The activin receptor-like kinase 1 gene: genomic structure and mutations in hereditary hemorrhagic telangiectasia type 2.

The activin receptor-like kinase 1 gene (ALK-1) is the second locus for the autosomal dominant vascular disease hereditary hemorrhagic telangiectasia (HHT). In this paper we present the genomic structure of the ALK-1 gene, a type I serine-threonine kinase receptor expressed predominantly in endothelial cells. The coding region is contained within nine exons, spanning < 15 kb of genomic DNA. All introns follow the GT-AG rule, except for intron 6, which has a TAG/gcaag 5' splice junction. The positions of introns in the intracellular domain are almost identical to those of the mouse serine-threonine kinase receptor TSK-7L. By sequencing ALK-1 from genomic DNA, mutations were found in six of six families with HHT either shown to link to chromosome 12q13 or in which linkage of HHT to chromosome 9q33 had been excluded. Mutations were also found in three of six patients from families in which available linkage data were insufficient to allow certainty with regard to the locus involved. The high rate of detection of mutations by genomic sequencing of ALK-1 suggests that this will be a useful diagnostic test for HHT2, particularly where preliminary linkage to chromosome 12q13 can be established. In two cases in which premature termination codons were found in genomic DNA, the mutant mRNA was either not present or present at barely detectable levels. These data suggest that mutations in ALK-1 are functionally null alleles.     

Characterization of the variable-number tandem repeats in vrrA from different Bacillus anthracis isolates.

PCR analysis of 198 Bacillus anthracis isolates revealed a variable region of DNA sequence differing in length among the isolates. Five polymorphisms differed by the presence of two to six copies of the 12-bp tandem repeat 5'-CAATATCAACAA-3'. This variable-number tandem repeat (VNTR) region is located within a larger sequence containing one complete open reading frame that encodes a putative 30-kDa protein. Length variation did not change the reading frame of the encoded protein and only changed the copy number of a 4-amino-acid sequence (QYQQ) from 2 to 6. The structure of the VNTR region suggests that these multiple repeats are generated by recombination or polymerase slippage. Protein structures predicted from the reverse-translated DNA sequence suggest that any structural changes in the encoded protein are confined to the region encoded by the VNTR sequence. Copy number differences in the VNTR region were used to define five different B. anthracis alleles. Characterization of 198 isolates revealed allele frequencies of 6.1, 17.7, 59.6, 5.6, and 11.1% sequentially from shorter to longer alleles. The high degree of polymorphism in the VNTR region provides a criterion for assigning isolates to five allelic categories. There is a correlation between categories and geographic distribution. Such molecular markers can be used to monitor the epidemiology of anthrax outbreaks in domestic and native herbivore populations.     

Cells resembling hair cells in developing rat olfactory and nasal respiratory epithelia

A hitherto ignored microvillous cell type, distinct from microvillous supporting cells and other microvillous cell types, was encountered in olfactory and respiratory epithelia of nasal turbinates of rat fetuses, near the transition between these two epithelia. The apex of the cell resembles the apices of vestibular hair cells. The cell has a cone-shaped bundle of microvilli, resembling the complex bundle of hair-cell stereocilia, accompanied by a cilium. Therefore we called this cell type the nasal hair cell. Cilium and microvilli seemed adhered. Cell numbers were very low, up to about 5 per turbinate. The cell's appearance is precocious compared to that of olfactory receptor and supporting cells. Also, while the apices of olfactory receptor and supporting cells and of ciliated respiratory cells underwent major morphological maturation during the developmental period from embryonic day 16 to day 21, the apical structures of the nasal hair cell only changed marginally from embryonic day 16, when they were first seen, through to at least embryonic day 21. The cell's location and precociously mature appearance suggests that it plays a special role in the development of nasal epithelia.     

Conservation of rice genetic resources: the role of the International Rice Genebank at IRRI

Rice genetic resources, comprising landrace varieties, modern and obsolete varieties, genetic stocks, breeding lines, and the wild rices, are the basis of world food security. The International Rice Genebank at the International Rice Research Institute in the Philippines conserves the largest and most diverse collection of rice germplasm. The facilities of the genebank ensure the long-term preservation of this important diversity. In field research, factors that affect long-term viability of rice seeds have been identified, leading to the introduction of modified practices for germplasm multiplication and regeneration. The value of conserved germplasm can be assessed in terms of useful traits for rice breeding and the economic impact that germplasm utilization has on rice production and productivity. The application of molecular markers is changing perspectives on germplasm management. International policies affecting access to and use of rice germplasm are discussed.     

