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PubMed1996

Direct and correlated responses to long-term selection for increased body weight and egg production in turkeys.

Lines of turkeys were selected long-term for increased egg production (E line; 34 generations) or increased 16-wk BW (F line; 28 generations). The E and F lines were started from randombred control populations (RBC1 and RBC2, respectively) that were also maintained to remove environmental variation among generations. Realized heritabilities (h2) +/- SE in the E line, based on regressions of response on cumulated actual selection differentials (selection differentials weighted for the number of offspring produced), for 180-d and 250-d egg production were 0.34 +/- 0.02 (17 generations) and 0.26 +/- 0.13 (8 generations), respectively. The realized h2 of 16-wk BW in the F line was 0.26 +/- 0.01. There was no consistent evidence of selection response reaching a plateau in either line. The genetic association of BW and egg production changed with selection in the E and F lines. The genetic correlation varied from near zero to strongly negative and fluctuated between these extremes in both lines even though they started from different base populations and selection criteria differed. Other correlated responses to selection for increased egg production were increased average clutch length (intensity of lay), and decreased broodiness (total days lost), egg weight, shell coloration, and rate of response to stimulatory lighting. Other correlated responses to selection for increased 16-wk BW in the F line included: increased egg weight (due to increased albumen), longer eating bouts, and decreased average clutch length, semen production, walking ability, and resistance to Pasteurella multocida and Newcastle disease virus. Selection within the E and F lines also changed the frequency of MHC haplotypes and the changes appeared to be in opposite directions in the two lines.

Animals↗
PubMed1994

Divergent selection for delayed-type wattle reaction of domestic fowls to BCG antigen.

1. Two-way selection for delayed-type hypersensitivity wattle reaction (DWR) competence to BCG antigen was carried out over 4 generations, using a flock of White Leghorn chickens. DWR was measured by intradermal injection of BCG into the wattle of chickens. 2. Selection for DWR was effective. The generation means of average selection differential, selection response and realized heritability were 1.15 mm, 0.77 mm and 0.70 respectively. Correlated responses were found in body weight, egg weight and hatchability. In all of these traits, the L line (selected for low wattle reaction) showed higher values than the H line (high reaction). 3. Specific trends in gene frequencies were observed at the major histocompatibility B and alkaline phosphatase Akp loci. 4. Significant line differences were found in graft-versus-host reaction competence and Marek's disease resistance. In both characters, the L line was higher than the H line. No line differences were found in phytohaemagglutinin response, phagocytic activity or immune responses.

Animals↗
PubMed1993

CD8 is needed for positive selection but differentially required for negative selection of T cells during thymic ontogeny.

During thymic development, immature thymocytes expressing major histocompatibility complex (MHC) class I-restricted T cell receptors (TcR) differentiate into CD8+ T cells with cytolytic functions. To evaluate the role of CD8 in positive and negative selection during thymic ontogeny, mice rendered CD8-null by gene targeting were bred with three lines of transgenic mice expressing unique MHC class I-restricted TcR. In all three instances CD8 was required for positive selection of MHC class I-restricted transgenic T cells. The efficiency of positive selection decreased in accordance with a reduced level of CD8 expression on thymocytes. Surprisingly, there was a differential requirement for CD8 expression in negative selection of MHC class I-restricted thymocytes, depending on the antigen specificity of TcR. These observations show that CD8 is essential for positive selection but is differentially required for negative selection of MHC class I-restricted T cells. Thus thymic selection, at least for negative selection, can occur in the absence of the CD8 accessory molecule.

Animals↗
PubMed1991

Detection of Streptococcus suis type 2 in tonsils of slaughtered pigs using improved selective and differential media.

New selective and differential media were devised for the isolation and identification of Streptococcus suis type 2. The selective medium (NNCC) agar) was Todd-Hewitt broth containing 1.5% Bactoagar and 5% defibrinated sheep blood with addition of sodium azide (50 micrograms/ml), nalidixic acid (25 micrograms/ml), colistin (12.5 micrograms/ml) and crystal violet (2 micrograms/ml). The differential medium consisted of heart infusion agar and antiserum specific only for S. suis type 2. In a total of 291 pigs tested by a combination of these media, S. suis type 2 was isolated and confirmed from 40 of them (13.7%).

