The bacterial cell cycle: DNA replication, nucleoid segregation, and cell division

Data on the bacterial cell cycle published in the last 10-15 years are considered, with a special stress on studies of nucleoid segregation between dividing cells. The degree of similarity between the eukaryotic mitotic apparatus and the apparatus performing nucleoid separation is discussed.     

Plant Cell Wall Is a Stumbling Stone for Molecular Biologists

Cell wall is a key structure of the plant organism engaged in numerous functions, and plants spend enormous resources on cell wall formation. Cell wall components are the most widespread organic substances on the Earth. However important is assembling plant cell wall polysaccharides, this process has been insufficiently studied by the methods of molecular genetics; in particular, too little is known of the genes that code for the relevant enzymes (glycosyltransferases, GT). The review addresses the current situation by expounding on GT classification, describing the characteristics of enzymes that synthesize cell wall polysaccharides, and summing up the existing knowledge of already identified and putative cellulose and callose synthases and GT localized in the Golgi apparatus. The methodology for searching and characterizing new genes that participate in cell wall formation is under discussion.__________Translated from Fiziologiya Rastenii, Vol. 52, No. 3, 2005, pp. 443–462.Original Russian Text Copyright © 2005 by Gorshkova, Nikolovski, Finaev.     

Volume and Rate Parameters of the Respiratory System and the State of the Vocal Apparatus

The parameters of permeability of the tracheobronchial tree were shown to determine the frequency characteristics of the voice and the functional state of the vocal apparatus.__________Translated from Fiziologiya Cheloveka, Vol. 31, No. 3, 2005, pp. 72–75.Original Russian Text Copyright © 2005 by Agadzhanyan, Smirnova.     

Changes in nucleoid viscosity following X-irradiation of rat thymic and splenic cells in vitro

Summary Unscheduled DNA synthesis (UDS) suggested a higher DNA repair capacity of X-irradiated rat thymic (T) cells when compared to splenic (S) cells (Tempel 1980). In the present investigations, damage and repair of DNA supercoiling was measured in T- and S-cells following X-irradiation in vitro by using the nucleoid sedimentation technique and a simplified low-shearing viscometric test. - X-irradiation resulted in a dose (0.6–19.2 Gy) - dependent reduction in sedimentation and viscosity of nucleoids. Within a post-irradiation period of 30–45 min after a challenge dose of 19.2 Gy, DNA repair was accompanied by an increase in nucleoid sedimentation and viscosity in T-cells by about 60 and 300, in S-cells by almost 40 and 100%, resp. The increase in nucleoid viscosity within a 30 min repair period could be reduced in a concentration-dependent manner by DNA polymerase - inhibitors and proteinase K. - The higher DNA repair capacity of T-cells as reflected by UDS is confirmed therefore by the nucleoid characteristics. Apart from this suggestion, measuring nucleoid viscosity may be considered as a sensitive, simple and rapid device to detect radiation-induced DNA supercoiling phenomena.     

First occurrence of Cochlodinium blooms in Sabah, Malaysia

Harmful algal blooms (HABs) resulting in red discoloration of coastal waters in Sepanggar Bay, off Kota Kinabalu, Sabah, East Malaysia, were first observed in January 2005. The species responsible for the bloom, which was identified as Cochlodinium polykrikoides, coincided with fish mortalities in cage-cultures. Determinations of cell density between January 2005 and June 2006 showed two peaks that occurred in March–June 2005 and June 2006. Cell abundance reached a maximum value of 6 × 10⁶ cells L⁻¹ at the fish cage sampling station where the water quality was characterized by high NO₃–N and PO₄–P concentrations. These blooms persisted into August 2005, were not detected during the north–east monsoon season and occurred again in May 2006. Favorable temperature, salinity and nutrient concentrations, which were similar to those associated with other C. polykrikoides blooms in the Asia Pacific region, likely promoted the growth of this species. Identification of C. polykrikoides as the causative organism was based on light and scanning microscopy, and confirmed by partial 18S ribosomal DNA sequences of two strains isolated during the bloom event (GenBank accession numbers DQ915169 and DQ915170).     

