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PubMed2004

Induction and characterization of taxol-resistance phenotypes with a transiently expressed artificial transcriptional activator library.

Phenotype-based functional genomic methods are useful for the identification of genes that are related to a particular biological function or disease. Essential to this approach is the ability to regulate the expression of selected genes. Artificial transcription factors (ATFs) are key molecular tools that selectively regulate gene expression in vivo. Here, we use an ATF library to identify genes that participate in rendering a cell resistant to the drug Taxol, a potent anti-cancer drug that binds to tubulin and inhibits cell division. The library, which encodes ATFs that activate (rather than inhibit) transcription, was introduced into a HeLa cell line, and Taxol-resistant cells were selected. After eight rounds of selection, we identified two ATFs that significantly increased the level of Taxol resistance (TR) in HeLa cells. Gene expression microarray experiments using these ATFs identified 37 co-regulated genes, including genes already known to participate in TR. This study demonstrates that ATF libraries can be used to induce phenotypic alterations in eukaryotic cells and then identify specific genes that are associated with the phenotype of choice.

Antineoplastic Agents, Phytogenic↗
PubMed1988

Measuring genetic change in a dairy herd using a control population.

A selection experiment was conducted to assess the change in production resulting from selection with artificial insemination using a randomly maintained control. The experiment continued for 16 yr with approximately 20 lactations in each of the two breeding groups annually. Selection and control production was compared using 1) intraseason herdmate comparisons (weighted) and 2) mixed model maximum likelihood estimates of year-season effects (adjusted). The regressions of differences in milk yield on years for the two approaches were 110 kg for milk (weighted) and 108 kg for milk (adjusted), corrected for inbreeding. The regressions for fat were 3.9 kg for fat (weighted) and 4.2 kg for fat (adjusted). These regression coefficients were 1.6 and 1.5% of the least squares means for milk (6987 kg) and fat (259 kg), respectively. Definitive trends were not evident for differences between the two groups in percent fat, percent SNF, days open, final type classification score, or heart girth. Even with the limited numbers in the closed control population, inbreeding, and nonrandomness in culling of females or in the choice of dams of bulls appeared to have little impact on control mean during the 16 yr.

Animals↗
PubMed2006

The use of artificial neural networks for the selection of the most appropriate thermal parameters and for the classification of a set of phenylcarbamic acid derivates.

The objective of this work was to apply artificial neural networks (ANNs) to the classification group of 43 derivatives of phenylcarbamic acid. To find the appropriate clusters Kohonen topological maps were employed. As input data, thermal parameters obtained during DSC and TG analysis were used. Input feature selection (IFS) algorithms were used in order to give an estimate of the relative importance of various input variables. Additionally, sensitivity analysis was carried out to eliminate less important thermal variables. As a result, one classification model was obtained, which can assign our compounds to an appropriate class. Because the classes contain groups of molecules structurally related, it is possible to predict the structure of the compounds (for example the position of the substitution alkoxy group in the phenyl ring) on the basis of obtained parameters.

Calorimetry, Differential Scanning↗
PubMed2006

Markers, selection, and media in yeast artificial chromosome cloning.

Yeast have proven to be a valuable and flexible host for cloning and manipulating large fragments of foreign genetic material, providing valuable reagents for the study of gene function and regulation in a variety of applications. However, this approach requires a familiarity with basic procedures derived from yeast genetics, and lack of experience can be a barrier to researchers with backgrounds limited to bacterial and mammalian culture systems. To address this issue, this chapter introduces and discusses the genetic markers and selection systems used in the genetic manipulation of yeast, with particular reference to yeast artificial chromosome (YAC) cloning and manipulation. Detailed descriptions of culture media are provided, allowing for the growth and selection of standard YAC strains, as well as for specialist applications.

Chromosomes, Artificial, Yeast↗
PubMed1981

A comparison of the reproductive and growth performances of offspring from broiler breeder males selected for early growth rate using artificial insemination and unselected males kept on deep litter.

Broiler breeder males were selected for early growth rate at 5 weeks of age (average weight + 0.5 SD). The reproductive and growth performances of the offspring of these males using artificial insemination with stored semen was compared with those from non-selected males kept on deep litter under conditions of natural mating. On three different occasions (31, 41 and 51 weeks of age), the eggs of the two treatments were incubated and, although the reproductive performances showed little difference over the entire period, hatchability of eggs set was significantly (p less than 0.01) higher for the field hens on the first occasion. The opposite was true after 50 weeks of age due to a serious decline in fertility in natural mating. At all periods, the selected males produced significantly (p less than 0.01) heavier offspring at six weeks of age.

Animals↗
PubMed1980

An autosomal centric fusion translocation in the Red Poll breed in Australia.

