Maximum Likelihood based comparison of the specific growth rates for P. aeruginosa and four mutator strains

The specific growth rate for P. aeruginosa and four mutator strains mutT, mutY, mutM and mutY-mutM is estimated by a suggested Maximum Likelihood, ML, method which takes the autocorrelation of the observation into account. For each bacteria strain, six wells of optical density, OD, measurements are used for parameter estimation. The data is log-transformed such that a linear model can be applied. The transformation changes the variance structure, and hence an OD-dependent variance is implemented in the model. The autocorrelation in the data is demonstrated, and a correlation model with an exponentially decaying function of the time between observations is suggested. A model with a full covariance structure containing OD-dependent variance and an autocorrelation structure is compared to a model with variance only and with no variance or correlation implemented. It is shown that the model that best describes data is a model taking into account the full covariance structure. An inference study is made in order to determine whether the growth rate of the five bacteria strains is the same. After applying a likelihood-ratio test to models with a full covariance structure, it is concluded that the specific growth rate is the same for all bacteria strains. This study highlights the importance of carrying out an explorative examination of residuals in order to make a correct parametrization of a model including the covariance structure. The ML method is shown to be a strong tool as it enables estimation of covariance parameters along with the other model parameters and it makes way for strong statistical tools for inference studies.     

Maximum likelihood estimation of population growth rates based on the coalescent.

We describe a method for co-estimating 4Nemu (four times the product of effective population size and neutral mutation rate) and population growth rate from sequence samples using Metropolis-Hastings sampling. Population growth (or decline) is assumed to be exponential. The estimates of growth rate are biased upwards, especially when 4Nemu is low; there is also a slight upwards bias in the estimate of 4Nemu itself due to correlation between the parameters. This bias cannot be attributed solely to Metropolis-Hastings sampling but appears to be an inherent property of the estimator and is expected to appear in any approach which estimates growth rate from genealogy structure. Sampling additional unlinked loci is much more effective in reducing the bias than increasing the number or length of sequences from the same locus.     

Exact and heuristic algorithms for the Indel Maximum Likelihood Problem.

Given a multiple alignment of orthologous DNA sequences and a phylogenetic tree for these sequences, we investigate the problem of reconstructing the most likely scenario of insertions and deletions capable of explaining the gaps observed in the alignment. This problem, that we called the Indel Maximum Likelihood Problem (IMLP), is an important step toward the reconstruction of ancestral genomics sequences, and is important for studying evolutionary processes, genome function, adaptation and convergence. We solve the IMLP using a new type of tree hidden Markov model whose states correspond to single-base evolutionary scenarios and where transitions model dependencies between neighboring columns. The standard Viterbi and Forward-backward algorithms are optimized to produce the most likely ancestral reconstruction and to compute the level of confidence associated to specific regions of the reconstruction. A heuristic is presented to make the method practical for large data sets, while retaining an extremely high degree of accuracy. The methods are illustrated on a 1-Mb alignment of the CFTR regions from 12 mammals.     

Changes in extracellular polysaccharide content and morphology of Microcystis aeruginosa at different specific growth rates

The cyanobacterium Microcystis mainly exists in colonies under natural conditions but as single cells in typical laboratory cultures. Understanding the mechanism by which single cells form small and large colonies can provide a deeper insight into the life history of Microcystis and the mechanisms of Microcystis bloom formation. In this paper, Microcystis aeruginosa cultured under varying light intensities and temperatures exhibited different specific growth rates. Correlations were found between the specific growth rate, extracellular polysaccharide (EPS) content, and morphology of M. aeruginosa. Under low light intensities and temperatures, M. aeruginosa formed small colonies (maximum colony size approximately 100 μm) and exhibited low specific growth rates. By contrast, standard culture conditions yielded single or paired cells with high specific growth rates. Moreover, the EPS content decreased dramatically with increasing specific growth rate. A significant positive linear relationship was observed between the EPS content per cell and colony size. High EPS content and colony formation were associated with low specific growth rates. The specific growth rate in laboratory cultures was higher than the in situ growth rate under natural conditions. This result may explain why Microcystis normally exists as single cells or (more rarely) as paired cells in axenic laboratory cultures after long-term cultivation, but forms colonies under natural conditions.     

