ploidyfrost: Reference-free estimation of ploidy level from whole genome sequencing data based on de Bruijn graphs

Polyploidy is ubiquitous and its consequences are complex and variable. A change of ploidy level generally influences genetic diversity and results in morphological, physiological and ecological differences between cells or organisms with different ploidy levels. To avoid cumbersome experiments and take advantage of the less biased information provided by the vast amounts of genome sequencing data, computational tools for ploidy estimation are urgently needed. Until now, although a few such tools have been developed, many aspects of this estimation, such as the requirement of a reference genome, the lack of informative results and objective inferences, and the influence of false positives from errors and repeats, need further improvement. We have developed ploidyfrost , a de Bruijn graph-based method, to estimate ploidy levels from whole genome sequencing data sets without a reference genome. ploidyfrost provides a visual representation of allele frequency distribution generated using the ggplot2 package as well as quantitative results using the Gaussian mixture model. In addition, it takes advantage of colouring information encoded in coloured de Bruijn graphs to analyse multiple samples simultaneously and to flexibly filter putative false positives. We evaluated the performance of ploidyfrost by analysing highly heterozygous or repetitive samples of Cyclocarya paliurus and a complex allooctoploid sample of Fragaria × ananassa. Moreover, we demonstrated that the accuracy of analysis results can be improved by constraining a threshold such as Cramér's V coefficient on variant features, which may significantly reduce the side effects of sequencing errors and annoying repeats on the graphical structure constructed.     

EFFECTS OF HELPER PROTEINS ENCODED BY p19 AND orf1-orf2 GENES ON Cyt1Aa PROTEIN EXPRESSION IN ACRYSTALLIFEROUS STRAIN OF BACILLUS THURINGIENSIS

A series of plasmids were constructed to examine the effects of p19 and orf1‐orf2 genes from Bacillus thuringiensis on Cyt1Aa synthesis and inclusion formation. The plasmids expressed the cyt1Aa gene along with either p19 or orf1‐orf2, or each of them coordinatively with p20 in the acrystalliferous strain of B. thuringiensis subsp. israelensis 4Q7. No effect on the expression of Cyt1Aa protein was found when P19 or Orf1‐Orf2 co‐expressed with Cyt1Aa. However, when including p20 gene, the constructs with p19 or orf1‐orf2 gene produced lower yield of Cyt1Aa proteins than without p19 or orf1‐orf2 gene. Electron microscopy observation and bioassay showed that P19 and Orf1‐Orf2 have no influence on the crystal size and toxicity of Cyt1Aa protein. It is presumed that P19 and Orf1‐Orf2 might have negative effects on Cyt1Aa synthesis in B. thuringiensis.     

Poplar (Populus nigra L.) plants transformed with aBacillus thuringiensis toxin gene: insecticidal activity and genomic analysis

Insect-resistant poplar (Populus nigra L.) plants have been produced by infecting leaves withAgrobacterium tumefaciens strains carrying a binary vector containing different truncated forms of aBacillus thuringiensis (B.t.) toxin gene under a duplicated CaMV 35S promoter. Putative transgenic plants were propagated by cuttings at two experimental farms (in Beijing and Xinjiang, China). At 2–3 years after transformation, 17 of them were selected on the bases of insect-tolerance and good silvicultural traits, and evaluated for insect resistance, for the presence of theB.t. toxin DNA fragment (Southern blots and PCR) and for the expression of the transgene (western and northern blots). Somaclonal variation, as suggested by the appearance of permanent changes in the shape of the leaves, was also investigated with molecular tools (RFLP (restriction fragment length polymorphism), RAPD (random amplified polymorphic DNA) and microsatellite DNA).Bioassays withApochemia cineraius andLymantria dispar on the leaves of the selected clones showed different and, in some cases, high levels of insecticidal activity. The molecular analysis demonstrated integration and expression of the foreign gene. Somatic changes were correlated to extensive genomic changes and were quantified in dendrograms, in terms of genomic similarity. The analysis of control plants suggested that genomic changes were correlated to thein vitro culture step necessary forA. tumefaciens-mediated gene transfer, rather than to the integration of the foreign genes.Three transgenic clones (12, 153 and 192), selected for insect resistance, reduced morphological changes and promising silvicultural traits, are now under large-scale field evaluation in six different provinces in China.     

A NEW SPECIES OF GENUS GRYPOCENTRUS RUTHE (HYMENOPTERA: ICHNEUMONIDAE)

Abstract  One new species of Grypocentrus , namely G. kasparyani , collected in Shenyang, China, is described.     

