New species of Pogonophryne (Pisces, Artedidraconidae) from the Bellingshausen Sea, Antarctica

A new species of notothenioid fish, Pogonophryne bellingshausenensis n. sp., is described from the Bellingshausen Sea, Antarctica. The new species belongs to the dorsally-spotted “mentella” group of the genus and is characterized by having a short (about 13% SL) mental barbel with a short (about 16% of barbel length), narrow (barely wider than the stalk), and relatively inconspicuous terminal expansion composed of short, irregular, fingerlike processes. Compared to most other dorsally-spotted species of Pogonophryne (“barsukovi”, “marmorata”, and “mentella” groups), P. bellingshausenensis has a relatively wide (about 7% SL) interorbital region. An unspotted patch on the median dorsal surface of the head, posterior to the posttemporal ridges and anterior to the first dorsal fin, has not been observed previously in any dorsally-spotted species. The holotype was collected at 1,947 m, one of the deepest records for any species of Pogonophryne. A revised key to the ten species of the “mentella” group of Pogonophryne is also provided.     

Evolutionary History of the 11p15 Human Mucin Gene Family

The four human mucin genes MUC6, MUC2, MUC5AC, and MUC5B are located at chromosome 11p15.5. It has been demonstrated that the three mucins MUC2, MUC5AC, and MUC5B contain several Cys-subdomains of 108 amino acid residues. In contrast, little information is available concerning MUC6. These Cys-subdomains contain 10 cysteine residues that have a highly conserved position. We present here a coherent probable evolutionary history of this human gene family after comparison of the nucleotide sequences of these Cys-subdomains. The three MUC loci MUC2, MUC5AC, and MUC5B may have evolved from a common ancestral gene by two successive duplications. Moreover, we can postulate that MUC5AC and MUC5B have evolved in a concerted manner, while MUC2 has evolved separately. Received: 30 January 1997 / Accepted: 17 April 1997     

Effects of N-uronoyl derivatives of neurotransmitter amino acids on rats under conditions of behavioral tests

Under conditions of a few behavioral tests on rats, we examined the psychotropic activity of novel N-uronoyl derivatives of amino acids: (i) N-(1,2:3,4-di-O-isopropylidene-α-D-galactopyranuronoyl-β-alanine (DAGU-Ala), (ii) DAGU-glycyl-D,L-glutamic acid (DAGU-Gly-Glu), and (iii) DAGU-glycyl-glycine (DAGU-Gly-Gly) injected i.p. in a 50 mg/kg dose. In an open-field test, DAGU-Gly-Glu and DAGU-GLy-Gly showed antistress properties (they decreased the intensity of locomotion, decreased the number of defecation acts, and intensified the research activity), while DAGU-Ala possessed a psychostimulating effect (intensification of locomotor and research activity and an increase in the number of defecations). In the “black-and-white chamber” test, only DAGU-Gly-Gly exerted an anxiolytic effect; it somewhat increased the frequency and duration of emergings of animals from the dark section and duration of visits to the illuminated section of the chamber. DAGU-GLy-Glu manifested antidepressant properties; it increased the time of active swimming of the animal in the Porsolt test and decreased the duration of passive “hanging” of rats in the “suspension by the tail” test. Neirofiziologiya/Neurophysiology, Vol. 39, No. 1, pp. 52–61, January–February, 2007.     

Neuropharmacological profile of a high-affinity ligand of 5-HT1A receptors, 4-phenyl-1-[4-(2-naphtalimido)butyl]-piperazine

The neuropharmacological profile of 4-phenyl-1-[4-(2-naphtalimido)butyl]-piperazine (PNBP), a compound that possesses a high affinity for the serotonin receptors of 1A-type (5-HT_1A) and lacks an anxiolytic action, has been studied. Intracerebral administration of PNBP to rats through implanted cannulae into the hippocampal region resulted in no substantial behavioral changes during “open field” and “conflict situation” tests, as compared with those of control animals. At the same time, the behavioral effects of intraperitoneal administration of 10 mg/kg buspirone were completely abolished if buspirone had been jointly administered with 10 mg/kg PNBP. Moreover, combined application of 0.3 mg/kg PNBP and 0.3 mg/kg 8-OH-DPAT, an agonist of 5-HT_1A receptors, almost completely abolished the components of “serotonin syndrome” (prone position and stamping of the forepaws) in animals under study. These findings allowed us to conclude that PNBP has the properties of a competitive antagonist of buspirone and 8-OH-DPAT.     

