Contrasting patterns of the 5S and 45S rDNA evolutions in the <Emphasis Type="Italic">Byblis liniflora</Emphasis> complex (Byblidaceae)

To clarify the evolutionary dynamics of ribosomal RNA genes (rDNAs) in the Byblis liniflora complex (Byblidaceae), we investigated the 5S and 45S rDNA genes through (1) chromosomal physical mapping by fluorescence in situ hybridization (FISH) and (2) phylogenetic analyses using the nontranscribed spacer of 5S rDNA (5S-NTS) and the internal transcribed spacer of 45S rDNA (ITS). In addition, we performed phylogenetic analyses based on rbcL and trnK intron. The complex was divided into 2 clades: B. aquatica–B. filifolia and B. guehoi–B. liniflora–B. rorida. Although members of the complex had conservative symmetric karyotypes, they were clearly differentiated on chromosomal rDNA distribution patterns. The sequence data indicated that ITS was almost homogeneous in all taxa in which two or four 45S rDNA arrays were frequently found at distal regions of chromosomes in the somatic karyotype. ITS homogenization could have been prompted by relatively distal 45S rDNA positions. In contrast, 2–12 5S rDNA arrays were mapped onto proximal/interstitial regions of chromosomes, and some paralogous 5S-NTS were found in the genomes harboring 4 or more arrays. 5S-NTS sequence type-specific FISH analysis showed sequence heterogeneity within and between some 5S rDNA arrays. Interlocus homogenization may have been hampered by their proximal location on chromosomes. Chromosomal location may have affected the contrasting evolutionary dynamics of rDNAs in the B. liniflora complex.     

Steady state growth space study of <Emphasis Type="Italic">Lactococcus lactis</Emphasis> in D-stat cultures

Growth space of Lactococcus lactis subsp. lactis IL1403 was studied at constant growth rate using D-stat cultivation technique. Starting from steady state conditions in a chemostat culture (μ = 0.2 h⁻¹), the pH and/or temperature were continuously changed in the range of 5.4–6.4 and 26–34°C, respectively, followed by the return to the initial environmental conditions. Based on substrate consumption and product formation yields and expression changes of 1,920 genes, it was shown that changes of physiological state were not dependent on the direction of movement (from pH 6.3 to 5.4 or from 5.4 to 6.3), showing that quasi steady state values in D-stat corresponded to the steady state values in chemostats. Relative standard deviation of growth characteristics in triplicate D-stat experiments was below 10%. Continuing the experiment and reestablishing initial growth conditions revealed in average 7% difference (hysteresis) in growth characteristics when comparing chemostat steady state cultures prior and after the change of environmental conditions. Similarly, shifts were also seen at gene expression levels. The large amount of quantitatively reliable data obtained in this study provided a new insight into dynamic properties of bacterial physiology, and can be used for describing the growth space of microorganisms by modeling cell metabolism.     

Extensive analysis of nuclear cistron rDNA sequence of <Emphasis Type="Italic">Paracyclopina nana</Emphasis> (Cyclopoida: Cyclopettidae)

As a special reference of the nuclear cistron rDNA of cyclopoid copepods, we obtained the entire DNA sequence of a single rDNA repeat unit from Paracyclopina nana (Cyclopoida: Cyclopettidae). The genomic organization of P. nana rDNA (7,974 bp, 51.7% of GC) was observed to be 18S–ITS1–5.8S–ITS2–28S–IGS in order. Comparative analyses of the rDNA between P. nana and other copepods showed that the intergenic spacer (IGS) was highly informative and divergent, while other coding regions are relatively conserved. We detected eleven poly(T) tracts in the IGS, demonstrating the high AT content in this region. In addition, many sub-repeat sequence patterns (e.g., AG, AT, GC, CCG, TC) such as microsatellites were identified from the rDNA IGS of P. nana. In this article, we show the first complete sequence of rDNA from the order Cyclopoida, providing a better understanding of molecular characteristics in molecular taxonomy.     

