Mutations of the rat growth hormone promoter which increase and decrease response to thyroid hormone define a consensus thyroid hormone response element

We have previously identified sequences required for thyroid hormone (T3) induction of the rat GH (rGH) promoter, which lie in a region from -188 to -164 upstream of the mRNA start site. Within this region, Domains A, -189 to -184 and B, -179 to -174, are imperfect direct repeats, and domain C, -172 to -167, is a divergent inverted copy that matches the A domain at 4/6 positions. A series of synthetic mutant versions of this sequence were inserted upstream of a truncated rGH promoter, or as a replacement for wild-type sequences in a synthetic 237 base pair rGH promoter or upstream of the heterologous thymidine kinase promoter. Mutations changing the B domain to a perfect copy of the A domain significantly increased T3 induction (21.3-fold) relative to the wild type (3.6-fold). A single point mutation making the C domain a better match to the A domain also increased T3 induction to 16.2-fold. Combining this up-mutation with any of three down-mutations in the A, B, or C domains strongly decreased response, showing that all three domains contribute to the amplified T3 response. Binding affinity of the various mutant oligonucleotides was assessed using in vitro translated receptor and affinity paralleled the functional responses for most binding site mutations. Requirements for in vitro binding were, however, less rigorous than those for functional T3 induction. Based on these results, we propose a consensus T3 receptor binding half-site, AGGT(C/A)A, at least two copies of which are required for a T3 response.(ABSTRACT TRUNCATED AT 250 WORDS)     

Cross-hybridizing snake satellite, Drosophila, and mouse DNA sequences may have arisen independently

Previous reports have interpreted hybridization between snake satellite DNA and DNA clones from a variety of distant taxonomic groups as evidence for evolutionary conservation, which implies common ancestry (homology) and/or convergence (analogy) to produce the cross- hybridizing sequences. We have isolated 11 clones from a genomic library of Drosophila melanogaster, using a cloned 2.5-kb snake satellite probe of known nucleotide sequence. We have also analysed published sequence data from snakes, mice, and Drosophila. These data show that (1) all of the cross-hybridization between the snake, fly, and mouse clones can be accounted for by the presence of either of two tandem repeats, [GATA]n and [GACA]n and (2) these tandem repeats are organized differently among the different species. We find no evidence that these sequences are homologous apart from the existence of the simple repeat itself, although their divergence from a common ancestral sequence cannot be ruled out. The sequences contain a variety of homogeneous clusters of tandem repeats of CATA, GA, TA, and CA, as well as GATA and GACA. We suggest that these motifs may have arisen by a self-accelerating process involving slipped-strand mispairing of DNA. Homogeneity of the clusters might simply be the result of a rate of accumulation of tandem repeats that exceeds that of other mutations.      

Structural comparison of fibroblast growth factor-specific heparan sulfates derived from a growing or differentiating neuroepithelial cell line

Heparan sulfate (HS) glycosaminoglycans are essential modulators of fibroblast growth factor (FGF) activity both in vivo and in vitro, and appear to act by cross-linking particular forms of FGF to appropriate FGF receptors. We have recently isolated and characterized two separate HS pools derived from immortalized embryonic day 10 mouse neuroepithelial 2.3D cells: one from cells in log growth phase, which greatly potentiates the activity of FGF-2, and the other from cells undergoing contact-inhibition and differentiation, which preferentially activates FGF-1. These two pools of HS have very similar functional activities to those species isolated from primary neuroepithelial cells at corresponding stages of active proliferation or differentiation. We present here a structural comparison between these cell line HS species to establish the nature of the changes that occur in the biosynthesis of HS. A combination of chemical and enzymatic cleavage, low pressure chromatography and strong anion-exchange HPLC were used to generate full chain models of each species. Overall, the HS pools synthesized in the dividing cell line pools possessed less complex sulfation than those derived from more differentiated, growth arrested cells.      

A novel retinoid X receptor-independent thyroid hormone response element is present in the human type 1 deiodinase gene.