Molecular Evolution of Nitrogen Fixation: The Evolutionary History of the nifD, nifK, nifE, and nifN Genes

The pairs of nitrogen fixation genes nifDK and nifEN encode for the α and β subunits of nitrogenase and for the two subunits of the NifNE protein complex, involved in the biosynthesis of the FeMo cofactor, respectively. Comparative analysis of the amino acid sequences of the four NifD, NifK, NifE, and NifN in several archaeal and bacterial diazotrophs showed extensive sequence similarity between them, suggesting that their encoding genes constitute a novel paralogous gene family. We propose a two-step model to reconstruct the possible evolutionary history of the four genes. Accordingly, an ancestor gene gave rise, by an in-tandem paralogous duplication event followed by divergence, to an ancestral bicistronic operon; the latter, in turn, underwent a paralogous operon duplication event followed by evolutionary divergence leading to the ancestors of the present-day nifDK and nifEN operons. Both these paralogous duplication events very likely predated the appearance of the last universal common ancestor. The possible role of the ancestral gene and operon in nitrogen fixation is also discussed. Received: 21 June 1999 / Accepted: 1 March 2000     

Evolution of major histocompatibility complex by “en bloc” duplication before mammalian radiation

Duplications are an important mechanism for the emergence of genetic novelties. Reports on duplicated genes are numerous, and mechanisms for polyploidization or local gene duplication are beginning to be understood. When a local duplication is studied, searches are usually done gene-by-gene, and the size of duplicated segments is not often investigated. Therefore, we do not know if the gene in question has duplicated alone or with other genes, implying that "en bloc" duplications are poorly studied. We propose a method for identification of "en bloc" duplication using mapping, phylogenetic and statistical analyses. We show that two segments present in the major histocompatibility complex (MHC) region of human chromosome 6 have resulted from an "en bloc" duplication that took place between divergence of amniotes and methaterian/eutherian separation. These segments contain members of the same multigenic families, namely olfactory receptors genes, genes encoding proteins containing B30.2 domain, genes encoding proteins containing immunoglobulin V domain and MHC class I genes. We will discuss the fact that olfactory receptors and MHC genes have undergone positive selection, which could have helped in fixation of the surrounding genes.     

Do slope orientation and sampling location determine soil biota composition?

“Evolution Canyon” is a typical Mediterranean-basin canyon with a summer dry stream at the bottom and large differences in vegetation cover and solar radiation between the north-facing slope (NFS) and the south-facing slope (SFS). It is known to act as an abiotic mediator influencing the community structure of soil fauna. The aim of this study was to determine the spatial dispersion of soil microbial and free-living nematode communities in the open sites (between shrubs) in the upper (0–10 cm) soil layer at four altitudes on both slopes. The combination of relative soil moisture availability and temperature, known to be one of the main triggers for soil biota activity, was explained by slope orientation. The above-mentioned differences were found to significantly affect microbial biomass and CO₂ evolution resulting in temporary stress, corresponding to higher values in metabolic quotient (qCO₂) values. These differences may represent microbial investment in energy in order to overcome stress resulting from the microclimatic differences between the two slopes. Moreover, the degree of substrate limitation (primary production due to the differences in plant cover) of microbial activity was explained by the difference in microbial functional groups. The total abundance of soil free-living nematodes was found to be 2-fold higher on the SFS than on the NFS. Thirty-nine genera, including 12 bacteria-feeders, 5 fungi-feeders, 12 plant-parasites, and 10 omnivore-predators, were found at the study site, with 34 genera on the NFS and 29 on the SFS. The generic diversity of the bacteriafeeding nematodes was higher on the SFS than on the NFS. This study elucidates the importance of slope orientation and its effect on the structural levels of soil microbial and nematode communities.     

The Evolutionary History of Carbamoyltransferases: A Complex Set of Paralogous Genes Was Already Present in the Last Universal Common Ancestor

