Romeu Cardoso Guimarães

tRNA-rRNA sequence homologies: A model for the origin of a common ancestral molecule, and prospects for its reconstruction

A model is proposed for the early evolution of the coding mechanism. A primordial RNA embodies the functions of todays nucleic acids in a single molecule. The molecule is generated by successive rounds of self-priming and-templating. After proximity is assured by enclosure in a cell, the functions can be partitioned among more efficient specializel molecules. The prediction of sequence homologies in later forms prompted a search for matches between t- and r-RNAs. These are described. Their distributions offer clues to their origins. The existance of overlapping homologies indicates an approach to the reconstruction of an ancestral molecule.

Possible hepatotoxicity of chronic marijuana usage

CONTEXT Hepatotoxicity is a potential complication from the usage of various illicit drugs, possibly consequent to their liver metabolism, but information on this is scarce in the medical literature. OBJECTIVE To study the occurrence of clinical and laboratory hepatic alterations in chronic marijuana users, from the use of marijuana on its own or in association with other legal or illicit drugs. TYPE OF STUDY transversal study SETTING Hospital Espírita de Marília, Marília, São Paulo, Brazil PARTICIPANTS The study was made among 123 patients interned in the Hospital Espírita de Marília from October 1996 to December 1998, divided into 3 groups: 26 (21%) using only marijuana, 83 (67.5%) using marijuana and crack, and 14 (11.4%) consuming marijuana and alcohol. PROCEDURES AND MAIN MEASUREMENTS: Patients were examined clinically with special emphasis on types of drugs used, drug intake route, age when consumption began, length and pattern of usage, presence of tattooing, jaundice, hepatomegaly and splenomegaly. Serum determinations of total proteins, albumin, globulin, total and fractions of bilirubin, aspartate (AST) and alanine (ALT) aminotransferases, alkaline phosphatase (AP), gamma-glutamyltransferase and prothrombin activity were performed. RESULTS Among users of only marijuana, hepatomegaly was observed in 57.7% and splenomegaly in 73.1%, and slightly elevated AST (42.3%), ALT (34.6%) and AP (53.8%). The three groups did not differ significantly in the prevalence of hepatomegaly, splenomegaly and hepatosplenomegaly. The group using both marijuana and alcohol showed the highest prevalence of alterations and highest levels of aminotransferases. Mean AP levels were above normal in all groups. CONCLUSIONS Chronic marijuana usage, on its own or in association with other drugs, was associated with hepatic morphologic and enzymatic alterations. This indicates that cannabinoids are possible hepatotoxic substances.

tRNA-rRNA sequence homologies: Evidence for a common evolutionary origin?

SummaryMany tRNAs ofE. coli and yeast contain stretches whose base sequences are similar to those found in their respective rRNAs. The matches are too frequent and extensive to be attributed to coincidence. They are distributed without discernible pattern along and among the RNAs and between the two species. They occur in loops as well as in stems, among both conserved and non-conserved regions. Their distributions suggest that they reflect common ancestral origins rather than common functions, and that they represent true homologies.

Structure of the genetic code suggested by the hydropathy correlation between anticodons and amino acid residues.

The correlation between hydropathies of anticodons and amino acids, detected by other authors utilizing scales of amino acid molecules in solution, was improved with the utilization of scales of amino acid residues in proteins. Three partitions were discerned in the correlation plot with the principal dinucleotides of anticodons (pDiN, excluding the wobble position). (a) The set of outliers of the correlation: Gly-CC, Pro-GG, Ser-GA and Ser-CU. The amino acids are consistently small, hydro-apathetic, stabilizers of protein N-ends, preferred in aperiodic protein conformations and belong to synthetases class II. The pDiN sequences are representative of the homogeneous sector (triplets NRR and NYY), distinguished from the mixed sector (triplets NRY and NYR), that depict a 70% correspondence to the synthetases class II and I, respectively. The triplet pairs proposed to be responsible for the coherence in the set of outliers are of the palindromic kind, where the lateral bases are the same, CCC: GGG and AGA: UCU. This suggests that UCU previously belonged to Ser, adding to other indications that the attribution of Arg to YCU was due to an expansion of the Arg-tRNA synthetase specificity. The other attributions produced two correlation sets. (b) One corresponds to the remaining pDiN of the homogeneous sector, containing both synthetase classes; its regression line overlapped the one formed by the remaining attributions to class II. (c) The other contains the pDiN of the mixed sector and produced steeper slopes, especially with the class I attributions. It is suggested that the correlation was established when the amino acid composition of the protein synthetases became progressively enriched and that the set of outliers were the earliest to have been fixed.