We identified two thyroid hormone response elements (TREs) in the 2.5-kb, 5'-flanking region of the human gene encoding type 1 iodothyronine deiodinase (hdio1), an enzyme which catalyses the activation of thyroxine to 3,5,3'-triiodothyronine (T3). Both TREs contribute equally to T3 induction of the homologous promoter in transient expression assays. The proximal TRE (TRE1), which is located at bp -100, has an unusual structure, a direct repeat of the octamer YYRGGTCA hexamer that is spaced by 10 bp. The pyrimidines in the -2 position relative to the core hexamer are both essential to function. In vitro binding studies of TRE1 showed no heterodimer formation with retinoid X receptor (RXR) beta or JEG nuclear extracts (containing RXR alpha) and bacterially expressed chicken T3 receptor alpha 1 (TR alpha) can occupy both half-sites although the 3' half-site is dominant. T3 causes dissociation of TR alpha from the 5' half-site but increases binding to the 3' half-site. Binding of a second TR to TRE1 is minimally cooperative; however, no cooperativity was noted for a functional mutant in which the half-sites are separated by 15 bp, implying that TRs bind as independent monomers. Nonetheless, T3 still causes TR dissociation from the DR+15, indicating that dissociation occurs independently of TR-TR contact and that rebinding of a T3-TR complex to the 3' half-site occurs because of its slightly higher affinity. A distal TRE (TRE2) is found at bp -700 and is a direct repeat of a PuGGTCA hexamer spaced by 4 bp. It has typical TR homodimer and TR-RXR heterodimer binding properties. The TRE1 of hdio1 is the first example of a naturally occurring TRE consisting of two relatively independent octamer sequences which do not require the RXR family of proteins for function.     

Effects of varying the position of thyroid hormone response elements within the rat growth hormone promoter: implications for positive and negative regulation by 3,5,3'-triiodothyronine

The thyroid hormone response element (T3RE) of the rat GH (rGH) promoter is located at -188 to -165 relative to the mRNA start site (TSS). Similar sites have been identified in other genes regulated by T3. We have investigated some of these T3REs in positions within the rGH promoter to assess the relative influences of DNA-binding site and position on positive and negative regulation by T3. Synthetic oligonucleotides were used with sequences from the rGH T3RE and proposed negative T3REs (nT3RE) from the rat and human alpha-subunit and rat beta TSH genes. The nT3REs were placed in the background of the wild-type rGH promoter in two positions, at -55 and down-stream of the TSS, with up- and down-mutations of the rGH T3RE. Rat GH T3RE elements were placed 700 basepairs up-stream of a basal rGH promoter and some also at the -55 and TSS positions. Constructions were tested in a transient transfection assay in rat pituitary tumor cells. Two copies of the rGHPAL (palindromic T3RE) placed 700 basepairs up-stream of the rGH promoter conferred 10-fold T3 induction. In the -55 position, the rGHPAL increased T3 induction compared to that in controls, whereas a fragment from the rat and human alpha-subunit gene in the same position reduced induction. Negative T3REs from rat beta TSH and human alpha-subunit reduced T3 induction 50% when placed at the TSS position of a rGH promoter containing an up-mutant T3RE. The T3REPAL placed at the same site increased T3 induction.(ABSTRACT TRUNCATED AT 250 WORDS)     

Time course of the luteinizing hormone surge in cannulated rats: quantitative variance estimates within individual rats over successive cycles

The present study was designed to compare quantitative variance estimates in the profile of the luteinizing hormone (LH) surge within individual rats over successive proestrous (PE) days (WITHIN) with the variability between rats (BETWEEN). Sprague-Dawley female rats were implanted under ether anesthesia with indwelling intracardiac cannulas. On successive PE afternoons of normal 4-day cycles, hourly blood samples (0.25 ml) were collected via the cannula from 1400-2000 h for radioimmunoassay of plasma LH. Three characteristics which reflected the profile of the LH surge were examined: the time of onset of LH release, the time of peak LH release, and the magnitude of peak LH release. Twenty-one animals yielded LH surge data on a total of 42 PE days with a mean (+/- SD) time of onset = 1534 h +/- 66 min, time of peak = 1730 h +/- 75 min, and magnitude of peak = 1176 +/- 441 ng NIAMDD-Rat LH-RP-1/ml plasma. Variance estimates BETWEEN and WITHIN animals were determined by analysis of variance and the method of Vaughan and Corballis (1969) for calculating percent of total variance. Differences BETWEEN in time of onset of LH release approached significance (P = 0.05-0.10) and contributed 50.5% of the total variance compared to a negative value for differences WITHIN. Differences BETWEEN in time of peak LH release were significant (P less than 0.05) and contributed 51.5% of total variance compared to a negative value for differences WITHIN. In contrast, for the magnitude of peak LH release, neither differences BETWEEN nor WITHIN contributed substantially to total variance (both negative values), with the major contribution from the residual term.(ABSTRACT TRUNCATED AT 250 WORDS)     

