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S L Johnson

Publications and source records attributed to S L Johnson.

At least 73 records · Page 4Linked to original sources

Centromere-linkage analysis and consolidation of the zebrafish genetic map.

The ease of isolating mutations in zebrafish will contribute to an understanding of a variety of processes common to all vertebrates. To facilitate genetic analysis of such mutations, we have identified DNA polymorphisms closely linked to each of the 25 centromeres of zebrafish, placed centromeres on the linkage map, increased the number of mapped PCR-based markers to 652, and consolidated the number of linkage groups to the number of chromosomes. This work makes possible centromere-linkage analysis, a novel, rapid method to assign mutations to a specific linkage group using half-tetrads.

Animals↗

Cdc53p acts in concert with Cdc4p and Cdc34p to control the G1-to-S-phase transition and identifies a conserved family of proteins.

Regulation of cell cycle progression occurs in part through the targeted degradation of both activating and inhibitory subunits of the cyclin-dependent kinases. During G1, CDC4, encoding a WD-40 repeat protein, and CDC34, encoding a ubiquitin-conjugating enzyme, are involved in the destruction of these regulators. Here we describe evidence indicating that CDC53 also is involved in this process. Mutations in CDC53 cause a phenotype indistinguishable from those of cdc4 and cdc34 mutations, numerous genetic interactions are seen between these genes, and the encoded proteins are found physically associated in vivo. Cdc53p defines a large family of proteins found in yeasts, nematodes, and humans whose molecular functions are uncharacterized. These results suggest a role for this family of proteins in regulating cell cycle proliferation through protein degradation.

Amino Acid Sequence↗

Microsatellite-centromere mapping in the zebrafish (Danio rerio).

Ten (CA)n microsatellite simple sequence repeat (SSR) markers, 1, 2, 12, 14, 16, 18, 20, 22, 26, and 29, were used to show high chiasma interference and to determine centromere-marker map distances in the zebrafish (Danio rerio). Of these, SSR 12 exhibited no recombinant tetratypes among 175 half-tetrad embryos, placing this marker within 1 cM of the centromere of Linkage Group XVII. Fractions of heterozygous half-tetrads for the remaining nine markers ranged from 0.64 to 0.89. Of these, six recombinant fractions were more than 0.67 (P < 0.05), indicating strong chiasma interference during female meiosis in the zebrafish. Consistent with previous mapping data, SSRs 2 and 20 of Linkage Group VI were tightly linked. Half-tetrad analysis will allow the mapping of the remaining centromeres and may be useful in the mapping of new genes and mutations in the zebrafish.

Animals↗

Genetic control of adult pigment stripe development in zebrafish.

Adult zebrafish stripes are formed from stripes of gold iridophores alternating with stripes of black melanocytes lying beneath silver stripes. Analysis of defects in pigment pattern development caused by sparse (spa, rose (ros), and leopard (leo) single and double mutant combinations suggests that spa+ and ros+ functions are required for development of separate populations of pigment cells in the adult and that leo+ functions to control assembly of melanocytes into stripes. Thus, between 2 and 3 weeks of zebrafish development, spa-dependent melanocytes differentiate throughout the flank, followed by leo-dependent assembly of these cells into stripes. Beginning at 3 weeks of development, a distinct ros-dependent population of melanocytes differentiates in the stripe. Both early and late differentiating melanocytes then affect the formation of the silver stripes, ensuring registration of melanocyte and iridophore stripes.

Animals↗

Life events and bipolar disorder: implications from biological theories.

Although a number of studies suggest that stressful life events play a role in bipolar disorder, methodological flaws impose serious limitations on this literature. Nonetheless, better designed studies indicate that life events influence the course of bipolar disorder. Little is known, however, about the nature of events that are of particular importance to this disorder. Given the strong biological vulnerability and the unique clinical aspects of bipolar disorder, certain forms of stress may have stronger interactions with vulnerability characteristics. Three major biological theories of bipolar disorder are discussed, with particular attention to their implications for investigations of life events. Although tenuous, these models suggest that greater attention needs to be paid to particular dimensions of life events and the course of disorder.

