Biomedical subjects

Lauren M McIntyre

Publications and source records attributed to Lauren M McIntyre.

15 recordsLinked to original sources

PubMed2006

Changes in skeletal muscle gene expression following clenbuterol administration.

BACKGROUND: Beta-adrenergic receptor agonists (BA) induce skeletal muscle hypertrophy, yet specific mechanisms that lead to this effect are not well understood. The objective of this research was to identify novel genes and physiological pathways that potentially facilitate BA induced skeletal muscle growth. The Affymetrix platform was utilized to identify gene expression changes in mouse skeletal muscle 24 hours and 10 days after administration of the BA clenbuterol. RESULTS: Administration of clenbuterol stimulated anabolic activity, as indicated by decreased blood urea nitrogen (BUN; P < 0.01) and increased body weight gain (P < 0.05) 24 hours or 10 days, respectively, after initiation of clenbuterol treatment. A total of 22,605 probesets were evaluated with 52 probesets defined as differentially expressed based on a false discovery rate of 10%. Differential mRNA abundance of four of these genes was validated in an independent experiment by quantitative PCR. Functional characterization of differentially expressed genes revealed several categories that participate in biological processes important to skeletal muscle growth, including regulators of transcription and translation, mediators of cell-signalling pathways, and genes involved in polyamine metabolism. CONCLUSION: Global evaluation of gene expression after administration of clenbuterol identified changes in gene expression and overrepresented functional categories of genes that may regulate BA-induced muscle hypertrophy. Changes in mRNA abundance of multiple genes associated with myogenic differentiation may indicate an important effect of BA on proliferation, differentiation, and/or recruitment of satellite cells into muscle fibers to promote muscle hypertrophy. Increased mRNA abundance of genes involved in the initiation of translation suggests that increased levels of protein synthesis often associated with BA administration may result from a general up-regulation of translational initiators. Additionally, numerous other genes and physiological pathways were identified that will be important targets for further investigations of the hypertrophic effect of BA on skeletal muscle.

Adrenergic beta-Agonists↗

PubMed2006

Sex-specific expression of alternative transcripts in Drosophila.

BACKGROUND: Many genes produce multiple transcripts due to alternative splicing or utilization of alternative transcription initiation/termination sites. This 'transcriptome expansion' is thought to increase phenotypic complexity by allowing a single locus to produce several functionally distinct proteins. However, sex, genetic and developmental variation in the representation of alternative transcripts has never been examined systematically. Here, we describe a genome-wide analysis of sex-specific expression of alternative transcripts in Drosophila melanogaster. RESULTS: We compared transcript profiles in males and females from eight Drosophila lines (OregonR and 2b, and 6 RIL) using a newly designed 60-mer oligonucleotide microarray that allows us to distinguish a large proportion of alternative transcripts. The new microarray incorporates 7,207 oligonucleotides, satisfying stringent binding and specificity criteria that target both the common and the unique regions of 2,768 multi-transcript genes, as well as 12,912 oligonucleotides that target genes with a single known transcript. We estimate that up to 22% of genes that produce multiple transcripts show a sex-specific bias in the representation of alternative transcripts. Sexual dimorphism in overall transcript abundance was evident for 53% of genes. The X chromosome contains a significantly higher proportion of genes with female-biased transcription than the autosomes. However, genes on the X chromosome are no more likely to have a sexual bias in alternative transcript representation than autosomal genes. CONCLUSION: Widespread sex-specific expression of alternative transcripts in Drosophila suggests that a new level of sexual dimorphism at the molecular level exists.

Alternative Splicing↗

PubMed2006

Mapping density response in maize: a direct approach for testing genotype and treatment interactions.

Maize yield improvement has been strongly linked to improvements in stress tolerance, particularly to increased interplant competition. As a result, modern hybrids are able to produce kernels at high plant population densities. Identification of the genetic factors responsible for density response in maize requires direct testing of interactions between genetic effects and density and evaluation of that response in multiple traits. In this article we take a broad view of the problem and use a general approach based upon mixed models to analyze data from eight segmental inbred lines in a B73 background and their crosses to the unrelated parent Mo17 (hybrids). We directly test for the interaction between treatment effects and genetic effects instead of the commonly used overlaying of results on a common map. Additionally, we demonstrate one way to handle heteroscedasticity of variances common in stress responses. We find that some SILs are consistently different from the recurrent parent regardless of the density, while others differ from the recurrent parent in one density level but not in the other. Thus, we find positive evidence for both main effects and interaction between genetic loci and density in cases where the approach of overlapping results fails to find significant results. Furthermore, our study clearly identifies segments that respond differently to density depending upon the inbreeding level (inbred/hybrid).

