Whole Proteome Prokaryote Phylogeny Without Sequence Alignment: A K-String Composition Approach

A systematic way of inferring evolutionary relatedness of microbial organisms from the oligopeptide content, i.e., frequency of amino acid K-strings in their complete proteomes, is proposed. The new method circumvents the ambiguity of choosing the genes for phylogenetic reconstruction and avoids the necessity of aligning sequences of essentially different length and gene content. The only parameter in the method is the length K of the oligopeptides, which serves to tune the resolution power of the method. The topology of the trees converges with K increasing. Applied to a total of 109 organisms, including 16 Archaea, 87 Bacteria, and 6 Eukarya, it yields an unrooted tree that agrees with the biologists tree of life based on SSU rRNA comparison in a majority of basic branchings, and especially, in all lower taxa.     

Comparative Study of Induction of iNOS mRNA Expression in Vascular Cells of Different Species

To determine the difference in induction of inducible nitric oxide synthase (iNOS) mRNA expression in cultured vascular cells of different species, the expression of iNOS genes and their regulatory mechanisms in rat, human, bovine, and rabbit vascular endothelial cells and smooth muscle cells (SMC) were studied by Northern blotting, chloramphenicol acetyltransferase (CAT) assay, and electrophoretic mobility shift assay (EMSA). Qualitative estimation of iNOS mRNA by Northern-blot analysis demonstrated that the combination of interleukin-1 (IL-1), tumor necrosis factor- (TNF-), and lipopolysaccharides (LPS) drastically induces iNOS expression in rat and human SMC, and a more moderate effect was observed for endothelial cells; the effect of IL-1 alone was much weaker than that of the three factors. IL-1 alone or a mixture of IL-1, TNF-, and LPS both showed negligible effect on iNOS expression in bovine and rabbit vascular endothelial cells and SMC. Results of CAT assay corresponded well with Northern analysis indicating 7-fold increase in CAT activity by the mixture of IL-1, TNF-, and LPS in SMC and more moderate, 2-fold increase, in endothelial cells. IL-1 alone produced an intermediate effect (less than 2-fold) on vascular SMC of rats and humans. The results of EMSA showed that two shifted bands appeared when the nuclear protein from rat and human vascular endothelial cells bound to the region from –1037 to –787 of the rat iNOS gene, while vascular SMC nuclear protein only produced a single shifted band under the same conditions. These results suggest that cell- and species-specific mechanisms exist in the induction of iNOS expression.     

On the manner in which crossbreeding takes place in bacteriophages and bacteria

Summary In order to explain several discrepancies between the gene-recombination phenomena in phages and in higher organisms, we assume that theT ₂ phage, after entering the bacterium, divides in three parts corresponding to the three chromosomes' whichHershey andRotman have traced in this phage. The three parts are supposed to be able to divide further by rupture or by the action of other chromosome fragments. Each fragment is supposed able to reproduce inside the bacterium as a more or less independent unit and before lysis of the bacterium the various parts are assumed to reunite in complete sets of genes each forming a new phage.After discussing the experimental facts supporting these assumptions, we show that the assumptions are in perfect agreement with the theory of the symbiosis of genes, a theory which seems necessary in order to explain the ability of the chromosome-fragments to reunite into complete phages.Also the problems arising with respect to the sexual reproduction in bacteria is discussed under the point of view of the symbiosis theory. The assumption is made that the hereditary material is transduced from bacterium to bacterium by ultramicroscopic virus-like particles genophores. In several lysogenic bacteria the genophores are supposed still able to act as parasites (phages) instead of symbiontes towards some other sensitive bacteria. The experimental facts supporting this assumption are analyzed, and new experimental tests suggested.     

Introduction

The only concrete basis for the discontinuous and hierarchical organization of extant organisms lies in their genealogical (i. e. germ line) relationships. Individuals and populations of common descent are called sib or stirps. Ideally, systematic classification is based on the formulas: (1) sib + taxonomic category + name = taxon, and (2) divergent genealogy of sibs + hierarchy of taxonomic categories + names = taxonomic system (Fig. 1).Presented at the symposium Speciation and the Species Concept during the XIIth International Botanical Congress, Leningrad, July 8, 1975.     