The karyotype 2n = 59,XY,t:1/29 was found in two pure bred Red Poll bulls originating from stock imported from Britain. Orthodox stained and G-banded karyotypes of the condition in this breed are presented for the first time. Non-return rates for one bull suggest no impairment of fertility when selected for artificial insemination. However, in a related herd infertility has become a serious problem. It is suggested that selection pressure does not operate to eliminate the translocation and that caution should be exercised in the use of animals.

Animals↗
PubMed2003

The use of artificial neural networks for the selection of the most appropriate formulation and processing variables in order to predict the in vitro dissolution of sustained release minitablets.

The objective of this work was to apply artificial neural networks (ANNs) to examine the relative importance of various factors, both formulation and process, governing the in-vitro dissolution from enteric-coated sustained release (SR) minitablets. Input feature selection (IFS) algorithms were used in order to give an estimate of the relative importance of the various formulation and processing variables in determining minitablet dissolution rate. Both forward and backward stepwise algorithms were used as well as genetic algorithms. Networks were subsequently trained using the back propagation algorithm in order to check whether or not the IFS process had correctly located any unimportant inputs. IFS gave consistent rankings for the importance of the various formulation and processing variables in determining the release of drug from minitablets. Consistent ranking was achieved for both indices of the release process; ie, the time taken for release to commence through the enteric coat (T(lag)) and that for the drug to diffuse through the SR matrix of the minitablet into the dissolution medium (T9(0-10)). In the case of the T(lag) phase, the main coating parameters, along with the original batch blend size and the blend time with lubricant, were found to have most influence. By contrast, with the T(90-10 phase), the amounts of matrix forming polymer and direct compression filler were most important. In the subsequent training of the ANNs, removal of inputs regarded as less important led to improved network performance. ANNs were capable of ranking the relative importance of the various formulations and processing variables that influenced the release rate of the drug from minitablets. This could be done for all main stages of the release process. Subsequent training of the ANN verified that removal of less relevant inputs from the training process led to an improved performance from the ANN.

Artificial Intelligence↗
PubMed2002

The selection of anterior teeth appropriate for the age and sex of the individual. How variable are dental staff in their choice?

As part of the development of a guide to aid the undergraduate in the selection of artificial teeth, the aim of this study was to investigate the variability in choice of dental staff to select teeth appropriate to the age and sex of the individual with the aid of a series of three-dimensional guides. Four three-dimensional guides were produced for use in the study. Fifty dentists were asked to complete a questionnaire designed to assess the variability in selection of anterior teeth appropriate for the age and sex of an individual. From this study it can be concluded that there was little consistency in the selection of the shade, mould and arrangement of anterior teeth appropriate for the age and sex of the individual by qualified dental staff. The development and implementation of an aesthetic proforma to guide dental staff, dental undergraduates and patients through the process of choosing tooth mould, shade and arrangement based on age and sex may be helpful.

Adult↗
PubMed1999

'Niche Selection' and the evolution of a complex behavior in a changing environment--a simulation.

One of the key problems in theoretical biology is the identification of the mechanisms underlying the evolution of complexity. This paper suggests that some difficulties in current models could be avoided by taking account of"niche selection"as proposed by Waddington [21] and subsequent authors [2]. Computer simulations, in which an evolving population of artificial organisms"selects"the niche(s) that maximize their fitness, are compared with a Control Model in which"Niche Selection"is absent. In the simulations the Niche Selection Model consistently produced a greater number of"fit"organisms than the Control Model; although the Niche Selection Model tended, in general, to produce organisms occupying simple niches, it was nonetheless more effective than the Control Model in producing well-adapted organisms inhabiting complex niches. It is shown that the production of these organisms is critically dependent on the rate of environmental change: Slow change leads to fit but undifferentiated populations, dominated by organisms occupying simple niches; differentiated populations, including well-adapted organisms living in complex niches, require rates of environmental change lying just beyond a mathematically well-defined critical value. In simulation"Niche Selection,"unlike conventional"Natural Selection,"provides a permanent selective bias in favor of simplicity. This tendency is counterbalanced by statistical forces favoring shifts from rare"simple niches"to commoner niches of greater complexity. Fit organisms inhabiting complex niches only emerge in conditions where the rate of environmental change is high enough to avoid the concentration of the population in very simple niches, but slow enough to permit step-by-step adaptation to niches of gradually increasing complexity. This result appears to be robust to changes in simulation parameters and assumptions, and leads to interesting conjectures about the real world behavior of biological organisms (and other complex adaptive systems). It is suggested that some of these conjectures might be relatively easy to test.

Animals↗
PubMed2000

[A study of the mechanism of effects of solution containing trace elements on remineralization layer formation of enamel carious lesions].