Chromosome Mapping↗

PubMed2005

Sex- and segment-specific modulation of gene expression profiles in Drosophila.

Homeotic and sex-determining genes control a wide range of morphological traits by regulating the expression of different target genes in different tissues. The identity of most of these target genes remains unknown, and it is not even clear what fraction of the genome is regulated in a segment- and sex-specific manner. In this report, we examine segment- and sex-specific gene expression in Drosophila pupal legs. The first and second legs in Drosophila have clearly distinguishable bristle patterns. Bristle pattern in the first leg also differs between males and females, whereas the second leg has no overt sexual dimorphism. To identify the genes responsible for these differences, we compared transcriptional profiles between male and female first and second legs during early pupal development. The extent of sexually dimorphic gene expression parallels morphological differences: over 100 genes are expressed sex specifically in the first leg, whereas no sexual differences are seen in the second leg. Segmental differences are less extensive than sexual dimorphism and involve fewer than 14 genes. We have identified a novel gene, CG13857, that is expressed exclusively in the first leg in a pattern that suggests this gene may play an important role in specifying segment- and sex-specific bristle patterns.

Animals↗

PubMed2005

Identification of co-regulated transcripts affecting male body size in Drosophila.

Factor analysis is an analytic approach that describes the covariation among a set of genes through the estimation of 'factors', which may be, for example, transcription factors, microRNAs (miRNAs), and so on, by which the genes are co-regulated. Factor analysis gives a direct mechanism by which to relate gene networks to complex traits. Using simulated data, we found that factor analysis clearly identifies the number and structure of factors and outperforms hierarchical cluster analysis. Noise genes, genes that are not correlated with any factor, can be distinguished even when factor structure is complex. Applied to body size in Drosophila simulans, an evolutionarily important complex trait, a factor was directly associated with body size.

Animals↗

PubMed2005

Model selection in binary trait locus mapping.

Quantitative trait locus (QTL) mapping methodology for continuous normally distributed traits is the subject of much attention in the literature. Binary trait locus (BTL) mapping in experimental populations has received much less attention. A binary trait by definition has only two possible values, and the penetrance parameter is restricted to values between zero and one. Due to this restriction, the infinitesimal model appears to come into play even when only a few loci are involved, making selection of an appropriate genetic model in BTL mapping challenging. We present a probability model for an arbitrary number of BTL and demonstrate that, given adequate sample sizes, the power for detecting loci is high under a wide range of genetic models, including most epistatic models. A novel model selection strategy based upon the underlying genetic map is employed for choosing the genetic model. We propose selecting the "best" marker from each linkage group, regardless of significance. This reduces the model space so that an efficient search for epistatic loci can be conducted without invoking stepwise model selection. This procedure can identify unlinked epistatic BTL, demonstrated by our simulations and the reanalysis of Oncorhynchus mykiss experimental data.

Animals↗

PubMed2005

Nematode-induced changes of transporter gene expression in Arabidopsis roots.

Root-knot plant-parasitic nematodes (Meloidogyne spp.) account for much of the damage inflicted to plants by nematodes. The feeding sites of these nematodes consist of "giant" cells, which have characteristics of transfer cells found in other parts of plants. Increased transport activity across the plasma membrane is a hallmark of transfer cells, and giant cells provide nutrition for nematodes; therefore, we initiated a study to identify the transport processes that contribute to the development and function of nematode-induced feeding sites. The study was conducted over a 4-week period, during which time the large changes in the development of giant cells were documented. The Arabidopsis ATH1 GeneChip was used to identify the many transporter genes that were regulated by nematode infestation. Expression of 50 transporter genes from 18 different gene families was significantly changed upon nematode infestation. Sixteen transporter genes were studied in more detail using real-time reverse-transcriptase polymerase chain reaction to determine transcript abundance in nematode-induced galls that contain giant cells and uninfested regions of the root. Certain genes were expressed primarily in galls whereas others were expressed primarily in the uninfested regions of the root, and a third group was expressed evenly throughout the root. Multiple transport processes are regulated and these may play important roles in nematode feeding-site establishment and maintenance.

