Recursion relation generation of probability profiles for specific-sequence macromolecules with long-range correlations

The problem of calculating detailed probability profiles giving the probability of each unit in the chain to be in the ordered state (and all other average quantities as well including the fraction of strand association) for specific-sequence macromolecules requiring statistical weights that correlate up to the total number of units in the chain (e.g., DNA, collagen) is formulated in terms of recursion relations for appropriate a priori and conditional probabilities, thus generalizing the approach of Lacombe and Simha for nearest-neighbor correlations in specific sequence macromolecules. The technique allows the probability profiles for chains of thousands of units to be calculated in minutes making no approximation in the basic model.     

Pseudo-steady state oxygen-concentration profiles in an agar slab containing growing Nitrobacter agilis

A dynamic model for growth and substrate consumption of immobilized cells is evaluated by comparing experimental and calculated psendo-steady-state oxygen-concentration profiles in the support material. For this, Nitrobacter agilis cells were immobilized and cultivated in agar slabs. The system was operated as a continuous submerged-bed reactor. At different growth states oxygen-concentration profiles were determined in the slabs with a microsensor. It was shown that simulated and measured profiles agreed very well, both in steady and in pseudo-steady states.     

Identification of functional links between genes using phylogenetic profiles

MOTIVATION: Genes with identical patterns of occurrence across the phyla tend to function together in the same protein complexes or participate in the same biochemical pathway. However, the requirement that the profiles be identical (i) severely restricts the number of functional links that can be established by such phylogenetic profiling; (ii) limits detection to very strong functional links, failing to capture relations between genes that are not in the same pathway, but nevertheless subserve a common function and (iii) misses relations between analogous genes. Here we present and apply a method for relaxing the restriction, based on the probability that a given arbitrary degree of similarity between two profiles would occur by chance, with no biological pressure. Function is then inferred at any desired level of confidence. RESULTS: We derive an expression for the probability distribution of a given number of chance co-occurrences of a pair of non-homologous orthologs across a set of genomes. The method is applied to 2905 clusters of orthologous genes (COGs) from 44 fully sequenced microbial genomes representing all three domains of life. Among the results are the following. (1) Of the 51 000 annotated intrapathway gene pairs, 8935 are linked at a level of significance of 0.01. This is over 30-fold greater than the 271 intrapathway pairs obtained at the same confidence level when identical profiles are used. (2) Of the 540 000 interpathway genes pairs, some 65 000 are linked at the 0.01 level of significance, some 12 standard deviations beyond the number expected by chance at this confidence level. We speculate that many of these links involve nearest-neighbor path, and discuss some examples. (3) The difference in the percentage of linked interpathway and intrapathway genes is highly significant, consistent with the intuitive expectation that genes in the same pathway are generally under greater selective pressure than those that are not. (4) The method appears to recover well metabolic networks. This is illustrated by the TCA cycle which is recovered as a highly connected, weighted edge network of 30 of its 31 COGs. (5) The fraction of pairs having a common pathway is a symmetric function of the Hamming distance between their profiles. This finding, that the functional correlation between profiles with near maximum Hamming distance is as large as between profiles with near zero Hamming distance, and as statistically significant, is plausibly explained if the former group represents analogous genes.     

Hormone profiles of obligate avian brood parasites during the breeding season

The ultimate explanations for avian brood parasitism have been studied intensively as a model system for coevolution, but little is known about the proximate mechanisms, for example hormonal regulation, underlying brood parasitic behaviour. In this study, we explored seasonal hormone profiles in two brood parasitic Cuculus species breeding in the Republic of Korea. As brood parasites have relatively simple breeding stages without incubation and provisioning, we predicted that during the breeding season individuals would exhibit similar levels of testosterone (T) and stress‐induced corticosterone (CORT), hormones that are known to be closely related to the transition of breeding stages. We also assessed how these hormone profiles were associated with traits such as body size and sex. Overall, male cuckoos showed similarly high T levels throughout the breeding season, as predicted, but individual variation became greater as the season progressed. Individual CORT levels tended to decrease as the season progressed, although the decrease was significant only in Common Cuckoos Cuculus canorus. We also found that male Lesser Cuckoos Cuculus poliocephalus showed a much higher level of T than females, as expected, but this sexual difference was not observed in Common Cuckoos. Our results suggest that the seasonal hormone profiles of avian brood parasites are likely to be similar to typical hormone profiles expected for non‐brood parasites during the breeding season. This may suggest that not only the breeding cycle but also other factors such as social interaction may be affected by hormonal changes. Further studies are needed to fully understand the proximate mechanism of avian brood parasitism.     