Phylogenetic Analysis of Heterothallic Neurospora Species

We examined the phylogenetic relationships among five heterothallic species of Neurospora using restriction fragment polymorphisms derived from cosmid probes and sequence data from the upstream regions of two genes, al-1 and frq. Distance, maximum likelihood, and parsimony trees derived from the data support the hypothesis that strains assigned to N. sitophila, N. discreta, and N. tetrasperma form respective monophyletic groups. Strains assigned to N. intermedia and N. crassa, however, did not form two respective monophyletic groups, consistent with a previous suggestion based on analysis of mitochondrial DNAs that N. crassa and N. intermedia may be incompletely resolved sister taxa. Trees derived from restriction fragments and the al-1 sequence position N. tetrasperma as the sister species of N. sitophila. None of the trees produced by our data supported a previous analysis of sequences in the region of the mating type idiomorph that grouped N. crassa and N. sitophila as sister taxa, as well as N. intermedia and N. tetrasperma as sister taxa. Moreover, sequences from al-1, frq, and the mating-type region produced different trees when analyzed separately. The lack of consensus obtained with different sequences could result from the sorting of ancestral polymorphism during speciation or gene flow across species boundaries, or both.     

Optimizing nutritional conditions for the liquid culture production of effective fungal biological control agents

Spores of fungal pathogens of weeds and insects are unique in their ability to actively infect and kill their pest host. While these capabilities are advantageous in terms of their use as a contact biological control agent, or biopesticide, they also require special consideration during spore production. Directed approaches to medium optimization must consider not only spore yield but also spore qualities such as desiccation tolerance, stability as a dry preparation, and biocontrol efficacy. Nutritional conditions during culture growth and sporulation should direct the accumulation of appropriate endogenous reserves so that newly formed spores possess these advantageous qualities. Studies with the bioherbicidal fungus Colletotrichum truncatum and with the bioinsecticidal fungus Paecilomyces fumosoroseus have demonstrated the impact of nutrition on spore ‘fitness’ for use as a biological control agent. The optimization strategy used in these nutritional studies as well as a comparison of the results are presented. Received 06 February 1997/ Accepted in revised form 29 May 1997     

Carolina Chickadee (Aves, Paridae, Poecile carolinensis) Vocalization Rates: Effects of Body Mass and Food Availability under Aviary Conditions

We evaluated the effect of body mass and several environmental factors on vocalization rates of Carolina chickadees ( Poecile carolinensis ) housed in an aviary. Two different nonsong vocalizations (tseet and chick-a-dee) and song (fee-bee fee-bay) were recorded. Food was delivered from a feeder and three different levels of food access were presented to each bird: 10, 40 and 55 min/d. Two scales of body mass were measured: 'dawn mass' and 'focal mass' (mass during a focal observation divided by dawn mass). Across all birds, there was a significant negative correlation between both nonsong vocalization rates and body mass (both dawn and focal mass) and the effect of mass on call rate was greatest for days when food was relatively abundant. Nonsong vocalizations were also given at higher rates when food was limited (10 min/d) than when food was more abundant (40 and 55 min/d). No changes in call rates with time of day were observed. Overall, song rates were substantially lower than nonsong rates. Unlike nonsong rates, song rates were highest in birds that had relatively high dawn mass. No significant correlation between song rates and focal mass was observed, and no significant correlation between song rates and time of day was observed. Finally, vocalizations from nonfocal birds had little effect on vocalization rates of focal birds. Our results suggest that nonsong communicative signals are more important for birds facing energetic stress, while song is more important for birds that are not energetically stressed.     

THE FATTY ACID AND STEROL COMPOSITION OF FIVE MARINE DINOFLAGELLATES

The fatty acid and sterol compositions of five species of marine dinoflagellates (Scrippsiella sp. Symbiodinium microadriaticum Freud, Gymnodinium sp., Gymnodinium sanguineum Hirasaki, and Fragilidium sp.) are reported. All contained the major fatty acids that are considered common in dinoflagellates, but the proportions were quite variable, and some species contained low contents of some polyunsaturated fatty acids. Concentration ranges for the major fatty acids were: 16:0 (9.0%–24.8%), 18:4(n-3) (2.5%–11.5%), 18:5(n-3) (7.0%–43.1%), 20:5(n-3) (EPA) (1.8%–20.9%), and 22:6(n-3) (DHA) (9.9%– 26.3%). Small amounts of novel very-long-chain highly unsaturated C₂₈ fatty acids occurred in all species. Each dinoflagellate contained a complex mixture of 4-methyl sterols and 4-desmethyl sterols. Four species contained cholesterol, although the amounts were highly variable (from 0.2% of total sterols in Scrippsiella sp. to 45.6% in Fragilidium sp.). All but G. sanguineum contained the 4-methyl sterol dinosterol, and all species contained sterols lacking a double bond in the ring system (i.e. stanols); in Scrippsiella sp. cholestanol composed 24.3% of the total sterols. Other common features of the 4-methylsterol profiles were the presence of 23,24-dimethyl alkylation and unsaturation at Δ²² in the side chain. In Scrippsiella sp., four steroidal ketones were identified: cholestanone, dinosterone, 4α,23,24-trimethyl-5α-cholest-8(14)-en-3-one, and dinostanone. The structures of these corresponded to the major sterols in this species, suggesting that the sterols and steroidal ketones are biosynthetically linked. Steroidal ketones were not detected in the other species. Although fatty acid profiles can be used to distinguish among algal classes, they were not useful for differentiating among dinoflagellate species. In contrast, whereas some taxonomic groupings of dinoflagellates display similar sterol patterns, others, such as the gymnodinoids studied here, clearly do not. The combination of fatty acid, sterol, and steroidal ketone profiles may be useful complementary chemotaxonomic tools for distinguishing morphologically similar species. The identification of steroidal ketones supports earlier suggestions that certain dinoflagellates might be a significant source of such components in marine environments.     