Forty-four sequences of ornithine carbamoyltransferases (OTCases) and 33 sequences of aspartate carbamoyltransferases (ATCases) representing the three domains of life were multiply aligned and a phylogenetic tree was inferred from this multiple alignment. The global topology of the composite rooted tree (each enzyme family being used as an outgroup to root the other one) suggests that present-day genes are derived from paralogous ancestral genes which were already of the same size and argues against a mechanism of fusion of independent modules. A closer observation of the detailed topology shows that this tree could not be used to assess the actual order of organismal descent. Indeed, this tree displays a complex topology for many prokaryotic sequences, with polyphyly for Bacteria in both enzyme trees and for the Archaea in the OTCase tree. Moreover, representatives of the two prokaryotic Domains are found to be interspersed in various combinations in both enzyme trees. This complexity may be explained by assuming the occurrence of two subfamilies in the OTCase tree (OTC α and OTC β) and two other ones in the ATCase tree (ATC I and ATC II). These subfamilies could have arisen from duplication and selective losses of some differentiated copies during the successive speciations. We suggest that Archaea and Eukaryotes share a common ancestor in which the ancestral copies giving the present-day ATC II/OTC β combinations were present, whereas Bacteria comprise two classes: one containing the ATC II/OTC α combination and the other harboring the ATC I/OTC β combination. Moreover, multiple horizontal gene transfers could have occurred rather recently amongst prokaryotes. Whichever the actual history of carbamoyltransferases, our data suggest that the last common ancestor to all extant life possessed differentiated copies of genes coding for both carbamoyltransferases, indicating it as a rather sophisticated organism.     

Ecological twin species and some obscure questions of hominidae evolutions

Ecological twin species are closely related species inhabiting the same ecological niche. Both micro- and macroevolutions proceed faster in a twin system than within a single species. One proposed hypothesis is that the acceleration of hominoid evolution was caused by the existence of ecological twin species. The complementary species for Homo habilis and Homo erectus were Australopithecus species. Both paleontological and cryptozoological data suggest that Homo sapiens has a complementary species as well. A small population of the latter may still exist today. Specific interaction within the system of two species explains the difficulty in detecting ecological twins of the species. The existence of a hypothetical human species provides the basis of popular talk of a “wildman”.     

Specific detection of green sulfur bacteria by in situ hybridization with a fluorescently labeled oligonucleotide probe

An oligodeoxynucleotide probe (GSB-532) specific for green sulfur bacteria was developed. Highly stringent hybridization conditions were established using whole cells of Chlorobium limicola DSM249 immobilized on glass slides. At a formamide concentration of 10%, the optimum specificity was reached at 47 °C. When a conventional fixation procedure was used, a conspicuous autofluorescence developed within the cells. This autofluorescence was due to the liberation of bacteriochlorophyll by the detergent Triton X-100 and a subsequent conversion to bacteriopheophytin and related compounds. The signal-to-noise ratio could be increased by a final dehydration of the samples with methanol. Finally, the method was adapted to the hybridization of natural samples collected on polycarbonate membrane filters. In situ hybridization of pure cultures, various enrichments, and natural samples from the chemocline of a freshwater lake confirmed that probe GSB-532 hybridized exclusively to cells of green sulfur bacteria. Our protocol allows the highly specific detection of green sulfur bacteria in water samples and a rapid screening of natural bacterial communities. Employing probe GSB-532, the phylogenetic affiliation of the epibionts in “Chlorochromatium aggregatum” and “Pelochromatium roseum” could be demonstrated for the first time. Received: 26 October 1998 / Accepted: 7 January 1999     

Bioaccumulation properties of nickel-, cadmium-, and chromium-resistant mutants of pseudomonas aeruginosa NBRI 4014 at alkaline pH

Nickel-, cadmium-, and chromium-resistant mutants of Psedomonas aeruginosa sp. NBRI 4014 are potent growth promontory strains. In the presence of metal(s), they have shown increased cell morphology and could accumulate nickel (2.0874 mM/g), cadmium (2.295 mM/g), and chromium (2.997 mM/g) at pH 9. However, chromium accumulation was maximum, but the toxicity levels of nickel, cadmium, and chromium was ranged from 90 to 504 μM of used metal(s). Bioaccumulation increases up to the fifth day at the highest used metal concentration and then became constant. This suggests their exploitation for detoxification and subsequently loaded biomass treatment for the recovery of accumulated metal(s).     