Effects of Copper on Root Growth, Cell Division, and Nucleolus of Zea Mays

The effects of different concentrations (10^–5 – 10^–2 M) of copper sulfate on root growth, cell division and nucleoli in root tip cells of Zea mays L. were investigated. 10^–5 M Cu stimulated root growth, but at higher concentrations (10^–4 – 10^–2 M) inhibited it. Cu had toxic effects on chromosomal morphology: c-mitosis, anaphase bridges, and chromosome stickiness were induced. Some nuclei had irregular shape and particles extruded from nucleoli to nuclei and finally from the nuclei into the cytoplasm.     

Variations in chloroplast nucleoid number during the cell cycle in the algaScenedesmus quadricauda grown under different light conditions

Summary Synchronous cultures of the green algaScenedesmus quadricauda were grown at different mean irradiances (ranging from 15 Wm^–2 to 130Wm^–2). At each irradiance, the algae were exposed to illumination regimes which differed in light duration and dark intervals (222 to 240 hours). The cells from these cultures were sampled during their cycles, stained with DAPI and the number of nuclei and chloroplast nucleoids estimated.The nucleoids divided semisynchronously in steps which represented doublings in their number. For each doubling a constant amount of light energy (defined as the product of irradiance and light duration) had to be converted by the cells to become committed to this division. The times to the start of the nucleoid divisions were therefore inversely proportional to the irradiances applied and the final number of nucleoids was proportional to the light duration.Temporal relationships between nuclear and nucleoid divisions were also light dependent. Shortage of light energy caused delay in nucleoid division. The cell division rate was higher than the rate of nucleoid division and consequently, the cells tended to decrease their nucleoid number with decreasing irradiance. With increasing irradiance the start of nucleoid division was gradually shifted toward the beginning of the cell cycle. The rate of nucleoid division exceeded the rate of nuclear and cellular division, thus with increasing irradiance cells with increasing numbers of nucleoids were formed.Abbreviations DAPI 46-diamidino-2-phenylindole - pt-DNA chloroplast DNA     

The application of a laboratory apparatus for the study of nutrient fluxes between sediment and water

Sediments of the river Elbe estuary have been studied to assess their impact on the total nitrogen budget of the estuary. A new laboratory incubation apparatus was used to provide a means of regulating important parameters such as temperature and oxygen concentrations. With this apparatus sediment cores from a typical shallow water area with high organic carbon content were incubated under varying oxygen concentrations in the overlying water. Measurements of ammonium, nitrite, nitrate and nitrous oxide in the water phase were carried out and the fluxes between sediment and water phase calculated. During aerobic conditions in the water phase overall nitrate fluxes between + 4 and –3.5 mmol Nm^–2d^–1 across the sediment/water interface were observed. Under anaerobic conditions the fluxes increased up to –10 mmol Nm^–2 d^–1. Nitrous oxide was formed within the sediment under both aerobic and anaerobic conditions. Fluxes into the water phase were highest when the oxygen concentrations in the water phase were low (between 0.1 and 0.6 mg l^–1).     

Establishment of Orthosiphon stamineus Cell Suspension Culture for Cell Growth

Callus of Orthosiphon stamineus could be induced successfully from petiole, leaf and stem tissues but not roots when cultured on MS medium containing different concentration of NAA (0–4.0 mg l^–1) and 2,4-D (0–2.0 mg l^–1). Highest fresh weight callus production was obtained from leaf explants and those with best friability were obtained on MS medium plus 1.0 mg l^–1 2,4-D plus 1.0 mg l^–1 NAA. Cell suspension cultures were established from these cultures. The appropriate cell inoculum size for the best cell growth was 0.75 g of cells in 20 ml culture medium. Cell suspension culture using MS medium supplemented with 1.0 mg l^–1 2,4-D promoted the best cell growth with maximum biomass of 8.609 g fresh weight and 0.309 g dry weight 24 days after inoculation. Cells that grew in MS medium supplemented with 1.0 mg l^–1 2,4-D reached the stationary growth phase in 15 days as compared to the cells that grew in MS medium supplemented with 1.0 mg l^–1 2,4-D + 1.0 mg l^–1 NAA reached the stationary phase in 24 days. MS medium supplemented with 1.0 mg l^–1 2,4-D was considered as the maintenance medium for maintaining the optimum cell growth of O. stamineus in the cell suspension cultures with 2-week interval subculture.     

