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.     

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.     

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.     

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.     

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.     

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 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.     

A Molecular approach to chromosome organization

A 315 kb walk in the genetically well characterized rosy region of the Drosophila chromosomes permits a molecular analysis of chromosome organization. Polytene chromosome bands in this region range from less than 7 kb to about 160 kb and the level of DNA replication is constant within bands and among bands and interbands. A good numerical and topographical correspondence is found between chromomeric units and genetic units.     

Replication variants of the human inactive X chromosome

The sequence of DNA replication was studied within the inactive X chromosome in human lymphocytes, by means of the FPG method. Several variants of the replication sequence were found. The number of variants in the cells of a single donor exceeded 2 in each of the 4 normal individuals studied. The phenomenon is discussed with respect to the regulation of DNA synthesis and to the cell differentiation process.     

Replication variants of the human inactive X chromosome

Replication variants of the inactive X chromosome were investigated in lymphocytes from six donors by means of terminal BrdU or thymidine incorporation. There were interindividual differences in the incidence of particular variants. In endoreduplicated and tetraploid cells both allocyclic X chromosomes showed the same replication sequence. The Xp22 band of the allocyclic X chromosome seemed to replicate later than the homologous material in some cells. Initiation time of DNA synthesis within the inactive X chromosome was found to be stable; termination time, however, varied greatly relative to the other chromosomes. Early completion of replication within the heterochromatic X chromosome could be demonstrated preferentially for the Xq25–27 terminal sequence, but other variants expressed the phenomenon also. A variable replication rate of the inactive X chromosome is believed to be responsible for its asynchronous, independent replication. The biological significance of the phenomenon is discussed with respect to cell differentiation.