Microbial Biogeography along an Estuarine Salinity Gradient: Combined Influences of Bacterial Growth and Residence Time

Shifts in bacterioplankton community composition along the salinity gradient of the Parker River estuary and Plum Island Sound, in northeastern Massachusetts, were related to residence time and bacterial community doubling time in spring, summer, and fall seasons. Bacterial community composition was characterized with denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA. Average community doubling time was calculated from bacterial production ([¹⁴C]leucine incorporation) and bacterial abundance (direct counts). Freshwater and marine populations advected into the estuary represented a large fraction of the bacterioplankton community in all seasons. However, a unique estuarine community formed at intermediate salinities in summer and fall, when average doubling time was much shorter than water residence time, but not in spring, when doubling time was similar to residence time. Sequencing of DNA in DGGE bands demonstrated that most bands represented single phylotypes and that matching bands from different samples represented identical phylotypes. Most river and coastal ocean bacterioplankton were members of common freshwater and marine phylogenetic clusters within the phyla Proteobacteria, Bacteroidetes, and Actinobacteria. Estuarine bacterioplankton also belonged to these phyla but were related to clones and isolates from several different environments, including marine water columns, freshwater sediments, and soil.     

An examination of the Cooper-Helmstetter theory of DNA replication in bacteria and its underlying assumptions

The relationship between the DNA content of an average bacterial cell in an exponential culture, the velocity of chromosome rePlication (C), the time between replication termination and cell division (D), and the doubling time (τ), originally derived by Cooper and Helmstetter, is shown to be independent of two assumptions made by those authors. That is, it is not necessary to assume an ideal age distribution of cells in an exponential culture, and replication need not initiate synchronously at every DNA origin sequence within the cell. This implies that the relationship has a more general validity than has been previously supposed, and that agreement of observations on exponential cultures with the Cooper-Helmstetter theory cannot be taken to prove the assumptions on which that theory was originally based.     

Correlation between lethality and DNA single-strand breaks in Bacillus subtilis cells treated with N-methyl-N'-nitro-N-nitrosoguanidine

The effects of N-methyl-N′-nitro-N-nitrosoguanidine (MNNG) treatment two Bacillus subtilis strains which exhibit different UV sensitivities were monitored at both the cellular (survival) and subcellular (DNA strand break) levels. The MNNG-induced single strand DNA breaks (SSB) in either strain, as measured by alkaline sucrose gradient centrifugation, were shown to be well correlated with lethality. These DNA lesions were shown by a computer simulation to be randomly induced. Cell survival after MNNG treatment is inversely related to the number of replication forks per cell which in turn depends upon the doubling time of the culture and the growth phase. The production of single-strand breaks and cell killing are proportional to the log of the initial MNNG concentration and may imply that decomposition of the mutagen is (pseudo) second order.     

Establishment of a neonate cell line from Epiphyas postvittana (Walker) (Lepidoptera: Tortricidae) that supports replication of E. postvittana nucleopolyhedrovirus

The lightbrown apple moth (Epiphyas postvittana) is a leafroller pest that damages horticultural crops in New Zealand. This paper documents the establishment of a primary cell line from neonate E. postvittana larvae to facilitate the development of E. postvittana nucleopolyhedrovirus (EppoNPV) for control of this pest. The cell line was cultured for 36 passages and a clonal derivative designated EpN1.10 was generated that had a doubling time of 36 h at 21 °C. The EpN1.10 cell line allowed for recovery of EppoNPV from transfected genomic DNA and virus passage, as determined by occlusion body production and restriction endonuclease analysis.     

Genetic toggle switch controlled by bacterial growth rate

Background

In favorable conditions bacterial doubling time is less than 20 min, shorter than DNA replication time. In E. coli a single round of genome replication lasts about 40 min and it must be accomplished about 20 min before cell division. To achieve such fast growth rates bacteria perform multiple replication rounds simultaneously. As a result, when the division time is as short as 20 min E. coli has about 8 copies of origin of replication (ori) and the average copy number of the genes situated close to ori can be 4 times larger than those near the terminus of replication (ter). It implies that shortening of cell cycle may influence dynamics of regulatory pathways involving genes placed at distant loci.

