Sequence comparison with concave weighting functions

We consider efficient methods for computing a difference metric between two sequences of symbols, where the cost of an operation to insert or delete a block of symbols is a concave function of the block's length. Alternatively, sequences can be optimally aligned when gap penalties are a concave function of the gap length. Two algorithms based on the ‘candidate list paradigm’ first used by Waterman (1984) are presented. The first computes significantly more parsimonious candidate lists than Waterman's method. The second method refines the first to the point of guaranteeingO(N ² lgN) worst-case time complexity, and under certain conditionsO(N ²). Experimental data show how various properties of the comparison problem affect the methods' relative performance. A number of extensions are discussed, among them a technique for constructing optimal alignments inO(N) space in expectation. This variation gives a practical method for comparing long amino sequences on a small computer. This work was supported in part by NSF Grant DCR-8511455.     

In vitro regeneration in Trifolium. 1. Direct somatic embryogenesis in T. rubens (L.)

The origin and development of zygotic and somatic embryos of Trifolium rubens L. was studied with the aid of paraffin sections and light microscopy. Zygotic embryos were collected, fixed and prepared daily from one to ten days after cross-pollination. Somatic embryos were obtained by plating petiole sections on modified L2 medium with 0.015 mgl^-1 picloram and 0.1 mgl^-1 6-BAP. Cultured petioles were collected and fixed daily from one to 25 days after plating. Two regions in the vascular bundle sheath of cultured petioles gave rise to callus. The first region was adjacent to the phloem fibers and produced friable callus. The second region gave rise to compact callus that was connected to the fascicular cambium. Somatic embryos originated from single cells in the cortex directly without intervening callus formation and from single cells in the friable callus. In addition, embryos arose from meristematic regions in compact callus. Many early stages of embryogenesis (one, two and four-celled stages) were observed in the cortex and friable callus. Zygotic embryogenesis in Trifolium differs from other legumes in that the suspensor is short and has a broad attachment. This arrangement was observed in zygotic embryos of T. rubens and in many somatic embryos. However, a continuum of somatic embryogenesis was observed where some young embryos had a Trifolium suspensor-like arrangement while others were attached to a long narrow suspensor-like structure more characteristic of Medicago.     

Human placental 3 beta-hydroxy-5-ene-steroid dehydrogenase and steroid 5----4-ene-isomerase: purification from microsomes, substrate kinetics, and inhibition by product steroids

In human pregnancy, placental 3 beta-hydroxy-5-ene-steroid dehydrogenase and steroid 5----4-ene-isomerase produce progesterone from pregnenolone and metabolize fetal dehydroepiandrosterone sulfate to androstenedione, an estrogen precursor. The enzyme complex was solubilized from human placental microsomes using the anionic detergent, sodium cholate. Purification (500-fold, 3.9% yield) was achieved by ion exchange chromatography (Fractogel-TSK DEAE 650-S) followed by hydroxylapatite chromatography (Bio-Gel HT). The purified enzyme was detected as a single protein band in sodium dodecylsulfate-polyacrylamide gel electrophoresis (monomeric Mr = 19,000). Fractionation by gel filtration chromatography at constant specific enzyme activity supported enzyme homogeneity and determined the molecular mass (Mr = 76,000). The dehydrogenase and isomerase activities copurified. Kinetic constants were determined at pH 7.4, 37 degrees C for the oxidation of pregnenolone (Km = 1.9 microM, Vmax = 32.6 nmol/min/mg) and dehydroepiandrosterone (Km = 2.8 microM, Vmax = 32.0 nmol/min/mg) and for the isomerization of 5-pregnene-3,20-dione (Km = 9.7 microM, Vmax = 618.3 nmol/min/mg) and 5-androstene-3,17-dione (Km = 23.7 microM, Vmax = 625.7 nmol/min/mg). Mixed substrate analyses showed that the dehydrogenase and isomerase reactions use the appropriate pregnene and androstene steroids as alternative, competitive substrates. Dixon analyses demonstrated competitive inhibition of the oxidation of pregnenolone and dehydroepiandrosterone by both product steroids, progesterone and androstenedione. The enzyme has a 3-fold higher affinity for androstenedione than for progesterone as an inhibitor of dehydrogenase activity. Based on these competitive patterns of substrate utilization and product inhibition, the pregnene and androstene activities of 3 beta-hydroxy-5-ene-steroid dehydrogenase and steroid 5----4-ene-isomerase may be expressed at a single catalytic site on one protein in human placenta.     

Blood pressure profile in two adult male populations.

Causal blood pressure measurements were recorded in two groups of men aged 40 to 64 years; of the 7024 men in metropolitan Saint John, NB, and the 4044 men in seven suburbs of Quebec who were asked, 5840 (83.1%) and 3097 (76.6%) respectively agreed to participate. Of the Saint John group 9.0% were taking antihypertensive drugs, as compared with only 3.3% of the Quebec group (p less than 0.0001). Among the treated subjects 33% in Saint John and 53% in Quebec still had a diastolic pressure greater than 95 mm Hg (p less than 0.01). Among the participants not taking antihypertensive drugs the systolic blood pressure increased with age, but the diastolic blood pressure increased only slightly up to 55 years of age and then decreased. On average the subjects in Saint John who were not being treated had a systolic pressure 6.2 mm Hg lower and a diastolic blood pressure 3.6 mm Hg lower than their Quebec counterparts (p less than 0.0001). This difference was observed in all the age groups and was not the result of the treatment of a greater proportion of the Saint John cohort. Despite the higher blood pressures and the smaller number receiving adequate treatment in the Quebec group, the rate of death due to coronary artery disease was 10% lower than that in the Saint John group. A bias in the data from Quebec may have influenced the magnitude of the differences between the two samples, but if present it should have underestimated the blood pressures in the Quebec group and therefore not have changed the outcome.     