Analysis of Variable Fractions Resulting from Microbial Counts

In microbiological studies various methods are employed to estimate fractions from paired counts of organisms. When the fraction (second count divided by first count) is constant among the paired counts, the maximum likelihood estimate is the ratio of the arithmetic means. In many practical applications this fraction may however not be constant, but vary substantially between pairs of counts.We discuss a statistical method that estimates the distribution of the fraction from pairs of counts, to allow for this variation. Four real data sets (concerning viability for growth and infection, recovery of a detection method, and removal in a treatment process) are analyzed by this method.Often, pairs of counts are not determined in the same physical sample, but the first count is made in one sample, and the second count in a second sample. We provide parametric models to deal with such a situation: the desired fraction is still estimated as a binomial probability, but the model includes sampling effects. This approach also allows for analysis of two distinct cases: paired observations, where the counts before and after are related in some way to each other, and unpaired observations, where they are not. The four models for separate samples: paired or unpaired observations, and binomial probability fixed or variable, are used to analyze the removal data.It is concluded that this approach of statistical analysis of fractions is more appropriate than often used calculations based on the ratio between the (geometric) means before and after. The implications for risk analysis are briefly discussed.     

Testis-specific β2 tubulins are identical in Drosophila melanogaster and D. hydei but differ from the ubiquitous β1 tubulin

In Drosophila as in many organisms tubulins are encoded by a gene family. We have determined the complete nucleotide sequences coding for the 1 and 2 tubulins of Drosophila melanogaster and the 2 tubulin of D. hydei, and found these insect tubulins to be highly conserved and like tubulins of other organisms. This is discussed with reference to the possible functional domains of these proteins. — The 1 tubulin gene of Drosophila is constitutively expressed, whereas the 2 tubulin is expressed specifically in the testes. In D. melanogaster the amino acid sequences of these proteins are 95% homologous, differing at only 25 positions. In the testes the 2 tubulin participates in different microtubules as shown by genetic analysis (Kemphues et al. 1982). Interestingly, all of the amino acids characteristic of the testis-specific 2 tubulin are also present in the corresponding gene of D. hydei. Of special interest is the high degree of conservation of the carboxy-terminal domain in these functionally equivalent tubulins.     

Causes,proximate and ultimate

Within evolutionary biology a distinction is frequently made between proximate and ultimate causes. One apparently plausible interpretation of this dichotomy is that proximate causes concern processes occurring during the life of an organism while ultimate causes refer to those processes (particularly natural selection) that shaped its genome. But ultimate causes are not sought through historical investigations of an organisms lineage. Rather, explanations referring to ultimate causes typically emerge from functional analyses. But these functional analyses do not identify causes of any kind, much less ultimate ones. So-called ultimate explanations are not about causes in any sense resembling those of proximate explanations. The attitude, implicit in the term ultimate cause, that these functional analyses are somehow superordinate to those involving proximate causes is unfounded. Ultimate causes are neither ultimate nor causes.     

Molecular pathways to parallel evolution: I. Gene nexuses and their morphological correlates

Aspects of the regulatory interactions among genes are probably as old as most genes are themselves. Correspondingly, similar predispositions to changes in such interactions must have existed for long evolutionary periods. Features of the structure and the evolution of the system of gene regulation furnish the background necessary for a molecular understanding of parallel evolution. Patently unrelated organs, such as the fat body of a fly and the liver of a mammal, can exhibit fractional homology, a fraction expected to become subject to quantitation. This also seems to hold for different organs in the same organism, such as wings and legs of a fly. In informational macromolecules, on the other hand, homology is indeed all or none. In the quite different case of organs, analogy is expected usually to represent attenuated homology. Many instances of putative convergence are likely to turn out to be predominantly parallel evolution, presumably including the case of the vertebrate and cephalopod eyes. Homology in morphological features reflects a similarity in networks of active genes. Similar nexuses of active genes can be established in cells of different embryological origins. Thus, parallel development can be considered a counter part to parallel evolution. Specific macromolecular interactions leading to the regulation of the c -fos gene are given as an example of a controller node defined as a regulatory unit. Quantitative changes in gene control are distinguished from relational changes, and frequent parallelism in quantitative changes is noted in Drosophila enzymes. Evolutionary reversions in quantitative gene expression are also expected. The evolution of relational patterns is attributed to several distinct mechanisms, notably the shuffling of protein domains. The growth of such patterns may in part be brought about by a particular process of compensation for controller gene diseases, a process that would spontaneously tend to lead to increased regulatory and organismal complexity. Despite the inferred increase in gene interaction complexity, whose course over evolutionary time is unknown, the number of homology groups for the functional and structural protein units designated as domains has probably remained rather constant, even as, in some of its branches, evolution moved toward higher organisms. In connection with this process, the question is raised of parallel evolution within the purview of activating and repressing master switches and in regard to the number of levels into which the hierarchies of genic master switches will eventually be resolved.     

