A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony

The method of evolutionary parsimony--or operator invariants--is a technique of nucleic acid sequence analysis related to parsimony analysis and explicitly designed for determining evolutionary relationships among four distantly related taxa. The method is independent of substitution rates because it is derived from consideration of the group properties of substitution operators rather than from an analysis of the probabilities of substitution in branches of a tree. In both parsimony and evolutionary parsimony, three patterns of nucleotide substitution are associated one-to-one with the three topologically linked trees for four taxa. In evolutionary parsimony, the three quantities are operator invariants. These invariants are the remnants of substitutions that have occurred in the interior branch of the tree and are analogous to the substitutions assigned to the central branch by parsimony. The two invariants associated with the incorrect trees must equal zero (statistically), whereas only the correct tree can have a nonzero invariant. The chi 2-test is used to ascertain the nonzero invariant and the statistically favored tree. Examples, obtained using data calculated with evolutionary rates and branchings designed to camouflage the true tree, show that the method accurately predicts the tree, even when substitution rates differ greatly in neighboring peripheral branches (conditions under which parsimony will consistently fail). As the number of substitutions in peripheral branches becomes fewer, the parsimony and the evolutionary-parsimony solutions converge. The method is robust and easy to use.      

Phylogenetic analysis of the South American electric fishes (order Gymnotiformes) and the evolution of their electrogenic system: a synthesis based on morphology, electrophysiology, and mitochondrial sequence data

The order Gymnotiformes (South American electric fishes) is a fascinating assemblage of freshwater fishes that share the unusual ability to produce and sense electric fields used for electrolocation and social communication. In the last few decades, the electrogenic and electrosensory systems (EES) of these fish have served as an excellent model to study motor and sensory physiology in vertebrates. In an attempt to the evolution of characters associated with the EES in the group, we applied maximum-parsimony (MP), minimum-evolution (ME), and maximum-likelihood (ML) methods to analyze 302 aligned bases of the mitochondrial 12S rRNA and 416 bases of the mitochondrial 16S rRNA of 19 gymnotiform genera representing all six recognized families. Six catfish genera (order Siluriformes) were also sequenced and used as outgroups. The phylogenetic hypothesis resultant from molecular data analysis differs in some respects from previous hypotheses based on morphological studies. Our results were most informative within the family level, as we were unable to elucidate the relationships among deeper branches in this order with sufficient confidence by using molecular data alone. The phylogenetic information of both mitochondrial DNA segments appears to be affected by functional constraints, and the resultant topologies were sensitive to different weighting schemes and the algorithm used. Nonetheless, we found unanimous support for the following phylogenetic relationships: (1) the family Sternopygidae is an unnatural group, and Sternopygus is the sole representative of a unique lineage within the order; (2) the family Hypopomidae is not monophyletic; and (3) the order Gymnotiformes is composed of at least six natural clades: Sternopygus, family Apteronotidae, a new clade consisting of the remaining sternopygids, families Hypopomidae + Rhamphicthyidae, family Electrophoridae, and family Gymnotidae. By combining molecular, morphological, and physiological information, we propose a new hypothesis for the phylogeny of this group and suggest a new family Eigenmanniidae n. (order Gymnotiformes).      

Formation of enlarged mitochondria in a liver cell line in response to a synthetic glucocorticoid

For a number of years it has been recognized that glucocorticoids cause alterations in liver cell morphology (6, 9). Several investigators have shown that in liver in vivo mitochondria can be enlarged to many times their normal volume by treatment with cortisone (13, 15). There is a concomitant decrease in mitochondrial number, and the results of Kimberg and Loeb suggest that this is due to mitochondrial fusion (7). However, the exact mechanism whereby mitochondrial volume is altered and whether in fact cortisone is the direct causal agent are not known due to the complexity of studying these questions in a whole animal system. We have found that dexamethasone sodium phosphate (dex), a synthetic glucocorticoid, causes the formation of enlarged mitochondria in a liver cell line RLC-GAI, which grows in defined medium. In this paper we present our observations on the amount of enlargement that occurs after 5 days of treatment. The formation of enlarged mitochondria is reversible upon removal of the hormone from the medium, and we have attempted to determine whether "mitochondrial" or "nonmitochondrial" inhibitors are more effective in blocking the return of mitochondria to their normal size when the hormone is removed.     