Bipolar Disorder↗

Physical activity and energy requirements.

Differences in physical activity represent the largest source of variability in energy requirements, both within and between individuals. Chronic changes in physical activity can produce chronic changes in energy requirements that, if not compensated for, can lead to changes in the level at which body weight and body composition are maintained over time. We present a model that can serve as a framework for understanding how energy and macronutrient balance are maintained in steady state conditions, and for illustrating the potential effect of a change in physical activity on these steady state conditions and on energy requirements. According to the model, a chronic change in physical activity forces changes in other aspects of energy and substrate utilization so that a steady state condition can be reestablished. The net effects of the change in physical activity on energy requirements will depend on how and over what period of time these new steady states are reached. Although we cannot at present predict, for any individual, the precise effect of changes in physical activity on energy requirements and on body weight and composition, our model provides a framework for further study of the factors that can influence energy requirements.

Body Weight↗

Half-tetrad analysis in zebrafish: mapping the ros mutation and the centromere of linkage group I.

Analysis of meiotic tetrads is routinely used to determine genetic linkage in various fungi. Here we apply tetrad analysis to the study of genetic linkage in a vertebrate. The half-tetrad genotypes of gynogenetic diploid zebrafish produced by early-pressure (EP) treatment were used to investigate the linkage relationships of two recessive pigment pattern mutations, leopard (leo) and rose (ros). The results showed that ros is tightly linked to its centromere and leo maps 31 cM from its centromere. Analysis of half-tetrads segregating for ros and leo in repulsion revealed no homozygous ros individuals among 32 homozygous leo half-tetrads--i.e., a parental ditype (PD) to nonparental ditype (NPD) ratio of 32:0. This result shows that ros is linked to leo, a mutation previously mapped to Linkage Group I. Investigation of PCR-based DNA polymorphisms on Linkage Group I confirmed the location of ros near the centromere of this linkage group. We propose an efficient, generally useful method to assign new mutations to a linkage group in zebrafish by determining which of 25 polymerase chain reaction (PCR)-based centromere markers shows a significant excess of PD to NPD in half-tetrad fish.

Animals↗

Temperature-sensitive mutations that cause stage-specific defects in Zebrafish fin regeneration.

When amputated, the fins of adult zebrafish rapidly regenerate the missing tissue. Fin regeneration proceeds through several stages, including wound healing, establishment of the wound epithelium, recruitment of the blastema from mesenchymal cells underlying the wound epithelium, and differentiation and outgrowth of the regenerate. We screened for temperature-sensitive mutations that affect the regeneration of the fin. Seven mutations were identified, including five that fail to regenerate their fins, one that causes slow growth during regeneration, and one that causes dysmorphic bumps or tumors to develop in the regenerating fin. reg5 mutants fail to regenerate their caudal fins, whereas reg6 mutants develop dysmorphic bumps in their regenerates at the restrictive temperature. Temperature-shift experiments indicate that reg5 and reg6 affect different stages of regeneration. The critical period for reg5 occurs during the early stages of regeneration before or during establishment of the blastema, resulting in defects in subsequent growth of the blastema and failure to differentiate bone-forming cells. The critical period for reg6 occurs after the onset of bone differentiation and during early stages of regenerative outgrowth. Both reg5 and reg6 also show temperature-sensitive defects in embryonic development or in ontogenetic outgrowth of the juvenile fin.

Animals↗

Differential induction of four msx homeobox genes during fin development and regeneration in zebrafish.