Agar↗
PubMed2004

The close relationship between estimated divergent selection and observed differentiation supports the selective origin of a marine snail hybrid zone.

To study the role of divergent selection in the differentiation of the two morphs in a hybrid zone of the intertidal snail Littorina saxatilis, we compared the strength of the divergent selection acting on a series of shell characters (as estimated by the viability of snails in a reciprocal transplant experiment) with the contribution of these characters to the phenotypic differences between the morphs. We found a close correlation between selection and differentiation, which suggests a cause-effect relationship, i.e. that all present differentiation is the result of past divergent selection. In addition, divergent selection was a very important component of the total natural selection acting on shell measures. These novel results support previous evidence, based on allozyme analysis, of a parapatric origin for this hybrid zone. We discuss possible limitations of this interpretation and the circumstances under which allopatric differentiation would produce the same results. Phenotypic analysis of divergent selection may be a useful method of investigating the evolutionary mechanisms involved in differentiation processes.

Animals↗
PubMed1986

Selective and differential medium for the primary isolation of members of the Proteeae.

A new differential and selective medium for the isolation of members of the Proteeae, PIM (Proteeae isolation medium) agar, was developed and evaluated. The medium relies on the ability of all members of the Proteeae (with the exception of a very few Morganella morganii strains) to produce a dark brown pigment in medium containing DL-tryptophan. An additional differential property, tyrosine degradation, was also demonstrated by the medium. Members of the Proteeae appeared as dark brown colonies with a halo of clearing of fine tyrosine crystals when cultured on PIM agar. Occasional strains of Citrobacter sp. and Pseudomonas aeruginosa may degrade tyrosine, but none has the ability to produce dark brown pigmentation on PIM agar. Quantitative recovery studies showed that the addition of 5 mg of clindamycin per liter suppressed gram-positive bacteria without inhibiting any strains of the Proteeae. The addition of 100 mg of colistin per liter made the medium highly selective for strains of the Proteeae, but approximately 10% of the strains were not isolated, thus making this formulation unsuitable for general surveys of the occurrence of members of the Proteeae. PIM agar should aid the investigation of episodes of cross infection caused by members of the Proteeae and the isolation of the new species of the Proteeae recently described.

Clindamycin↗
PubMed1984

Differential and selective antagonism of the slow-inhibitory postsynaptic potential and slow-excitatory postsynaptic potential by gallamine and pirenzepine in the superior cervical ganglion of the rabbit.

Two cholinergic antagonists, gallamine and pirenzepine, agents that have been shown to bind selectively to different subpopulations of the muscarinic receptor, were found to antagonize selectively and differentially the amplitudes of the slow-inhibitory and slow-excitatory postsynaptic potentials in the superior cervical ganglion of the rabbit. Incubation of ganglia with gallamine resulted in a concentration-dependent suppression of the slow-inhibitory postsynaptic potential. The pharmacological action of gallamine was highly specific. At concentrations which reduced the amplitude of the slow-inhibitory postsynaptic potential by as much as 70-90%, there was no reduction of the amplitudes of the muscarinic slow-excitatory postsynaptic potential, the nicotinic fast-excitatory postsynaptic potential, noncholinergic slow-slow-excitatory postsynaptic potential, or post-stimulus hyperpolarizing afterpotentials. The amplitude of the slow-excitatory postsynaptic potential was actually facilitated in the presence of gallamine, presumably as a result of suppression of the overlapping slow-inhibitory postsynaptic potential. In contrast to the action of gallamine, pirenzepine produced a selective suppression of the amplitude of the slow-excitatory postsynaptic potential. Pirenzepine had very little influence on the amplitude of the slow-inhibitory postsynaptic potential at concentrations sufficient to reduce the amplitude of the slow-excitatory postsynaptic potential by as much as 50%, and had no effect on the amplitudes of the nicotinic fast-excitatory postsynaptic potential or noncholinergic slow-slow-excitatory postsynaptic potential. The evidence presented suggests that multiple muscarinic recognition sites, previously identified by studies of the affinities of pharmacological agents for the muscarinic receptor, may actually be involved in synaptic transmission and functionally coupled to cellular effector mechanisms.