Early development of the self-fertilizing mangrove killifish <Emphasis Type="Italic">Rivulus marmoratus</Emphasis> reared in the laboratory

The mangrove killifish Rivulus marmoratus was reared at 25°±1°C and 17ppt salinity from 0 to 100 days after hatching (DAH), and its early development was described by examining growth and morphometric parameters, meristic characters (vertebral and fin-ray counts), bone-cartilage development, and pigmentation. Growth was isometric for preanal length, head length, snout length, body depth, pectoral-fin length, dorsal-fin length, anal-fin length, and caudal-peduncle depth. Negative allometric growth was observed in eye diameter and gape size. Meristic counts (mean±SD) for vertebrae (34.2±0.4) and dorsal- (8.6±0.5), anal- (11.4±0.5), and caudal-fin rays (30.2±0.8) were complete at 0 DAH (n=5), whereas pectoral-fin rays and pelvic-fin rays were complete by 30 DAH (14.5±0.4, n=5) and 60 DAH (4.2±0.8, n=5). Full ossification of meristic elements proceeded in the following sequence: vertebrae (by 30 DAH), caudal-, dorsal-, and anal-fin rays (by 60 DAH), pectoral-fin rays (between 60 DAH and 100 DAH), and pelvic-fin rays (by 100 DAH). Both morphological characters and meristic counts indicate that this species can be considered to be a juvenile after 9.8mm in standard length (20 DAH).     

Survival and viability of nonculturableEscherichia coli andVibrio cholerae in the estuarine and marine environment

Plating methods for estimating survival of indicator organisms, such asEscherichia coli, and water-borne pathogens includingVibrio cholerae, have severe limitations when used to estimate viable populations of these organisms in the aquatic environment. By combining the methods of immunofluorescent microscopy, acridine orange direct counting, and direct viable counting, with culture methods such as indirect enumeration by most probable number (MPN) estimation and direct plating, it was shown that bothE. coli andV. cholerae undergo a nonrecoverable stage of existence, but remain viable. Following 2-week incubations in saltwater (5–25%o NaCl) microcosms, total counts, measured by direct microscopic examination of fluorescent antibody and acridine orange stained cells, remained unchanged, whereas MPN estimates and plate counts exhibited rapid decline. Results of direct viable counting, a procedure permitting estimate of substrate-responsive viable cells by microscopic examination, revealed that a significant proportion of the nonculturable cells were, indeed, viable. Thus, survival of pathogens in the aquatic environment must be re-assessed. The die-off or decay concept may not be completely valid. Furthermore, the usefulness of the coliform and fecal coliform indices for evaluating water quality for public health purposes may be seriously compromised, in the light of the finding reported here.     

The carotenoids of Flavobacterium strain R1560

The main carotenoid of Flavobacterium strain R1560 has been identified as (3R,3R)-zeaxanthin. Also present were small amounts of 15-cis-phytoene, phytofluene, -carotene (7,8,7,8-tetrahydro-, -carotene plus 7,8,11,12-tetrahydro-, -carotene), neurosporene, lycopene, -zeacarotene, -carotene, -carotene, -cryptoxanthin, rubixanthin, 3-hydroxy--zeacarotene and several apo-carotenals. Zeaxanthin production was inhibited by nicotine (10 mM), and lycopene and rubixanthin accumulated. The biosynthesis of zeaxanthin is discussed in terms of pathways and also of half-molecule reaction sequences. The presence of zeaxanthin may be a characteristic of a group of Flavobacterium species, and may thus be useful in the taxonomic classification of these organisms.     

