Biomedical subjects

Jennifer J Smith

Publications and source records attributed to Jennifer J Smith.

17 recordsLinked to original sources

PubMed2006

Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast.

Transcriptional noise is known to be an important cause of cellular heterogeneity and phenotypic variation. The extent to which molecular interaction networks may have evolved to either filter or exploit transcriptional noise is a much debated question. The yeast genetic network regulating galactose metabolism involves two proteins, Gal3p and Gal80p, that feed back positively and negatively, respectively, on GAL gene expression. Using kinetic modeling and experimental validation, we demonstrate that these feedback interactions together are important for (i) controlling the cell-to-cell variability of GAL gene expression and (ii) ensuring that cells rapidly switch to an induced state for galactose uptake.

Computer Simulation↗

PubMed2006

Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism.

Cells respond to fatty acid exposure by metabolic reorganization and proliferation of peroxisomes. Described here is the development and application of a genome-wide screen to identify nonessential yeast genes necessary for efficient metabolism of myristic and oleic acids. Comparison of the resultant fitness data set with an integrated data set of genes transcriptionally responsive to fatty acids revealed very little overlap between the data sets. Furthermore, the fitness data set enriched for genes involved in peroxisome biogenesis and other processes related to cell morphology, whereas the expression data set enriched for genes related to metabolism. These data suggest that in response to fatty acid exposure, transcriptional control is biased towards metabolic reorganization, and structural changes tend to be controlled post-transcriptionally. They also suggest that fatty acid responsive metabolic networks are more robust than those related to cell structure. Statistical analyses of these and other global data sets suggest that the utilization of distinct control mechanisms for the execution of morphological versus metabolic responses is widespread.

Fatty Acids↗

PubMed2005

The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control.

Nuclear pore complexes (NPCs) govern macromolecular transport between the nucleus and cytoplasm and serve as key positional markers within the nucleus. Several protein components of yeast NPCs have been implicated in the epigenetic control of gene expression. Among these, Nup2p is unique as it transiently associates with NPCs and, when artificially tethered to DNA, can prevent the spread of transcriptional activation or repression between flanking genes, a function termed boundary activity. To understand this function of Nup2p, we investigated the interactions of Nup2p with other proteins and with DNA using immunopurifications coupled with mass spectrometry and microarray analyses. These data combined with functional assays of boundary activity and epigenetic variegation suggest that Nup2p and the Ran guanylyl-nucleotide exchange factor, Prp20p, interact at specific chromatin regions and enable the NPC to play an active role in chromatin organization by facilitating the transition of chromatin between activity states.

Active Transport, Cell Nucleus↗

PubMed2005

A data integration methodology for systems biology.

Different experimental technologies measure different aspects of a system and to differing depth and breadth. High-throughput assays have inherently high false-positive and false-negative rates. Moreover, each technology includes systematic biases of a different nature. These differences make network reconstruction from multiple data sets difficult and error-prone. Additionally, because of the rapid rate of progress in biotechnology, there is usually no curated exemplar data set from which one might estimate data integration parameters. To address these concerns, we have developed data integration methods that can handle multiple data sets differing in statistical power, type, size, and network coverage without requiring a curated training data set. Our methodology is general in purpose and may be applied to integrate data from any existing and future technologies. Here we outline our methods and then demonstrate their performance by applying them to simulated data sets. The results show that these methods select true-positive data elements much more accurately than classical approaches. In an accompanying companion paper, we demonstrate the applicability of our approach to biological data. We have integrated our methodology into a free open source software package named POINTILLIST.

Informatics↗

PubMed2005

A data integration methodology for systems biology: experimental verification.

The integration of data from multiple global assays is essential to understanding dynamic spatiotemporal interactions within cells. In a companion paper, we reported a data integration methodology, designated Pointillist, that can handle multiple data types from technologies with different noise characteristics. Here we demonstrate its application to the integration of 18 data sets relating to galactose utilization in yeast. These data include global changes in mRNA and protein abundance, genome-wide protein-DNA interaction data, database information, and computational predictions of protein-DNA and protein-protein interactions. We divided the integration task to determine three network components: key system elements (genes and proteins), protein-protein interactions, and protein-DNA interactions. Results indicate that the reconstructed network efficiently focuses on and recapitulates the known biology of galactose utilization. It also provided new insights, some of which were verified experimentally. The methodology described here, addresses a critical need across all domains of molecular and cell biology, to effectively integrate large and disparate data sets.

Chromatin Immunoprecipitation↗

PubMed2004

The brassinosteroid growth response in pea is not mediated by changes in gibberellin content.