Characterization of serotypes and outer membrane protein profiles in enteroaggregative Escherichia coli strains.

Twenty-four Escherichia coli strains mainly isolated from children with diarrhea in São Paulo, and showing characteristics of enteroaggregative E. coli (EAEC), were characterized by serotyping and outer membrane protein (OMP) profiles. The relationship between these characteristics was evaluated, as well as the usefulness of OMP profiles in the clonal analysis of EAEC strains. All strains presented aggregative adherence to HeLa cells and were classified in two groups based on their interaction with the EAEC DNA probe. A diversity of serotypes and OMP profiles was observed in both groups studied. Although no significant correlation between serotypes and OMP profiles was observed, unique OMP profiles were identified in 80% of the probe-positive strains which were distributed in only 4 OMP profiles. This result may indicate the presence of a few clones in the probe-positive group. On the other hand, probe-negative strains seem to constitute a more diverse group. In general, the observed heterogeneity in serotypes and OMP profiles described in the present study suggest a great genetic diversity in EAEC isolates of either the same or different serotypes and in strains presenting the same EAEC markers identified in our community.     

Gene-expression profiles for five key glycosylation genes for galactose-fed CHO cells expressing recombinant IL-4/13 cytokine trap

Recombinant protein glycosylation profiles have been shown to affect the in-vivo half-life, and therefore the efficacy and economics, for many therapeutics. While much research has been conducted correlating the effects of various stimuli on recombinant protein glycosylation characteristics, relatively little work has examined glycosylation-related gene-expression profiles. In this study, the effects of galactose feeding on the gene-expression profiles for five key glycosylation-related genes were determined for Chinese hamster ovary cells producing a recombinant IL-4/13 cytokine trap fusion. The genes investigated were sialidase, a putative alpha2,3-sialyltransferase, CMP-sialic acid transporter, beta1,4-galactosyltransferase, and UDP-galactosyltransferase. Additionally, the sialic acid content (sialylation) of the recombinant protein was examined. The peak sialic acid content of the IL-4/13 cytokine trap fusion protein was observed to be similar for the control and galactose-fed cultures. The gene-expression profiles for four of the glycosylation genes were observed to be sensitive to the glucose concentration and not significantly different for the control and galactose-fed cultures prior to glucose depletion. However, the sialidase gene-expression profiles were different for the control and galactose-fed cultures. The sialidase gene-expression profile increased significantly for the galactose-fed cultures prior to glucose depletion, whereas for the control cultures, the sialidase gene-expression profiles did not increase until the late stationary phase. The intracellular sialidase enzyme activity decreased exponentially with time for the control cultures; however, for the galactose-fed cultures, the intracellular sialidase enzyme activity decreased initially and then remained relatively high compared to the control cultures. These results indicate that the galactose feeding may increase the potential for desialylation, which offsets any improvements in the sialylation rate due to increased substrate levels. Thus, galactose feeding is an unnecessary expense for the production of the IL-4/13 cytokine trap fusion protein in a batch process.     

Prediction of band profiles of mixtures of bradykinin and kallidin from data acquired by competitive frontal analysis

The competitive adsorption isotherms of two closely related peptides, bradykinin and kallidin, were measured by frontal analysis on a Zorbax SB-C18 microbore column. An aqueous soluton at 20% acetonitrile (0.1% TFA) was used as the mobile phase. The competitive isotherm data were fitted to four different models: Langmuir, Bilangmuir, Langmuir-Freundlich, and Toth. These data fitted best to a Bilangmuir isotherm model. The influence of the pressure on the retention factors of the two peptides was found to be small and was not investigated in detail. The band profiles of large samples of the single components and of their mixtures were recorded. The overloaded profiles calculated using either the equilibrium-dispersive or POR model are in excellent agreement with the experimental profiles in all cases. Our results confirm that the competitive isotherm data derived from mixtures may suffice for a reasonably accurate prediction of the band profiles of all mixtures of the two components, provided their composition is close to 1/1.     

Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities

Terminal restriction fragment (TRF) analysis of 16S rRNA genes is an increasingly popular method for rapid comparison of microbial communities, but analysis of the data is still in a developmental stage. We assessed the phylogenetic resolution and reproducibility of TRF profiles in order to evaluate the limitations of the method, and we developed an essential analysis technique to improve the interpretation of TRF data. The theoretical phylogenetic resolution of TRF profiles was determined based on the specificity of TRFs predicted from 3,908 16S rRNA gene sequences. With sequences from the Proteobacteria or gram-positive division, as much as 73% of the TRFs were phylogenetically specific (representing strains from at most two genera). However, the fraction decreased when sequences from the two divisions were combined. The data show that phylogenetic inference will be most effective if TRF profiles represent only a single bacterial division or smaller group. The analytical precision of the TRF method was assessed by comparing nine replicate profiles of a single soil DNA sample. Despite meticulous care in producing the replicates, numerous small, irreproducible peaks were observed. As many as 85% of the 169 distinct TRFs found among the profiles were irreproducible (i.e., not present in all nine replicates). Substantial variation also occurred in the height of synonymous peaks. To make comparisons of microbial communities more reliable, we developed an analytical procedure that reduces variation and extracts a reproducible subset of data from replicate TRF profiles. The procedure can also be used with other DNA fingerprinting techniques for microbial communities or microbial genomes.     

Improvement in prediction of solvent accessibility by probability profiles

The capability of predicting folding and conformation of a protein from its primary structure is probably one of the main goals of modern biology. An accurate prediction of solvent accessibility is an intermediate step along this way. A new method for predicting solvent accessibility from single sequence and multiple alignment data is described. The method is based on probability profiles calculated on an amino acid sequence centred on the residue whose accessibility has to be predicted. A profile is constructed for each exposure category considered so as to calculate the probability of a sequence being generated by the different profiles. Prediction accuracy was tested on a variety of protein sets with two- and three-state models. Different thresholds were used according to those adopted by the authors proposing the data sets. The prediction accuracy is significantly improved over existing methods.     

Influence of protein fermentation on gas production profiles

With modern equipment, accurate gas-production profiles can be obtained reflecting the organic-matter fermentation in rumen fluid. Although the gas production caused by fermentation of carbohydrates is well understood and described, ignoring the influence of protein fermentation may lead to misinterpretation of the gas-production data. Gas-production profiles, from grass samples differing in growing days, and hence in protein content, showed an unexpected low gas production for the young samples compared to the old ones. The influence of protein fermentation on gas-production profiles was studied by incubation of mixtures of casein with glucose, Zulkovsky starch and/or potato starch. After prolonged incubation, the fermentation of casein produced only 32% gas compared with carbohydrates and it was calculated that each percentage of protein caused a reduction in gas production of 2.48 ml g⁻¹ organic matter. Relative to potato starch, casein was fermented in an earlier stage of incubation.After correction for the influence of protein fermentation, gas production of the youngest grass sample was the highest and of the oldest sample the lowest. It showed that protein fermentation influenced gas production mainly in the initial hours of incubation, because the major part of protein is part of the soluble fraction. It is concluded that a comparison of gas-production profiles of feed samples differing largely in protein content may lead to a misinterpretation, which necessitates correction for protein fermentation.     

Microelectrode measurement of ammonium profiles in freshwater sediments

Abstract Ammonium microprofiles in two dominant types of lake sediment were measured using ion-selective microelectrodes. These profiles enabled establishment of local fluxes and convensions. Comparison of ammonium profiles obtained from the analysis of sediment slices with those measured with microelectrodes showed the superior spatial resolution of the latter method. Flux measurements with microelectrodes were confirmed by laboratory incubation experiments. In both sediments ammonium consumption was restricted to the oxic surface layer. In sandy sediments ammonium was only consumed, while in silty sediment both ammonium production and consumption were observed. In silty sediment ammonium production by anaerobic mineralization was not balanced by ammonium consumption in the oxic surface layer.     