Complex phylogeographic history of central African forest elephants and its implications for taxonomy

Background

The mitochondrial genomes of snakes are characterized by an overall evolutionary rate that appears to be one of the most accelerated among vertebrates. They also possess other unusual features, including short tRNAs and other genes, and a duplicated control region that has been stably maintained since it originated more than 70 million years ago. Here, we provide a detailed analysis of evolutionary dynamics in snake mitochondrial genomes to better understand the basis of these extreme characteristics, and to explore the relationship between mitochondrial genome molecular evolution, genome architecture, and molecular function. We sequenced complete mitochondrial genomes from Slowinski's corn snake (Pantherophis slowinskii) and two cottonmouths (Agkistrodon piscivorus) to complement previously existing mitochondrial genomes, and to provide an improved comparative view of how genome architecture affects molecular evolution at contrasting levels of divergence.

Results

We present a Bayesian genetic approach that suggests that the duplicated control region can function as an additional origin of heavy strand replication. The two control regions also appear to have different intra-specific versus inter-specific evolutionary dynamics that may be associated with complex modes of concerted evolution. We find that different genomic regions have experienced substantial accelerated evolution along early branches in snakes, with different genes having experienced dramatic accelerations along specific branches. Some of these accelerations appear to coincide with, or subsequent to, the shortening of various mitochondrial genes and the duplication of the control region and flanking tRNAs.

Conclusion

Fluctuations in the strength and pattern of selection during snake evolution have had widely varying gene-specific effects on substitution rates, and these rate accelerations may have been functionally related to unusual changes in genomic architecture. The among-lineage and among-gene variation in rate dynamics observed in snakes is the most extreme thus far observed in animal genomes, and provides an important study system for further evaluating the biochemical and physiological basis of evolutionary pressures in vertebrate mitochondria.     

Anti-cyclooxygenase effects of lipid extracts from the New Zealand green-lipped mussel, Perna canaliculus

Total lipid extracts of P. canaliculus (a bivalve marine mollusc native to New Zealand, commonly called the green-lipped mussel) and Mytilus edulis (commonly called the common blue mussel) moderately inhibited ovine COX-1 and COX-2 pure enzymes in vitro. The inhibition was increased after the mussel extracts were saponified by KOH hydrolysis. Protease- and protease-lipase-hydrolysed lipid extracts of P. canaliculus exhibited similarly strong COX inhibition as the KOH-hydrolysed extract. Lyprinol(R) (a commercial extract from P. canaliculus) also exhibited strong inhibition of both COX isoforms, an effect that was increased 10-fold upon subsequent hydrolysis. In contrast, fish oil was not as anti-COX active as Lyprinol. The Lyprinol free fatty acid fraction, and to a lesser extent the Lyprinol triglyceride fraction, were the only lipid classes of Lyprinol to exhibit strong inhibition of the COX isoforms. The purified PUFA extracts were all bioactive, potently inhibiting COX-1 and COX-2. Incubation of Lyprinol in the absence of exogenous arachidonic acid (AA) showed the appearance of alternate prostaglandin metabolites, confirming Lyprinol PUFA as a competitive substrate inhibitor of AA metabolism.     