Genotyping and sequence analysis of apolipoprotein E isoforms

Apolipoprotein E (apoE), a polymorphic plasma protein, is essential for catabolism of lipoproteins by receptor-mediated endocytosis. One of the apoE isoforms (E2) differs in its binding affinity to specific receptors and contributes to variations in lipoprotein metabolism. Diagnosis of apoE isoforms is done by isoelectric focusing, but it is hindered by various degrees of post-translational sialylation of the apoE protein. Electrophoretically silent structural variations may also escape detection by this technique. We describe a method for genotyping apoE based on hybridization of allele-specific oligonucleotides with enzymatically amplified genomic DNA, which permits unambiguous diagnosis of six common apoE phenotypes within 24 h. Among 100 E2 alleles present in 81 unrelated individuals genotyped by this technique, we found two rare structural mutants of apoE in addition to the common E2 form, E2(158Arg----Cys). Automated sequencing of amplified DNA identified the rare mutants as E2(136Arg----Ser) and E2(145Arg----Cys). The genotypic method may complement or even replace isoelectric focusing for routine determination of apoE phenotypes and for identification of rare structural variants.     

A linkage group of five DNA markers on human chromosome 10

Five chromosome 10 DNA markers (D10S1, D10S3, D10S4, D10S5, and RBP3) were typed in five large pedigrees with multiple endocrine neoplasia type 2A (MEN-2A) and in five non-MEN-2A pedigrees. Linkage analyses showed that these loci and the locus for MEN-2A (MEN2A) are in one linkage group spanning at least 70 cM. The order of the marker loci is RBP3-D10S5-D10S3-D10S1-D10S4, with interlocus recombination frequencies of 7, 13-19, 19, and 19%, respectively, all on the same side of MEN2A. Analyses of sex-specific recombination frequencies indicated no significant differences between males and females for any of the map intervals studied. Previous localization of D10S5 and RBP3 to the proximal region of the long arm and the pericentric region, respectively, comparison of results with other studies, and our preliminary results with other chromosome 10 markers suggest that the D10S4 end of the map extends into the long arm. Our linkage map has been constructed using only two- and three-locus analyses. It will be possible to combine our results with those of other groups to construct a more detailed and accurate genetic map of chromosome 10.     

Optimal alignments in linear space

Space, not time, is often the limiting factor when computingoptimal sequence alignments, and a number of recent papers inthe biology literature have proposed space-saving strategies.However, a 1975 computer science paper by Hirschberg presenteda method that is superior to the new proposals, both in theoryand in practice. The goal of this paper is to give Hirschberg'sidea the visibility it deserves by developing a linear-spaceversion of Gotoh's algorithm, which accommodates affine gappenalties. A portable C-software package implementing this algorithmis available on the BIONET free of charge. Received on October 14, 1987; accepted on December 19, 1987     

Effect of vasopressin administration and deficiency upon 3H-AVP binding sites in the CNS and periphery during development.

Arginine8-vasopressin (AVP, 40 micrograms/100 g b.wt., SC) was administered to male Long-Evans (LE) pups from day 1 to 7 of life and the pups were sacrificed on day 8 or 60. 3H-AVP binding was performed on membranes prepared from the liver, kidney, and septum. No significant changes were observed in the kidney or septum of animals 8 or 60 days old. However, the chronic AVP treatment did result in a significant increase in the density of 3H-AVP binding sites in the liver when compared to control day 8 pups (control 44 +/- 2 vs. AVP 56 +/- 3 fmol/mg protein), with no change in affinity. This effect was maintained into adulthood, as the day 60 AVP-treated LE rats also showed a significant increase in liver 3H-AVP binding sites compared to control (control 186 +/- 9 vs. AVP 239 +/- 14 fmol/mg protein), with no change in affinity. A comparison of 3H-AVP binding sites in 8-day-old LE, heterozygous Brattleboro (HET-BB), and homozygous Brattleboro rats (HOM-BB) was performed to assess the effect of complete (HOM-BB) and partial (HET-BB) VP deficiency on binding sites in the CNS and periphery. The liver again was the only tissue in which a change in 3H-AVP binding characteristics was noted. The HOM-BB rat (Bmax 144 +/- 6 fmol/mg protein) displayed a significant increase in AVP binding sites from the LE rat (Bmax 100 +/- 7 fmol/mg protein), while the 3H-AVP binding sites in the HET-BB rat liver (Bmax 69.8 +/- 9 fmol/mg protein) were significantly lower than LE rats. Thus hepatic AVP receptors appear most sensitive to the presence or absence of vasopressin during the early postnatal period.     

Recruiting physicians to rural practice. Suggestions for success.

Medical school graduates from 1986 to 1988 and current residents in 12 family practice residency programs in the Northwest (N = 302) were surveyed to identify important factors in the recruitment process for their first postresidency placement. The study sought to compare the recruitment practices of rural communities and urban sites. Specific questions addressed in the study concerned sources of information about practice opportunities, stage in training when job search was initiated, factors related to unsuccessful site visits, and activities scheduled in the visit. Results indicated that referrals from faculty were the most valued source of information. Most job searches were initiated in the first 6 months of the third year in training. An unreceptive physician community and a reluctant spouse or partner were substantial problems for residents making site visits to rural communities. Rural sites tended to provide a broader mix of professional and personal activities during the visit.