Evolutionary History of 4.5SI RNA and Indication That It Is Functional

To date, the small nuclear 4.5S_I RNA has only been studied in the rat (Rattus norvegicus). Combining PCR and hybridization analyses, we have revealed 4.5S_I RNA homologues sequences in the genomes of four myomorph rodent families (Muridae, Cricetidae, Spalicidae, and Rhizomyidae), and not in other myomorph families (Dipodidae, Zapodidae, Geomyidae, and Heteromyidae) or sciuromorph and caviomorph rodents. By Northern-hybridization, 4.5S_I RNA has been detected in the common rat (R. norvegicus, Muridae), golden hamster (Mesocricetus auratus, Cricetidae), and Russian mole rat (Spalax microphthalmus, Spalacidae), but not in the related great jerboa (Allactaga jaculus, Dipodidae) or in four non-myomorph rodent species tested. cDNA derived from 4.5S_I RNA of M. auratus and S. microphthalmus has been cloned and sequenced. The hamster RNA is found to differ from rat 4.5S_I RNA by only one nucleotide substitution. For the mole rat, two variants of 4.5S_I RNA are detected: short (S) and long (L) with length 101 and 108 nt, respectively. The L variant differs from the S variant as well as from murid and cricetid 4.5S_I RNAs by both a 7 nt insertion and a varying number of nucleotide substitutions. The sequence similarity between the spalacid S-variant and murid/crecitid variants of 4.5S_I RNA is 90%. Judging from species distribution, 4.5S_I RNA genes emerged during the same period of time as the related short interspersed element B2 arose. This occurred after the divergence of Dipodidae lineage but before the branching of Spalicidae/Rhizomyidae lineage from a common myomorph rodent stem. S variant genes seemed to emerge in a common ancestor of spalacids and rhizomyds whereas L variant genes formed in spalacids following the divergence of these two families. The low rate of evolutionary changes of 4.5S_I RNA, at least, in murids and cricetids (6 × 10⁻⁴ substitutions per site per million years), suggests that this RNA is under selection constraint and have a function. This is a remarkable fact if the recent origin and narrow species distribution range of 4.5S_I RNA genes is taken into account. Genes with narrow species distribution are proposed to be referred to as stenogenes. Received: 11 December 2000 / Accepted: 27 August 2001     

Reconstructing the Complex Evolutionary History of Hepatitis B Virus

A detailed analysis of the evolutionary history of hepatitis B virus (HBV) was undertaken using 39 mammalian hepadnaviruses for which complete genome sequences were available, including representatives of all six human genotypes, as well as a large sample of small S gene sequences. Phylogenetic trees of these data were ambiguous, supporting no single place of origin for HBV, and depended heavily on the underlying model of DNA substitution. In some instances genotype F, predominant in the Americas, was the first to diverge, suggesting that the virus arose in the New World. In other trees, however, sequences from genotype B, prevalent in East Asia, were the most divergent. An attempt was also made to determine the rate of nucleotide substitution in the C open reading frame and then to date the origin of HBV. However, no relationship between time and number of substitutions was found in two independent data sets, indicating that a reliable molecular clock does not exist for these data. Both the pattern and the rate of nucleotide substitution are therefore complex phenomena in HBV and hinder any attempt to reconstruct the past spread of this virus. Received: 5 December 1998 / Accepted: 23 February 1999     

Evolutionary History of B1 Retroposons in the Genus Mus

Short interspersed DNA elements (SINEs) amplify by retroposition either by (i) successive waves of amplification from one or a few evolving master genes or by (ii) the generation of new master genes that coexist with their progenitors. Individual, highly conserved, elements of the B1 SINE family were identified from the GenBank nucleotide database using various B1 subfamily consensus query sequences to determine their integration times into the mouse genome. A comparison of orthologous loci in various species of the genus Mus demonstrated that four subfamilies of B1 elements have been amplifying within the last 1–3 million years. Therefore, B1 sequences are generated by coexisting source genes. Additionally, three B1 subfamilies have been concurrently propagated during subspecies divergence and strain formation in Mus, indicating very recent activity of this retroposon family. The patterns of intra- and interspecies variations of orthologous loci demonstrate the usefulness of B1 integrations as a phylogenetic tool. A single inconsistency in the phylogenetic trends was depicted by the presence of a B1 insert in an orthologous locus exclusively in M. musculus and M. pahari. However, DNA sequence analysis revealed that these were independent integrations at the same genomic site. One highly conserved B1 element that integrated at least 4–6 million years ago suggests the possibility of occasional function for B1 integrations. Received: 25 February 2000 / Accepted: 5 June 2000     

Evolutionary History of MHC Class I Genes in the Mammalian Order Perissodactyla

We carried out an analysis of partial sequences from expressed major histocompatibility complex (MHC) class I genes isolated from a range of equid species and more distantly related members of the mammalian order Perissodactyla. Phylogenetic analysis revealed a minimum of six groups, five of which contained genes and alleles that are found in equid species and one group specific to the rhinoceros. Four of the groups contained only one, or very few sequences, indicating the presence of relatively nonpolymorphic loci, while another group contained the majority of the equid sequences identified. These data suggest that a diversification of MHC genes took place after the split between the Equidae and the Rhinocerotidae yet before the speciation events within the genus Equus. Received: 17 November 1998 / Accepted: 7 April 1999     

