A molecular and cytogenetic survey of major repeated DNA sequences in tomato (Lycopersicon esculentum)

Summary The major families of repeated DNA sequences in the genome of tomato (Lycopersicon esculentum) were isolated from a sheared DNA library. One thousand clones, representing one million base pairs, or 0.15% of the genome, were surveyed for repeated DNA sequences by hybridization to total nuclear DNA. Four major repeat classes were identified and characterized with respect to copy number, chromosomal localization by in situ hybridization, and evolution in the family Solanaceae. The most highly repeated sequence, with approximately 77000 copies, consists of a 162 bp tandemly repeated satellite DNA. This repeat is clustered at or near the telomeres of most chromosomes and also at the centromeres and interstitial sites of a few chromosomes. Another family of tandemly repeated sequences consists of the genes coding for the 45 S ribosomal RNA. The 9.1 kb repeating unit in L. esculentum was estimated to be present in approximately 2300 copies. The single locus, previously mapped using restriction fragment length polymorphisms, was shown by in situ hybridization as a very intense signal at the end of chromosome 2. The third family of repeated sequences was interspersed throughout nearly all chromosomes with an average of 133 kb between elements. The total copy number in the genome is approximately 4200. The fourth class consists of another interspersed repeat showing clustering at or near the centromeres in several chromosomes. This repeat had a copy number of approximately 2100. Sequences homologous to the 45 S ribosomal DNA showed cross-hybridization to DNA from all solanaceous species examined including potato, Datura, Petunia, tobacco and pepper. In contrast, with the exception of one class of interspersed repeats which is present in potato, all other repetitive sequences appear to be limited to the crossing-range of tomato. These results, along with those from a companion paper (Zamir and Tanksley 1988), indicate that tomato possesses few highly repetitive DNA sequences and those that do exist are evolving at a rate higher than most other genomic sequences.     

Distributions of polymorphisms among pathways of carbohydrate metabolism in the earthworm Eisenia fetida (Oligochaeta).

1. Activities and genetic banding patterns of 36 isozymes in carbohydrate metabolism were detected by spectrophotometry and starch-gel electrophoresis, respectively, in the earthworm Eisenia fetida. 2. Polymorphisms were not distributed randomly among metabolic pathways, activity levels, or gene copy numbers. 3. In glycolysis and the Krebs cycle, 16% of the loci were polymorphic and polymorphisms occurred only when multiple copies of the loci existed. 4. In other pathways, 45% of the loci were polymorphic and the distribution of polymorphisms was independent of gene copy number. 5. Polymorphisms may affect metabolic phenotypes and natural selection may have led to conserved biochemical activity in glycolysis and the Krebs cycle.     

Application of automated DNA sizing technology for genotyping microsatellite loci.

Highly polymorphic microsatellite loci offer great promise for gene mapping studies, but fulfillment of this potential will require substantial improvements in methods for accurate and efficient genotyping. Here, we report a genotyping method based on fluorescently labeled PCR primers and size characterization of PCR products using an automated DNA fragment analyzer. We capitalize on the availability of three distinct fluorescent dyes to label uniquely loci that overlap in size, and this innovation increases by threefold the number of loci that can be analyzed simultaneously. We label size standards with a fourth dye and combine these with the microsatellite PCR products in each gel lane. Computer programs provide very rapid and accurate sizing of microsatellite alleles and efficient data management. In addition, fluorescence signals are linear over a much greater range of intensity than conventional autoradiography. This facilitates multiplexing of loci (since signal intensities often vary greatly) and helps distinguish major peaks from artifacts, thereby improving genotyping accuracy.     

The respiratory response to heat shock in Neurospora crassa

A sharp decrease in oxygen uptake occurred in Neurospora crassa cells that were transferred from 30 degrees C to 45 degrees C, and the respiration that resumed later at 45 degrees C was cyanide-insensitive. Energization of mitochondria, measured in vivo with fluorescence microscopy and a carbocyanine dye, also declined sharply in cells at 45 degrees C. Electron microscopy showed no changes in mitochondrial complexity; however, the cytoplasm of heat-shocked cells was deficient in glycogen granules.     