Changes in biodiversity of phytoplankton,zooplankton, fishes and macrobenthos in the Southern Caspian Sea after the invasion of the ctenophore <Emphasis Type="Italic">Mnemiopsis Leidyi</Emphasis>

Monitoring for 6 years (2001–2006) showed that the population explosion of the alien ctenophore Mnemiopsis leidyi in the southern Caspian Sea coincided with a decline in the abundance and species number of mesozooplankton. While this decline appeared to have reduced the nourishment of sprat (also known as kilka), it seemed to have affected phytoplankton favorably mainly due to the decrease in grazing pressure. During 2001–2002, when M. leidyi abundance and biomass were at their highest levels, abundance of dinoflagellates and cyanophytes exceeded that of diatoms. Before the invasion (1996) and in some years after the invasion (2003, 2004 and 2006) diatom abundance was higher than the abundance of other groups. In September 2005, an unprecedented bloom of the toxic cyanophyte Nodularia sp. was observed in the southern Caspian Sea. Disappearance of edible zooplankton such as Eurytemora spp. was among the first changes observed after the expansion of M. leidyi in the area. Some changes in the macrobenthic fauna were also conspicuous after the increase of this ctenophore. While the biomass of some deposit feeders, such as the polychaete Nereis diversicolor and oligochaete species increased, benthic crustaceans decreased sharply in abundance during 2001–2003 and completely disappeared during 2004–2006. Iranian catches of kilka, the most abundant and widespread zooplanktivorous fish, decreased significantly in the southern Caspian Sea after 1999. Iranian landings of kilka dropped ~70% from 69,070 ± 20,270 t during 1995–2000 to 23,430 ± 12,240 t during 2001–2006, resulting in a loss of at least 125 million US dollars to the economy. There were also changes in the total catches of large predators such as the kutum and mullet, which mainly feed on kilka, between 1991 and 2006.     

Systematic review of the genus <Emphasis Type="Italic">Bothrocara</Emphasis> Bean 1890 (Teleostei: Zoarcidae)

The systematics of the eelpout genus Bothrocara Bean 1890 is reviewed on the basis of 941 specimens. Eight mostly eurybathic, demersal species are recognized, distributed mainly along the continental slopes of the North and South Pacific oceans, with one species entering the South Atlantic. Distributions are: B. brunneum ranges from the Sea of Okhotsk to the Gulf of Panama at depths of 199–1,829 m; B. elongatum ranges from the Gulf of Panama to Chile at depths of 720–1,866 m; B. hollandi ranges from the Sea of Japan to the southeastern Bering Sea at depths of 150–1,980 m; B. molle ranges from the western Bering Sea to the South Atlantic at depths of 106–2,688 m; B. nyx is known only from the eastern Bering Sea at depths of 790–1,508 m; B. pusillum ranges from the northern Bering Sea to British Columbia, Canada, at depths of 55–642 m; B. tanakae is found along the northern coasts of Honshu and Hokkaido islands, Japan, at depths of 274–892 m; B. zestum ranges from the Izu Islands, Japan, and central Honshu, Japan, to the Gulf of Alaska at depths of 199–1,620 m (an unidentifiable specimen from off Taiwan may be B. zestum). The species are distinguished from one another mainly on the basis of head pore patterns, gill raker morphology, coloration and various meristic and morphometric values. A determination key to the species is provided.     

Recurrent high-biomass blooms of <Emphasis Type="Italic">Alexandrium taylorii</Emphasis> (Dinophyceae), a HAB species expanding in the Mediterranean

Summer outbreaks of the dinoflagellate Alexandrium taylorii Balech are recurrent events in nearshore waters of Sicily (Italy)—a central region in the Mediterranean Sea—producing dense yellowish–green patches. Beyond the local phenomenon, the problem covers a broader geographic scale, involving also other European localities, mostly in Spain. Biological, environmental, and molecular data are reported here from a semi-closed bay of Sicily (Vulcano Island, Tyrrhenian Sea, 2000–2003), showing in summer the recurrence of high-biomass blooms and events of water discolouration. Without underestimating the setbacks to the tourism industry, the ecological impact of A. taylorii blooms may be important considering the high levels of biomass produced (West Bay, Vulcano: up to a magnitude order of 10⁷ cells l⁻¹, 50–180 μg-Chla l⁻¹, June 2002 and 2003) and coincident conditions of oxygen supersaturation of the waters (130–170%). Trophic trends in the Tyrrhenian site indicate high amounts of nutrients linked to the increased anthropogenic activity in summer, although recently there has been an apparent shift of the marked eutrophic conditions towards a slighter eutrophy. Genetic data on isolates of A. taylorii from the Mediterranean Sea are also discussed. Molecular analyses implied the sequencing of target rDNA regions (5.8S rDNA and ITS regions) of several isolates from different Mediterranean localities, as well as the application of species-specific PCR assays for rapid species identification in preserved field samples. The confirmation of the specific identity provided new insights into the biogeography of this species and further evidence of the occurrence of A. taylorii in a number of Mediterranean localities, both in the western side (the Catalan coast of Spain) and the eastern area (Greece). Analyses of the molecular diversity of geographically distinct isolates of A. taylorii from Italy, Spain, and Greece based on the 5.8S rDNA-ITS region sequences showed a high level of similarity, indicating the existence of an unique Mediterranean population.     