To study the genetic regulation of growth control and pattern formation during fin development and regeneration, we have analysed the expression of four homeobox genes, msxA, msxB, msxC and msxD in zebrafish fins. The median fin fold, which gives rise to the unpaired fins, expresses these four msx genes during development. Transcripts of the genes are also present in cells of the presumptive pectoral fin buds. The most distal cells, the apical ectodermal ridge of the paired fins and the cleft and flanking cells of the median fin fold express all these msx genes with the exception of msxC. Mesenchymal cells underlying the most distal cells express all four genes. Expression of the msx genes in the fin fold and fin buds is transient and, by 3 days after fertilization, msx expression in the median fin fold falls below levels detectable by in situ hybridization. Although the fins of adult zebrafish normally have levels of msx transcripts undetectable by in situ hybridization, expression of all four genes is strongly reinduced during regeneration of both paired and unpaired fins. Induction of msx gene expression in regenerating caudal fins occurs as early as 30 hours postamputation. As the blastema forms, the levels of expression increase and reach a maximum between the third and fifth days. Then, msx expression progressively declines and disappears by day 12 when the caudal fin has grown back to its normal size. In the regenerating fin, the blastema cells that develop at the tip of each fin ray express msxB and msxC. Cells of the overlying epithelium express msxA and msxD, but do not express msxB or msxC. Amputations at various levels along the proximodistal axis of the fin suggest that msxB expression depends upon the position of the blastema, with cells of the rapidly proliferating proximal blastema expressing higher levels than the cells of the less rapidly proliferating distal blastema. Expression of msxC and msxD is independent of the position of the blastema cell along this axis. Our results suggest distinct roles for each of the four msx genes during fin development and regeneration and differential regulation of their expression.

Amino Acid Sequence↗

Effects of reduced exposure on computed radiography: comparison of nodule detection accuracy with conventional and asymmetric screen-film radiographs of a chest phantom.

OBJECTIVE: Radiographic exposure has been thought to have little impact on the diagnostic quality of chest computed radiography because of automatic digital control of global optical density. The objectives of this study were to compare images obtained with two different exposures in computed radiography with conventional and asymmetric screen-film images of the chest for the detection of simulated lung nodules by use of receiver operating characteristic analysis and to relate differences in observer performance to parameters of image noise measured for each receptor condition. MATERIALS AND METHODS: At 110 kVp (fixed), exposures for the two screen-film systems were those necessary to achieve adequate optical densities over the lung and mediastinal regions of an anthropomorphic phantom. The two exposures used for the computed radiographs corresponded to the exposure used for the conventional chest screen-film system and an exposure 22% lower. An anthropomorphic phantom constructed of materials matched to the muscle, lung, and bone attenuation of a muscular adult man was used. Soft-tissue-equivalent plastic nodules of various sizes were secured at multiple sites on the phantom to simulate lung nodules. The chest phantom was imaged in 50 configurations with a total of 70 superimposed nodules. The perceptual performances of five radiologists were compared by use of receiver operating characteristic analysis. The signal-to-noise ratio in the mediastinum and the coefficient of variation of noise were measured for all four image conditions by use of a step wedge technique to provide an explanation for differences in diagnostic accuracy. RESULTS: We found no significant differences in the detection of lung nodules between the two screen-film systems or between the conventional screen-film images and the standard-exposure computed radiographs. However, there was a significant decrease in nodule detection on computed radiographs obtained at a reduced exposure; this result was associated with a 21% decrease in the signal-to-noise ratio. CONCLUSION: Our results show that underexposure of computed radiographs decreases the detection of low-contrast objects such as lung nodules. Although consistent global optical density on computed radiographs is achieved over a wide range of exposures, the alterations in signal-to-noise ratio that result from underexposure can reduce the diagnostic quality of computed radiographs.

Adult↗

A genetic linkage map for the zebrafish.