Sequence comparison and phylogenetic analysis by the Maximum Likelihood method of ribosome-inactivating proteins from angiosperms

Ribosome-inactivating proteins (RIPs) from angiosperms are rRNA N-glycosidases that have been proposed as defence proteins against virus and fungi. They have been classified as type 1 RIPs, consisting of single-chain proteins, and type 2 RIPs, consisting of an A chain with RIP properties covalently linked to a B chain with lectin properties. In this work we have carried out a broad search of RIP sequence data banks from angiosperms in order to study their main structural characteristics and phylogenetic evolution. The comparison of the sequences revealed the presence, outside of the active site, of a novel structure that might be involved in the internal protein dynamics linked to enzyme catalysis. Also the B-chains presented another conserved structure that might function either supporting the beta-trefoil structure or in the communication between both sugar-binding sites. A systematic phylogenetic analysis of RIP sequences revealed that the most primitive type 1 RIPs were similar to that of the actual monocots (Poaceae and Asparagaceae). The primitive RIPs evolved to the dicot type 1 related RIPs (like those from Caryophyllales, Lamiales and Euphorbiales). The gene of a type 1 RIP related with the actual Euphorbiaceae type 1 RIPs fused with a double beta trefoil lectin gene similar to the actual Cucurbitaceae lectins to generate the type 2 RIPs and finally this gene underwent deletions rendering either type 1 RIPs (like those from Cucurbitaceae, Rosaceae and Iridaceae) or lectins without A chain (like those from Adoxaceae).     

Cross sensitivity of mutator strains to physical and chemical mutagens.

Ten different mutator strains of Saccharomyces cerevisiae were tested for cross sensitivity to two alkylaitng agents, ethylmethanesulfonate (EMS) and methylmethanesulfonate (MMS), to determine if any of them are defective in the repair systems which normally deal with damage caused by these agents. For one of the mutators, namely mut2-1, it was shown by genetic analysis that mutator activity and MMS sensitivity are both controlled by the same gene. Two mutants, mut2-1 and mut7-1, were found to be sensitive to MMS but normal to ultraviolet and gamma-rays. Another group is represented by mut1, mut6 and mut8 which are not sensitive to any of the mutagens tested so far. Mutator strain mut2-1 was also shown not to be significantly altered for levels of UV-induced forward and reverse mutations. These observations lend support to the idea of multiple repair systems that deal with DNA damage caused by different agents and also show that mutator activity can often result from the loss of normal cellular repair systems.     

Human anti-Pseudomonas aeruginosa outer membrane proteins IgG cross-protective against infection with heterologous immunotype strains of P. aeruginosa.

In order to develop an effective means to treat and prevent Pseudomonas aeruginosa infections, we have purified P. aeruginosa outer membrane protein (Oprs)-specific human IgG antibody using a large-scale affinity column. In this study, we investigated the cross-protective activity of the purified anti-Oprs IgG against various immunotype strains of P. aeruginosa. The anti-Oprs IgG reacted with Oprs isolated from seven Fisher-Devlin immunotype strains of P. aeruginosa and was able to promote opsonophagocytic killing of all seven immunotype strains by human phagocytic cells. Administration of 500 microg anti-Oprs IgG to mice raised the LD50 of the P. aeruginosa strains by 8-250-fold, indicating the protective capacity against heterologous P. aeruginosa strains as well as homologous strains. In contrast, despite high titers against P. (aeruginosa Oprs, total serum IgG isolated from burn patient sera was no better than normal serum IgG in protecting mice from infection with P. aeruginosa. These data demonstrate that the affinity-purified human anti-Oprs IgG could afford protection against heterologous immunotype P. aeruginosa strains and provide a rationale to use anti-Oprs IgG as an adjunct for treatment of P. aeruginosa infections in humans.     

Insertion and replication of the Pseudomonas aeruginosa mutator phage D3112

D3112 is a temperate bacteriophage of P. aeruginosa with heterogeneous sequences at one extremity of the virion DNA molecule. Infection of strain PAOl with phage D3112 results in a 40- to 65-fold increase in the frequency of ami mutants resistant to fluoroacetamide. Nine ami::D3112 prophages have been mapped to distinct sites within the ami locus by Southern blotting experiments with a cloned ami+ probe. All prophages have the same restriction map as the D3112 genome extracted from phage particles. The position of D3112 insertions correlates with the phenotype and reversion behavior of the ami mutants. Induction of D3112cts prophages results in amplification of internal prophage segments as discrete restriction fragments before the terminal viral fragments are visible as sharp hybridizing species. This indicates that D3112 replication is accompanied by recombination of prophage termini to numerous sites in the bacterial genome. Chromosomal junction fragments of an ami::D3112cts prophage are maintained through most of the replication cycle but are cleaved shortly before cell lysis, apparently by the viral encapsidation system.     