Results

We analyze this effect in a model of a genetic toggle switch, i.e. a system of two mutually repressing genes, one localized in the vicinity of ori and the other localized in the vicinity of ter. Using a stochastic model that accounts for cell growth and divisions we demonstrate that shortening of the cell cycle can induce switching of the toggle to the state in which expression of the gene placed near ter is suppressed. The toggle bistability causes that the ratio of expression of the competing genes changes more than two orders of magnitude for a two-fold change of the doubling time. The increasing stability of the two toggle states enhances system sensitivity but also its reaction time.

Conclusions

By fusing the competing genes with fluorescent tags this mechanism could be tested and employed to create an indicator of the doubling time. By manipulating copy numbers of the competing genes and locus of the gene situated near ter, one can obtain equal average expression of both genes for any doubling time T between 20 and 120 min. Such a toggle would accurately report departures of the doubling time from T.

     

Effect of Initiation Time of Hydrostatic Pressure Shock on Chromosome Set Doubling of Tetraploidization in Turbot <Emphasis Type="Italic">Scophthalmus maximus</Emphasis>

The objective of the study was to clarify the effects of initiation time on chromosome set doubling induced by hydrostatic pressure shock through nuclear phase fluorescent microscopy in turbot Scophthalmus maximus. The ratio of developmentally delayed embryo and chromosome counting was used to assess induction efficiency. For the embryos subjected to a pressure of 67.5 MPa for 6 min at prometaphase (A group), chromosomes recovered to the pre-treatment condition after 11-min recovering. The first nuclear division and cytokinesis proceeded normally. During the second cell cycle, chromosomes did not enter into metaphase after prometaphase, but spread around for about 13 min, then assembled together and formed a large nucleus without anaphase separation; the second nuclear division and cytokinesis was inhibited. The ratio of developmentally delayed embryo showed that the second mitosis of 78% A group embryo was inhibited. The result of chromosome counting showed that the tetraploidization rate of A group was 72%. For the embryos subjected to a pressure of 67.5 MPa for 6 min at anaphase (B group), chromosomes recovered to the pre-treatment condition after about 31-min recovering. Afterwards, one telophase nucleus formed without anaphase separation; the first nuclear division was inhibited. The time of the first cleavage furrow occurrence of B group embryos delayed 27 min compared with that of A group embryos. With the first cytokinesis proceeding normally, 81.3% B group embryos were at two-cell stage around the middle of the second cell cycle after treatment. Those embryos were one of the two blastomeres containing DNA and the other without DNA. The first nuclear division of those embryos was inhibited. During the third cell cycle after treatment, 65.2% of those abovementioned embryos were at four-cell stage, cytokinesis occurred in both blastomeres, and nuclear division only occurred in the blastomere containing DNA. Of those abovementioned embryos, 14.0% were at three-cell stage and cytokinesis only occurred in the blastomere containing DNA. The result of chromosome counting showed that the tetraploidization rate of B group was only 7%. To summarize what had been mentioned above, mechanisms on chromosome set doubling of tetraploid induction would be different with different initiation time of hydrostatic pressure treatment. Chromosome set doubling was mainly due to inhibition of the second mitosis when hydrostatic pressure treatment was performed at prometaphase. Otherwise, chromosome set doubling was mainly due to inhibition of the first nuclear division when hydrostatic pressure treatment was performed at anaphase. Induction efficiency of tetraploidization resulted from inhibition of the second cleavage was higher than which resulted from inhibition of the first nuclear division. This study was the first to reveal biological mechanisms on the two viewpoints of chromosome set doubling through effect of initiation time of hydrostatic pressure treatment on chromosome set doubling in tetraploid induction.     