To facilitate molecular genetic analysis of vertebrate development, haploid genetics was used to construct a recombination map for the zebrafish Danio (Brachydanio) rerio. The map consists of 401 random amplified polymorphic DNAs (RAPDs) and 13 simple sequence repeats spaced at an average interval of 5.8 centimorgans. Strategies that exploit the advantages of haploid genetics and RAPD markers were developed that quickly mapped lethal and visible mutations and that placed cloned genes on the map. This map is useful for the position-based cloning of mutant genes, the characterization of chromosome rearrangements, and the investigation of evolution in vertebrate genomes.

Animals↗

Identification of RAPD primers that reveal extensive polymorphisms between laboratory strains of zebrafish.

The zebrafish has recently emerged as a useful system for understanding vertebrate developmental genetics, despite the lack of a linkage map. To identify DNA-based genetic polymorphisms for constructing a genetic map, we have screened a collection of RAPD primers for their utility in identifying genetic polymorphisms between two laboratory strains of zebrafish. Here, we report 116 primers that identify 721 strain-specific genetic markers and show how they can be used in haploid genetics of zebrafish.

Animals↗

Clinical characteristics associated with interpersonal depression: symptoms, course and treatment response.

A range of theories, including environmental, personality and cognitive theories, have suggested that loss may be a particularly critical form of stress in the etiology and expression of depression. The current study examines whether interpersonal depression predicted a unique clinical presentation and course in subjects with major depression. Subjects who became depressed following a severe interpersonal event were contrasted with two control groups: patients without antecedent stressors and patients with major non-interpersonal stressors. The hypothesized interpersonal subgroup was differentiated from the control groups only in the speed of treatment response. Proposals for future research are discussed.

Adult↗

Parents' and children's adiposity and eating style.

OBJECTIVE: To investigate children's ability to self-regulate energy intake and to determine whether individual differences in the precision of food intake regulation are related to children's anthropometric measures. We collected information pertaining to parental adiposity and dieting practices, as well as mothers' child-feeding practices. Of special interest was the degree of control imposed by mothers over their children's food intake. Our intent was to explore whether these variables might influence children's regulation of energy intake. SUBJECTS AND SETTING: Seventy-seven 3-5-year-old children who attended a university preschool setting and their parents participated in this experiment. MEASUREMENTS AND MAIN RESULTS: Children completed controlled, two-part meals used to estimate their ability to adjust food intake in response to changes in caloric density of the diet. An eating index, reflecting children's precision in the ability to regulate energy intake, was correlated to children's anthropometric measures. These correlations provided evidence for a relation between children's body fat stores and their responsiveness to caloric density cues: Pearson correlation coefficients revealed that children with greater body fat stores were less able to regulate energy intake accurately. The best predictor of children's ability to regulate energy intake was parental control in the feeding situation: mothers who were more controlling of their children's food intake had children who showed less ability to self-regulate energy intake (r = -.67, P < .0001). CONCLUSIONS: These findings suggest that the optimal environment for children's development of self-control of energy intake is that in which parents provide healthy food choices but allow children to assume control of how much they consume.

Body Weight↗

Children's lunch intake: effects of midmorning snacks varying in energy density and fat content.

To determine the effects of preloads differing in energy density and fat content on subsequent lunch intake, 24 preschool children consumed 113 g ice-cream preloads as mid-morning snacks (containing 0, 12, or 18 g of fat, and 4 g of protein), followed nearly 2 h later by an ad libitum lunch consisting of a variety of foods. A fat-free baseline preload, consisting of dry cereal and apple juice, was also included. The baseline, fat-free, medium and high-fat preloads contained 334, 740, 953, and 1150 kJ per serving. All three ice-cream preloads produced significant but equivalent suppression of ad libitum lunch intake relative to baseline; lunch intake was not related to the fat content or energy density of the ice-cream preloads. Compensation at lunch was not macronutrient specific; children did not increase their fat intake at lunch following the fat-free preload. As energy and fat content of the preloads increased, children consumed significantly fewer foods at lunch, confirming previous findings. These changes in the variety of foods consumed were related to preference: regardless of preload, children continued to consume their preferred foods, while non-preferred foods tended to be eliminated following the higher energy preloads. Because compensation for energy was incomplete, energy intake of meals plus snacks increased with the energy content of the preload. Additional research is required to determine whether manipulating the fat and energy content of snacks produces similar effects when the unit of analysis is the child's total daily diet, rather than a single meal.

