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PubMed2006

IgV gene intraclonal diversification and clonal evolution in B-cell chronic lymphocytic leukaemia.

Intraclonal diversification of immunoglobulin (Ig) variable (V) genes was evaluated in leukaemic cells from a B-cell chronic lymphocytic leukaemia (B-CLL) case over a 2-year period at four time points. Intraclonal heterogeneity was analysed by sequencing 305 molecular clones derived from polymerase chain reaction amplification of B-CLL cell IgV heavy (H) and light (C) chain gene rearrangements. Sequences were compared with evaluating intraclonal variation and the nature of somatic mutations. Although IgV intraclonal variation was detected at all time points, its level decreased with time and a parallel emergence of two more represented V(H)DJ(H) clones was observed. They differed by nine nucleotide substitutions one of which only caused a conservative replacement aminoacid change. In addition, one V(L)J(L) rearrangement became more represented over time. Analyses of somatic mutations suggest antigen selection and impairment of negative selection of neoplastic cells. In addition, a genealogical tree representing a model of clonal evolution of the neoplastic cells was created. It is of note that, during the period of study, the patient showed clinical progression of disease. We conclude that antigen stimulation and somatic hypermutation may participate in disease progression through the selection and expansion of neoplastic subclone(s).

Aged↗
PubMed2004

PyEvolve: a toolkit for statistical modelling of molecular evolution.

BACKGROUND: Examining the distribution of variation has proven an extremely profitable technique in the effort to identify sequences of biological significance. Most approaches in the field, however, evaluate only the conserved portions of sequences - ignoring the biological significance of sequence differences. A suite of sophisticated likelihood based statistical models from the field of molecular evolution provides the basis for extracting the information from the full distribution of sequence variation. The number of different problems to which phylogeny-based maximum likelihood calculations can be applied is extensive. Available software packages that can perform likelihood calculations suffer from a lack of flexibility and scalability, or employ error-prone approaches to model parameterisation. RESULTS: Here we describe the implementation of PyEvolve, a toolkit for the application of existing, and development of new, statistical methods for molecular evolution. We present the object architecture and design schema of PyEvolve, which includes an adaptable multi-level parallelisation schema. The approach for defining new methods is illustrated by implementing a novel dinucleotide model of substitution that includes a parameter for mutation of methylated CpG's, which required 8 lines of standard Python code to define. Benchmarking was performed using either a dinucleotide or codon substitution model applied to an alignment of BRCA1 sequences from 20 mammals, or a 10 species subset. Up to five-fold parallel performance gains over serial were recorded. Compared to leading alternative software, PyEvolve exhibited significantly better real world performance for parameter rich models with a large data set, reducing the time required for optimisation from approximately 10 days to approximately 6 hours. CONCLUSION: PyEvolve provides flexible functionality that can be used either for statistical modelling of molecular evolution, or the development of new methods in the field. The toolkit can be used interactively or by writing and executing scripts. The toolkit uses efficient processes for specifying the parameterisation of statistical models, and implements numerous optimisations that make highly parameter rich likelihood functions solvable within hours on multi-cpu hardware. PyEvolve can be readily adapted in response to changing computational demands and hardware configurations to maximise performance. PyEvolve is released under the GPL and can be downloaded from http://cbis.anu.edu.au/software.

Animals↗
PubMed2006

Tempo and mode of spliceosomal intron evolution in actin of foraminifera.