Life history characteristics of the clam<Emphasis Type="Italic"> Mya arenaria</Emphasis> in the White Sea

Dynamics of Mya arenaria beds in two bights of the Chupa Inlet (Kandalaksha Bay, White Sea) were studied on a long-term basis. Observations were carried out at 1– to 3-year intervals from 1979 up to 1999. The studied soft-shell clam beds were characterised by a substantial instability of age structure. Since 1988, only one year-class has dominated in the beds while other generations have been scarce and recruitment was not observed. This pattern of Mya bed dynamics was related neither to interannual environmental changes nor to differential reproduction success or predation effects in the benthic assemblages. Favourable conditions for spat formation in 1988 (low abundance of other M. arenaria generations), as well as for juvenile survival during the following winter, resulted in high abundance of juveniles in both investigated locations in 1989. The mortality rate (μ) in this 1988 generation varied throughout the period of investigation and was related to age. The mortality level decreased for the first 2–4 years of the life cycle, then stabilised for the next 3–4 years, and eventually increased in subsequent years. Overall μ values ranged from 0 to 1.68 year^–1. The oldest specimens observed were 17 years old and had a maximum shell length of 79 mm. Significant differences in average growth rates were observed between molluscs of different locations. Communicated by H.-D. Franke     

Recent phytoplankton productivity of the northern Bering Sea during early summer in 2007

Although the northern Bering Sea is one of the most productive regions in the northern North Pacific Ocean and currently considered a declining productivity region, no recent primary productivity measurements have been collected in this region. Phytoplankton productivity was measured in the northern Bering Sea in 2007 using a dual ¹³C–¹⁵N isotope tracer technique to quantify present rates of primary productivity and to assess changes under recent environmental conditions in this area. We found that large diatoms (mostly Fragilaria sp.) dominated the phytoplankton during the initial part of the cruise, whereas unidentified nano + pico phytoplankton largely dominated at the surface about 2 weeks later (at “revisited stations”). At the 1% light depth, diatoms and Phaeocystis sp. were the dominant species, whereas diatoms and unidentified nano + pico cells were dominant at the revisited sites. Based on nitrate and ammonium uptake rates, the estimated f-ratios (the ratio of nitrate uptake rate/nitrate + ammonium uptake rates of phytoplankton) were high (0.65–0.74), indicating that nitrate was an important nitrogen source supporting primary production in the northern Bering Sea during the cruise in 2007. Compared with previous studies performed several decades ago, we found significantly lower chlorophyll-a concentrations and carbon uptake rates of phytoplankton in the northern Bering Sea in 2007. This is consistent with recent studies that have shown lower rates of production in the Chukchi Sea and declines in benthic biomass and sediment oxygen uptake in the northern Bering Sea.     

Chromosomal distribution of 18S-25S rDNA in four <Emphasis Type="Italic">Lupinus</Emphasis> species visualized by fluorescence <Emphasis Type="Italic">in situ</Emphasis> hybridization

The number and position of 18S–25S rDNA sites in 4 selected Lupinus species are reported for the first time. L. atlanticus, L. subcarnosus and L. paniculatus had two rDNA loci, while L. albus exhibited only one loci. Among these 4 species, all of them exhibited one large pair of strong signals that extends from the short arm to a NOR on a chromosome satellite. L. atlanticus, L. subcarnosus, L. paniculatus had one more locus of 18–25S rDNA, but a pair of weak hybridization signals were observed in L. paniculatus when 18S–25S rDNA was used as probe. The results are discussed in terms of the evolutionary relationships among these species.     