Amino Acids↗

PubMed2004

Persistent bacteremia due to methicillin-resistant Staphylococcus aureus infection is associated with agr dysfunction and low-level in vitro resistance to thrombin-induced platelet microbicidal protein.

BACKGROUND: The causes of persistent bacteremia (PB) due to methicillin-resistant Staphylococcus aureus (MRSA) are poorly understood. This investigation examined potential associations between PB with key clinical features and several in vitro bacterial genotypic and phenotypic characteristics, in isolates from 1 institution. METHODS: Pulsed-field gel electrophoresis (PFGE) relatedness, thrombin-induced platelet microbicidal protein (tPMP)-susceptibility phenotype, accessory gene regulator (agr) genotype and functionality (via delta-lysin production), and autolysis phenotypes were assessed in MRSA isolates from the bloodstream of 21 prospectively identified patients with PB (blood cultures positive after > or =7 days of therapy) and of 18 patients with resolving bacteremia (RB) (sterile blood cultures within the first 2-4 days of therapy) due to MRSA. RESULTS: The 2 groups had comparable baseline characteristics but differed in their clinical courses (e.g., endocarditis was more frequent in patients with PB than in those with RB [43% vs. 0%, respectively; P=.0016]); isolates from patients with PB exhibited higher rates of (1) survival in vitro after exposure to tPMP (22.4+/-14.8% vs. 11.6+/-6.5%, respectively; P=.005); (2) defective delta-lysin production (71.4% vs. 38.9%, respectively; P=.057); (3) non-agr genotype II profile (100% vs. 77.8%, respectively; P=.037); and (4) overrepresentation of a specific PFGE genotype (85.7% vs. 44.4%, respectively; P=.015). CONCLUSIONS: Isolates from patients with PB differed from those in patients with RB, in several in vitro characteristics. Further studies will be necessary to define how these factors might affect clinical outcome.

Anti-Bacterial Agents↗

PubMed2004

Common pattern of evolution of gene expression level and protein sequence in Drosophila.

Sequence divergence scaled by variation within species has been used to infer the action of selection upon individual genes. Applying this approach to expression, we compared whole-genome whole-body RNA levels in 10 heterozygous Drosophila simulans genotypes and a pooled sample of 10 D. melanogaster lines using Affymetrix Genechip. For 972 genes expressed in D. melanogaster, the transcript level was below detection threshold in D. simulans, which may be explained either by sequence divergence between the primers on the chip and the mRNA transcripts or by down-regulation of these genes. Out of 6,707 genes that were expressed in both species, transcript level was significantly different between species for 534 genes (at P < 0.001). Genes whose expression is under stabilizing selection should exhibit reduced genetic variation within species and reduced divergence between species. Expression of genes under directional selection in D. simulans should be highly divergent from D. melanogaster, while showing low genetic variation in D. simulans. Finally, the genes with large variation within species but modest divergence between species are candidates for balancing selection. Rapidly diverging, low-polymorphism genes included those involved in reproduction (e.g., Mst 3Ba, 98Cb; Acps 26Aa, 63F; and sperm-specific dynein). Genes with high variation in transcript abundance within species included metallothionein and hairless, both hypothesized to be segregating in nature because of gene-by-environment interactions. Further, we compared expression divergence and DNA substitution rate in 195 genes. Synonymous substitution rate and expression divergences were uncorrelated, whereas there was a significant positive correlation between nonsynonymous substitution rate and expression divergence. We hypothesize that as a substantial fraction of nonsynonymous divergence has been shown to be adaptive, much of the observed expression divergence is likewise adaptive.

Amino Acid Sequence↗

PubMed2004

Using alpha wisely: improving power to detect multiple QTL.