Animals↗
PubMed1997

Identification of new tag sequences with differential and selective recognition properties for the anti-FLAG monoclonal antibodies M1, M2 and M5.

The FLAG peptides DYKDDDDK and MDYKDDDDK are widely used affinity tags. Here we describe new variants of the FLAG peptides which, in direct ELISA, showed selective and differential binding to the commercially available anti-FLAG monoclonal antibodies M1, M2 and M5. Variants of the FLAG peptides were synthesized on polymer-grafted plastic pins, and in an ELISA incubated with mAbs M1, M2 and M5. Among the newly identified tag sequences are those that bind only one of the anti-FLAG mAbs and those that bind only two or all three of the anti-FLAG mAbs. Examples of new tag sequences are MDFKDDDDK (which binds mAb M5 and does not bind mAbs M1 and M2) and MDYKAFDNL (which binds mAb M2 and does not bind mAbs M1 and M5). The sensitivity in direct ELISA of some variants was increased, e.g. using mAb M2 it was found that replacing DDDDK in MDYKDDDDK by AFDNL increased the sensitivity in ELISA at least 10-fold. The activity of this peptide was studied in more detail. In different direct ELISAs, in which MDYKAFDNL was synthesized on polyethylene pins, coated onto polystyrene microtiter plates or onto nitrocellulose paper, the activity of this peptide was similar, i.e. increased at least 10-fold over that of MDYKDDDDK. Remarkably, in competitive ELISA the binding activity of soluble MDYKAFDNL was decreased 10-fold over those of soluble MDYKDDDDK or DYKDDDDK. The results seem to suggest that, in solution, the conformation of MDYKAFDNL is more 'unstructured' compared to its conformation when coated or linked to a carrier. We postulate that the newly described tag sequences may be used as affinity tags to separately detect, quantify and purify multiple co-expressed proteins and/or subunits.

Affinity Labels↗
PubMed1998

Conformer selection and differential restriction of ligand mobility by a plant lectin--conformational behaviour of Galbeta1-3GlcNAcbeta1-R, Galbeta1-3GalNAcbeta1-R and Galbeta1-2Galbeta1-R' in the free state and complexed with galactoside-specific mistletoe lectin as revealed by random-walk and conformational-clustering molecular-mechanics.

To study conformational parameters of ligands before and after complex formation with the galactoside-binding agglutinin of Viscum album L. (VAA) in solution, combined computer-assisted random walk molecular mechanics (RAMM) calculations extended by conformational clustering analysis (CCA), molecular dynamics (MD) simulations as well as two-dimensional rotating-frame nuclear Overhauser effect (ROE) and two-dimensional nuclear Overhauser effect (NOE) spectroscopy NMR experiments were employed. Derivatives of the naturally occurring disaccharides Galbeta1-3GlcNAcbeta1-R and Galbeta1-3GalNAcbeta1-R as well as of a synthetic high-affinity binding partner, i.e. the disaccharide Galbeta1-2Galbeta1-R', were chosen as ligands in this study. The disaccharides displayed inherent flexibility in the valley of the global minimum between phi/psi combinations of (40 degrees/60 degrees) and (40 degrees/-60 degrees). Calculations of the de-N-acetylated sugars revealed that presence of this group did not markedly influence the distribution of low-energy conformers in the phi, psi, epsilon plot. Occupation of side minima at phi/psi (180 degrees/0 degrees) or (0 degrees/180 degrees) is either unlikely or low according to the results of MD simulations and RAMM calculations extended by CCA. Notably, these side minima define conformations which are not stable during a MD simulation. Transitions to other minima occur already a few picoseconds after the start of the simulation. NMR experiments of the free-state ligand confirmed the validity of the data sets obtained by the calculations. Following the description of the conformational space in the free-state NMR experiments were performed for these disaccharides complexed with VAA. They yielded two interresidual contacts for Galbeta1-3GlcNAcbeta1-R and Galbeta1-2Galbeta1-R'. The ligand conformations in the complex did not deviate markedly from those of a minimum conformation in the free state. One- and two-dimensional transferred nuclear Overhauser enhancement (TRNOE) experiments at different mixing times excluded the influence of spin-diffusion effects. When the NOE build-up curves in the three studied cases were compared, the residual mobility of the penultimate carbohydrate unit of Galbeta1-3GalNAcbeta1-R was observed to be higher than that of the respective hexopyranose unit of the other two bound ligands. Due to the availability of the conformational parameters of Galbeta1-2Galbeta1-R' in association with a galectin, namely the beta-galactoside-binding protein from chicken liver, it is remarkable to note that this ligand displays different conformations in the binding sites of either the plant or the animal lectin. They correspond to local energy-minimum conformations in the phi,psi, epsilon plot and substantiate differential conformer selection by these two lectins with identical nominal monosaccharide specificity.