Chromosome phylogeny of <Emphasis Type="Italic">Zamia</Emphasis> and <Emphasis Type="Italic">Ceratozamia</Emphasis> by means of Robertsonian changes detected by fluorescence <Emphasis Type="Italic">in situ</Emphasis> hybridization (FISH) technique of rDNA

 Appearance and location of 45S rDNA and 5S rDNA signals were compared in chromosomes of nine species of the aneuploid Zamia and their taxonomically and phylogenetically closely related Ceratozamia mexicana. The 45S rDNA signal was detected in the proximal region of six chromosomes in Zamia angustifolia, Z. integrifolia, Z. pumila and Z. pygmaea (all 2n=16); in the proximal region of 6–14 chromosomes in Z. furfuracea, Z. loddigesii, Z. skinneri and Z. vazquezii (all 2n=18); and on the proximal region of 20 chromosomes in Z. muricata (2n=23). The 5S rDNA signals were commonly seen near the terminal region of the short arm of two metacentric chromosomes in the four species with 2n=16 and Z. furfuracea, Z. loddigesii and Z. vazquezii with 2n=18. Other 5S rDNA signals were seen near the terminal region of two terminal-centromeric chromosomes in Z. skinneri and near the terminal region of a metacentric and a telocentric chromosomes in Z. muricata. In contrast, those with 45S and 5S rDNA signals were exhibited in chromosomes of Ceratozamia mexicana in a different manner from those in the nine species of Zamia; the 45S rDNA signal in the terminal region of four metacentric and two submetacentric chromosomes and the 5S rDNA signal near the proximal region of two metacentric chromosomes. Received November 1, 1999 Accepted January 10, 2001     

Mackerel from the northern indian ocean and the red sea arescomber australasicus, notscomber japonicus

The population ofScomber from the Red Sea and northern Indian Ocean (gulfs of Aden and Oman) is identified asS. australasicus rather thanS. japonicus based on having 30–33 vs. 26–29 interneural bones under the first and second dorsal fins and the combination of interneural bone counts of 16–20 under the first dorsal fin (vs. 13–16) and first dorsal fin spine counts of 10–13 (vs. 9–10). These are the best morphological characters to distinguish these two species. This change in identification constitutes a major range extension forS. australasicus which was thought to be restricted to the Pacific Ocean and the southeastern Indian Ocean around Western Australia.     

RFLP analyses of severalBrassica representatives

Molecular variability was determined between, 17Brassica napus cultivars, 8 new selections 4 F₁ hybrids, 5 cultivars ofB. oleracea, B. campestris andB. peruvianum with 4 rDNA probes fromLycopersicon esculentum, 3 probes from a PstI library ofB. oleracea, 3 probes from EcoRI libraries ofB. napus andB. oleracea and the acetolactatsynthase gene fromNicotiana tabacum. Sporadic interspecific and rare intraspecific variability was detected. Contribution presented to the 5^th Czechoslovak Seminar “Plant Gene Engineering”, organized by the Institute of Plant Molecular Biology in České Budějovice, 2–13 September 1991.     

Effect of snow depth on under-ice irradiance and growth of <Emphasis Type="Italic">Aulacoseira baicalensis</Emphasis> in Lake Baikal

Lake Baikal freezes for 4–5 months each year; yet the planktonic diatoms that grow under the ice include some of the largest species found in freshwater. An important factor influencing their growth is the depth of snow. In this study, a population of Aulacoseira baicalensis developed where there was little or no snow on the ice but declined where there was 10 cm of snow, because 99% of the available light was attenuated. Culture studies of light response showed that A. baicalensis was adapted to relatively low light intensities (<40 μmol m⁻² s⁻¹) that were close to the average that a cell experiences in L. Baikal when mixed vertically by convection to depths that can exceed 100 m. On sunny days, cell division could be inhibited down to >10 m depth but narrow (<15 μm) diameter cells trapped in high light intensities in sub-ice layers switched to auxosporulation and size regeneration.     

