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PubMed2003

Results from nine generations of selection for increased litter size in swine.

Direct selection for increased litter size was done for nine generations. The select line consisted of approximately 15 sires and 60 dams per generation, and selection was based on estimated breeding values for number of live pigs. A control line of approximately 10 sires and 30 dams was maintained with stabilizing selection. Heritabilities estimated in the select line using restricted maximal likelihood procedures, daughter-dam regression within sires, and half-sib analysis were 0.01, 0.04, and 0.00 for number of pigs born alive (NBA) and 0.02, 0.16, and 0.00 for total born per litter (TB). Corresponding estimates for the control line were 0.01, 0.06, and 0.23 and 0.02, 0.07, and 0.09 for NBA and TB, respectively. Realized heritabilities for NBA from multiple regression were 0.09 +/- 0.08 in the select line and 0.11 +/- 0.166 in the control line. Heritability estimated from regression of differences in response between lines on differences in cumulative selection differentials was 0.13 +/- 0.07. At Generation 9, litter sizes, estimated breeding values, and cumulative selection differentials were 0.86 (P < 0.05), 0.63 (P < 0.01), and 9.05 (P < 0.01) pigs larger for the select line than for the control line. Phenotypic differences between lines for TB, adjusted backfat (BF), and days to 104 kg (DAYS) were not significant. Genetic trends in the select line were 0.053 +/- 0.002 pigs/yr for NBA, 0.054 +/- 0.013 mm/yr for BF, and 0.398 +/- 0.110 d/yr for DAYS. Corresponding phenotypic trends were 0.145 +/- 0.051 pigs/yr, -0.012 +/- 0.089 mm per yr, and 0.307 +/- 0.278 d/yr, respectively. Genetic trends in the control line were -0.026 +/- 0.004 pigs/yr for NBA, 0.026 +/- 0.022 mm/yr for BF, and -0.532 +/- 0.182 d/yr for DAYS. Corresponding phenotypic trends were 0.001 +/- 0.085 pigs/yr, -0.043 +/- 0.147 mm/yr, and -0.519 +/- 0.462 d/yr, respectively. Litter size can be increased by direct selection using breeding values estimated from an animal model, in conjunction with rearing selected gilts in litters of 10 pigs or less.

Adipose Tissue↗
PubMed1987

Selection by differential molecular survival: a possible mechanism of early chemical evolution.

A model is proposed to account for selective chemical evolution, progressing from a relatively simple initial set of abiotic synthetic phenomena up to the elaborately sophisticated processes that are almost certainly required to produce the complex molecules, such as replicatable RNA-like oligonucleotides, needed for a Darwinian form of selection to start operating. The model makes the following assumptions: (i) that a small number of micromolecular substances were present at high concentration; (ii) that a random assembly mechanism combined these molecules into a variety of multimeric compounds comprising a wide repertoire of rudimentary catalytic activities; and (iii) that a lytic system capable of breaking down the assembled products existed. The model assumes further that catalysts supplied with substrates were significantly protected against breakdown. It is shown that, by granting these assumptions, an increasingly complex network of metabolic pathways would progressively be established. At the same time, the catalysts concerned would accumulate selectively to become choice substrates for elongation and other modifications that could enhance their efficiency, as well as their survival. Chemical evolution would thus proceed by a dual process of metabolic extension and catalytic innovation. Such a process should be largely deterministic and predictable from initial conditions.

Biochemical Phenomena↗
PubMed2002

An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences.

Positive selection or adaptive evolution is thought to be responsible, at least some of the time, for the rapid accumulation of advantageous changes in protein-coding genes. The origin of new enzymatic functions, erection of barriers to heterospecific fertilization, and evasion of host response by pathogens, among other things, are thought to be instances of adaptive evolution. Detecting positive selection in protein-coding genes is fraught with difficulties. Saturation for sequence change, codon usage bias, ephemeral selection events and differential selective pressures on amino acids all contribute to the problem. A number of solutions have been proposed with varying degrees of success, however they suffer from limitations of not being accurate enough or being prohibitively computationally intensive. We have developed a character-based method of identifying lineages that undergo positive selection. In our method we assess the possibility that for each internal branch of a phylogenetic tree an event occurred that subsequently gave rise to a greater number of replacement substitutions than might be expected. We classify these replacement substitutions into two categories - whether they subsequently became invariable or changed again in at least one descendent lineage. The former situation indicates that the new character state is under strong selection to preserve its new identity (directional selection), while the latter situation indicates that there is a persistent pressure to change identity (non-directional selection). The method is fast and accurate, easy to implement, sensitive to short-lived selection events and robust with respect to sampling density and proportion of sites under the influence of positive selection.