Adaptive response of the chicken embryo to low doses of x-irradiation

Chicken embryos were x-irradiated in ovo with 5–30 cGy (=priming dose) at the 13th–15th day of development. After 3–48 h, brain- and liver-cell suspensions were x-irradiated in vitro with (challenge) doses of 4–32 Gy. Significantly less radiation damage was observed when the radiation response was measured by scheduled DNA synthesis, nucleoid sedimentation and viscosity of alkaline cell lysates 12–36 h after the priming exposure. In vivo, pre-irradiation with 10 cGy enhanced regeneration as evidenced by the DNA content of chicken embryo brain and liver 24 h following a challenge dose of 4 Gy. From nucleoid sedimentation analyses in brain and liver cells immediately after irradiation with 16 Gy and after a 30-min repair period in the presence of aphidicolin, dideoxythymidine and 3-aminobenzamide or in the absence of these DNA repair inhibitors, it is concluded that a reduction of the initial radiation damage is the dominant mechanism of the radio-adaptive response of the chicken embryo. Sedimentation of nucleoids from ethidium bromide (EB) (0.75–400 µg/ml)-treated cells suggests a higher tendency of radio-adapted cells to undergo positive DNA supercoiling in the presence of high EB concentrations.     

The mantle, ink sac, ink, arm hooks and soft body debris associated with the shells in Late Triassic coleoid cephalopod Phragmoteuthis from the Austrian Alps

Fragmentarily preserved shells – mainly pro-ostraca, in several cases also phragmocones – occurring together with arm hooks and the ink sac of the Carnian (Late Triassic) coleoid cephalopod Phragmoteuthis bisinuata (Bronn) from Lunz (Austria) are examined with the scanning electron microscope and energy-dispersive spectrometer. The pro-ostracum bears black, shiny, pitch-like sheets. The black sheets, the ink sac content and the arm hooks have a granular ultrastructure of 0.1–1 μm grain size. The arm hooks and black sheets are micro-laminated; each lamina consists of fibres. The ink consists of an agglomerate of grains. On the ventral (internal) side of the pro-ostracum, the black sheets occasionally bear agglomerates of homogeneous, ink-like material along with heterogeneous structures. The pro-ostracum has crystal-shaped units with lamello-columnar ultrastructure of the inner layer and plate ultrastructure of the outer layer. This resembles the Late Triassic Lunzoteuthis [Doguzhaeva, L.A., Mutvei, H., Summesberger, H., 2005a. A Late Triassic coleoid from the Austrian Alps: the pro-ostracum viewpoint. In: Kostak, M., Marek, J. (Eds.), Proceedings of the 2nd International Symposium on Coleoid Cephalopods Through Time. Short Papers/Abstracts Vol. Prague, 26–29 September, 2005, pp. 55–59] and Early Jurassic Belemnotheutis [Doguzhaeva, L.A., Donovan, D.T., Mutvei, H., 2005b. The rostrum, conotheca and pro-ostracum in the Jurassic coleoid Belemnotheutis Pearce from Wiltshire, England. In: Kostak, M., Marek, J. (Eds.), Proceedings of the 2nd International Symposium on Coleoid Cephalopods Through Time. Short Papers/Abstracts Vol. Prague, 26–29 September, 2005, pp. 45–49]. The black sheets, the material on their inner surface, the ink and the arm hooks consist of carbon, occasionally with minor amounts of sulfur. The shell is of calcium carbonate.Based on their organic composition, position in the shell and lamello-fibrillar ultrastructure, the black sheets are considered to be remains of the mantle, sometimes with ink sac and soft body debris. The carbon composition and granular ultrastructure of arm hooks, ink, and soft tissue remains indicate that the non-mineralized structures are pseudomorphosed by carbon (carbonization), possibly due to C-accumulating bacteria.     