Molecular sequencing and analysis of soluble methane monooxygenase gene clusters from methanotroph <Emphasis Type="Italic">Methylomonas</Emphasis> sp<Emphasis Type="Italic">.</Emphasis> GYJ3

Summary A methanotroph Methylomonas sp. GYJ3 was isolated, whose sMMO genes and 16S rDNA were sequenced and analysed, demonstrating that the bacterium might be a type I methanotroph (γ-Proteobacteria) and was closer to Methylomonas sp. KSWIII/KSPIII. This result was consistent with the result previously determined by biochemistry and morphological taxonomy. Sequence comparison among six open reading frames and the deduced amino acid sequences of the sMMO genes from six strains revealed that the strain GYJ3 had highly conserved regions in MMOX with other strains, amounting to 78–99% homology at protein level and 71–97% homology at DNA level. Highly conserved sequences lay in two iron-binding regions. Furthermore, scanning electron microscopy of the strain GYJ3 showed rod shapes with a slightly bent configuration on the even surfaces and with plump bodies.     

Cloning of ribosomal RNA genes from an Indian isolate ofGiardia lamblia and the use of intergenic nontranscribing spacer regions in the differentiation ofGiardia from other enteric pathogens

The ribosomal RNA genes from an Indian isolate ofGiardia lamblia have been cloned and characterized with respect to size, composition and copy number. Southern blotting and rDNA cloning ofGiardia lamblia revealed that genes coding for ribosomal RNA (rRNA) are exceptionally small and are encoded within a 5.6 kb genome fragment repeat. The rDNA repeat unit of this isolate was found to be highly G-C rich like other human isolates and the physical map showed severalSmaI sites. There are 132 copies of the rDNA repeat unit per cell in a head to tail arrangement. Two fragments corresponding to intergenic (0.2 kb and 0.3 kb) region and one (0.8 kb) containing both an intergenic region and a small part of the small subunit ribosomal RNA (SS rRNA) have been identified within the rDNA. These were used in heterogeneity studies ofGiardia isolated from two geographic locations as well as in the analysis of cross reactivity with other enteric organisms. In Southern blots, all the three fragments were found to be highly specific for the differential diagnosis ofGiardia spp. from the other enteric pathogens. These findings should help in developing a sensitive and more specific method for the diagnosis of giardiasis over currently available techniques.     

DNA sequence homology analysis of<Emphasis Type="Italic">ars</Emphasis> genes in arsenic-resistant bacteria

Homology ofars (arsenic-resistance system) genes was examined among the indigenous bacteria isolated from the soils and sediments of two abandened Au mines, which are highly contaminated with arsenic. The DNA and amino acid sequence homology of thears determinants were investigated using anars genotype. The isolated showed As(III)-oxidation ability containedarsAB genes encoding the efflux pump as well asarsR andarsD regulator genes. ThearsR andarsD leader gene are required for an arsenic resistance system when the high-homology genes (arsR; pl258 52.09% andarsD;Shewanell sp. 42.33%) are controlled by thears inducer-independent regulatory amino acid sequence. These leader gene were observed under weak acidic conditions in the Myoung-bong (pH; 5.0 to 6.0) and Duck-um (pH; 4.0 to 7.0) mines In addition, the strains with the ability of As (V)-reduction involved thearsC gene homologues, as in the strain CW-16 (Pseudomonas putida). The arsenic-resistance genes in the isolated indigenous bacteria showed varying degrees of amino acid similarity to the homologous genes found in the database (GenBank) such asP. putida KT2440: 39–53% forarsR, 22–42% forarsD, 16–84% forarsA, 26–45% forarsB, 17–44% forarsAB, 37–41% forarsC, and 14–47% forarsH. These findings suggested that the function of the variousars gene in indigenous bacteria existing in weakly oxidative conditions may be the key factor for redox mechanisms and biogeochemical systems in arsenic contaminated soils.     

Distribution of cells in different stages of the cell cycle and some age-related physiological characteristics in dependence on the dilution rate in chemostat cultures ofCandida utilis

Position of cells in their cell cycle was determined microscopically in chemostat cultures ofCandida utilis. Proportion of cells in phase G₁ decreased in a linear manner from 86% to 58% with dilution rate. Proportion of cells in phase S increased in the same range ofD from 5.6 to 13.5% and in the (G₂+M) phase from 8.4 to 28.5%, again linearly. Differential centrifugation was used to separate chemostat cultures to mother and daughter cells. Analyses showed that, relative to mother cells, daughter cells contain 2.1–11.9% more protein and 25.5–34.6% more RNA in dry matter. Their mass is 34.4–5.6% lower and volume is 154–19% smaller.