Dry to wet weight biomass conversion constant for Tetrahymena elliotti (Ciliophora,Protozoa)

Summary The wet and dry weights of both axenic and monoxenic cultures of the ciliate Tetrahymena were determined directly. These estimates are dependent upon the method of volume determination. Assuming a prolate spheroidal shape for the ciliate, we calculate a mean wet weight of 0.4157±0.0713 pg m^-3 and a mean dry weight of 0.2793±0.0652 pg m^-3. Using electronic cell sizing, our estimates are 0.7869±0.1659 pg m^-3 and 0.5239±0.1101 pg m^-3, respectively. Independent of the method of volume determination, we estimate a mean biomass conversion ratio (dry weight/wet weight) of 0.59±0.08.     

Idioms of distress: Kinship and sickness among the people of the Kingdom of Tonga

Idioms of distress refers to the popular expression of emotional tension that arises in the relationship between sickness and kinship. By reference to case studies and discussions among the Polynesian people of Tonga, the author shows where such tension arises and how it influences the sickness process. Sickness is necessarily a collective phenomenon which can best be understood not simply as a clinical event, but as an experience that is part of the experience of family. Various ways of expressing distress as a reflexive encounter between personal and cultural meaning systems are reviewed, as are several new concepts such as doing sickness as kinship, and turning in the process of decision making in the kinship management of sickness. The explanatory models of sickness in Tonga are shown to encompass culturally sanctioned expressions of distress as part of the adaptive coping mechanisms in that society. Distress frequently emerges in somatic form, as a number of studies have shown. However, the author emphasizes the kinship meaning of sickness, kinship management and sickness therapy, the adaptive process of idiomatic expressions of distress, which are expanded here and offered as potential avenues for elaboration in other cultural milieu. Two aspects of the notion idioms of distress are noted, and the phenomenon is understood as a process which acts as a prime mover in social change.     

Fine structure studies of the ocelli of Polyorchis penicillatus (Hydrozoa,Anthomedusae) and their connection with the nerve ring

Summary The fine structure of the small compact ocelli (50–100 m in diameter) of Polyorchis penicillatus is described. The ocellar cup is formed of pigment cells and receptor cells. The pigment cells occur in approximately a 2:1 ratio to the receptor cells. Each pigment cell has a process that may pass through the presumed photosensory region. Pigment cells are connected to adjacent receptor cell processes by septate junctions. The sensory cells are bipolar with the apical part forming the receptor process and the basal part forming an axon 8–15 m long and 1–2 m in diameter. Each receptor cell axon forms a synapse with a single second order neuron but the sensory cells are also connected to the second order neurons postsynaptically. There are also synapses between adjacent second order neurons. The second order neurons lie outside the ocellar cup, next to the tentacular mesogloea. Each second order neuron forms an axon of about 1 m thickness. The axons on each side group together to form an optic nerve having 30–40 axons that travel around the tentacle base on either side and enter the outer nerve ring independently.     

On the stabilization of animal numbers. Problems of testing

Summary It is tried to remove some misunderstandings about the regulation of animal numbers by density-dependent processes. Staying between limits is called stabilization, and only when this results from density-dependent processes it is considered regulation. We discuss two tests that may be used to detect the existence of regulation: the parametric tests of Bulmer and a nonparametric permutation test. The powers of these tests are compared. The first test of Bulmer and the permutation test do not differ very much in power, but the second test of Bulmer has hardly any power and therefore cannot be used in cases where densities were only estimated. The arguments from which Bulmer's second test is derived are critically discussed and found not to be very convincing. We propose, rather than using Bulmer's second test, to correct the test statistic of his first test for estimation error, and present a possible solution for this. In a following paper this method will be applied to some long series of population counts of univoltine insects, for, a basic assumption of all regulation-tests is, that the sequence of population counts is a realization of a piece of first-order Markov chain. This highly restricts the usefulness of regulation-tests. Some other recent attempts to construct such tests are discussed within the present context     