Algorithms↗
PubMed1997

Stem cells in prostatic epithelia.

The normal prostate is, structurally and functionally, a highly complex glandular tissue in which populations of epithelial and stromal cells interact, one with the other, and are under a constant state of proliferation, differentiation, elimination and selective secondary replenishment so that functional integrity of the tissue is maintained. The ability of normal prostatic tissue to maintain its structure and function is dependent upon retention of cells, generally regarded as 'stem cells', which are able to respond by proliferation and selective differentiation within a wide range of phenotypic alternatives. With respect to cells in the epithelial compartment, replenishment is possible at several levels from within distinct pathways of normal cellular differentiation. It is now appreciated that fully differentiated prostatic epithelial cells retain a far greater degree of phenotypic 'plasticity' than was earlier apparent from morphological examination of the intact tissue. This inherent plasticity, coupled with the ability of the intact tissue to respond to diverse environmental (particularly humoral) stimuli by regenerating a wide and divergent spectrum of functional prostatic epithelial phenotypes is its strength--but also its weakness. Disturbance and distortion of the homeostatic regulatory mechanisms, whether physical or humoral, which control the normal sequence of epithelial proliferation, differentiation and elimination exposes these cells, particularly multipotent 'stem cells', to an increased probability of genetic change, thus resulting in either transient, or permanent, neoplastic transformation.

Basement Membrane↗
PubMed2001

cDNA array analysis of cag pathogenicity island-associated Helicobacter pylori epithelial cell response genes.

Helicobacter pylori strains containing the cag pathogenicity island (PAI) induce NF-kappaB activation and interleukin-8 secretion in gastric epithelial cells. The aim of this study was to investigate changes in epithelial gene expression induced by cag PAI-positive and -negative strains of H. pylori using high-density cDNA array hybridization technology. Radio-labeled cDNA prepared from H. pylori-infected Kato 3 gastric epithelial cells was hybridized to high-density cDNA arrays to identify changes in epithelial gene expression compared to noninfected controls. In vivo expression of selected, differentially expressed genes was examined by reverse transcription-PCR analysis of H. pylori-positive and -negative gastric mucosa. Screening of ca. 57,800 cDNAs identified 208 known genes and 48 novel genes and/or expressed sequence tags of unknown function to be differentially expressed in Kato 3 cells following H. pylori infection. Marked differences in gene expression profiles were observed following cag PAI-positive and cag PAI-negative infection with 15 novel cDNAs and 92 known genes being differentially expressed. H. pylori was found to change the expression of genes encoding growth factors and cytokine/chemokines and their receptors, apoptosis proteins, transcription factors and metalloprotease-disintegrin proteins (ADAMs), and tissue inhibitors of metalloproteinases. Gastric differential expression of selected known genes (amphiregulin and ADAM 10) and a novel gene (HPYR1) was confirmed in vivo in patients with H. pylori infection. Confirmation of the in vivo expression of selected genes demonstrates the usefulness of this approach for investigating pathogen-induced changes in host gene expression.

ADAM Proteins↗
PubMed1979

A genetic study of cryptorchidism and scrotal hernia in pigs.

The genetic parameters of cryptorchidism and scrotal hernia were estimated. The heritability of liability to cryptorchidism identified at birth was about 0.5 and that identified to be normal at birth, but recognized to be abnormal later was almost zero. The heritabilities of scrotal hernia estimated in two herds were 0.65 and 0.86. The genetic correlation between these two defects was 0.20. An equation for calculating selection differentials for family selection was derived and expected changes of incidence resulting from individual, full-sib and half-sib family selection calculated. Practical culling plans were discussed from the aspect of selection response and possible culling rate.

Animals↗
PubMedDate not supplied

Optimizing purebred selection for crossbred performance using QTL with different degrees of dominance.

A method was developed to optimize simultaneous selection for a quantitative trait with a known QTL within a male and a female line to maximize crossbred performance from a two-way cross. Strategies to maximize cumulative discounted response in crossbred performance over ten generations were derived by optimizing weights in an index of a QTL and phenotype. Strategies were compared to selection on purebred phenotype. Extra responses were limited for QTL with additive and partial dominance effects, but substantial for QTL with over-dominance, for which optimal QTL selection resulted in differential selection in male and female lines to increase the frequency of heterozygotes and polygenic responses. For over-dominant QTL, maximization of crossbred performance one generation at a time resulted in similar responses as optimization across all generations and simultaneous optimal selection in a male and female line resulted in greater response than optimal selection within a single line without crossbreeding. Results show that strategic use of information on over-dominant QTL can enhance crossbred performance without crossbred testing.