Spliceosomal introns are present in almost all eukaryotic genes, yet little is known about their origin and turnover in the majority of eukaryotic phyla. There is no agreement whether most introns are ancestral and have been lost in some lineage or have been gained recently. We addressed this question by analyzing the spatial and temporal distribution of introns in actins of foraminifera, a group of testate protists whose exceptionally rich fossil record permits the calibration of molecular phylogenies to date intron origins. We identified 24 introns dispersed along the sequence of two foraminiferan actin paralogues and actin deviating proteins, an unconventional type of fast-evolving actin found in some foraminifera. Comparison of intron positions indicates that 20 of 24 introns are specific to foraminifera. Four introns shared between foraminifera and other eukaryotes were interpreted as parallel gains because they have been found only in single species belonging to phylogenetically distinctive lineages. Moreover, additional recent intron gain due to the transfer between the actin paralogues was observed in two cultured species. Based on a relaxed molecular clock timescale, we conclude that intron gains in actin took place throughout the evolution of foraminifera, with the oldest introns inserted between 550 and 500 million years ago and the youngest ones acquired less than 100 million years ago.

Actins↗
PubMed2005

Fast apoptosis and erythroid differentiation induced by imatinib mesylate in JURL-MK1 cells.

We compare the effects of Imatinib mesylate (Glivec) on chronic myeloid leukemia derived cell lines K562 and JURL-MK1. In both cell lines, the cell cycle arrests in G(1)/G(0) phase within 24 h after the addition of 1 microM Imatinib. This is followed by a decrease of Ki-67 expression and the induction of apoptosis. In JURL-MK1 cells, the apoptosis is faster in comparison with K562 cells: the caspase-3 activity reaches the peak value (20 to 30 fold of the control) after about 40 h and the apoptosis proceeds to its culmination point, the DNA fragmentation, within 48 h following 1 microM Imatinib addition. Unlike K562 cells, JURL-MK1 cells possess a probably functional p53 protein inducible by TPA (tetradecanoyl phorbol acetate) or UV-B irradiation. However, no increase in p53 expression was observed in Imatinib-treated JURL-MK1 cells indicating that the difference in the apoptosis rate between the two cell lines is not due to the lack of p53 in K562 cells. Imatinib also triggers erythroid differentiation both in JURL-MK1 and K562 cells. Glycophorin A expression occurred simultaneously with the apoptosis, even at the single cell level. In K562 cells, but not in JURL-MK1 cells, the differentiation process involved increased hemoglobin synthesis. However, during spontaneous evolution of JURL-MK1 cells in culture, the effects produced by Imatinib progressively changed from the fast apoptosis to the more complete erythroid differentiation. We suggest that the apoptosis and the erythroid differentiation are parallel effects of Imatinib and their relative contributions, kinetics and completeness are related to the differentiation stage of the treated cells.

Antineoplastic Agents↗
PubMed2002

Short-term rhythmic proliferation of human breast cancer cell lines: surface effects and fractal growth patterns.

Kinetic studies of cell proliferation rates shed light on the growth dynamics of cancer. Most such studies are based on measurements of cell numbers that were evaluated in time intervals of about 12 h. Studies of the initial tumour growth with short measuring intervals are rare. This study was therefore designed with 1 h measuring intervals over a 24 h period. Human breast cancer cell lines (ZR-75-1, SK-BR-3, MCF-7) and a benign cell line (HBL-100) were used to study the hourly thymidine uptake as a measure of cells in synthesis. In parallel experiments, the same cell lines were also exposed to tumour necrosis factor alpha (TNF-alpha) to explore the effect of an apoptosis-inducing substance on initial tumour growth kinetics. In time-evolution plots, there was an oscillation of the labelling index of thymidine uptake for all investigated cell lines, with and without TNF-alpha. Based on the results obtained, a mathematical model was developed mimicking the real experiment. To describe the system dynamically a cellular automaton model was studied. The growth kinetics revealed by the simulation were in accordance with our experimental data. Two- and three-dimensional growth simulations of this computer model yielded objects morphologically similar to real images of human breast cancer. Almost identical fractal dimensions of the virtual and real tumours further supported this visual similarity. The cellular automata models could, therefore, be seen as a bridge towards realistic in vivo scenarios. From a clinical point of view, the results obtained may be applicable not only to primary tumours, but even to tumour cell microfoci and small metastases, which are a major concern in early metastasizing tumours such as breast cancer.

