Genome conservation among three legume genera detected with DNA markers.

A set of 219 DNA clones derived from mungbean (Vigna radiata), cowpea (V. unguiculata), common bean (Phaseolus vulgaris), and soybean (Glycine max) were used to generate comparative linkage maps among mungbean, common bean, and soybean. The maps allowed an assessment of linkage conservation and collinearity among the three genomes. Mungbean and common bean, both of the subtribe Phaseolinae, exhibited a high degree of linkage conservation and preservation of marker order. Most linkage groups of mungbean consisted of only one or two linkage blocks from common bean (and vice versa). The situation was significantly different with soybean, a member of the subtribe Glycininae. Mungbean and common bean linkage groups were generally mosaics of short soybean linkage blocks, each only a few centimorgans in length. These results suggest that it would be fruitful to join maps of mungbean and common bean, while knowledge of conserved genomic blocks would be useful in increasing marker density in specific genomic regions for all three genera. These comparative maps may also contribute to enhanced understanding of legume evolution.     

Insertion and excision of Bacteroides conjugative chromosomal elements.

Many strains of Bacteroides harbor large chromosomal elements that can transfer themselves from the chromosome of the donor to the chromosome of the recipient. Most of them carry a tetracycline resistance (Tcr) gene and have thus been designated Tcr elements. In the present study, we have used transverse alternating field electrophoresis to show that all but one of the Tcr elements screened were approximately 70 to 80 kbp in size. The exception (Tcr Emr 12256) was 150 to 200 kbp in size and may be a hybrid element. All of the Tcr elements inserted in more than one site, but insertion was not random. The Tcr elements sometimes cotransfer unlinked chromosomal segments, or nonreplicating Bacteroides units (NBUs). Transverse alternating field electrophoresis analysis showed that insertion of NBUs was not random and that the NBUs did not insert near the Tcr element. Although attempts to clone one or both ends of a Tcr element have not been successful, ends of a cryptic element (XBU4422) were cloned previously and shown to be homologous to the ends of Tcr elements. We have obtained DNA sequences of junction regions between XBU4422 and its target from several different insertions. Comparison of junction sequences with target sequences showed that no target site duplication occurred during insertion and that XBU4422 carried 4 to 5 bp of adjacent chromosomal DNA when it excised from the chromosome and inserted in a plasmid. We identified a short region of sequence similarity between one of the ends of XBU4422 and its target site that may be important for insertion. This sequence contained an 8-bp segment that was identical to the recombinational hot spot sequence on Tn21. XBU4422 could exise itself from plasmids into which it inserted. In most cases, the excision left a single additional A behind in the target site, but precise excision was seen in one case.     

The assessment of cellular proliferation by immunohistochemistry: A review of currently available methods and their applications

Summary Immunohistochemical methods using antibodies to cell cycle-related antigens may be used as a means of assessing various aspects of proliferation in tissue, and have the important advantage of preserving the spatial orientation of proliferating cells in histological sections. Currently, the most widely available antibodies for this purpose are antibodies to bromodeoxyuridine (BrdU), Ki67 and antibodies to proliferating cell nuclear antigen (PCNA). BrdU is a thymidine analogue incorporated during the S phase of the cell cycle, which can be introduced by in vivo administration or by in vitro incubation, and monoclonal antibodies are available to display its localization. Ki67 demonstrates a nuclear antigen expressed in all phases of the cell cycle, except G₀ and early G₁, but can only be applied to frozen tissue. PCNA is a nuclear antigen which is essential for DNA synthesis, two commercially available antibodies to PCNA work in paraffin-embedded tissue, but may have different staining characteristics under different conditions of fixation. The main advantages and disadvantages of these different techniques are discussed, together with their main applications to date.     