上海四膜虫接合生殖期间皮层细胞骨架蛋白的研究

本文采用生化抽提,结合电泳及显微技术,对上海四膜虫（Ｔｅｔｒａｈｙｍｅｎａｓｈａｎｇｈａｉｅｎｓｉｓ）Ｓ１皮层细胞骨架（ｃｏｒｔｉｃａｌｃｙｔｏｓｋｅｌｅｔｏｎ）的蛋白组份,及其在接合生殖期间的变化进行了一系列的研究,初次探索了Ｓ１株上海四膜虫在接合生殖中皮细胞骨架的蛋白组份及含量,并分析了它们与间期,接合分开时期同类蛋白相互间的差异,发现在接合生殖时期７６－８８ｋＤ蛋白有突出的表现,而９０ｋＤ和     

Exfoliative cytology in the evaluation of interferon treatment of cervical intraepithelial neoplasia

Local interferon injection in four patients with cervical intraepithelial neoplasia (CIN) regularly elicited progressive regression of the lesions. The response was observed with exfoliative cytology after each injection, guided by colposcopic examination. The cytologic changes showed a cytocidal effect mainly on the dyskaryotic cells, preceded by cellular degeneration not unlike that of nonspecific inflammation and accompanied by an increase in neutrophil infiltration. The cytologic response was closely correlated with partial or complete clinical regression based on the absence of viable or degenerated dyskaryotic cells in the cervical smears. Three patients showed complete clinical regression after treatment. One patient showed recurrent viable dyskaryotic cells when the dosage was reduced, and treatment was suspended temporarily although her lesion had regressed completely after five injections. Clinical recurrence was noted one week after viable dyskaryotic cells reappeared in her smears. These observations suggest that cytology may be a useful means of monitoring interferon treatment in CIN.     

Stereochemistry of the incorporation of valine methyl groups into methylene groups in cephalosporin C.

'Chiral methyl valines', i.e. samples of valine labelled stereospecifically in the methyl groups with 2H and 3H, were incorporated into cephalosporin C by a suspension of washed cells of Cephalosporium acremonium. Analysis by 3H n.m.r. of the cephalosporin C produced showed that the conversion of the 3-pro-S-methyl group of valine into the acetoxymethyl side-chain was a highly stereospecific process. By contrast, conversion of the 3-pro-R-methyl group into the endocyclic methylene group of the dihydrothiazine ring was shown to proceed by a non-stereospecific process.     

Pharmacological comparison of bPTH-(1–34) and other hypotensive peptides in the dog

The purpose of the present study was to compare the potency, effectiveness and duration of action of synthetic bPTH-(1–34) with those of other known hypotensive peptides in the anesthetized dog. Of sixteen peptides tested in the present study only 8 were demonstrated to possess hypotensive activity. While bPTH-(1–34) was one of the least potent of the hypotensive peptides, it was equal to or greater than the other peptides in terms of effectiveness and duration of action. Of all the peptides studied, substance P and eledoisin were the most potent in terms of their hypotensive action. It is suggested that perhaps substance P and eledoisin might act at a different site or through different mechanisms than do vasoactive intestinal peptide (V.I.P.), corticotropin inhibiting peptide (C.I.P.), neurotensin, xenopsin, bradykinin and bPTH-(1–34).     

HLA genotypes and HLA-linked genetic markers in Italian patients with classical 21-hydroxylase deficiency

Summary HLA genotype and HLA-linked marker data for 40 unrelated patients from central Italy and 2 unrelated patients from Sardinia with congenital adrenal hyperplasia due to 21-hydroxylase deficiency (21-OH-def) were analyzed. The results confirm that the HLA-linked 21-OH-def gene is associated with several different HLA determinants and complete HLA haplotypes, although the only determinant with significantly increased frequency was the complement C2 allele C2B. The HLA antigens B8 and DR3 were found in significantly decreased frequencies. The haplotype A3, Cw6, Bw47, BfF, DR7, which is exceptionally rare in the general population but which has been found in many other 21-OH-def patients from diverse geographical origins, was also found in one of the Italian patients. This and other HLA haplotype associations found among the Italian patients may represent mutations that have occurred on HLA haplotypes with genetic linkage disequilibrium or, alternatively, may represent mutations that have not yet had time to become randomly associated with different HLA complex determinants. The marked negative associations with B8 and DR3 could, however, result from an interaction between the gene products of the HLA complex and the 21-OH-def phenotype.