Breast Neoplasms↗
PubMed1991

Molecular behavior of water in a flour-water baked model system.

The molecular behavior of water in complex food systems, via bonding and solvation reactions with low molecular weight solutes or high molecular weight macromolecules, is intimately linked with both the palatability and storage stability of those systems. Due to the difficulty in interpreting data derived from multicomponent finished food products, water behavior in a baked flour-water "matzo" model system was studied. Water behavior was assessed from high resolution [1H] nuclear magnetic resonance (NMR) spin-spin relaxation studies and differential scanning calorimetric (DSC) measurements of unfreezable water content. The unfreezable water capacity of "matzo" model crackers, as measured by DSC, ranged from ca. 24-30% (w/w). These results were corroborated by NMR data. Only one exponent (less than 0.46 msec greater than) is required to fit spin-echo evolution curves below a total moisture content of ca. 20% (w/w), whereas two exponents (less than 0.46 greater than and 1.6 msec) are observed when the moisture content exceeds 20% (w/w). Expert sensory texture assessments parallel unfreezable (= total) water contents between 2.9% (w/w) and 20.1% (w/w). This relationship may be explained by the known tendency for water to plasticize biological polymers, e.g. wheat starch and proteins, and to render these macromolecules incrementally more mobile with increasing water concentration. The similarities (if any) between water of plasticization, immobile water, and "bound" water are discussed, in terms of theoretical physicochemical "states" of water and the various techniques utilized to assess (define) those "states."

Chemical Phenomena↗
PubMed2000

Sediment toxicity assessment: comparison of standard and new testing designs.

Standard methods of sediment toxicity testing are fairly well accepted; however, as with all else, evolution of these methods is inevitable. We compared a standard ASTM 10-day amphipod toxicity testing method with smaller, 48- and 96-h test methods using very toxic and reference sediments. In addition we compared parallel exposures of single species, either the amphipod Ampelisca abdita or the mysid Americamysis bahia, to multiple species, mysid, and amphipod, cohabiting the same types of chambers. These comparisons were performed for both water-only and sediment-water tests. Results of the comparison of the standard ASTM 10-day amphipod test with the smaller, 48- and 96-h test chambers indicate that survival was high in both test designs using the reference sediment. With toxic sediments, complete mortality occurred in less than 48 h using the smaller experimental chambers and only after 96 h in the larger experimental chambers. We concluded that although time to death is shorter in the smaller, shorter exposure chambers, there was no overall change in mortality for the organisms, and that the smaller chambers were predictive of the results obtained with larger chambers and longer exposures. For multiple species testing in whole sediment exposures there was no change in toxicity to either the amphipod or the mysid when they cohabited the same chamber. In contrast, for water-only exposures, A. bahia demonstrated less sensitivity when cohabiting the same chamber as A. abdita. Therefore, during whole sediment testing we can add A. bahia and A. abdita to the same test chamber without changing the toxicity to either species; however, in our 10-ml water-only exposures, the species should be tested separately.

Animals↗
PubMed1999

Protein plasticity to the extreme: changing the topology of a 4-alpha-helical bundle with a single amino acid substitution.

BACKGROUND: Conventional wisdom has it that two proteins sharing 98.4% sequence identity have nearly identical three-dimensional structures. Here we provide a counter-example to this statement by showing that a single amino acid substitution can change the topology of a homodimeric 4-alpha-helical bundle protein. RESULTS: We have determined the high-resolution crystal structure of a 4-alpha-helical protein with a single alanine to proline mutation in the turn region, and show that this single amino acid substitution leads to a complete reorganisation of the whole molecule. The protein is converted from the canonical left-handed all-antiparallel form, to a right-handed mixed parallel and antiparallel bundle, which to the best of our knowledge and belief represents a novel topological motif for this class of proteins. CONCLUSIONS: The results suggest a possible new mechanism for the creation and evolution of topological motifs, show the importance of loop regions in determining the allowable folding pathways, and illustrate the malleability of protein structures.