Changes in LHβ-gene and FSHβ-gene expression in the ram pars tuberalis according to season and castration

Luteinizing hormone beta (LH) and follicle stimulating hormone beta (FSH) subunits and their mRNAs were studied in the ram pars tuberalis following different seasonal (winter vs summer) and experimental (intact vs castrated animals) conditions. Hormone-containing cells were identified by immunohistochemistry, and mRNAs for LH and FSH by in situ hybridization using homologous double-stranded ³⁵S-cDNAs. The labelling was quantified by image analysis. Immunohistochemical staining showed that cells containing LH and FSH were localized mainly in the ventral part of the pars tuberalis but that, in the summer, additional LH-containing cells were present in the dorsal part in intact rams. On the other hand, LH-mRNA labelling was found in the whole pars tuberalis in wethers but only in the ventral part in intact rams. The magnitude of LH-mRNA labelling was significantly greater in summer than in winter rams, and in castrated than in intact animals (P<0.001). However, the number of labelled cells was found to be the greatest in the winter (P<0.001) and was not affected by castration. FSH-mRNA expression was similar to that of LH-mRNA except that the level and extent were considerably lower. Thus, our results show an increase in the magnitude of gonadotropin subunit-mRNA in the summer and following castration; this increase appears to involve the entire pars tuberalis.     

Further cytogenetic analyses of the Croatian triploid shallot “Ljutika” (Allium cepa var.viviparum, Alliaceae) and its comparison with the Indian triploid “Pran”

Feulgen and silver-stained karyotypes and meiosis of two triploid viviparous onion forms (Allium cepa var.viviparum), the Croatian Ljutika and the Indian Pran, were comparatively analyzed. The results of chromosome measurements show that Ljutika and Pran are karyologically not identical, although significant similarities were found in the morphology of their chromosomes. Five geographically distant clones of Ljutika showed good agreement in the number and gross morphology of the chromosomes and in the number and position of NORs and interphase nucleoli. Heterotrivalents were predominant in meiosis of Ljutika but a relatively high frequency of higher multivalents together with univalents and bivalents were also observed. The relationship between Ljutika and Pran and their possible origin are discussed.     

Multiple Phosphorylation Sites and Quaternary Organization of Guanine-Nucleotide Exchange Complex of Elongation Factor-1 (EF-1βγδ/ValRS) Control the Various Functions of EF-1α

The eukaryotic guanine-nucleotide exchange factor commonly called elongation factor-1 (EF-1), comprises four different subunits including valyl-tRNA synthetase (EF-1/ValRS). The factor is multiply-phosphorylated by three different protein kinases, protein kinase C, casein kinase II and cyclin dependent kinase 1 (CDK1). EF-1/ValRS is organized as a macromolecular complex for which we propose a new structural model. Evidence that EF-1/ValRS is a sophisticated supramolecular complex containing many phosphorylation sites, makes it a potential regulator of any of the functions of its partner EF-1, not only involved in protein synthesis elongation, but also in many other cellular functions.     

Engineering of zinc finger and MHC motifs to locked-in tertiary folds

The assembly of helical and -sheet peptide blocks containing reactive chain ends results inhighly branched chain architectures (locked-in folds) mimicking native tertiary structures.This molecular kit strategy allows to bypass the protein folding problem in protein de novodesign and gives access to protein mimetics of high thermodynamic stability. The validity ofthis concept is exemplified for the design and synthesis of locked-in folds mimicking the zincfinger and MHC folding motifs.     

Polygonal inequalities as a key to neuronic equations

Neuronic or decision equations, first proposed as a mathematical model of neural activity, have shown, after their exact, compact solution was found, typical behaviours that make them natural tools for General Systems studies. It is shown here that their mathematical investigation is remarkably furthered by generalizing the triangular inequality to polygonal ones. These permit the immediate computation of the tensorial expansion of linearly separable boolean functions, and exhibit clearly the connection between their continuous and discontinuous aspects.