The Differential Contribution by Individual Enzymes of Glycolysis and Protein Catabolism to the Relationship between Heterozygosity and Growth Rate in the Coot Clam, Mulinia Lateralis

The locus-specific effects of heterozygosity upon individual growth rate were determined for 15 polymorphic enzymes among 1906 individuals from a single cohort sample of the marine bivalve Mulinia lateralis. Two measures of individual growth rate (total wet weight and shell length) were made at collection and after a period of growth in the laboratory. The correlation between heterozygosity and growth rate was independently determined for each locus using multiple linear regression, thereby providing a rank of individual locus effects; these differed significantly. The four estimated rankings of relative locus effects (initial length, initial weight, length added in the laboratory, and added weight) were not statistically different. That is, a locus with a large effect of heterozygosity on growth rate in nature had a similarly large effect on laboratory growth rate. The effect of a locus was not related to heterozygosity per se; some highly heterozygous loci had no detectable correlation with growth rate. The data contained two pairs of relatively tightly linked loci; in both cases one locus of a pair had significant effects on growth rate, while the other had no effect. Loci with large and significant correlations with growth rate synthesize enzymes which function in protein catabolism or glycolysis; heterozygosity in enzymes of the pentose shunt, redox balance, or other miscellaneous metabolic roles was not correlated with growth rate. Since the metabolic basis for the correlation is known to derive from individual differences in net energy status, particularly energetic costs of whole-body protein turnover, these data indicate that phenotypic effects (e.g., variation in growth rate) are determined by heterozygosity at the studied genes, not other linked loci.     

Growth curve models of repeated binary response

Experimental designs that include repeated measures of binary response variables over time and under different conditions are common in biology. In such settings, it is often desirable to characterize the response pattern over time. When response variables are continuous, this characterization can be made in terms of a growth model such as the Potthoff-Roy growth curve model. We illustrate how a similar growth curve modeling strategy can be implemented using weighted least squares (WLS) methods for binary response data. The growth models are constructed in terms of polynomial functions across marginal response. However, when growth models are fit to repeated binary response, the nonsignificant higher-order polynomial functions are dropped from the model, rather than used as covariates. Dropping the nonsignificant polynomials from the model will reduce the number of response functions, and help avoid small-sample problems that can occur when the number of correlated response functions is large and sample sizes are small. The reduced set of response functions are then modeled using WLS methods. We illustrate such models with an example of binary fly oviposition response (accept or reject) exhibited by two populations of flies at four ages to two types of fruit.     

MATCH-UP/MATRIX: a microcomputer program designed to search for protein primary structure homology

MATCH-UP/MATRIX is a program designed to aid the investigatorinterested in determining primary protein structure. It is writtenin Applesoft BASIC for the Apple lle microcomputer. MATCH-UPwill survey any set of proteinaceous materials for amino acidsequence homology; however, it is primarily intended to comparethe structures of newly sequenced peptides with the establishedstructure of a protein with suspected homology. Any peptide-to-proteinalignment which shows a homology greater than or equal to thepercentage specified by the user will result in output. MATRIXwill compare the sequences of two proteins (peptides) in whateveralignment specified by the user and is intended to spot insertionsand/or deletions between structures. Received on December 2, 1985; accepted on March 10, 1986     

Sparing effects of intrauterine treatment with prostaglandin E2 on luteal function in cycling gilts

Twelve crossbred gilts, 8 to 9 months of age, were used to study the effects of prostaglandin E2 (PGE2) on luteal function during the estrous cycle. Intrauterine and jugular vein catheters were surgically placed before day 7 of the treatment estrous cycle and gilts were randomly assigned to 1 of 3 treatment groups. Groups I and II received constant intrauterine infusion of vehicle (6.0 ml/24 hr) or PGE2 (2400 micrograms/day; 6.0 ml/24 hr) respectively; while group III was given intrauterine infusions of 400 micrograms PGE2 every 4 hr. All infusions were initiated on day 7 and continued until estrus or through day 23. Jugular blood samples were collected twice daily from days 7 to 30 for progesterone analysis. Intrauterine infusion of PGE2 at the dose and frequencies given in this study delayed the decline in jugular plasma progesterone and resulted in prolongation of the estrous cycle length. The results of this study have shown that PGE2 at the dosage and frequency of administration used was capable of extending corpus luteum function.