The increase in the number of available markers for many experimental populations has led to QTL studies with ever increasing marker numbers and densities. The resulting conundrum is that as marker density increases, so does the multiple testing problem. It is important to re-examine the detection of multiple QTL in light of increasing marker density. We explore through simulation whether existing methods have achieved the maximum possible power for detecting multiple QTL and whether increasing the marker density is an effective strategy for locating multiple QTL. In addition to existing methods, such as the maximum, the CET, and the Benjamini-Hochberg and Benjamini-Yekutieli procedures, we propose and evaluate the complete set of order statistics with their corresponding empirical joint distribution. We examine these statistics in conjunction with a novel application of the alpha-spending approach, providing a less conservative solution to the problem of controlling the false discovery rate (FDR) in multiple tests. We conducted a simulation study to assess the relative power of these approaches as well as their ability to control FDR. We find that several of the new approaches have a reasonable FDR, and can substantially improve the experimenter's ability to detect multiple QTL compared to existing approaches in many cases; however, the Benjamini-Hochberg procedure remains a very reasonable choice. The methods are applied to a nine-trait Oat vernalization dataset.

Journal Article↗

PubMed2004

Differential gene expression in response to hydrogen peroxide and the putative PerR regulon of Synechocystis sp. strain PCC 6803.

We utilized a full genome cDNA microarray to identify the genes that comprise the peroxide stimulon in the cyanobacterium Synechocystis sp. strain PCC 6803. We determined that a gene (slr1738) encoding a protein similar to PerR in Bacillus subtilis was induced by peroxide. We constructed a PerR knockout strain and used it to help identify components of the PerR regulon, and we found that the regulatory properties were consistent with the hypothesis that PerR functions as a repressor. This effort was guided by finding putative PerR boxes in positions upstream of specific genes and by careful statistical analysis. PerR and sll1621 (ahpC), which codes for a peroxiredoxin, share a divergent promoter that is regulated by PerR. We found that isiA, encoding a Chl protein that is induced under low-iron conditions, was strongly induced by a short-term peroxide stress. Other genes that were strongly induced by peroxide included sigD, sigB, and genes encoding peroxiredoxins and Dsb-like proteins that have not been studied yet in this strain. A gene (slr1894) that encoded a protein similar to MrgA in B. subtilis was upregulated by peroxide, and a strain containing an mrgA knockout mutation was highly sensitive to peroxide. A number of genes were downregulated, including key genes in the chlorophyll biosynthesis pathway and numerous regulatory genes, including those encoding histidine kinases. We used PerR mutants and a thioredoxin mutant (TrxA1) to study differential expression in response to peroxide and determined that neither PerR nor TrxA1 is essential for the peroxide protective response.

Bacterial Proteins↗

PubMed2003

Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis.

BACKGROUND: It has been reported in the quantitative trait locus (QTL) literature that when testing for QTL location and effect, the statistical power supporting methodologies based on two markers and their estimated genetic map is higher than for the genetic map independent methodologies known as single marker analyses. Close examination of these reports reveals that the two marker approaches are more powerful than single marker analyses only in certain cases. Simulation studies are a commonly used tool to determine the behavior of test statistics under known conditions. We conducted a simulation study to assess the general behavior of an intersection test and a two marker test under a variety of conditions. The study was designed to reveal whether two marker tests are always more powerful than intersection tests, or whether there are cases when an intersection test may outperform the two marker approach.We present a reanalysis of a data set from a QTL study of ovariole number in Drosophila melanogaster. RESULTS: Our simulation study results show that there are situations where the single marker intersection test equals or outperforms the two marker test. The intersection test and the two marker test identify overlapping regions in the reanalysis of the Drosophila melanogaster data. The region identified is consistent with a regression based interval mapping analysis. CONCLUSION: We find that the intersection test is appropriate for analysis of QTL data. This approach has the advantage of simplicity and for certain situations supplies equivalent or more powerful results than a comparable two marker test.

Animals↗

PubMed2003

Microarray analysis of the genome-wide response to iron deficiency and iron reconstitution in the cyanobacterium Synechocystis sp. PCC 6803.