Alleles↗
PubMed2006

Differentiation of selected Salmonella enterica serovars by Fourier transform mid-infrared spectroscopy.

Salmonella enterica serovars include pathogens responsible for high numbers of foodborne salmonellosis. Fourier transform infrared (FT-IR) spectroscopy can be used to rapidly and accurately identify microorganisms based on unique spectra of bacterial cell components. The objectives of this study were to discriminate closely related Salmonella enterica serovars by using FT-IR spectroscopy and multivariate analysis and to compare the performance of three techniques for differentiating among Salmonella serovars. Selected serovars of S. enterica were streaked onto plate count agar and incubated (37 degrees C, 24 h). Isolated colonies were suspended in phosphate buffer or 50% ethanol (10 microL). Suspensions were placed on (1) ZnSe crystals for transmission, (2) disposable polyethylene membranes (DPM) for transmission, and (3) diamond crystal plate for attenuated total reflectance (ATR) analyses; all samples were dried under vacuum. Classification models, soft independent modeling of class analogy (SIMCA), from derivatized infrared spectra (1300-900 cm(-1)), discriminated among Salmonella serovars presumably attributed to cell's lipopolysaccharides (1000-980 cm(-1)). Samples on DPM required high cell density for reliable spectra. High-quality spectra were obtained when a single colony was suspended in ethanol or buffer and mounted on ZnSe crystals for transmission or diamond plate for ATR analysis. Prediction of unknowns, representative of serovars used to construct classification models, showed that all techniques were suitable for the rapid and accurate differentiation of Salmonella serovars.

Algorithms↗
PubMed1984

A new selective and differential agar medium for Escherichia coli and coliform organisms.

An enriched lauryl sulphate-aniline blue agar medium which is selective for Escherichia coli and coliform organisms is described. From faecal samples, the medium gave higher counts of colonies producing acid from lactose than media containing bile salts. From contaminated water and food samples, the medium gave comparable or higher counts of colonies identified as E. coli than standard media. Colonies of E. coli were more readily differentiated from those of other coliform organisms.

Agar↗
PubMedDate not supplied

Hypothermic effect of ethanol in mice selected for differential sleep-time response to pentobarbital.

The hypothermic action of ethanol was investigated in genetically distinct lines of mice selected for sleep-time response to pentobarbital for six generations. Ethanol (3 g/kg, intraperitoneally) was administered to alcohol-naive males and females from each of the unselected control, long-, and short-sleep mouse lines. Rectal temperatures were measured immediately before, and at 15, 30, 60, 90, 120, and 240 min after ethanol injection. Eight female and eight male mice from each line were sacrificed at each time point, and trunk blood was collected for plasma ethanol analysis. The results show that short-sleep mice were less hypothermic (p < 0.05) compared to long-sleep mice at 15 and 30 min after ethanol administration. However, plasma ethanol concentrations were not significantly different between the mouse lines at any time point. Therefore, the line-dependent differential ethanol-induced hypothermia observed may be a result of differences in "brain sensitivity" rather than in the rates of ethanol metabolism among the mouse lines.

Animals↗
PubMed2005

Extracellular loop 3 (EL3) and EL3-proximal transmembrane helix 7 of the mammalian type I and type II gonadotropin-releasing hormone (GnRH) receptors determine differential ligand selectivity to GnRH-I and GnRH-II.

Mammalian type I and II gonadotropin-releasing hormone (GnRH) receptors (GnRHRs) show differential ligand preference for GnRH-I and GnRH-II, respectively. Using a variety of chimeric receptors based on green monkey GnRHR-2 (gmGnRHR-2), a representative type II GnRHR, and rat GnRHR, a representative type I GnRHR, this study elucidated specific domains responsible for this ligand selectivity. A chimeric gmGnRHR-2 with the extracellular loop 3 (EL3) and EL3-proximal transmembrane helix 7 (TMH7) of rat GnRHR showed a great increase in ligand sensitivity to GnRH-I but not to GnRH-II. Point-mutation studies indicate that four amino acids, Leu/Phe(7.38), Leu/Phe(7.43), Ala/Pro(7.46), and Pro/Cys(7.47) in TMH7 are critical for ligand selectivity as well as receptor conformation. Furthermore, a combinatory mutation (Pro(7.31)-Pro(7.32)-Ser(7.33) motif to Ser-Glu-Pro in EL3 and Leu(7.38), Leu(7.43), Ala(7.46), and Pro(7.47) to those of rat GnRHR) in gmGnRH-2 exhibited an approximately 500-fold increased sensitivity to GnRH-I, indicating that these residues are critical for discriminating GnRH-II from GnRH-I. [Trp(7)]GnRH-I and [Trp(8)]GnRH-I but not [His(5)]GnRH-I exhibit a higher potency in activating wild-type gmGnRHR-2 than native GnRH-I, indicating that amino acids at positions 7 and 8 of GnRHs are more important than position 5 for differential recognition by type I and type II GnRHRs. As a whole, these data suggest a molecular coevolution of ligands and their receptors and facilitate the understanding of the molecular interaction between GnRHs and their cognate receptors.