Bacterial Proteins↗
PubMed2000

The current management of infectious diseases in the liver transplant recipient.

The spectrum of major infections after transplantation has undergone a striking evolution. The epidemiologic trends in infectious diseases through the last decade have been most notable for a dramatic decrease in the incidence of several opportunistic infections, largely because of advances in prophylaxis against these pathogens. Paralleling these trends has been an exponential rise in the proportion of infections caused by antimicrobial-resistant bacteria. These multiresistant organisms have now emerged as leading pathogens at many transplant centers, and their management is a daunting challenge.

Bacterial Infections↗
PubMed1997

Imprinting effects of proline containing dipeptides (proline-glycine, proline-leucine, proline-valine and their retro variants) in tetrahymena. Evolutionary conclusions.

Proline-glycine, proline-leucine and proline-valine dipeptides and their retro variants were used in the experiments to study the effects of pretreatment (imprinting) in Tetrahymena, by investigating fluorescein isothiocyanate (FITC)-conjugated peptide binding. The protozoan organism could differentiate between the proline-dipeptides containing different partner amino-acids and between the dipeptides having the amino acids in reversed positions. The effect of imprinting was positive or negative and this was dependent on the type of the partner amino acid and on its position. Pro-Gly and Pro-Leu induced positive imprinting (elevated FITC-dipeptide binding) and Pro-Val induced negative imprinting (decrease of FITC-peptide binding). There was positive imprinting induction in two cases for the retro FITC-peptide and in one case for the FITC-conjugate of the imprinter peptide itself. The highest positive imprinting (almost 60% increase) was induced by Pro-Gly for FITC-Gly-Pro. Considering earlier--chemotaxis--experiments, the results of the present--binding--studies run parallel with the physiological effects. The experiments call attention to the sharp differentiating ability of small peptides at a unicellular level, that could have some role in the selection of molecules for hormone formation, during evolution.

Animals↗
PubMedDate not supplied

Environmental implications of gene flow from sugar beet to wild beet--current status and future research needs.

Gene flow via seed or pollen is a basic biological process in plant evolution. The ecological and genetic consequences of gene flow depend on the amount and direction of gene flow as well as on the fitness of hybrids. The assessment of potential risks of transgenic plants should take into account the fact that conventional crops can often cross with wild plants. The precautionary approach in risk management of genetically modified plants (GMPs) may make it necessary to monitor significant wild and weed populations that might be affected by transgene escape. Gene flow is hard to control in wind-pollinated plants like beet (Beta vulgaris). In addition, wild beet populations potentially can undergo evolutionary changes which might expand their geographical distribution. Unintended products of cultivated beets pollinated by wild beets are weed beets that bolt and flower during their first year of planting. Weed beets cause yield losses and can delay harvest. Wild beets are important plant genetic resources and the preservation of wild beet diversity in Europe has been considered in biosafety research. We present here the methodology and research approaches that can be used for monitoring the geographical distribution and diversity of Beta populations. It has recently been shown that a century of gene flow from Beta vulgaris ssp. vulgaris has not altered the genetic diversity of wild Beta vulgaris L. ssp. maritima (L.) Arcang. in the Italian sugar beet seed production area. Future research should focus on the potential evolution of transgenic wild beet populations in comparison to these baseline data. Two monitoring models are presented describing how endpoints can be measured: (1) "Pre-post" crop commercialization against today's baseline and (2) "Parallel" to crop commercialization against GMP free reference areas/ populations. Model 2 has the advantage of taking ongoing changes in genetic diversity and population dynamics into account. Model 1 is more applicable if gene flow is so strong that most areas/populations contain GMPs. Important traits that may change the ecology of populations are genes that confer tolerance to biotic and abiotic stress. An assessment of environmental effects can realistically only be based on endpoints and consequences of gene introgression, which may include economic values of biodiversity in littoral and other ecosystems containing wild beet. In general, there is still a great need to harmonize worldwide monitoring systems by the development of appropriate methods to evaluate the environmental impact of introgressed transgenes.