Binding Sites↗
PubMed2005

A theoretical analysis of the selection of differentially expressed genes.

A great deal of recent research has focused on the challenging task of selecting differentially expressed genes from microarray data ("gene selection"). Numerous gene selection algorithms have been proposed in the literature, but it is often unclear exactly how these algorithms respond to conditions like small sample sizes or differing variances. Choosing an appropriate algorithm can therefore be difficult in many cases. In this paper we propose a theoretical analysis of gene selection, in which the probability of successfully selecting differentially expressed genes, using a given ranking function, is explicitly calculated in terms of population parameters. The theory developed is applicable to any ranking function which has a known sampling distribution, or one which can be approximated analytically. In contrast to methods based on simulation, the approach presented here is computationally efficient and can be used to examine the behavior of gene selection algorithms under a wide variety of conditions, even when the number of genes involved runs into the tens of thousands. The utility of our approach is illustrated by comparing three widely-used gene selection methods.

Algorithms↗
PubMed1999

Selective estrogen receptor modulators: tissue selectivity and differential uterine effects.

Selective estrogen receptor modulators (SERMs) are compounds that bind to estrogen receptors and produce estrogen-like (agonist) effects in some tissues and estrogen-blocking (antagonist) effects in other tissues. One of the goals of SERM research has been to develop compounds that provide the potential benefits of estrogen in the skeleton and cardiovascular system, but avoid the negative effects of estrogen in other tissues. Estrogen therapy has been consistently associated with endometrial stimulation, including glandular proliferation, hyperplasia and cancer. In contrast, the presence or degree of endometrial stimulation observed with SERMs varies by compound. The purpose of this review is to differentiate the endometrial effects of compounds that display a SERM-like profile. Molecular mechanisms involving SERM binding to estrogen receptors, preclinical uterine effects in both tissue culture and animal models, and endometrial findings in clinical experience are discussed. There are several SERMs commercially available or in development. The favorable safety profile of raloxifene in the uterus differentiates it from the others. Future SERM development will continue to focus on finding compounds that exhibit minimal endometrial stimulation.

Animals↗
PubMed2006

An analysis of continent-wide patterns of sexual selection in a passerine bird.

Patterns of selection are widely believed to differ geographically, causing adaptation to local environmental conditions. However, few studies have investigated patterns of phenotypic selection across large spatial scales. We quantified the intensity of selection on morphology in a monogamous passerine bird, the barn swallow Hirundo rustica, using 6495 adults from 22 populations distributed across Europe and North Africa. According to the classical Darwin-Fisher mechanism of sexual selection in monogamous species, two important components of fitness due to sexual selection are the advantages that the most attractive males acquire by starting to breed early and their high annual fecundity. We estimated directional selection differentials on tail length (a secondary sexual character) and directional selection gradients after controlling for correlated selection on wing length and tarsus length with respect to these two fitness components. Phenotype and fitness components differed significantly among populations for which estimates were available for more than a single year. Likewise, selection differentials and selection gradients differed significantly among populations for tail length, but not for the other two characters. Sexual selection differentials differed significantly from zero across populations for tail length, particularly in males. Controlling statistically for the effects of age reduced the intensity of selection by 60 to 81%, although corrected and uncorrected estimates were strongly positively correlated. Selection differentials and gradients for tail length were positively correlated between the sexes among populations for selection acting on breeding date, but not for fecundity selection. The intensity of selection with respect to breeding date and fecundity were significantly correlated for tail length across populations. Sexual size dimorphism in tail length was significantly correlated with selection differentials with respect to breeding date for tail length in male barn swallows across populations. These findings suggest that patterns of sexual selection are consistent across large geographical scales, but also that they vary among populations. In addition, geographical patterns of phenotypic selection predict current patterns of phenotypic variation among populations, suggesting that consistent patterns of selection have been present for considerable amounts of time.