Clinical significance of gene amplification studied in human neuroblastoma xenografts: relationship with tumor growth rate, chemotherapeutic sensitivities and levels of neuron-specific enolase

Tumor doubling time, sensitivity to chemotherapeutic agents and concentrations of neuron-specific enolase were studied in nine human neuroblastoma xenografts, in which amplifications of N-myc, clones 8 and G21 were known; N-myc was amplified in eight, clone 8 in five and clone G21 in four of these nine xenografts. Tumor doubling time was longest in one xenograft, TNB10, which lacks the amplification of either N-myc or clone 8 or G21, and shortest in TNB1 in which all three DNA sequences are amplified with a DNA rearrangement in clone 8. No correlations were found between genomic amplification of N-myc, clones 8 and G21 and effectiveness of five chemotherapeutic drugs tested, except for cis-platinum. cis-Platinum was found to be effective on all but the one xenograft, TNB10, with the longest tumor doubling time. Concentration of neuron-specific enolase in tumor extract was lowest in TNB1 and correlated with the length of the tumor doubling time.     

Prolongation of replication time after doublings of the DNA content of polytene chromosome bands of Chironomus

Using ³H-thymidine autoradiography, labeling frequency of homologous asynapsed chromosome bands of the hybrid of Chironomus th. thummi and Chironomua th. piger has been studied. In a number of these bands the DNA content of the thummi bands is 2, 4, 8 or 16 times as large as that of the homologous piger bands (Keyl, 1965). Those bands of Ch. th. thummi which show one doubling of their DNA content in comparison with the homologous piger bands are also labeled two times more frequently than piger. In contrast to this such a correlation between increase of labeling frequency (i.e. prolongation of replication time) and doubling of the DNA content is not observed, when thummi bands have 4, 8 or 16 times more DNA than their homologues in piger. In these cases replication time is also prolonged after each doubling. Duration of DNA synthesis increases linearly but always by a smaller factor as the corresponding DNA content is increased.     

A microspectrofluorometric analysis of nuclear and chloroplast DNA in Volvox

Nuclear division immediately follows nuclear DNA doubling in all stages of the life cycle examined in the green alga Volvox; fluorescence microfluorometry of individual cells revealed no evidence of prolonged accumulation of nuclear DNA prior to mitosis in reproductive cells. Somatic cell nuclear DNA quantity is unaffected by developmental events in gonidia of the same spheroid; it remains constant from the end of cleavage until the death of the cell. In reproductive cells, chloroplast DNA replication precedes nuclear replication. The sites of plastid DNA accumulation, made visible by use of the fluorochrome 4′,6-diamidino-2-phenylindole, increase in number during the prolonged growth phase of the V. carteri gonidium. Microspectrofluorometry of fluorochrome-stained DNA in situ shows that plastid DNA increases exponentially throughout this phase. The continuous plastid DNA accumulation during gonidial growth appears to represent a prokaryote-like instead of a eukaryote-like control of DNA synthesis. Most somatic cells contain plastid DNA, and this does not increase in amount during colony growth and reproduction. Most sperm cells also contain plastid DNA, although approximately 5% of somatic cells and up to 20% of sperm cells have no discernable plastid DNA. This is the second group of organisms in which DNA-free plastids have been observed.     

Effects of salinity on synthesis of DNA,acidic polysaccharide,and ichthyotoxin in Gymnodinium breve

A Florida red tide organism, Gymnodinium breve Davis, an unarmored dinoflagellate, was grown in enriched sea water media at salinities 20–43% and constant illumination. Use of lowest (23%) and highest (43%) salinities resulted in death within 24 hr of inoculation, though good growth was obtained at all intermediate salinities (29–39%), in accord with field observation. Rates of synthesis of DNA, acidic polysaccharide and ichthyotoxin were determined as a function of salinity and growth constant (K₁₀). The relative rate of' synthesis of DNA or polysaccharide increased linearly with growth constant. Mean cell volumes, determined during log-phase growth, showed a positive correlation with doubling time. Hemolytic activity was detected in cell extracts only at high toxin concentrations (0.35–2.05 mg of ichthyotoxin). No significant difference was noted in hemolytic activity of extracts of cells grown in high (34%) or low (26%) salinity. The rate of toxin synthesis showed a linear decrease with the rate of DNA or polysaccharide synthesis.     