On the mechanics of mucociliary flows. III. Flow-velocity profiles in frog palate mucus

Flow-velocity profiles over excised frog ciliated epithelium were obtained for the region within about 600 micron of the mucosa. Fluorescent particles were used as flow tracers. Both a control and an autologous mucus suspension were observed. The control culture medium was bounded by the walls of the observation chamber, and mucus was deposited on the epithelium as a blob after mixing it with tracers. In spite of the difference in boundary conditions the two profiles, normalized to maximum particle velocity and solution depth, were indistinguishable at heights over 60 micron from the mucosa. The near-mucosa profiles in contrast were unalike with mucus exhibiting a greater shear gradient than the control culture medium. It was concluded that ciliary contact is not necessary for generation of mucus flow provided the ciliary shear is not negated by the mucus "flake" or "slab" being in simultaneous contact with significant ciliostatic patches which would act as anchors.     

Phage types, plasmid profiles and chromosomal restriction profiles of Salmonella enterica subsp. enterica ser. enteritidis (S. enteritidis) isolated in Poland in 1999-2000]

Salmonella Enteritidis strains are the most often isolated Salmonella serovars in Poland. In the present study, phage typing, plasmid profile analysis, and PFGE have been applied to characterize 140 Polish S. Enteritidis isolates originated from human cases of salmonellosis and from other sources. The typing phages of Ward and colleagues scheme were used to type a total of 140 S. Enteritidis strains coming from Poland. All 140 strains were typable and six different phage types were observed. A total of 125 (89%) of 140 isolates examined belonged to PT 4. The others PTs were represented by small amount of strains (PT1-2, PT6-6, PT7-1, PT8-4 and PT21-2 strains). Among all tested isolates six different plasmid profiles were observed. Of the 140 examined strains, 128 (91.4%) contained the 57 kb plasmid alone. After XbaI digestion four distinct pulse field chromosomal restriction profiles among studied S. Enteritidis were observed. XbaI and SpeI chromosomal restriction profiles of S. Enteritidis PT4 were identical with reference strain profiles. Our findings confirmed earlier suggestions that the increase of human salmonellosis cases in Poland was caused by S. Enteritidis PT4 and was due to consumption of contaminated food. This study confirmed the importance of using PFGE in combination with phage typing, plasmid typing and antibiotic resistance testing for studying the epidemiology of S. Enteritidis.     

Designing gene libraries from protein profiles for combinatorial protein experiments

Protein combinatorial libraries provide new ways to probe the determinants of folding and to discover novel proteins. Such libraries are often constructed by expressing an ensemble of partially random gene sequences. Given the intractably large number of possible sequences, some limitation on diversity must be imposed. A non-uniform distribution of nucleotides can be used to reduce the number of possible sequences and encode peptide sequences having a predetermined set of amino acid probabilities at each residue position, i.e., the amino acid sequence profile. Such profiles can be determined by inspection, multiple sequence alignment or physically-based computational methods. Here we present a computational method that takes as input a desired sequence profile and calculates the individual nucleotide probabilities among partially random genes. The calculated gene library can be readily used in the context of standard DNA synthesis to generate a protein library with essentially the desired profile. The fidelity between the desired profile and the calculated one coded by these partially random genes is quantitatively evaluated using the linear correlation coefficient and a relative entropy, each of which provides a measure of profile agreement at each position of the sequence. On average, this method of identifying such codon frequencies performs as well or better than other methods with regard to fidelity to the original profile. Importantly, the method presented here provides much better yields of complete sequences that do not contain stop codons, a feature that is particularly important when all or large fractions of a gene are subject to combinatorial mutation.     

High-resolution vertical profiles of pelagic tunicates

The objectives of our research were to obtain high-resolutionvertical profiles of the abundance of pelagic tunicates andto relate their distribution to physical and biological variables.The abundance of doholids (Tunicata: Thaliacea) from near thesurface to near the seafloor was determined by obtaining continuousvideotape recording from a descending submersible. These verticalprofiles, accompanied by temperature and fluorescence measurements,revealed (i) pronounced changes in dololiolid concentrationwithin 2 m depth intervals, and (ii) two general modes of verticaldistribution, one characterized by a peak in abundance in thethennocline and the second by a more or less even distributionthroughout much of the water column. This in situ approach canprovide estimates of zooplankton abundance in near real-time