Age Factors↗
PubMed2004

The Global Error Assessment (GEA) model for the selection of differentially expressed genes in microarray data.

MOTIVATION: Microarray technology has become a powerful research tool in many fields of study; however, the cost of microarrays often results in the use of a low number of replicates (k). Under circumstances where k is low, it becomes difficult to perform standard statistical tests to extract the most biologically significant experimental results. Other more advanced statistical tests have been developed; however, their use and interpretation often remain difficult to implement in routine biological research. The present work outlines a method that achieves sufficient statistical power for selecting differentially expressed genes under conditions of low k, while remaining as an intuitive and computationally efficient procedure. RESULTS: The present study describes a Global Error Assessment (GEA) methodology to select differentially expressed genes in microarray datasets, and was developed using an in vitro experiment that compared control and interferon-gamma treated skin cells. In this experiment, up to nine replicates were used to confidently estimate error, thereby enabling methods of different statistical power to be compared. Gene expression results of a similar absolute expression are binned, so as to enable a highly accurate local estimate of the mean squared error within conditions. The model then relates variability of gene expression in each bin to absolute expression levels and uses this in a test derived from the classical ANOVA. The GEA selection method is compared with both the classical and permutational ANOVA tests, and demonstrates an increased stability, robustness and confidence in gene selection. A subset of the selected genes were validated by real-time reverse transcription-polymerase chain reaction (RT-PCR). All these results suggest that GEA methodology is (i) suitable for selection of differentially expressed genes in microarray data, (ii) intuitive and computationally efficient and (iii) especially advantageous under conditions of low k. AVAILABILITY: The GEA code for R software is freely available upon request to authors.

Algorithms↗
PubMed1985

Selective and differential medium for detecting Clostridium botulinum.

A selective and differential growth medium was developed for detection of Clostridium botulinum types A, B, and F. The medium consisted of peptone-glucose-yeast extract agar supplemented with cycloserine, 250 micrograms/ml; sulfamethoxazole, 76 micrograms/ml; and trimethoprim, 4 micrograms/ml as selective inhibitors and various types and levels of botulinal antibodies for type differentiation in the immunodiffusion reaction. Growth of proteolytic types of C. botulinum were not affected by the incorporation of the selective agents, but some nonproteolytic types were suppressed. Cross-reactions between types A and B were visually distinguishable, whereas cross-reactions between type F and Clostridium sporogenes did not occur at the optimum antibody titer. Optimum antibody titer varied with toxin type. The proposed selective differential medium should be valuable in isolating and typing of proteolytic C. botulinum types A, B, and F from samples containing mixed microbial populations.

Antitoxins↗
PubMed2002

Nitric oxide preferentially induces type 1 T cell differentiation by selectively up-regulating IL-12 receptor beta 2 expression via cGMP.

Nitric oxide plays an important role in immune regulation. We have shown that although high concentrations of NO generally were immune-suppressive, low concentrations of NO selectively enhanced the differentiation of T helper (Th)1 cells but not Th2 cells. This finding provided an explanation for the crucial role of NO in defense against intracellular pathogens. However, the mechanism for the selective induction of Th1 cells was unknown. We report here that at low concentrations, NO activates soluble guanylyl cyclase, leading to the up-regulation of cGMP, which selectively induces the expression of IL-12 receptor beta2 but has no effect on IL-4 receptor. Because IL-12 and IL-4 are the key cytokines for induction of Th1 and Th2 cells, respectively, these results, therefore, provide the mechanism for the selective action of NO on T cell subset differentiation. Furthermore, this selectivity also applies to CD8+ cytotoxic and human T cells and, thus, demonstrates the general implication of this observation in immune regulation. Our results also provide an example of the regulation of cytokine receptor expression by NO. The selectivity of such action via cGMP suggests that it is amenable to therapeutic intervention.