Host determinants of DNA alkylation and DNA repair activity in human colorectal tissue: O(6)-methylguanine levels are associated with GSTT1 genotype and O(6)-alkylguanine-DNA alkyltransferase activity with CYP2D6 genotype.

There is increasing evidence that alkylating agent exposure may increase large bowel cancer risk and factors which either alter such exposure or its effects may modify risk. Hence, in a cross-sectional study of 78 patients with colorectal disease, we have examined whether (i) metabolic genotypes (GSTT1, GSTM1, CYP2D6, CYP2E1) are associated with O(6)-methyldeoxyguanosine (O(6)-MedG) levels, O(6)-alkylguanine-DNA alkyltransferase (ATase) activity or K-ras mutations, and (ii) there was an association between ATase activity and O(6)-MedG levels. Patients with colon tumours and who were homozygous GSTT1(*)2 genotype carriers were more likely than patients who expressed GSTT1 to have their DNA alkylated (83 versus 32%, P=0.03) and to have higher O(6)-MedG levels (0.178+/-0.374 versus 0.016+/-0.023 micromol O(6)-MedG/mol dG, P=0.04) in normal, but not tumour, DNA. No such association was observed between the GSTT1 genotype and the frequency of DNA alkylation or O(6)-MedG levels in patients with benign colon disease or rectal tumours. Patients with colon tumours or benign colon disease who were CYP2D6-poor metabolisers had higher ATase activity in normal tissue than patients who were CYP2D6 extensive metabolisers or CYP2D6 heterozygotes. Patients with the CYP2E1 Dra cd genotype were less likely to have a K-ras mutation: of 55 patients with the wild-type CYP2E1 genotype (dd), 23 had K-ras mutations, whereas none of the 7 individuals with cd genotype had a K-ras mutation (P=0.04). No other associations were observed between GSTT1, GSTM1, CYP2D6 and CYP2E1 Pst genotypes and adduct levels, ATase activity or mutational status. O(6)-MedG levels were not associated with ATase activity in either normal or tumour tissue. However, in 15 patients for whom both normal and tumour DNA contained detectable O(6)-MedG levels, there was a strong positive association between the normal DNA/tumour DNA adduct ratio and the normal tissue/tumour tissue ATase ratio (r(2)=0.66, P=0.001). These results indicate that host factors can affect levels both of the biologically effective dose arising from methylating agent exposure and of a susceptibility factor, the DNA repair phenotype.     

Determination of twin zygosity: a comparison of DNA with various questionnaire indices.

This study examined cross-validation and test-retest reliability of questions and questionnaire indices commonly used for twin zygosity classification. Mothers of 58 monozygotic (MZ) and 52 dizygotic (DZ) same sex twin pairs were interviewed by telephone to answer questions regarding the similarity of their twins (mean age = 14.6 +/- 2.8 years). A logistic regression equation correctly classified 91% of both MZ and DZ twin pairs in our sample using 7 of the 12 zygosity questions. The internal consistency for the total questionnaire (Cronbach's alpha) was 0.88. The median two month temporal stability estimate for the individual questions was r = .56 and r = .79 for the test total. For the cross-validation, zygosity classification indices taken from 9 previous studies were applied to our sample and compared to classification according to DNA microsatellite analyses (agreement range = 44 to 100%). The accuracy of the classification indices was significantly lower than the original studies for 62% of the comparisons. If zygosity determination with DNA markers or blood group typing for all subjects is not feasible, rather than using classification indices based on other studies, an optimal classification scheme can be achieved by using a zygosity questionnaire of which the reliability and validity of the questions is established in a random subsample of the same twin cohort.