Age and composition of carbonate shoreface sediments, Kailua Bay, Oahu, Hawaii

The origin, age, and dynamics of carbonate sediments in Kailua Bay on Oahu, Hawaii, are described. The shoreface (from shoreline to 4 km offshore) consists of a broad (5 km²) fringing coral reef ecosystem bisected by a sinuous, shore-normal, sand-filled paleostream channel 200–300 m wide. The median grain diameter of surface sands is finest on the beach face (<0.3 mm) and increases offshore along the channel axis. Kailua sands are >90% biogenic carbonate, dominated by skeletal fragments of coralline algae (e.g. Porolithon, up to 50%) followed by the calcareous green alga Halimeda (up to 32%), coral fragments (1–24%), mollusc fragments (6–21%), and benthic foraminifera (1–10%). Sand composition and age across the shoreface are correlated to carbonate production. Corals and coralline algae, principal builders of the reef framework, are younger and more abundant in sands along the channel axis and in offshore reefal areas, while Halimeda, molluscs, and foraminifera are younger and more dominant in nearshore waters shoreward of the main region of framework building. Shoreface sediments are relatively old. Of 20 calibrated radiocarbon dates on skeletal constituents of sand, only three are younger than 500 years b.p.; six are 500–1000 years b.p.; six are 1000–2000 years b.p.; and five are 2000–5000 years b.p. Dated fine sands are older than medium to coarse sands and hence may constitute a reservoir of fossil carbonate that is distributed over the entire shoreface. Dominance of fossiliferous sand indicates long storage times for carbonate grains, which tend to decrease in size with age, such that the entire period of relative sea-level inundation (∼5000 years) is represented in the sediment. Despite an apparently healthy modern coral ecosystem, the surficial sand pool of Kailua Bay is dominated by sand reflecting an antecedent system, possibly one that existed under a +1–2 m sea-level high stand during the mid- to late Holocene. Accepted: 20 December 1999     

Sucrose metabolism in spring and winter wheat in response to high irradiance, cold stress and cold acclimation

Effects of low‐temperature stress, cold acclimation and growth at high irradiance in a spring (Triticum aestivum L. cv. Katepwa) and a winter wheat (Triticum aestivum L. cv. Monopol) were examined in leaves and crowns with respect to the sucrose utilisation and carbon allocation. Light‐saturated and carbon dioxide (CO₂)‐saturated rates of CO₂ assimilation were decreased by 50% in cold‐stressed spring and winter wheat cultivars. Cold‐ or high light‐acclimated Katepwa spring wheat maintained light‐saturated rates of CO₂ assimilation comparable to those of control spring wheat. In contrast, cold‐ or high light‐acclimated winter wheat maintained higher light and CO₂‐saturated rates of CO₂ assimilation than non‐acclimated controls. In leaves, during either cold stress, cold acclimation or acclimation to high irradiance, the sucrose/starch ratio increased by 5‐ to 10‐fold and neutral invertase activity increased by 2‐ to 2.5‐fold in both the spring and the winter wheat. In contrast, Monopol winter wheat, but not Katepwa spring wheat, exhibited a 3‐fold increase in leaf sucrose phosphate synthase (SPS) activity, a 4‐fold increase in sucrose:sucrose fructosyl transferase activity and a 6.6‐fold increase in acid invertase upon cold acclimation. Although leaves of cold‐stressed and high light‐grown spring and winter wheat showed 2.3‐ to 7‐fold higher sucrose levels than controls, these plants exhibited a limited capacity to adjust either sucrose phosphate synthase or sucrose synthase activity (SS[s]). In addition, the acclimation to high light resulted in a 23–31% lower starch abundance and no changes at the level of fructan accumulation in leaves of either winter or spring wheat when compared with controls. However, high light‐acclimated winter wheat exhibited a 1.8‐fold higher neutral invertase activity and high light‐acclimated spring wheat exhibited an induction of SS(d) activity when compared with controls. Crowns of Monopol showed higher fructan accumulation than Katepwa upon cold and high light acclimation. We suggest that the differential adjustment of CO₂‐saturated rates of CO₂ assimilation upon cold acclimation in Monopol winter wheat, as compared with Katepwa spring wheat, is associated with the increased capacity of Monopol for sucrose utilisation through the biosynthesis of fructans in the leaves and subsequent export to the crowns. In contrast, the differential adjustment of CO₂‐saturated rates of CO₂ assimilation upon high light acclimation of Monopol appears to be associated with both increased fructan and starch accumulation in the crowns.