A full-genome microarray of the (oxy)photosynthetic cyanobacterium Synechocystis sp. PCC 6803 was used to identify genes that were transcriptionally regulated by growth in iron (Fe)-deficient versus Fe-sufficient media. Transcript accumulation for 3,165 genes in the genome was analyzed using an analysis of variance model that accounted for slide and replicate (random) effects and dye (a fixed) effect in testing for differences in the four time periods. We determined that 85 genes showed statistically significant changes in the level of transcription (P </= 0.05/3,165 = 0.0000158) across the four time points examined, whereas 781 genes were characterized as interesting (P </= 0.05 but greater than 0.0000158; 731 of these had a fold change >1.25 x). The genes identified included those known previously to be Fe regulated, such as isiA that encodes a novel chlorophyll-binding protein responsible for the pigment characteristics of low-Fe (LoFe) cells. ATP synthetase and phycobilisome genes were down-regulated in LoFe, and there were interesting changes in the transcription of genes involved in chlorophyll biosynthesis, in photosystem I and II assembly, and in energy metabolism. Hierarchical clustering demonstrated that photosynthesis genes, as a class, were repressed in LoFe and induced upon the re-addition of Fe. Specific regulatory genes were transcriptionally active in LoFe, including two genes that show homology to plant phytochromes (cph1 and cph2). These observations established the existence of a complex network of regulatory interactions and coordination in response to Fe availability.

Cyanobacteria↗

PubMed2002

Prognostic significance of molecular genetic aberrations on chromosome segment 11p15.5 in non-small-cell lung cancer.

PURPOSE: The assessment of prognosis and decisions on treatment for patients with non-small-cell lung cancer (NSCLC) are determined on the basis of disease stage and performance status. NSCLC frequently manifests loss of heterozygosity (LOH) at chromosome segment 11p15.5. Whether LOH at 11p15.5 is an independent prognostic variable has yet to be determined. PATIENTS AND METHODS: We developed five novel markers, which can be assessed by polymerase chain reaction and restriction enzyme digestion. LOH at 11p15.5 was assessed in 193 patients who underwent surgical resection for pathologic stage I and II of the disease. RESULTS: LOH at 11p15.5 was associated with poor survival (P =.021). Multivariate logistic regression analysis showed that after disease stage, performance status, weight loss, sex, age at diagnosis, and smoking history were controlled for, patients with LOH were two times more likely to die than those without LOH (relative risk [RR] = 2.01, P =.021). Cox regression analysis with disease stage and LOH revealed that the survival of patients with stage I disease and LOH was similar to the survival of patients with stage II disease, and it was significantly worse than the survival of stage I patients without LOH (RR = 2.38, P =.038). CONCLUSION: LOH in a 310-kb region on chromosome segment 11p15.5 that includes the gene for the regulatory subunit of the enzyme ribonucleotide reductase is highly predictive of poor survival from NSCLC. The future utility of analysis of the allelic status of this region may involve treatment decisions, such as the use of neoadjuvant and adjuvant chemotherapy for patients with stage I disease.

Carcinoma, Non-Small-Cell Lung↗

PubMed2002

Evidence for an evolutionarily conserved interaction between cell wall biosynthesis and flowering in maize and sorghum.

BACKGROUND: Factors that affect flowering vary among different plant species, and in the grasses in particular the exact mechanism behind this transition is not fully understood. The brown midrib (bm) mutants of maize (Zea mays L.), which have altered cell wall composition, have different flowering dynamics compared to their wild-type counterparts. This is indicative of a link between cell wall biogenesis and flowering. In order to test whether this relationship also exists in other grasses, the flowering dynamics in sorghum (Sorghum bicolor (L.) Moench) were investigated. Sorghum is evolutionarily closely related to maize, and a set of brown midrib (bmr) mutants similar to the maize bm mutants is available, making sorghum a suitable choice for study in this context. RESULTS: We compared the flowering time (time to half-bloom) of several different bmr sorghum lines and their wild-type counterparts. This revealed that the relationship between cell wall composition and flowering was conserved in sorghum. Specifically, the mutant bmr7 flowered significantly earlier than the corresponding wild-type control, whereas the mutants bmr2, bmr4, bmr6, bmr12, and bmr19 flowered later than their wild-type controls. CONCLUSION: The change in flowering dynamics in several of the brown midrib sorghum lines provides evidence for an evolutionarily conserved mechanism that links cell wall biosynthesis to flowering dynamics. The availability of the sorghum bmr mutants expands the germplasm available to investigate this relationship in further detail.

Body Height↗