Solid phase isotope exchange with spillover hydrogen in amino acids,peptides, and proteins

We summarize here information on the theoretical and experimental study of high-temperature (150–200°C) solid phase catalytic isotope exchange (HSCIE) carried out with amino acids, peptides, and proteins under the action of spillover hydrogen. Main specific features of the HSCIE reaction, its mechanism, and its use for studying spatial interactions in polypeptides are discussed. A virtually complete absence of racemization makes this reaction a valuable preparative method. The main regularities of the HSCIE reaction with the participation of spillover tritium have been revealed in the case of peptides and proteins, and the dependence of reactivity of peptide fragments on the spatial organization of their molecules has been studied. An important peculiarity of this reaction is that HSCIE proceeds at 150–200°C with a high degree of chirality retention in amino acids and peptides. This is provided by its reaction mechanism, which consists in a synchronous one-center substitution at the saturated carbon atom characterized by the formation of pentacoordinated carbon and a three-center bond between the carbon and the incoming and outgoing hydrogen atoms.Translated from Bioorganicheskaya Khimiya, Vol. 31, No. 1, 2005, pp. 3–21.Original Russian Text Copyright © 2005 by Zolotarev, Dadayan, Borisov.     

Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy

A small container of several to a few hundred µm³ (i.e. bacterial cells and eukaryotic nuclei) contains extremely long genomic DNA (i.e. mm and m long, respectively) in a highly organized fashion. To understand how such genomic architecture could be achieved, Escherichia coli nucleoids were subjected to structural analyses under atomic force microscopy, and found to change their structure dynamically during cell growth, i.e. the nucleoid structure in the stationary phase was more tightly compacted than in the log phase. However, in both log and stationary phases, a fundamental fibrous structure with a diameter of ~80 nm was found. In addition to this ‘80 nm fiber’, a thinner ‘40 nm fiber’ and a higher order ‘loop’ structure were identified in the log phase nucleoid. In the later growth phases, the nucleoid turned into a ‘coral reef structure’ that also possessed the 80 nm fiber units, and, finally, into a ‘tightly compacted nucleoid’ that was stable in a mild lysis buffer. Mutant analysis demonstrated that these tight compactions of the nucleoid required a protein, Dps. From these results and previously available information, we propose a structural model of the E.coli nucleoid.     

Cell wall composition and synthesis via Golgi-directed scale formation in the marine eucaryote,Schizochytrium aggregatum,with a note on Thraustochytrium sp.

Summary Cell walls of Schizochytrium aggregatum and Thraustochytrium sp. were mechanically isolated and subjected to chemical analysis. On a dry weight basis the cell walls contain 21–36% carbohydrate and 30–43% protein. The principal sugar (>95%) of the Schizochytrium wall is l-galactose, while the Thraustochytrium cell wall contains l-galactose, d-galactose and xylose with l-galactose predominating. Ultrastructurally the cell walls of both organisms consist of a laminated structure which yields thin, flexible, nearly circular scales (0.5–1.1 in diameter) upon sonic disintegration. Structures presumed to be developing wall scales are found within cisternae of the Golgi apparatus in both organisms. The chemical composition and method of formation of the cell wall in these two protists is distinctly different from that found in the Saprolegniales (Oomycetes), the group with which these organisms have hitherto been aligned.     

Effect of nickel on growth,proliferation, and differentiation of root cells in <Emphasis Type="Italic">Triticum aestivum</Emphasis> seedlings

The effect of 10^–6 and 10^–4 M NiSO₄ on cell growth, proliferation, and differentiation was studied over 48 h in seminal and lateral roots of five-day-old Triticum aestivum seedlings. 10^–6 M NiSO₄ did not significantly affect the root system, whereas 10^–4 M NiSO₄ inhibited its development. However, 10^–6 M NiSO₄ disturbed the contacts between the groups of closely related cells of the rhizodermis in the meristem. In the exodermis, an additional layer of cells was formed. At the nickel concentration of 10^–4 M, cell divisions in the outer layers of the root cells and metaxylem ceased earlier than in other root tissues positioned both centripetally and acropetally. Differentiation of protophloem sieve elements was completed in the meristem but at a greater distance from the root tip. Cell elongation started at the same distance from the root tip as in control plants. The rate of elongation decreased, and acropetally it stopped. Therefore, the cells of the xylem and metaphloem started to differentiate, and primordia of lateral roots were initiated and formed closer to the root tip. At a lethal concentration (10^–4 M), nickel induced necroses of elongating cells of the endodermis and pericycle. Nickel is supposed to enter the tissues of the central cylinder predominantly via the protoxylem and rapidly translocate along the xylem. As a result, the incubation of the roots at this concentration for 48 h almost did not affect the development of the phloem and probably sugar unloading, that makes possible to maintain the growth of meristematic cells and the cell division of the most important tissues for longer time.Translated from Fiziologiya Rastenii, Vol. 52, No. 2, 2005, pp. 250–258.Original Russian Text Copyright © 2005 by N. Demchenko, Kalimova, K. Demchenko.This revised version was published online in April 2005 with a corrected cover date.     