Polyamine Biosynthetic Enzymes in the Cell Cycle of Chlorella: Correlation between Ornithine Decarboxylase and DNA Synthesis at Different Light Intensities

During the life cycle of Chlorella vulgaris Beijerinck var vulgaris fa. vulgaris growing synchronously, the specific activity of ornithine decarboxylase peaked at the 2nd hour of the cycle, whereas that of arginine decarboxylase changed only slightly, increasing towards the end of the cycle. The endogenous level of putrescine and spermidine on a per cell basis increased gradually up to the 8th hour of the cycle, and declined thereafter. Thus, the peak of ornithine decarboxylase activity and the polyamine increase preceded both DNA replication (which took place between the 6th and 8th hours of the cycle) and autospore release (which started at the 8th hour). A 2-fold increase in the light intensity caused doubling of the DNA content, resulting in doubling of the number of autospores per mother cell. It also brought about a 2-fold increase in the specific activity of ornithine decarboxylase and polyamine content, the peaks being at the same hour of the cycle under high and low light intensities. The increase in cell number and polyamine content in a Chlorella culture grown under high light intensity was inhibited by α-difluoromethyl ornithine, a specific inhibitor of ornithine decarboxylase, this inhibition being partially reversed by putrescine.

It is suggested that in C. vulgaris the sequence of events which relates polyamine biosynthesis to cell division is as follows: increased ornithine decarboxylase activity, accumulation of polyamines, DNA replication, and autospore release.

     

Chromosome diminution in Ascaris suum: Chromatin structure

Ascaris suum loses 56% of its nuclear DNA during chromosome diminution. Measured values of histones per nucleus are relatively constant, resulting in an approximate doubling of histone: DNA ratios during this process. Experiments were performed in an effort directed towards ascertaining the location of the increased histones. Repeat lengths of micrococcal nuclease protected pre- and post-diminution DNA were determined. Nuclear sap proteins from post-diminution nuclei were also examined in order to test the possibility of nuclear pools of free histones.     

Synchrony of Nuclear Replication in Individual Hyphae of Aspergillus nidulans

The synchrony of nuclear replication in individual, multinucleate hyphae of Aspergillus nidulans has been investigated. Samples were taken from cultures of germinating conidiospores, and the relative frequency of hyphae containing two to eight nuclei was determined. Because the conidiospores are mononucleate, complete synchrony will yield populations of hyphae containing only 2ⁿ nuclei, n being the number of doublings after germination. The appearance of hyphae with total numbers of nuclei other than 2ⁿ will indicate lack of synchrony. The relative frequency of hyphae not having 2ⁿ nuclei will depend on the degree of synchrony in the individual hyphae; numerical aspects of this relation are discussed. In two different strains, replication of the nuclei in any one hypha was highly synchronized when the dry weight doubling time was 1.4 to 1.8 hr. As the doubling time was made longer by changing the nitrogen or carbon source, synchrony was progressively lost. At the slowest growth rate tested, the interval between the division of the fastest and the slowest nucleus equaled 48% of the dry weight doubling time. The active replication of some nuclei in a hypha where other nuclei were resting suggested that nuclear duplication in this eukaryotic organism may be controlled by specific initiators.     