A self-referential model for the formation of the genetic code

A model for the formation of the genetic code is presented where protein synthesis is directed initially by tRNA dimers. Proteins that are resistant to degradation and efficient RNA-binders protect the RNAs. Replication becomes elongational producing poly-tRNAs from which the mRNAs and ribosomes are derived. Attributions are successively fixed to tRNAs paired through the perfect palindromic anticodons, with the same bases at the extremities (5′ANA: UNU 3′; GNG: CNC; principal dinucleotides, pDiN). The 5′ degeneracy is then developed. The first pairs to be encoded correspond to the hydropathy correlation outliers (Gly-CC: Pro-GG and Ser-GA: Ser-CU) and to the sector of homogeneous pDiN, composed by two pyrimidines or two purines. These amino acids are preferred in the N-ends of proteins, stabilizers of proteins against catabolism and strong RNA-binders. The next pairs complete the sector of homogeneous pDiN (Asp, Glu-UC: Leu-AG and Asn, Lys-UU: Phe-AA). This set of nine amino acids forms the protein cores with the predominant aperiodic conformation. Next enter the pairs with mixed pDiN (one purine and one pyrimidine), the RY attributions composing the protein N-ends and the YR attributions the C-ends. The last pair contains the main punctuation signs (Ile, Met, iMet-AU: Tyr, Stop-UA). The model indicates that genetic information emerged during the process of formation of the coding/decoding system and that genes were defined by the proteins. Stable proteins constructed the nucleoprotein system by binding to the RNAs that produced them. In this circular rationale, genes are memories in a metabolic system for production of proteins that stabilize it. The simplicity and the highly deterministic character of the process suggest that the Last Universal Common Ancestor populations could be composed, in early stages, of lineages bearing similar genetic codes.

Metabolic Basis for the Self-Referential Genetic Code

An investigation of the biosynthesis pathways producing glycine and serine was necessary to clarify an apparent inconsistency between the self-referential model (SRM) for the formation of the genetic code and the model of coevolution of encodings and of amino acid biosynthesis routes. According to the SRM proposal, glycine was the first amino acid encoded, followed by serine. The coevolution model does not state precisely which the first encodings were, only presenting a list of about ten early assignments including the derivation of glycine from serine—this being derived from the glycolysis intermediate glycerate, which reverses the order proposed by the self-referential model. Our search identified the glycine-serine pathway of syntheses based on one-carbon sources, involving activities of the glycine decarboxylase complex and its associated serine hydroxymethyltransferase, which is consistent with the order proposed by the self-referential model and supports its rationale for the origin of the genetic code: protein synthesis was developed inside an early metabolic system, serving the function of a sink of amino acids; the first peptides were glycine-rich and fit for the function of building the early ribonucleoproteins; glycine consumption in proteins drove the fixation of the glycine-serine pathway.

Three-Dimensional Algebraic Models of the tRNA Code and 12 Graphs for Representing the Amino Acids

Three-dimensional algebraic models, also called Genetic Hotels, are developed to represent the Standard Genetic Code, the Standard tRNA Code (S-tRNA-C), and the Human tRNA code (H-tRNA-C). New algebraic concepts are introduced to be able to describe these models, to wit, the generalization of the 2n-Klein Group and the concept of a subgroup coset with a tail. We found that the H-tRNA-C displayed broken symmetries in regard to the S-tRNA-C, which is highly symmetric. We also show that there are only 12 ways to represent each of the corresponding phenotypic graphs of amino acids. The averages of statistical centrality measures of the 12 graphs for each of the three codes are carried out and they are statistically compared. The phenotypic graphs of the S-tRNA-C display a common triangular prism of amino acids in 10 out of the 12 graphs, whilst the corresponding graphs for the H-tRNA-C display only two triangular prisms. The graphs exhibit disjoint clusters of amino acids when their polar requirement values are used. We contend that the S-tRNA-C is in a frozen-like state, whereas the H-tRNA-C may be in an evolving state.

ETIOPATHOGENESIS OF PEPTIC ULCER: back to the past?