OBJECTIVE: To study the effects of several remineralization solutions with different composition on the artificial demineralization lesions of bovine enamel and the mechanism of remineralization layer formation. METHODS: 36 bovine teeth were selected and artificial carious lesions were formed with lactic acid gel. Then all specimens were divided into 4 groups which contained no fluoride, fluoride, fluoride-calcium-phosphate-tin, and de-ionic water separately, and the de-ionic group was taken as control. The structure and composition of the sediments on the enamel surface were evaluated and detected by X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). Histological change of enamel section was examined by polarized microscopy. RESULTS: Compared with the control group, all the solutions had remineralization effects, especially the solutions containing trace elements. XPS showed that there were sediments formed on the surface of carious lesion, the compositions of the sediments were CaF2, HAP and non-specifically absorbed fluoride (NSAF). Irregular, crystal deposits were also found under SEM on the enamel surface. The polarized microscopy results showed that the observed demineralization areas decreased after exposure to the solutions. CONCLUSION: Solutions containing fluoride and trace elements were effective on remineralization. The possible mechanism is that CaF2 and NSAF, instead of FA formed in the remineralization layer. Moreover, the remineralization effects of the fluoride solutions containing trace elements are more outstanding than that without trace elements. The potential mechanism is the synergistic action of fluoride and trace elements.

Animals↗
PubMed1995

Characterization of a human chromosome 22 enriched bacterial artificial chromosome sublibrary.

Selection of chromosomal sublibraries from total human genomic libraries is critical for chromosome-based physical mapping approaches. We have previously reported a method of screening total human genomic library using flow sorted chromosomal DNA as a hybridization probe and selection of a human chromosome 22-enriched sublibrary from a total human bacterial artificial chromosome (BAC) library (Nucleic Acids Res 1995; 23: 1838-39). We describe here further details of the method of construction as well as characterization of the chromosome 22-enriched sublibrary thus constructed. Nearly 40% of the BAC clones that have been mapped by fluorescence in situ hybridization (FISH) analysis were localized to chromosome 22. By screening the sublibrary using chromosome 22-specific hybridization probes, we estimated that the sublibrary represents at least 2.5 x coverage of chromosome 22. This is in good agreement with the results from FISH mapping experiments. FISH map data also indicate that chromosome 22-specific BACs in the sublibrary represent all the subregions of chromosome 22.

Animals↗
PubMed2004

A site-selective dual anchoring strategy for artificial metalloprotein design.

Introducing nonnative metal ions or metal-containing prosthetic groups into a protein can dramatically expand the repertoire of its functionalities and thus its range of applications. Particularly challenging is the control of substrate-binding and thus reaction selectivity such as enantioselectivity. To meet this challenge, both non-covalent and single-point attachments of metal complexes have been demonstrated previously. Since the protein template did not evolve to bind artificial metal complexes tightly in a single conformation, efforts to restrict conformational freedom by modifying the metal complexes and/or the protein are required to achieve high enantioselectivity using the above two strategies. Here we report a novel site-selective dual anchoring (two-point covalent attachment) strategy to introduce an achiral manganese salen complex (Mn(salen)), into apo sperm whale myoglobin (Mb) with bioconjugation yield close to 100%. The enantioselective excess increases from 0.3% for non-covalent, to 12.3% for single point, and to 51.3% for dual anchoring attachments. The dual anchoring method has the advantage of restricting the conformational freedom of the metal complex in the protein and can be generally applied to protein incorporation of other metal complexes with minimal structural modification to either the metal complex or the protein.

Animals↗
PubMed1994

Dynamics of genetic variability in two-locus models of stabilizing selection.

We study a two locus model, with additive contributions to the phenotype, to explore the dynamics of different phenotypic characteristics under stabilizing selection and recombination. We demonstrate that the interaction of selection and recombination results in constraints on the mode of phenotypic evolution. Let Vg be the genic variance of the trait and CL be the contribution of linkage disequilibrium to the genotypic variance. We demonstrate that, independent of the initial conditions, the dynamics of the system on the plane (Vg, CL) are typically characterized by a quick approach to a straight line with slow evolution along this line afterward. We analyze how the mode and the rate of phenotypic evolution depend on the strength of selection relative to recombination, on the form of fitness function, and the difference in allelic effect. We argue that if selection is not extremely weak relative to recombination, linkage disequilibrium generated by stabilizing selection influences the dynamics significantly. We demonstrate that under these conditions, which are plausible in nature and certainly the case in artificial stabilizing selection experiments, the model can have a polymorphic equilibrium with positive linkage disequilibrium that is stable simultaneously with monomorphic equilibria.

Animals↗
PubMed1995

Effect of artificial tears on cultured keratocytes in vitro.

