practically free of technical variables coherent with C-band technique and, therefore, it was possible to use the size of an euchromatic segment of a chromosome as a reference standard. LBA variants were observed in about 50% of the members of the remaining 12 pairs of chromosomes, i.e., 2, 5, 6, 7, 8, 10, 11, 12, 17, 18, 19, and 20.     

LBA technique in the detection of chromosome variants

Summary A method is described (LBA method) which uses DNA replication pattern in the detection of chromosome variants in man. In Part I, results on chromosomes with known sites of Q-variants, i.e., 5 pairs of acrocentrics, as well as 3 and 4, were presented.Fourty-one variants were detected in a total of 40 acrocentrics. Twentyeight of them were detected only by the LBA technique; 11 of them being in short arms and 17 of them in centromeres. Seven variants, including 4 of those in satellites, were detected only in QFQ-stained metaphases. Six short-arm variants were observed by both methods. It appears that a sequential QFQ-LBA technique is very useful in the detection of variants in D- or G-group chromosomes.     

Expression in lymphocyte and fibroblast culture of the fragile X chromosome: A new technical approach

Summary By studying those conditions most favourable for the expression of the fragile site fra(X)(q28) in lymphocytes and in fibroblasts, we have been able to develop a reliable and standardised technique. The technique which gave the best results in lymphocytes was culture in TC 199 for 96 h with addition of methotrexate 10 mg/l for the final 24 h. These same two factors, prolongation of the culture time in TC 199 and addition of methotrexate, gave satisfactory results in fibroblasts.Supported by grants from I.N.S.E.R.M. (A.T.P. 79-110)     

A new approach to biochemical evaluation of brain dopamine metabolism

1. Dopaminergic neurotransmission in brain is receiving increased attention because of its known involvement in Parkinson's disease and new methods for the treatment of this disorder and because of hypotheses relating several psychiatric disorders to abnormalities in brain dopaminergic systems. 2. Chemical assessment of brain dopamine metabolism has been attempted by measuring levels of its major metabolite, homovanillic acid (HVA), in cerebrospinal fluid, plasma, or urine. Because HVA is derived in part from dopamine formed in noradrenergic neurons, plasma levels and urinary excretion rates of HVA do not adequately reflect solely metabolism of brain dopamine. 3. Using debrisoquin, the peripheral contributions of HVA to plasma or urinary HVA can be diminished, but the extent of residual HVA formation in noradrenergic neurons is unknown. By measuring the levels of methoxy-hydroxyphenylglycol (MHPG) in plasma or of urinary norepinephrine metabolites (total MHPG in monkeys; the sum of total MHPG and vanillyl mandelic acid (VMA) in humans) along with HVA, it is possible to estimate the degree of impairment by debrisoquin of HVA formation from noradrenergic neuronal dopamine and thereby better assess brain dopamine metabolism. 4. This method was applied to a monkey before and after destruction of the nigrostriatal pathway by the administration of MPTP.     

A new chromosome model

We present a new model of the three-dimensional structure of chromosomes. With DNA and protein staining it could be shown by high-resolution scanning electron microscopy that metaphase chromosomes are mainly composed of DNA packed in "chromomeres" (coiled solenoides) and a dynamic matrix formed of parallel protein fibers. In the centromeric region, the chromomeres are less densely packed, giving insight into the matrix fibers. We postulate that chromosome condensation is achieved by the binding of solenoids to matrix fibers which have contact sites to one another and move antiparallel to each other. As condensation progresses, loops of solenoids accumulate to form additional chromomeres, causing chromosomes to become successively shorter and thicker as more chromomeres are formed. For sterical reasons, a tension vertical to the axial direction forces the chromatids apart. The model can simply explain the enormous variety of chromosome morphology in plant and animal systems by varying only a few cytological parameters. Primary and secondary constrictions and deletions are defined as regions devoid of chromomeres. Even in the highly condensed metaphase, all genes would be easily accessible.     

Structural aberrations of the X chromosome in man

Summary Among 209 patients with Shereshevsky-Turner syndrome, 69 women with structural aberrations of X chromosome were detected: 46,X, i(Xq)-11; 45,X/46,X,i(Xq)-24; 45,X/46,X,r(X)-14; 45,X/46,X,f(X or Y)-10; 45,X/46,X,del(Xq)-4; 45,X/46,X,del(Xp)-2; 45,X/46,X,idic(X)-2; 46,X,idic(X)-1; and 46,X,t(X,2)-1. All the patients with structural abnormalities of X chromosome were short in stature, but in no group was it as low on the average as in 45,X cases. Somatic signs were noticed in all structural changes of X, but they were less frequent and less pronounced. In some patients with r(X) and i(Xq), spontaneous menstrual bleeding and breast development was found.The structurally abnormal X chromosome appears to be functionally inactive, the phenotype of patients with structural rearrangements being close to the phenotype of patients with X monosomy. At the same time, the abnormal X might have certain effects in early embryogenesis which mitigated the further development of the Shereshevsky-Turner syndrome.