Isolation and characterization of mutator strains of Escherichia coli K-12.

A selection procedure was devised to select for mutants of Escherichia coli K-12 with enhanced rates of spontaneous frameshift mutation. Three types of mutants were isolated. Two of the mutations apparently represent alleles of previously isolated mutL13 and mutS3. The third type of mutation, represented by two alleles, lies between lysA and thyA, and has been designated mutR. mutR increases the rate of spontaneous frameshift mutation and also the rate of base substitution mutations. The mutator phenotype is recessive. Reversion of a lac amber mutation located on an episome is increased in the presence of the mutator, indicating that mutR can act in trans. No change in sensitivity to ultraviolet irradiation or mitomycin C could be found when mutR34 was compared to the isogenic mutR+ strain. The mutator's activity was little affected by the type of medium in which the strain was grown. Deoxyribonucleoside triphosphate pools were normal in mutR34. Intergenic recombination frequencies were the same in mutR and mutR and mutR+ strains, but a two- to threefold increase in intragenic recombination was observed in Hfr times Fminus crosses when the recipeint was mutR34 as compared with mutR+. This increase appeared independent of the distance between the two markers within the gene in which the crossover took place.     

Bromouracil mutagenesis and mismatch repair in mutator strains of Escherichia coli.

A screening procedure based on the formation of papillae on individual bacterial colonies was used to isolate mutants of Escherichia coli with high mutation rates in the presence of bromouracil. Most of the mutants obtained had high spontaneous mutation rates and mapped close to the previously known mutators mutT, mutS, mutR, uvrE and mutL. Except for mutants of mutT type, these mutators also showed high mutability by bromouracil. Transfection experiments were performed with heteroduplex lambda DNA to test for mismatch repair. The results suggest a reduced efficiency of repair of mismatched bases in mutators mutS, mutR, uvrE and mutL, whereas mutants mapping as mutT appear normal. The results support a connection between spontaneous and bromouracil-induced mutability and repair of mismatched bases in DNA.     

Differences in growth,pigment composition and photosynthetic rates of two phenotypes Microcystis aeruginosa strains under high and low iron conditions

This paper provided insight into the influence of iron on the growth of Microcystis aeruginosa strains related to different phenotypes of this species. In this research it was intended to compare the growth, pigment composition, photosynthetic efficiency and extracellular polysaccharides production of unicellular and colonial strains of M. aeruginosa. A significantly growth inhibition under iron-limited condition on unicellular M. aeruginosa was noted, whereas the colonial strain could maintain a steady growth along with the culture time. This observation was reconfirmed by the content of chlorophyll a. Compared with unicellular strain; the colonial strain exhibited a higher PSII maximum light energy transformation, photosynthetic oxygen evolution and extracellular polysaccharides (EPS) production in iron-limited condition. Further, in order to gain more information about the accessibility of iron in the two phenotypic Microcystis, we found the two strains could produce hydroxamate-type siderophores, the content of siderophores produced by the colonial strain was more than those in unicellular strain under the iron-limited condition. It was interpreted as an adaptation to the dilute environment. Our results demonstrated that the colonial phenotypes possessed stronger ability to endure iron-limited condition than unicellular strain by higher pigment contents, higher photosynthetic activities, higher EPS production and higher siderophores secretion. It might elucidate that the colonial M. aeruginosa bloom can sustain in eutrophic reservoirs and lakes.     

Specific ion effects on the growth rates of Staphylococcus aureus and Pseudomonas aeruginosa

Motivated by recent advances in the physical and chemical basis of the Hofmeister effect, we measured the rate cell growth of S. aureus--a halophilic pathogenic bacterium--and of P. aeruginosa, an opportunistic pathogen, in the presence of different aqueous salt solutions at different concentrations (0.2, 0.6 and 0.9 M). Microorganism growth rates depend strongly on the kind of anion in the growth medium. In the case of S. aureus, chloride provides a favorable growth medium, while both kosmotropes (water structure makers) and chaotropes (water structure breakers) reduce the microorganism growth. In the case of P. aeruginosa, all ions affect adversely the bacterial survival. In both cases, the trends parallel the specific ion, or Hofmeister, sequences observed in a wide range of physico-chemical systems. The correspondence with specific ion effect obtained in other studies, on the activities of a DNA restriction enzyme, of horseradish peroxidase, and of Lipase A (Aspergillus niger) is particularly striking. This work provides compelling evidence for Hofmeister effects, physical chemistry in action, in these organisms.     