Alterations in the cell cycle of Drosophila imaginal disc cells precede metamorphosis

Flow cytometric analyses of imaginal disc and brain nuclei of Drosophila melanogaster have been made throughout the third larval instar. In wing, haltere, and leg discs the proportion of cells in the G₂M phase of the cell cycle (tetraploid cells) increases with larval age. In contrast, in the eye disc and in brain the proportion of tetraploid cells, already low at the outset of the instar, declines further. Measurement of growth rates for disc and brain tissue during the same developmental period was carried out by the cell counting procedure of Martin (1982). Our results are consistent with the conclusion that imaginal discs grow exponentially with an apparent doubling time of 5–10 hr from the resumption of cell division (in the first or second larval instar) until about 95 hr, when the apparent doubling time increases. Cell numbers increase until at least 5 hr after formation of white prepupae (122 hr), but during the preceding 10 hr the rate of increase is low. Thus, for wing and leg discs, but not for the eye disc and brain, the declining growth rate is associated with an increase in the proportions of tetraploid cells. In conjunction with cell counts and flow cytometry, fluorometric determination of disc DNA content at 112 hr indicated that the diploid DNA content of imaginal disc nuclei is 0.45 pg.     

Rate of increase of Autographa californica nuclear polyhedrosis virus in Trichoplusia ni larvae determined by DNA:DNA hybridization

The rate of increase and doubling time of the HOB clone of Autographa californica nuclear polyhedrosis virus (AcMNPV-HOB) in neonate Trichoplusia ni larvae was determined by measuring the increase in viral DNA through time following inoculation with average doses of 50 or 17,400 occlusion bodies per larva. Changes in total DNA and viral DNA through time were followed by fluorescence spectroscopy and quantitative slot-blot DNA:DNA hybridization, respectively. Total DNA content (i.e., larval DNA and viral DNA) of larvae infected with the intermediate dose lagged behind that of noninfected larvae 30 hr post-inoculation (p.i), reached a maximum at 51 hr p.i., and stayed constant thereafter. The total DNA content of larvae inoculated with the high dose lagged behind that of the control group from 18 hr p.i. and increased slowly until death of the larvae (ca. 48 hr p.i.). The amount of viral DNA in larvae inoculated with the intermediate dose increased exponentially between 15 and 42 hr p.i., reached a maximum at 48 hr p.i., and stayed constant until 68 hr p.i., by which time most larvae had died. The amount of viral DNA in larvae inoculated with the high dose did not increase exponentially; initially the rate of increase was the same as that for larvae inoculated with the intermediate dose but became progressively lower after 13 hr p.i. Calculations of the rate of increase for AcMNPV-HOB in neonate T. ni larvae inoculated with the intermediate dose and incubated at 29 degrees C resulted in a value of 0.264 hr-1 (doubling time: 2.63 hr).(ABSTRACT TRUNCATED AT 250 WORDS)     

NapA (Rv0430), a Novel Nucleoid-Associated Protein that Regulates a Virulence Operon in Mycobacterium tuberculosis in a Supercoiling-Dependent Manner

Comparison of Mycobacterium tuberculosis with Escherichia coli reveals a reduction in the diversity of DNA-managing proteins, such as DNA topoisomerases, although genome sizes are similar for the two species. The same is true for nucleoid-associated proteins (NAPs), important factors in bacterial chromosome compaction, chromosome remodeling, and regulation of gene expression. In a search for still uncharacterized NAPs, we found that M. tuberculosis protein Rv0430 has NAP-like features: it binds to DNA in a length- and supercoil-dependent fashion, prefers A/T-rich DNA sequences, protects DNA from damaging agents, and modulates DNA supercoiling. At a ratio of 1 dimer/40 bps of DNA, Rv0430 bridges distant DNA segments; at 1 dimer/20 bps, it coats DNA, forming inflexible rods. Rv0430 also stimulates the DNA relaxation activity of topoisomerase I. Remarkably, Rv0430 stimulates its own promoter in a supercoil-dependent manner. It is the first gene of an operon harboring two regulators of M. tuberculosis virulence (virR and sodC), and controls the expression of these downstream virulence regulators and therefore itself is a virulence regulator. The sensitivity of rv0430 expression to supercoiling is consistent with supercoiling being important for infection by M. tuberculosis. Thus, Rv0430 is a novel NAP, doubling up as a topology modulator of M. tuberculosis.     