The role of endothelial cell biology in endocarditis

The treatment of endocarditis remains a challenge for physicians, even in times of modern antibiotic treatment. Depending on its cause, endocarditis can either be of infectious or non-infectious origin. Infective endocarditis is caused by bacterial (or fungal) pathogens, and the clinical course is critically dependent on the virulence factors of the specific microorganisms involved. Therefore, the clinical type of endocarditis can be divided into an acute and more aggressive form and a subacute form (endocarditis lenta). Much of our knowledge regarding the pathogenesis of infective endocarditis is based on studies of the virulence of Staphylococcus aureus, which has become the most frequent cause of infective endocarditis nowadays. However, independently of the underlying cause of endocarditis (infectious or noninfectious), the pathogenesis involves the damage and disturbance of endothelial function and the formation of associated “vegetation”. Surprisingly little is known about the specific role of the endothelium in the pathogenesis of endocarditis. This review will thus give insights into current knowledge of the pathogenesis of endocarditis with a focus on the role of the endothelium.     

Allometric Effects of <Emphasis Type="Italic">Agriophyllum squarrosum</Emphasis> in Response to Soil Nutrients,Water, and Population Density in the Horqin Sandy Land of China

We monitored the allometric effects for greenhouse-grown Agriophyllum squarrosum plants in response to variations in population density and the availability of soil nutrients and water. Biomass allocations were size-dependent. The plasticity of roots, stems, leaves, and reproductive effort was “true” in response to changes in nutrient content. At a low level of soil minerals, plants allocated more resources to the development of roots and reproductive organs than to leaves, but data for stem allocations were consistent for tradeoffs between the effects of nutrients and plant size. The plasticities of leaf allocation and reproductive effort were “true” whereas those of root and stem allocations were “apparent” in response to fluctuations in soil water, being a function of plant size. Decreasing soil water content was associated with higher leaf allocation and lower reproductive effort. Except for this “apparent” plasticity of leaf allocation, none was detected with population density on biomass allocation. Architectural traits were determinants of the latter. For roots, the determining trait was the ratio of plant height to total biomass; for stems and reproduction, plant height; and for leaves, the ratio of branch numbers to plant height.     

Species composition and distribution of algae on the fringing coral reef of Sesoko Island (Ryukyu Archipelago) before and after the natural catastrophe of 1998

The species composition and distribution of marine plants on the fringing reef of Secoko Island were studied before and after the mass coral mortality in 1998. The study showed that changes in the bottom communities that occurred after bleaching of corals were caused by the presumed development of marine plants substituting reef-building corals on the bottom. The number of algal species grew from 211 to 345. The projective cover (PC) of hard substrate with macroalgae increased: in 1998, it was 1–10% in the subtidal zone and 20–50% in the intertidal zone, while in 2002 through 2005, the PC reached 71% in the subtidal and 40–85% in the intertidal zone. It is assumed that the phase of the “plant reef” on Sesoko Island is a temporary event, and that the coral reef can recover within several decades, unless a natural catastrophe occurs again.     

Molecular Evidence on the Evolutionary and Biogeographical Patterns of European Cyprinids

The phylogenetic relationships of 106 European cyprinid taxa were determined based on the complete nucleotide sequence (1140 bp) of the mitochondrial cytochrome b gene. The molecular phylogeny was used (1) to revise the current systematics of European cyprinids, (2) to establish the phylogenetic utility of traditional morphological characters that are widely used in Cyprinidae systematics, and (3) to discuss alternative hypotheses on the biogeography of the family in Europe. The age of the major lineages within European cyprinids was tentatively estimated with a molecular clock and showed full agreement with the fossil record of the group. Moreover, the results provided unambiguous evidence for a close phylogenetic affinity of some Caucasian and Greek endemic cyprinid taxa (e.g., B. capito and B. brachycephalus and Leuciscus keadicus, Barbus graecus, and B. albanicus, respectively) to Iberian and North African, but not Central European, cyprinids. The existence of such unexpected phylogenetic relationships refutes the classical hypothesis on the biogeography of European cyprinids, which assumes a dispersal of the cyprinid fauna from central Europe to southern Europe and northern Africa during the Miocene (and, hence, predicts a close phylogenetic relationship of all Caucasian, Greek, Iberian, and North African cyprinids to central European taxa). Instead, the existence of a Mediterranean realm independent of the central European route seems plausible based on the molecular evidence. It is likely that the new biogeographical scenario proposed here might apply to other primary freshwater European animals with low dispersal abilities, including fish, amphibians, and invertebrates. Received: 2 February 1999 / Accepted: 16 March 1999