BIOGENESIS OF MITOCHONDRIA : XI. A Comparison of the Effects of Growth-Limiting Oxygen Tension, Intercalating Agents, and Antibiotics on the Obligate Aerobe Candida Parapsilosis

Growth under conditions of oxygen restriction results in a generalized decrease in the definition of the mitochondrial membranes, a decrease in the mitochondrial cytochromes, and a decrease in citric acid cycle enzymes of the obligate aerobic yeast Candida parapsilosis. Addition of unsaturated fatty acids and ergosterol to cultures exposed to limited oxygen results in improved definition of the mitochondrial membranes and an increase in the total mitochondrial cytochrome content of the cells. Euflavine completely inhibits mitochondrial protein synthesis in vitro. Its in vivo effect is to cause the formation of giant mitochondrial profiles with apparently intact outer membranes and modified internal membranes; the cristae (in-folds) appear only as apparently disorganized remnants while the remainder of the inner membrane seems intact. Cytochromes a, a₃, b, and c₁ are not synthesized by the cells in the presence of euflavine. Ethidium appears to have effects identical to those of euflavine, whereas chloramphenicol, lincomycin, and erythromycin have similar effects in principle but they are less marked. The effects of all the inhibitors are freely reversible after removal of the drugs. The results are discussed in terms of a functionally three-membrane model of the mitochondrion. In addition, the phylogenetic implications of the observed differences between this organism and the facultative anaerobic yeasts are considered.     

Glutamate dehydrogenase (GDH) and respiratory electron-transport-system (ETS) activities in Gulf of Mexico zooplankton

Ratios of GDH activity: NH₄⁺ excretion and ETS activity: oxygenconsumption were measured in western Gulf of Mexico zooplanktonand averaged 18.7 ? 4.3 and 2.65 ? 0.55, respectively. Theseratios were used to estimate NH₄₊ excretion and respirationrates of two natural zooplankton assemblages sampled quantitativelyfor GDH and ETS activity with a Multiple Opening and ClosingNet and Environmental Sensing System (MOCNESS). Greater than80% of the total GDH and ETS activity 0–200 m was concentratedin depth strata above the chlorophyll maximum, suggesting astrong zooplankton-phytoplankton grazing interaction. GDH activityper unit of zooplankton protein biomass was 3-fold greater inthe upper 100 m than between 100 – 200 m, while ETS activityper unit of zooplankton protein biomass showed no consistentpattern with increasing depth. O:N metabolic quotients wereestimated for the zooplankton sampled with the MOCNESS by ratioingGDH-excretion and ETS-respiratory by atoms. Lowest O:N quotientsoccurred in depth strata above the chlorophyll maximum, suggestinga predominance of protein-based grazing and/or predation. ¹Contribution No. 81-013 from the Bigelow Laboratory for OceanSciences     

Effects of chronic administration of phencyclidine on stereotyped and ataxic behaviors in the rat

After chronic administration of Phencyclidine (PCP) to rats, a high test dose (15 mg/kg) of PCP produced increases in stereotypic and ataxic behaviors, and a lower test dose of PCP (5 mg/kg) produced decreases in these behaviors, compared to behavioral responses of control rats. Rearing behavior in rats chronically administered PCP was increased at all test doses of the drug. Rats treated chronically with 15 mg/kg PCP for 9 days showed marked increases in most of these behaviors, whereas, rats receiving 5 mg/kg PCP for 9 days showed less change in several stereotypic and ataxic behaviors. Rats receiving 10 mg/kg PCP on a once-weekly schedule also exhibited more rearing and ataxic behavioral responses after the 3rd or 4th weekly PCP injection. Chronic PCP rats did not show more stereotypic or ataxic behavior after administration of apomorphine or amphetamine than control rats. These results suggest that chronic administration of PCP augments sensitivity to the stereotypic inducing effects of high doses, and decreases sensitivity to low doses of PCP.     

Response of 19 cultivars of soybeans to ultraviolet-B irradiance

Nineteen soybean cultivars were grown for four weeks in controlled environmental chambers with artificial daylight supplemented by five UV-B irradiance regimes to determine the range of growth and development responses of seedlings. Data from nine plant characteristics were assessed: leaf area, dry weight of leaves, stems and roots, total plant dry weight, height, ratio of roots to shoots and leaf area to weight and rating of leaves for damage. Significant differences were observed in the responses noted. Stunting, leaf chlorosis and loss of apical dominance were three general symptoms apparent on all cultivars which received UV-B irradiance. Varying degrees of reduced leaf area and dry weight of the plants and altered ratios of weights of leaves per unit area and weight of roots to shoots were also found. It was concluded that different soybean cultivars demonstrate a marked difference in sensitivity to UV-B radiation under the artificial conditions of controlled environmental growth chambers and this may indicate a genetic basis for variability in sensitivity of soybean cultivars to this waveband. However, the sensitivity to UV-B radiation was increased by the lower than normal photon fluence of photosynthetically active radiation (225 μE m⁻² s⁻¹).     