We investigated the effects of artificial tears on cultured rabbit and human keratocytes in vitro. The cells were exposed to seven nonpreserved commercially available artificial tear formulations and examined under phase-contrast microscopy for 60 min. After 5-min exposures to the solutions, rabbit keratocytes were fixed for transmission electron microscopy (TEM). In rabbit keratocytes, phase-contrast microscopy and TEM demonstrated that Aqua Site (CIBA Vision Ophthalmics, Atlanta, GA, U.S.A.), Hypo Tears PF (Johnson & Johnson, Claremont, CA, U.S.A.), and Tears Naturale Free (Alcon, Humacao, Puerto Rico, U.S.A.) immediately induced intracytoplasmic vacuoles and cell swelling, and subsequent cell degeneration. Rabbit cells exposed to the other artificial tears, which contained Ca2+ and did not contain EDTA, maintained their normal shape and appearance for 60 min. Phase-contrast microscopy of human keratocytes showed that Aqua Site and Hypo Tears PF induced mild and delayed cellular swelling, but the other artificial tears tested did not affect the cell shape for the entire 60-min observation period. Electrolyte balance and osmolarity of artificial tears appear to be critical for keratocyte survival. Maintenance of keratocyte integrity may be an important factor to consider when selecting an artificial tear preparation to be used when corneal epithelium is not intact.

Animals↗
PubMed2005

Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat.

The current view of wheat genome composition is that genes are compartmentalized into gene-rich and gene-poor regions. This model can be tested by analyzing randomly selected bacterial artificial chromosome (BAC) clones for gene content, followed by placement of these BACs onto physical and genetic maps. Map localization could be difficult for BACs that consist entirely of repeated elements. We therefore developed a technique where repeat junctions are used to generate unique markers. Four BAC clones from hexaploid wheat variety Chinese Spring were randomly selected and sequenced at 4- to 6-fold redundancy. About 50% of the BAC sequences corresponded to previously identified repeats, mainly LTR-retrotransposons, whereas most of the remaining DNA consisted of sequences with unknown origin or function. The average gene content was <1%, although each BAC contained one or two identified genes. Repeat boundaries were amplified and used to map each clone to a chromosome arm. Extrapolation from wheat-rice comparative knowledge suggests that three of the four BAC clones originate from "gene-rich" regions of the wheat genome. Nevertheless, because these BACs carry only a single gene (two BACs) or two genes (one BAC), the predicted gene density is approximately 1 gene per 75 kb, which is considerably lower than previously estimated gene densities (one gene per 5-20 kb) for gene-rich regions in wheat. This analysis of randomly selected wheat BAC clones suggests that genes are more evenly distributed in wheat than previously believed and substantiates the need for large-scale random BAC sequencing to determine wheat genome organization.

Bread↗
PubMed2006

[Uncontrolled genetic processes in artificial populations: proving the leading role of selection in evolution].

The review considers studies examining artificially maintained populations as models for understanding biological evolution. The key factors of gene pool evolution-random processes, interspecific hybridization, migration, mutation, and selection--are analyzed. We present evidence indicating that selection is the leading evolutionary factor that regulates the operation of other factors, directly or through genetic systems.

Animals↗
PubMed1997

Sequence-selective RNA scission by oligoamine--DNA conjugates (1).

Ethylenediamine and diethylenetriamine, which are active for RNA hydrolysis, are attached to the 5'-ends of synthetic oligonucleotides by urethane linkages. The resultant artificial ribonucleases selectively hydrolyze the substrate RNA at the target phosphodiester linkage. Acid/base cooperation in the oligoamines for the catalysis is confirmed in terms of kinetic evidences.

Base Sequence↗
PubMed1984

Selection against genetic defects in semen donors.

Artificial insemination donor selection requires predicting which men are likely to beget the healthiest offspring. Methods are developed for calculating the "offspring excess recurrence risk", delta R, for an anomaly in the offspring of an afflicted father. Mainly from published family survey and population data delta R is computed for 38 disorders. From a small survey a value for the with-treatment "affliction burden", Bt, is assigned to each anomaly. For each disorder the "offspring excess burden expectation" is delta RBt. Defects such as cataract, hereditary Parkinson disease, psoriasis, seropositive rheumatoid arthritis, and schizophrenia have such a high delta RBt that they are individually sufficient cause for rejecting a donor candidate. A candidate may be rejected because of a combination of lesser defects with sigma delta RBt exceeding an acceptable limit. A limit should also be placed on Bt, because the affliction burden for Tay-Sachs disease or cystic fibrosis is intolerable, however infrequent. Most of the important hereditary defects are late onset, and for the older donor the opportunity to select more directly against late-onset disorders offsets the added risk of newly-arising gene mutations. The most careful donor selection cannot completely eliminate the risk of a child inheriting some disorder, but selection can reduce the average total burden by as much as 17%.

Genetic Diseases, Inborn↗