RFLP Mapping in Soybean: Association between Marker Loci and Variation in Quantitative Traits

Quantitative trait loci (QTLs) have been mapped to small intervals along the chromosomes of tomato (Lycopersicon esculentum), by a method we call substitution mapping. The size of the interval to which a QTL can be mapped is determined primarily by the number and spacing of previously mapped genetic markers in the region surrounding the QTL. We demonstrate the method using tomato genotypes carrying chromosomal segments from Lycopersicon chmielewskii, a wild relative of tomato with high soluble solids concentration but small fruit and low yield. Different L. chmielewskii chromosomal segments carrying a common restriction fragment length polymorphism were identified, and their regions of overlap determined using all available genetic markers. The effect of these chromosomal segments on soluble solids concentration, fruit mass, yield, and pH, was determined in the field. Many overlapping chromosomal segments had very different phenotypic effects, indicating QTLs affecting the phenotype(s) to lie in intervals of as little as 3 cM by which the segments differed. Some associations between different traits were attributed to close linkage between two or more QTLs, rather than pleiotropic effects of a single QTL: in such cases, recombination should separate desirable QTLs from genes with undesirable effects. The prominence of such trait associations in wide crosses appears partly due to infrequent reciprocal recombination between heterozygous chromosomal segments flanked by homozygous regions. Substitution mapping is particularly applicable to gene introgression from wild to domestic species, and generally useful in narrowing the gap between linkage mapping and physical mapping of QTLs.     

Rat cerebral cortical synaptoneurosomal membranes. Structure and interactions with imidazobenzodiazepine and 1,4-dihydropyridine calcium channel drugs.

Small angle x-ray scattering has been used to investigate the structure of synaptoneurosomal (SNM) membranes from rat cerebral cortex. Electron micrographs of the preparation showed SNM with classical synaptic appositions intact, other vesicles, occasional mitochondria, and some myelin. An immunoassay for myelin basic protein placed the myelin content of normal rat SNM at less than 2% by weight of the total membrane present. X-Ray diffraction patterns showed five diffraction orders with a unit cell repeat for the membrane of 71 to 78 A at higher hydration states. At lower hydration, 11 orders appeared; the unit cell repeat was 130 A, indicating that the unit cell contained two membranes. Electron density profiles for the 130-A unit cell were determined; they clearly showed the two opposed asymmetrical membranes of the SNM vesicles. SNM membrane/buffer partition coefficients (Kp) of imidazobenzodiazepine and 1,4-dihydropyridine (DHP) calcium channel drugs were measured; Kp's for DHP drugs were approximately five times higher in rabbit light sarcoplasmic reticulum than in SNM. Ro 15-1788 and the DHP BAY K 8644 bind primarily to the outer monolayer of vesicles of intact SNM membranes. Nonspecific equilibrium binding of Ro 15-1788 occurs mainly in the upper acyl chain of the bilayer in lipid extracts of SNM membrane.     

Chemotactic Responses of Marine Vibrio sp. Strain S14 (CCUG 15956) to Low-Molecular-Weight Substances under Starvation and Recovery Conditions

The chemotactic responses by starved cells of marine Vibrio sp. strain S14 differed from those elicited by cells that were not nutrient limited. The rate of chemotaxis at different concentrations of several attractants varied for starved and growing cells. Vibrio sp. strain S14 showed positive chemotaxis to leucine, valine, arginine, and glucose at the onset of energy and nutrient deprivation. A continued, though decreased, positive response was demonstrated fro leucine, arginine, and glucose at 10 h of starvation. Cells starved for 3 h displayed a stronger response to glucose than those starved for shorter or longer times. However, cells starved for 5 and 10 h responded more strongly to a lower concentration of glucose than did cells starved for 0 and 3 h. Starvation for 24 h elicited no measurable chemotaxis to leucine, arginine, or glucose. The motility decreased by over 95% in the cell population after 24 h of starvation, which resulted in a low sensitivity in the chemotaxis assay. A switch in the response to valine was observed by 3 h of starvation. The addition of nutrients of 22-h-starved cells elicited a temporary positive chemotactic response to leucine by 2 and 4 h of nutrient recovery, while cells at 1 and 6 h of recovery showed no response. At 2 h of recovery, the greatest response was recorded to 10⁻⁴ M leucine, whereas at 4 h it was to 10⁻² M leucine. Ten to fifty percent of the 22-h-starved cell population regained their motility after 4 h of nutrient-aided recovery. It is possible that two types of chemosensory systems exist in marine bacteria. Starved and growing cells responded to different concentrations of the attractant, and growing cells displayed a saturated chemotactic system with leucine as the attractant, unlike the response during starvation.     