DNA-Binding Proteins and Structural Characteristics of Chloroplast Nucleoids

A comparative analysis of proteins from chloroplast nucleoids was performed in two higher-plant species (Pisum sativumL. andArabidopsis thalianaL.) and a green alga Chlamydomonas reinhardtiiDang. In the nucleoids of the higher plants and the alga, 26–27 proteins were detected with their mol wts ranging from 10 to more than 94 kD. In all the species tested, the distribution of nucleoid proteins by their mol wts was similar, especially between the predominant proteins with mol wts of 10 to 40 kD. Six DNA-binding proteins (12–18 kD) were detected in nucleoids fromCh. reinhardtiichloroplasts after in vivocovalent cross-linking between chloroplast DNA and proteins. Under an electron miscroscope, some regular structures resembling nucleosome-like particles of bacterial cells were revealed.     

Stephen Angus Hutchinson, 1914–2005: an appreciation

Stephen A. Hutchinson (1914–2005), who spent most of his academic career at the University of Glasgow, served as President of the British Mycological Society in 1970, as Honorary Treasurer from 1961–85, and as a Trustee from 1967–99. A synopsis of his academic contributions and other activities is presented, along with a complete list of his publications.     

Genetic Mechanisms of Cell Transdifferentiation

Studies have been considered, which concern identification of regulatory genes in adult newts and their expression during retinal and lens regeneration. B.L. Astaurov repeatedly urged to join efforts of geneticists and embryologists in studies of the mechanisms underlying biological phenomena. This was also true for studies of regeneration. Such studies became possible only after introduction of molecular biology methods. Studies of the mechanisms underlying regeneration have been recently carried out jointly by geneticists and developmental biologists. This review presented at the conference dedicated to the 100th anniversary of B.L. Astaurov deals with these aspects in studies of regeneration.__________Translated from Ontogenez, Vol. 36, No. 4, 2005, pp. 292–299.Original Russian Text Copyright © 2005 by Mitashov.     

Three classes of spiny-(Clathrin-) coated vesicles in rodent liver based on size distributions

Summary Clathrin-coated vesicles in rodent (rat and mouse) liver distribute into three distinct populations based on measurements of vesicle diameter. The first population consists of 60–80 nm vesicles found almost exclusively within the Golgi apparatus region. The second population is of 100–160 nm coated vesicles located within 100–500 nm of the cell surface. A third population of coated vesicles of intermediate diameter (ca. 90 nm) is present both at the Golgi apparatus and at the cell surface. We speculate that clathrin and clathrin-coated vesicles within the region of the Golgi apparatus and of the cell surface exist in two recycling populations. The third population of vesicles of intermediate diameter could represent a shuttle to link the two major compartments.     

Effect of culture medium composition on the activity of extracellular lectins of <Emphasis Type="Italic">Lentinus edodes</Emphasis>

The time course of lectin production in culture liquid of the basidial fungus Lentinus edodes strain F-249 in different media under submerged culture conditions was studied. The activity of agglutinins depended on the ratio between carbon and nitrogen sources and the pH of the culture medium. The lectin activity in culture medium was maximal when the fungus was grown in a medium containing L-arabinose as a source of carbon and L-asparagine as a source of nitrogen (C:N ratio, (9.5–12):1) on day 15–18 of culturing at pH 8.0–9.0.Translated from Prikladnaya Biokhimiya i Mikrobiologiya, Vol. 41, No. 2, 2005, pp. 200–203.Original Russian Text Copyright © 2005 by Tsivileva, Nikitina, Garibova.