Beta vulgaris↗
PubMed2005

Blast count and cytogenetics correlate and are useful parameters for the evaluation of different phases in chronic myeloid leukemia.

Staging of chronic myeloid leukemia (CML) phases is based on cytomorphological criteria that vary considerably between different staging systems. Thus, staging of CML is heterogeneous and causes problems with respect to the comparison of therapeutical strategies and clinical outcome. We evaluated 59 patients with CML in different stages of the disease. In order to define which cytomorphological parameters correlate with cytogenetics we investigated cytomorphology and cytogenetics in parallel in all cases. As a result, bone marrow blast count demonstrated a highly significant correlation with the respective cytogenetic results of the patients and was clearly linked to the frequency and complexity of clonal evolution. We therefore propose to focus staging systems of CML on the correlation of the percentage of bone marrow blasts and the cytogenetic results.

Blast Crisis↗
PubMed1999

Methicillin-resistant and borderline methicillin-resistant asymptomatic Staphylococcus aureus colonization in children without identifiable risk factors.

BACKGROUND: The recent evolution in the epidemiology of methicillin-resistant asymptomatic Staphylococcus aureus (MRSA) infections in children, whereby children without traditional risk factors for MRSA have been hospitalized in increasing numbers, prompted us to establish whether a parallel increase in "asymptomatic" MRSA colonization had occurred. METHODS: We cultured the nares and perineum of 500 children attending our Pediatric Emergency Department. RESULTS: One hundred thirty-two (26.4%) of these children were colonized with S. aureus. Eleven (8.3%) of the S. aureus isolates were MRSA; 4 (36.4%) of the 11 subjects colonized with MRSA had no risk factors. Seven (5.3%) of the 132 S. aureus isolates were borderline methicillin-resistant S. aureus (BRSA); 5 (71.4%) of the 7 subjects colonized with BRSA had no MRSA risk factors. CONCLUSIONS: These findings indicate that MRSA and BRSA isolates are circulating in the community and that MRSA isolates are no longer confined to children with frequent contact with a health care environment.

Adolescent↗
PubMed1997

Factor VII, cholesterol, and triglycerides. The CARDIA Study. Coronary Artery Risk Development in Young Adults Study.

Cross-sectional studies have shown that factor VII coagulant activity (VIIc) is positively associated with plasma total cholesterol (TC), LDL cholesterol, and triglycerides (TG) as well as body mass index (BMI) and diastolic blood pressure. To determine whether changes in VIIc parallel changes in coronary risk factors over a period of 2 years, we examined data from 1514 participants in the Coronary Artery Risk Development in Young Adults Study (CARDIA), an ongoing investigation of lifestyles and evolution of cardiovascular risk factors. Subjects were 23 to 35 years old at the year 5 examination. Cross-sectional analyses at these examinations showed that VIIc was positively correlated (P < .001) with TC and TG in all race/sex groups except for TC in black women at the year 5 examination. Changes in VIIc over the 2-year period were correlated positively with changes in TC in all except black men and TG in all groups; the association of VIIc change with change in TC and TG was reduced only slightly with adjustment for age and BMI at year 5 and 2-year change in BMI. To determine whether the higher levels of VIIc in subjects with higher lipid values were due to activation of the factor or to an increase in the concentration of the factor VII clotting protein, we measured factor VII antigen (VIIag) in a randomly selected subsample of 223 subjects at the year 7 examination. In all sex/race groups, VIIag correlated with VIIc (r = .69 to 0.81). After adjustment for sex and race, the partial correlation coefficient between TG and VIIc was .28 (P = .0001); between TG and VIIag, .35 (P = .0001); between TC and VIIc, .39 (P = .0001); and between TC and VIIag, 0.43 (P = .0001). No associations were observed between lipid levels and the ratio of VIIc to VIIag. We conclude that the raised VIIc with higher lipid levels occurs in blacks as well as whites, in men and women, persists over time, and represents a true increase in the plasma concentration of this clotting factor.