Child Nutritional Physiological Phenomena↗

An automatic method for enhancing the display of different tissue densities in digital chest radiographs.

Digital chest radiographs are often too bright and/or lack contrast when viewed on a video display. This often occurs in radiographs taken of patients with dense lungs, or when incorrect x-ray exposure techniques or inappropriate image preprocessing operations are performed (eg, by the computed radiography system or laser scanner). This article describes a method to automatically provide brightness and contrast adjustments to selectively enhance either soft or dense tissues. This method reduces viewer interaction and improves displayed image quality. The algorithm analyzes the gray-level histogram of a chest radiograph and determines the breakpoints that separate the region outside the patient (background), the radiographically soft tissues, and the radiographically dense tissues. From these breakpoints, a series of piecewise linear look-up tables (LUTs) is generated to selectively enhance either the soft tissues or the dense tissues. This is performed by: (1) varying the contrast in the patient background to achieve the desired overall brightness, (2) selectively increasing the contrast of the tissue region of interest, and (3) reducing or maintaining the contrast of the remaining region. The resulting LUTs are applied to the original image via video display.

Algorithms↗

Effects of a nonenergy fat substitute on children's energy and macronutrient intake.

To determine whether children adjusted their energy intake in response to covert manipulations in the proportion of energy from dietary fat, 24-h food intake of 29 2- to 5-y-old children was measured over four 2-d blocks. In this within-subject crossover design, in the first three meals of the first day of each block, children consumed foods containing dietary fat or a nonenergy fat substitute, which provided 10% of total daily energy intake. Children compensated for the missing energy; cumulative energy intake differed by only 100 kJ over 2 d. Substitution for dietary fat reduced the percent of energy from fat from 38.7% to 36.4%. Children's intake at individual meals was highly variable (mean CV 24.7%) relative to the variability of total daily energy intake (CV = 8.6%). To produce this pattern, children adjusted energy intake across successive meals. Use of a fat substitute at 10% of energy from dietary fat did not significantly reduce 24-h energy intake.

Analysis of Variance↗

TSF1 to TSF6, required for silencing the Saccharomyces cerevisiae GAL genes, are global regulatory genes.

The Saccharomyces cerevisiae GAL1 and GAL10 genes are controlled in response to the availability of galactose and glucose by multiple activating and repressing proteins bound at adjacent or overlapping sites in UASG. Negative control elements in UASG, designated GAL operators GALO1 to GALO6, are required to silence basal level transcription of GAL1 and GAL10 when galactose is absent. We isolated and characterized recessive mutations in six nuclear genes, TSF1 to TSF6, that impair silencing of GAL1 and GAL10 gene expression. Surprisingly, the results of several experiments suggest that the TSF genes encode global regulatory factors. tsf1 to tsf6 mutations derepressed expression from yeast CYC-GAL hybrid promoters (fused to lacZ) that harbor a variety of operator sequences, and caused pleiotropic defects in cell growth, mating, and sporulation. S1 mapping and Northern blot results for tsf3 suggest that the molecular defect is at the transcriptional level. Mutant phenotypes were additive in certain combinations of tsf double mutants, implying that more than one silencing pathway is involved in TSF1 to TSF6 function. Most significantly, mutations in all six TSF1 to TSF6 genes activated expression from GAL1 and CYC1 promoters (fused to lacZ) lacking upstream activating sequences. Combined, the simplest interpretation of these results is that TSF1 to TSF6 encode factors that control the function of the basic RNA polymerase II transcriptional machinery.

Base Sequence↗