Relationships of Initial Population Densities of Meloidogyne incognita and M. hapla to Yield of Tomato

Microplots 80 × 100 cm, infested with varying initial population densities (P_i) of Meloidogyne incognita or M. hapla, were planted to tomato at two locations. Experiments were conducted in a sandy loam soil at Fletcher, N. C. (mountains) where the mean temperature for May to September is ca 20.7 C, and in a loamy saml at Clayton, N. C. (coastal plain) where the mean temperature for May to Septemher is ca 24.8 C. In these experimentally infested plots, M. incognita and M. hapla caused maximunt yield losses of 20-30%, at lhe mountain site with Pi of 0-12,500 eggs and larvae/500 cm³ of soil. In the coaslal plain, M. incognita suppressed yields up to 85%, and M. hapla suppressed yields up to 50% in comparison with the noninfested control. A part of the high losses at this site apparently was due to M. incognita predisposing tomato to the early blight fungus. In a second experintent, in which a nematicide was used to obtain a range of P_is (with P_i as high as 25,000/50 cm³ of soil) at Fletcher, losses due to M. incognita were as great as 50%, but similar densities of M. hapla suppressed yields by only 10-25%. Approximate threshold densities for both species ranged from 500 to 1,000 larvae and eggs (higher for surviving larvae) for the mountain site, whereas nutnbers as low as 20 larvae/500 cm³ of soil of either species caused signiticant damage in the coastal plain. Chemical soil treatments proved useful in obtaining various initial population densities; however, problems were encountered in measuring effective inoculum after such treatments, especially in the heavier soil.     

Quantitation of conductance pathways in antral gastric mucosa

The magnitude of cellular and shunt conductance of Necturus gastric antral mucosa was studied by (a) comparing the cellular PD response to transepithelial PD response during changes of ionic activity in the serosal bathing solution and (b) by measurement of current spread within the epithelial sheet. Using constant product KCl changes cellular resistance was 6,788 omegacm2 and shunt resistance was 1,803 omegacm2. Deletion of HCO3- from the serosal solution produced similar but quantitatively smaller changes in PD. Using HCO3- deletion cellular resistance was 7,338 omegacm2 and shunt resistance was 1,973 omegacm2. Measurement of current spead within the mucosa avoids changing ionic gradients yet gave very similar results; cellular resistance was 8,967 omegacm2 and shunt resistance was 2,947 omegacm2. The shunt contribution to transepithelial conductance ranged from 75.2 to 79.0%. Shunt selectivity was assessed using KCl dilution potentials, where mucosal dilution gave a small change in tissue PD compatible with an anion/cation selectivity ratio of 1.16 across the shunt, whereas serosal dilution effect was dominated by a PD change across the serosal membrane of the cell.     

Evolutionary conservation of DNA methylation in CpG sites within ultraconserved noncoding elements

Ultraconserved noncoding elements (UCNEs) constitute less than 1 Mb of vertebrate genomes and are impervious to accumulating mutations. About 4000 UCNEs exist in vertebrate genomes, each at least 200 nucleotides in length, sharing greater than 95% sequence identity between human and chicken. Despite extreme sequence conservation over 400 million years of vertebrate evolution, we show both ordered interspecies and within-species interindividual variation in DNA methylation in these regions. Here, we surveyed UCNEs with high CpG density in 56 species finding half to be intermediately methylated and the remaining near 0% or 100%. Intermediately methylated UCNEs displayed a greater range of methylation between mouse tissues. In a human population, most UCNEs showed greater variation than the LINE1 transposon, a frequently used epigenetic biomarker. Global methylation was found to be inversely correlated to hydroxymethylation across 60 vertebrates. Within UCNEs, DNA methylation is flexible, conserved between related species, and relaxed from the underlying sequence selection pressure, while remaining heritable through speciation.