Animals↗
PubMed1996

[Simultaneous isolation of MRSA and Pseudomonas aeruginosa using a novel selective and differential PMAC agar].

PMAC agar, a novel, selective and differential medium has been developed and was subjected for evaluation of its selective and differential capability of methicillin resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa from other bacteria such as Bacillus, Micrococcus, Gram-negative bacteria and drug resistant ones. Growth of MRSA and P. aeruginosa on PMAC agar was facilitated and their colonies were easily differentiated. Colonies of MRSA after 24 approximately 48 h incubation at 35 degrees C were small (2 to 4 mm in diameter), smooth and egg-yolk reaction positive. On the other hand, P. aeruginosa with pigment production (pyocianin, fluorescin or pyomelanin) formed large (2.5 to 7.0 mm in diameter), brownish black or brown colonies with a creamy edge. PMAC agar did not allow to grow unwanted bacteria tested except certain species formerly classified to Pseudomonas such as Burkholderia and Stenotrophomonas. However multi-drug resistant strains such as Enterobacter cloacae, Serratia marcescens and Acinetobacter calcoaceticus formed extremely small colonies. PMAC agar is recommended as a novel, useful medium for isolation, differentiation and presumptive identification of MRSA and P. aeruginosa from clinical and environmental sources.

Bacteriological Techniques↗
PubMed1990

Efficiency of selection strategies for halothane-negative gene.

Use of a method to estimate the frequency of the halothane-negative allele in boars is illustrated for different sampling schemes for boar testing programs and for testing within closed breeding populations. This method uses information not only on the individual, but also on all mates and relatives including parents, siblings and offspring. Accuracy of the estimates of the allelic frequency in boars was measured through use of Monte Carlo simulation. The selection differential in real frequency of the halothane-negative allele when boars were selected on estimated allelic frequency was used as the criterion for accuracy. In the progeny testing situation, phenotypes of base boars and one generation of offspring were available. The average selection differentials with 90% selection (i.e., culling 10% of boars on estimated allelic frequency) when 2 and 10 litters of two boars each were tested were .017 and .044 in base boars and .013 and .025 in the offspring. The value of the boar's own phenotype was small. Higher selection differentials were found in the closed herd situation, where data on two generations were available. The selection differential in base boars when 10 litters were tested increased from .046 to .066 when the proportion of boars selected decreased from 90% to 50%. No improvement in selection differential with proportion selected was found in the progeny testing situation. Intense selection is most effective when the number of litters per boar is large and data over several generations are used. The estimation procedure for allelic frequencies in boars should improve current screening and selection programs to reduce halothane sensitivity in pigs.

Alleles↗
PubMed1985

Development and evaluation of a flow-dividing unit for differential ventilation and selective PEEP.

Differential ventilation with selective positive end-expiratory pressure (PEEP) was studied in a two-compartment lung model, using one ventilator and a flow-dividing unit consisting of inspiratory flow resistors and an inspiratory threshold valve. The compliance of each lung compartment was varied between 0.15 and 0.23 1 X kPa-1 and the resistance was varied from 0 to 3.5 kPa X 1(-1) X s. The minute volume was 12 1 and the respiratory frequency 12/min, with an inspiratory:expiratory ratio of 1:2. An even distribution of ventilation to the two lung compartments was obtained with the inspiratory flow resistors or the threshold valve under all conditions studied. However, a stepwise increase in the inspiratory resistance of one lung compartment from 1.0 to 2.5 or from 2.5 to 3.5 kPa X 1(-1) X s required readjustment of the inspiratory flow resistor to achieve an even distribution of ventilation, whereas the inspiratory threshold valve needed no readjustment. Large differences in the inspiratory impedance of the two lung compartments caused asynchronous gas delivery when the ventilation distribution was adjusted by means of the flow resistors. Use of the threshold valve resulted in synchronous gas delivery. The flow-dividing unit consists of non-active elements and can thus be connected to any ventilator.

Humans↗