Amino Acid Sequence↗
PubMed2001

Tumor necrosis factor alpha and interleukin 11 secreted by malignant breast epithelial cells inhibit adipocyte differentiation by selectively down-regulating CCAAT/enhancer binding protein alpha and peroxisome proliferator-activated receptor gamma: mechanism of desmoplastic reaction.

The dense layer of fibroblasts that accumulate around malignant breast epithelial cells (i.e., desmoplastic reaction) arises from the breast adipose tissue and provides structural and biochemical support for breast cancer. We report herein a number of epithelial-stromal interactions responsible for desmoplastic reaction in breast cancer using cultured 3T3-L1 murine fibroblasts and human adipose fibroblasts, which can be activated with a mixture of hormones to differentiate to mature adipocytes. Adipocyte differentiation was inhibited by coculturing fibroblasts with various breast cancer cell lines (T47D, MCF-7, SSC202, SSC78, and SSC30) completely or by breast cancer cell conditioned media in a dose-dependent manner; on the other hand, adipocyte differentiation was not inhibited by coculturing with normal human primary mammary epithelial cell conditioned medium. This tumor effect was eliminated using neutralizing antibodies against tumor necrosis factor (TNF)-alpha or interleukin (IL)-11. TNF-alpha and IL-11 levels were 2.5-3 times higher in T47D conditioned medium compared with control medium, and TNF-alpha transcripts were detectable in T47D but not in 3T3-L1 cells in culture, indicating that the malignant epithelial cell is the major site of cytokine production. This was confirmed in vivo in mastectomy specimens, where immunoreactive TNF-alpha and IL-11 were readily detectable in malignant epithelial cells but not in the majority of the surrounding fibroblasts. Adipocyte differentiation is mediated by the expression of a cascade of adipogenic transcription factors, including CCAAT/enhancer binding protein (C/EBP)beta, C/EBPdelta, peroxisome proliferator-activated receptor (PPAR)gamma and C/EBPalpha. C/EBPalpha and PPARgamma are essential for this process. We demonstrated by Northern analysis that exposure of activated 3T3-L1 cells to T47D cell conditioned medium strikingly decreased the levels of PPARgamma and C/EBPalpha transcripts and increased the levels of C/EBPbeta and C/EBPdelta transcripts. In these 3T3-L1 cells, inhibition of differentiation was also confirmed by markedly suppressed levels of aP2 mRNA, which is an adipocyte-specific gene. These in vitro observations were confirmed in sections of human malignant breast tumors, where immunoreactive C/EBPalpha was readily detectable in adipose flbroblasts distant to the tumor but not in intratumoral fibroblasts. Treatment of 3T3-L1 cells with T47D cell conditioned medium or TNF-alpha changed neither the numbers of cells in G0-G1, S, and G2 phases nor the rate of [3H]thymidine incorporation, thus ruling out a proliferative effect of malignant cells on the surrounding fibroblasts. In summary, desmoplastic reaction primarily occurs via the action of cytokines (TNF-alpha and IL-11) secreted by the malignant epithelial cells to inhibit differentiation of adipose fibroblasts to mature adipocytes. This tumor-induced block in adipocyte differentiation is mediated by the selective inhibition of expression of the essential adipogenic transcription factors, i.e., PPARgamma and C/EBPalpha.

3T3 Cells↗
PubMed1985

Social class mortality differentials: artefact, selection or life circumstances?