OBJECTIVES To review some aspects of the etiopathogenesis of peptic ulcerous disease especially on the basis of studies on its correlation with Helicobacter pylori (H. pylori). METHODS A search was made in the data bases MEDLINE, LILACS and PubMed, and in Brazilian and foreign books, referring to the incidence and prevalence of infection by H. pylori and of peptic ulcerous disease in various populations of different countries. RESULTS It was observed that the prevalence of H. pylori infection is similar in individuals with peptic ulcerous disease and the general population. There are differences between countries with respect to the prevalence of infection and of gastric or duodenal peptic ulcers. In many countries the prevalence of infection by H. pylori shows stability while the prevalence of peptic ulcerous disease is declining. The prevalence of peptic ulcerous disease without H. pylori infection varies between 20% and 56% in occidental countries. DISCUSSION The observations might be suggestive of H. pylori being only one more factor to be summed together with other aggressive components in the genesis of peptic ulcerous disease. We would therewith be returning to the classic concept that peptic gastric and duodenal ulcers have multifactorial etiology and would result from imbalance between aggressive and defensive factors. The focus of studies should be enriched with the identification of the defensive factors and of other aggressive factors besides the well known H. pylori and non-steroidal anti-inflammatory drugs, since these two aggressors do not exhaust the full causal spectrum.

Self-Referential Formation of the Genetic System

Formation of the genetic code is considered a part of the process of establishing precise nucleoprotein associations. The process is initiated by tRNA dimers paired through the perfect palindromic anticodons, which are at the same time codons for each other; the amino acid acceptor ends produce the transferase function, in a manner similar to the reaction occurring in ribosomes. The connections between nucleic acids and proteins are bidirectional, forming a self-feeding system. In one direction, proteins that are resistant to degradation and efficient RNA-binders stabilize the tRNAs that are specifically involved with their production; in the other direction, these tRNAs become fixed with the correspondences which are the amino acid codes. Replication of the stabilized tRNAs becomes elongational, forming polytRNAs, the precursors of the mRNA strings (genes), and of ribosomes. The linear order in the gene sequences follows the temporal succession of the encoding of tRNA pairs. The whole encoding process is oriented by the tRNA pairs. The core sequence of proteins shows the predominant aperiodic conformation and the anticodonic principal dinucleotides (pDiN) are composed of two purines or two pyrimidines: (1a) Gly / Pro; (1b) Ser / Ser; (2a) Asp, Glu / Leu; (2b) Asn, Lys / Phe. Members of the following pairs, with pDiN composed of a purine and a pyrimidine [(3a) Ala / Arg; (3b) Val / His, Gln; (3c) Thr / Cys, Trp; (4) Ile, Met / Tyr, and iMet / Stop], are added, respectively, to the mRNA heads / tails. It is indicated that: (a) The Last Universal Common Ancestor populations could, at some early stages, be composed of lineages bearing similar genetic codes, due to the simple and highly deterministic character of the process; (b) Genetic information was created during the process of formation of the coding/decoding subsystem, inside a proto-metabolic system already producing some amino acids and tRNA-like precursors; (c) Genes were defined by the proteins that stabilized the system, as memories for their production.

Indicators of inflammation and cellular damage in chronic asymptomatic or oligosymptomatic alcoholics: correlation with alteration of bilirubin and hepatic and pancreatic enzymes

Biochemical and hematimetric indicators of inflammation and cell damage were correlated with bilirubin and hepatic and pancreatic enzymes in 30 chronic male alcoholics admitted into psychiatric hospital for detoxification and treatment of alcoholism. Aspartate aminotransferase, alanine aminotransferase, gamma-glutamyltransferase, alkaline phosphatase, and total bilirubin were altered, respectively, in 90%, 63%, 87%, 23% and 23% of the cases. None of the indicators of inflammation (lactic dehydrogenase, altered in 16% of the cases; alpha-1 globulin, 24%; alpha-2 globulin, 88%; leucocyte counts, 28%) was correlated with alterations of bilirubin or liver enzymes. Lactic dehydrogenase was poorly sensitive for detection of hepatocytic or muscular damage. Alterations of alpha-globulins seemed to have been due more to alcohol metabolism-induced increase of lipoproteins than to inflammation. Among indicators of cell damage, serum iron, increased in 40% of the cases, seemed to be related to liver damage while creatine phosphokinase, increased in 84% of the cases, related to muscle damage. Hyperamylasemia was found in 20% of the cases and significantly correlated with levels of bilirubin, alkaline phosphatase and gamma-glutamyltransferase. It was indicated that injuries of liver, pancreas, salivary glands, and muscle occurred in asymptomatic or oligosymptomatic chronic alcoholics.