Augmentation mammaplasty: a comparative analysis

With the continuation of augmentation mammaplasty as a desirable operation for a large segment of the female population in the United States, the problem of fibrous capsular contracture that has been present since the inception of the operation has persisted. Various approaches to the problem have been entertained, and a lessening of the incidence has occurred as reviewed in our earlier report, which follows augmentation mammaplasty in our clinic from 1962 through 1979. In this retrospective study, no significant difference in contracture rate was seen based on patient smoking habits, operative approach used, or implant type. It is important to note that the total experience with the low-bleed implant was significantly lower in terms of number of patients meeting the criteria of this retrospective study than the standard gel mammary implant. Greater follow-up time and number of patients will be evaluated in future retrospective studies. We have demonstrated in this study that placement of the implant beneath the pectoral muscle has significantly diminished the incidence of capsular contracture both as Baker grades II, III, and IV and as Baker grades III and IV. The retropectoral site has become the preferred location for the prosthesis in our clinic. There is no appreciable alteration in the overall shape of the breasts from this approach, and therefore, it will continue to be the preferred method. Rates of incidence of hematoma, the most frequent adverse reaction after contracture, were not significantly different between the retropectoral and retromammary implant sites.(ABSTRACT TRUNCATED AT 250 WORDS)     

Does progressive nuclear staining with hemalum (alum hematoxylin) involve DNA,and what is the nature of the dye-chromatin complex?

Previous investigators have disagreed about whether hemalum stains DNA or its associated nucleoproteins. I review here the literature and describe new experiments in an attempt to resolve the controversy. Hemalum solutions, which contain aluminum ions and hematein, are routinely used to stain nuclei. A solution containing 16 Al³⁺ ions for each hematein molecule, at pH 2.0–2.5, provides selective progressive staining of chromatin without cytoplasmic or extracellular “background color.” Such solutions contain a red cationic dye-metal complex and an excess of Al³⁺ ions. The red complex is converted to an insoluble blue compound, assumed to be polymeric, but of undetermined composition, when stained sections are blued in water at pH 5.5–8.5. Staining experiments with DNA, histone and DNA + histone mixtures support the theory that DNA, not histone, is progressively colored by hemalum. Extraction of nucleic acids, by either a strong acid or nucleases at near neutral pH, prevented chromatin staining by a simple cationic dye, thionine, pH 4, and by hemalum, with pH adjustments in the range, 2.0–3.5. Staining by hemalum at pH 2.0–3.5 was not inhibited by methylation, which completely prevented staining by thionine at pH 4. Staining by hemalum and other dye-metal complexes at pH ≤ 2 may be due to the high acidity of DNA-phosphodiester (pK_a ~ 1). This argument does not explain the requirement for a much higher pH to stain DNA with those dyes and fluorochromes not used as dye-metal complexes. Sequential treatment of sections with Al₂(SO₄)₃ followed by hematein provides nuclear staining that is weaker than that attainable with hemalum. Stronger staining is seen if the pH is raised to 3.0–3.5, but there is also coloration of cytoplasm and other materials. These observations do not support the theory that Al³⁺ forms bridges between chromatin and hematein. When staining with hematein is followed by an Al₂(SO₄)₃ solution, there is no significant staining. Taken together, the results of my study indicate that the red hemalum cation is electrostatically attracted to the phosphate anion of DNA. The bulky complex cation is too large to intercalate between base pairs of DNA and is unlikely to fit into the minor groove. The short range van der Waals forces that bind planar dye cations to DNA probably do not contribute to the stability of progressive hemalum staining. The red cation is precipitated in situ as a blue compound, insoluble in water, ethanol and water-ethanol mixtures, when a stained preparation is blued at pH > 5.5.     

Phylogenetic analysis of carbamoylphosphate synthetase genes: complex evolutionary history includes an internal duplication within a gene which can root the tree of life

Carbamoylphosphate synthetase (CPS) catalyzes the first committed step in pyrimidine biosynthesis, arginine biosynthesis, or the urea cycle. Organisms may contain either one generalized or two specific CPS enzymes, and these enzymes may be heterodimeric (encoded by linked or unlinked genes), monomeric, or part of a multifunctional protein. In order to help elucidate the evolution of CPS, we have performed a comprehensive phylogenetic analysis using the 21 available complete CPS sequences, including a sequence from Sulfolobus solfataricus P2 which we report in this paper. This is the first report of a complete CPS gene sequence from an archaeon, and sequence analysis suggests that it encodes an enzyme similar to heterodimeric CPSII. We confirm that internal similarity within the synthetase domain of CPS is the result of an ancient gene duplication that preceded the divergence of the Bacteria, Archaea, and Eukarya, and use this internal duplication in phylogenetic tree construction to root the tree of life. Our analysis indicates with high confidence that this archaeal sequence is more closely related to those of Eukarya than to those of Bacteria. In addition to this ancient duplication which created the synthetase domain, our phylogenetic analysis reveals a complex history of further gene duplications, fusions, and other events which have played an integral part in the evolution of CPS.