Data from 10 years follow up of mortality in the OPCS Longitudinal Study are used to relate deaths of men in 1976-81 to their social class as recorded by the 1971 census. Explanations of social class mortality differentials are critically reviewed in the light of these new data. The similarity between the class differentials observed for men aged 15-64 years in this study and those reported in the 1970-2 Decennial Supplement on Occupational Mortality indicate that the published gradients were not in fact grossly distorted by numerator denominator biases. Distortions to gradients observed in the early years of the longitudinal study and ascribed to selective health related mobility out of employment from the principal social classes to the permanently sick had largely worn off after five years of follow up. Sharp gradients at ages over 75 years, similar to those at younger ages, suggest that, for men aged over 50 years, selective health related mobility between social classes does not contribute to differentials in mortality.

Adolescent↗
PubMed1998

Sensitivity to cocaine and amphetamine among mice selectively bred for differential cocaine sensitivity.

Selective breeding of mice for differences in response to a drug offers a powerful means for testing hypotheses regarding underlying mechanisms and relationships between drug-induced behaviors. Starting from a heterogeneous stock of mice, we have selectively bred lines of mice for extreme differences in their locomotor response to 10 mg/kg cocaine HCl. Selection pressure has been maintained for 12 generations and has resulted in two cocaine sensitive (CAHI) and two cocaine insensitive (CALO) lines. Across the generations of selection, the CAHI lines showed progressively greater amounts of cocaine-induced locomotion, with mice from the S12 generation traveling over 21,000 cm/30 min. following 10 mg/kg cocaine. The CALO lines, in contrast, did not substantially diverge from control values until the S8 generation. By generation 12, however, the LO lines traveled no further following 10 mg/kg cocaine (7000 cm/30 min), than they did following an initial saline injection. Cocaine and amphetamine dose-response analyses were conducted on drug-naive mice from the tenth generation. The CAHI lines were extremely sensitive to the locomotor activating effects of all doses of cocaine, displaying from 2- to 6-fold greater amounts of cocaine-induced locomotion than the CALO lines. The CALO lines, in contrast, were completely insensitive to the psychomotor stimulant effects of cocaine. The CAHI lines were also more sensitive to the locomotor activating effects of amphetamine. Both lines showed dose-dependent amphetamine-induced locomotion that peaked at 3 mg/kg. However, at all doses, the CAHI lines showed a 2- to 4-fold greater amount of locomotion than CALO lines. Thus, the sensitivity to cocaine developed through selection using a single dose of cocaine has generalized to a range of doses of cocaine and to at least one other psychostimulant.

Amphetamine↗
PubMed1998

Herpes simplex virus type 1 inhibits in vitro differentiation and selected functions of human blood-derived monocytes.

We have studied the effect of herpes simplex virus type 1 (HSV1) infection on in vitro differentiation of blood-derived human monocytes into macrophages using morphological, functional and biochemical parameters that alter during macrophage differentiation. Purified preparations of HSV modified the monocyte-macrophage differentiation, in spite of the fact that the virus did not replicate in monocytes. Disappearance of expression of a monocyte-specific surface antigen and the typical development of morphological appearance were delayed in HSV- infected cells. Production of the lysosomal enzyme acid phosphatase, which normally increases during differentiation, was also reduced in infected cells. Transcription of the oncogenes c-myc and c-fos, and the Hsp70 gene was modified in cells from some donors but not in other cell preparations. Possible mechanisms of these effects are discussed.

Acid Phosphatase↗
PubMed2005

ISER: selection of differentially expressed genes from DNA array data by non-linear data transformations and local fitting.

SUMMARY: This report describes an algorithm (intensity-dependent selection of expression ratios or ISER) developed to analyse DNA array data by optimizing the selection of genes with the most significant variations in expression amongst two RNA samples. The algorithm is designed for use when little or no replication of array hybridizations is available.

Algorithms↗
PubMed1988

Transduction of Escherichia coli in soil.

Bacteriophage P1-mediated generalized transduction of Escherichia coli K-12 was assessed in nonsterile soil. Auxotrophic recipient cells (thr- leu- thi- rpsL) were incubated in a sandy and a silty clay loam soil, and the transducing phage lysates from prototrophic strains carrying transposon 10(Tn10) in either purE or aroL regions were added. At intervals, the bacterial populations derived from the soils were plated on selective-differential media to enumerate prototrophic (thr+, leu+, or Tcr) transductants. Of 100 bacterial isolates obtained on the selective-differential media, 58 (14 thr+; 11, leu+; 33 Tcr) were confirmed E. coli transductants. The frequency of transduction in soil was ca. 10(-6). These data demonstrate the potential use of bacteriophage P1 to genetically manipulate E. coli in situ.

Escherichia coli↗