Adult↗
PubMed1989

[Prophylactic measures at work sites in respect of the adaptation of working personnel].

The paper shows the importance and role played by medicine in the orientation and solving of the adaptation processes of the individual at the working site and in modern life, under the conditions of variability and complexity of industrial development. Correct knowledge of work and of efficiency achieved provides the elements of a complete appreciation of the workers' adaptation, with the possibility of improving those conditions on which the formation of the dynamic stereotype depends. The efficiency parallels the training, being influenced by the adaptation of the respiratory and cardiovascular functions, elimination of useless movements during the working process and increase of muscular strength. Lack of adaptation may be noticed by inadequate evolution of the indices mentioned and the appearance of general phenomena--fatigue, neuro-psychical disturbances etc. Observation of the unfavourable effects of the working conditions upon the body should lead to application of prophylactic measures concerning rhythm and regimen of work. The results obtained in the adaptability process, followed up in the inpatient medical unit are reported.

Adaptation, Physiological↗
PubMed1981

[Dynamics of the changes in the acid-base state in acquired heart defects].

One hundred thirty nine patients with acquired valvular defects were examined, 72 of them followed up dynamically. The dynamic changes in the indices of ABS were studied as well as the pressure of arterial blood gases, some electrolytes in blood serum, the basic indices of external respiration, diffusion capacity of lungs for CO, alveolar-arterial gradients for O2, functional and true shunts, etc. The results showed that the disorders found in ABS were, to a great extent, reversible after complex treatment carried out. Most intensive was the dynamics of recovery at stage IIB and the poorest stage IIA of cardiac insufficiency. The changes in respiratory function play a leading role in the genesis of ABS disorders. The diuretics and electrolyte deviations are of secondary importance. The dynamic investigations on ABS in parallel with some indices of respiratory function provide an early and accurate assessment of the functional state of the respiration system in acquired valvular defects, a more complete estimation of the results from the treatment, evolution and prognosis, revealing some of the complicated mechanisms of those disorders.

Acid-Base Imbalance↗
PubMed1995

Temperature-induced functional and structural transformations of the photosystem II oxygen-evolving complex in spinach subchloroplast preparations.

Heat inactivation of the process of O2 evolution, temperature-induced Mn2+ release and structural transitions revealed by differential scanning calorimetry (DSC) were studied in photosystem II (PSII) enriched subchloroplast fragments, granal thylakoids and the isolated oxygen-evolving pigment-lipoprotein complexes (OEC). It was found that the temperature of semi-inactivation of O2 evolution, which coincided with Mn2+ release, declined from 45 degrees C to 40 degrees C and 34 degrees C in this series of preparations, in accordance with the decreased structural stability of OEC. This was paralleled by a decrease in the content of light harvesting complex (LHC) and by an increase in the accessibility of OEC to hydrophilic electron acceptors. Thermoinactivation processes were accompanied by a two-fold decrease in PSII particle size on the EFs surface of membrane fragments. A "bi-core" oxygen-evolving complex model is proposed to account for these findings.

Calorimetry, Differential Scanning↗
PubMed1996

The adenoma-carcinoma sequence in colorectal neoplasia.

In this article the epidemiologic, pathologic, molecular, and clinical evidence for the adenoma-carcinoma sequence is reviewed. The authors describe the morphologic evolution of the precursor adenomas, from the earliest discernible abnormality of the colon to adenomas with advanced pathologic features, the factors that determine the risk of progression of adenomas to adenocarcinoma, the molecular events that parallel or underlie the morphologic changes, the outcome of clinical interventions that have tested this hypothesis, and the time frame within which this progression is likely to occur.

Adenocarcinoma↗