Control of membrane protein synthesis in bacillus subtilis

In synchronous cultures of Bacillus subtilis 168/S grown on succinate as a sole carbon source (mean generation time 115 min), chromosome initiation occurs at the beginning of the cell cycle but the rate of membrane protein synthesis doubles in mid-cycle more or less coincident with nuclear segregation. In glucose-grown cultures, the doubling in rate of membrane protein synthesis occurs at about the same time as nuclear segregation and DNA initiation at the beginning of the cycle. Control of the rate of membrane synthesis by the chromosome has been demonstrated by inhibiting DNA synthesis using thymine starvation and showing that membrane protein synthesis continues at a constant rate, whereas the rate of cytoplasmic protein synthesis almost doubles.I suggest that the replication of a region at or close to the chromosome terminus is required to allow the doubling in rate of membrane synthesis.     

Effect of Medium Composition on the Denitrification of Nitrate by Paracoccus denitrificans

The course of denitrification of nitrate in static cultures of Paracoccus denitrificans was studied. Reduction of nitrate to gaseous nitrogen without accumulation of nitrite because of parallel and balanced activities of nitrate and nitrite reductases was observed in nutrient broth. In minimal liquid cultures supplemented with either methanol, acetate, or ethanol as a sole carbon source, substantial amounts of nitrite (up to 70%) accumulated. The reduction in nitrite concentration began just after the transformation of nitrate to nitrite was completed. The addition of some growth factors to minimal media shortened the bacterial biomass doubling time. A correlation coefficient of 0.71 between the doubling time and the amount of accumulated nitrite in cultures was found. My results indicated that the type of denitrification carried out by P. denitrificans is not stable and depends on the nutritional composition of the culture medium.     

Trypanosoma cruzi: interaction with vertebrate cells in vitro. 3. Selection for biological characteristics following intracellular passage

Two strains of Trypanosoma cruzi, House 510 and Limbo Tree Platform, were studied to determine whether maintenance in vertebrate cell culture would alter their biological characteristics. After having been maintained for several years in alternate mouse-insect passage using NIH general purpose male white mice and Rhodnius prolixus, respectively, the parasites were transferred into primary bovine embryo skeletal muscle cell culture and their intracellular doubling time and generation number quantified.A significant change appeared in the doubling time of each strain. Initially, the doubling times of the House 510 and Limbo Tree Platform strains were not significantly different. They were 8.6 ± 0.8 hr and 7.5 ± 0.5 hr, respectively. After a varying period in cell culture, these values changed to 11.4 ± 1.6 and 11.5 ± 1.3 hr, respectively. Other observations, unrelated to length of time in cell culture, included the appearance of many broad, trypomastigote forms with a decreased ability to reach host cells and a varying generation number ranging from 7 to 9.     

Delayed termination of nuclear histone doubling after premeiotic DNA synthesis inTriturus vulgaris male meiosis

It has been shown by means of double wavelength cytophotometry of DNA (Feulgen reaction) and histone (fast green, pH 8.2) inTriturus vulgaris spermatocytes that the doubling of DNA content in nuclei terminates at the end of preleptotene to beginning of leptotene whereas the doubling of histone content begun at premeiotic interphase is delayed and proceeds till the end of leptotene to beginning of zygotene. As a result preleptotene spermatocytes contain approximately 4C DNA and only 3C histone. Histone content in leptotene amounts to 93% of 4C, and in zygotene, pachytene and metaphase I both DNA and histone contents equal 4C. Thus, the temporal pattern of nucleo-histone doubling in meiotic chromosomes ofT. vulgaris differs from the synchronous DNA and histone doubling in mitotic chromosomes of all previously studied species. The delay of histone doubling inT. vulgaris meiocytes is less pronounced than in the previously studied insectsAcheta domestica andPyrrhocoris apterus where the histone content amounts to 3C in leptotene—zygotene and the equal histone/DNA ratio is restored only in pachytene.—Responsibilities for this phenomenon and its biolgoical sinnificance are discussed in connection with recent hypotheses concerning mechanisms of homologous chromosome pairing.