Image processing technique for measuring specific growth rates of Gibberella fujikuroi

Summary Two methods were compared for estimating of Gibberella fujikuroi grown with different proportions of glucose and starch. They were, =Ln2 (V_r/Le) on Petri dish (V_r= rate of tip extension and L_e= mean hyphal length) and, ₂=d (LnX)/dt in stirred fermenter. Values of ₁ and ₂ were in close agreement with each other.     

A comparison of specific growth rates of periphytic diatoms of varying cell size under laboratory and field conditions

Diatom species grown under non-limiting nutrient availability in multispecific biofilms were sampled from glass substrates immersed in the field and in experimental freshwater microcosms, and their growth responses were determined. The major species that developed on the substrates were common to both experiments and the specific growth rates (k) ranged from 0.06 to 0.41 division day⁻¹. An inverse relationship between k and cell sizes was observed, which is in accordance with allometry results reported by several authors. Although found in lower amounts, the large, slow-growing species accounted significantly in total community biovolume, underlying their significance for ecological purposes. From growth characteristics data, life history strategies were drawn for the dominant species recorded, from small pioneer species to large taxa that are more favoured by high resource supply. Kinetic data measured in both laboratory and in situ experiments stressed that the difficulties to mimic the field in laboratory experiments may have a strong impact on growth kinetics. Handling editor: J. Padisak     

Finite Sample Properties of the Maximum Likelihood Estimator and of Likelihood Ratio Tests in Hidden Markov Models

Hidden Markov models were successfully applied in various fields of time series analysis, especially for analyzing ion channel recordings. The maximum likelihood estimator (MLE) has recently been proven to be asymptotically normally distributed. Here, we investigate finite sample properties of the MLE and of different types of likelihood ratio tests (LRTs) by means of simulation studies. The MLE is shown to reach the asymptotic behavior within sample sizes that are common for various applications. Thus, reliable estimates and confidence intervals can be obtained. We give an approximative scaling function for the estimation error for finite samples, and investigate the power of different LRTs suitable for applications to ion channels, including tests for superimposed hidden Markov processes. Our results are applied to physiological sodium channel data.     

Diagnosing lactic acid fermentation based on specific rates of growth,substrate consumption and product formation

The on-line calculated specific rates of growth, substrate consumption and product formation were used to diagnose microbial activities during a lactic acid fermentation. The specific rates were calculated from on-line measured cell mass, and substrate and product concentrations. The specific rates were more sensitive indicators of slight changes in fermentation conditions than such monitored data as cell mass or product concentrations.List of Symbols 1/h specific rate of cell growth - 1/h specific rate of substrate consumption - 1/h specific rate of product formation - ^* dimensionless specific rate of cell growth - ^* dimensionless specific rate of substrate consumption - ^* dimensionless specific rate of product formation - _max 1/h maximum specific rate of cell growth - _max 1/h maximum specific rate of substrate consumption - _max 1/h maximum specific rate of product formation - X g/l cell mass concentration - S g/l substrate concentration - S ^* dimensionless substrate concentration - S ₀ g/l initial substrate concentration - P g/l product concentration     

Heterogeneity of the mutation rates of influenza A viruses: isolation of mutator mutants.

The rates of mutation to the mar (monoclonal antibody-resistant) genotype of individual influenza virus plaque isolates, obtained from a stock generated after two successive cloning steps, have been determined by the fluctuation test. When a random sample of 60 clones was analyzed, 7 contained a proportion of mar mutants significantly higher than the average, and among them, 2 showed a mutation rate two to three times higher than the average value obtained for the virus population when the hemagglutinin-specific monoclonal antibody 2G10 was used. In order to look for mutants with higher mutation rates, a systematic search was carried out with a nonmutagenized virus stock, and several clones with increased mutation rates were isolated. One of them (mut43) was characterized further and was shown to have a mutation rate three to four times higher than that of the virus population at the sites defined by two nonoverlapping, hemagglutinin-specific monoclonal antibodies as well as at the site defined by a neuraminidase-specific monoclonal antibody. These results indicate that the mutation rate of an influenza virus is a weighted average of the contributions of a heterogeneous population. The consequences of this fact for the adaptive evolution of influenza viruses are discussed.