The objective of this study was to increase our understanding of the relationship between brassinosteroids (BRs) and gibberellins (GAs) by examining the effects of BR deficiency on the GA biosynthesis pathway in several tissue types of pea (Pisum sativum L.). It was suggested recently that, in Arabidopsis, BRs act as positive regulators of GA 20-oxidation, a key step in GA biosynthesis [Bouquin et al. (2001) Plant Physiol 127:450-458]. However, this may not be the case in pea as GA20 levels were consistently higher in all shoot tissues of BR-deficient (lk and lkb) and BR-response (lka) mutants. The application of brassinolide (BL) to lkb plants reduced GA20 levels, and metabolism studies revealed a reduced conversion of GA19 to GA20 in epi-BL-treated lkb plants. These results indicate that BRs actually negatively regulate GA20 levels in pea. Although GA20 levels are affected by BR levels, this does not result in consistent changes in the level of the bioactive GA, GA1. Therefore, even though a clear interaction exists between endogenous BR levels and the level of GA20, this interaction may not be biologically significant. In addition to the effect of BRs on GA levels, the effect of altered GA1 levels on endogenous BR levels was examined. There was no significant difference in BR levels between the GA mutants and the wild type (wt), indicating that altered GA1 levels have no effect on BR levels in pea. It appears that the BR growth response is not mediated by changes in bioactive GA levels, thus providing further evidence that BRs are important regulators of stem elongation.

Arabidopsis↗

PubMed2004

Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane.

We have combined classical subcellular fractionation with large-scale quantitative mass spectrometry to identify proteins that enrich specifically with peroxisomes of Saccharomyces cerevisiae. In two complementary experiments, isotope-coded affinity tags and tandem mass spectrometry were used to quantify the relative enrichment of proteins during the purification of peroxisomes. Mathematical modeling of the data from 306 quantified proteins led to a prioritized list of 70 candidates whose enrichment scores indicated a high likelihood of them being peroxisomal. Among these proteins, eight novel peroxisome-associated proteins were identified. The top novel peroxisomal candidate was the small GTPase Rho1p. Although Rho1p has been shown to be tethered to membranes of the secretory pathway, we show that it is specifically recruited to peroxisomes upon their induction in a process dependent on its interaction with the peroxisome membrane protein Pex25p. Rho1p regulates the assembly state of actin on the peroxisome membrane, thereby controlling peroxisome membrane dynamics and biogenesis.

Actins↗

PubMed2004

A dominant mutation in the pea PHYA gene confers enhanced responses to light and impairs the light-dependent degradation of phytochrome A.

Phytochrome A (phyA) is an important photoreceptor controlling many processes throughout the plant life cycle. It is unique within the phytochrome family for its ability to mediate photomorphogenic responses to continuous far-red light and for the strong photocontrol of its transcript level and protein stability. Here we describe a dominant mutant of garden pea (Pisum sativum) that displays dramatically enhanced responses to light, early photoperiod-independent flowering, and impaired photodestruction of phyA. The mutant carries a single base substitution in the PHYA gene that is genetically inseparable from the mutant phenotype. This substitution is predicted to direct the replacement of a conserved Ala in an N-terminal region of PHYA that is highly divergent between phyA and other phytochromes. This result identifies a region of the phyA photoreceptor molecule that may play an important role in its fate after photoconversion.

Amino Acid Sequence↗

PubMed2004

Brassinosteroid deficiency due to truncated steroid 5alpha-reductase causes dwarfism in the lk mutant of pea.

The endogenous brassinosteroids in the dwarf mutant lk of pea (Pisum sativum) were quantified by gas chromatography-selected ion monitoring. The levels of castasterone, 6-deoxocastasterone, and 6-deoxotyphasterol in lk shoots were reduced 4-, 70-, and 6-fold, respectively, compared with those of the wild type. The fact that the application of brassinolide restored the growth of the mutant indicated that the dwarf mutant lk is brassinosteroid deficient. Gas chromatography-selected ion monitoring analysis of the endogenous sterols in lk shoots revealed that the levels of campestanol and sitostanol were reduced 160- and 10-fold, respectively, compared with those of wild-type plants. These data, along with metabolic studies, showed that the lk mutant has a defect in the conversion of campest-4-en-3-one to 5alpha-campestan-3-one, which is a key hydrogenation step in the synthesis of campestanol from campesterol. This defect is the same as that found in the Arabidopsis det2 mutant and the Ipomoea nil kbt mutant. The pea gene homologous to the DET2 gene, PsDET2, was cloned, and it was found that the lk mutation would result in a putative truncated PsDET2 protein. Thus it was concluded that the short stature of the lk mutant is due to a defect in the steroidal 5alpha-reductase gene. This defect was also observed in the callus induced from the lk mutant. Biosynthetic pathways involved in the conversion of campesterol to campestanol are discussed in detail.

3-Oxo-5-alpha-Steroid 4-Dehydrogenase↗

PubMed2004

Bacterial meningitis and brain abscesses secondary to infectious disease processes involving the head in horses: seven cases (1980-2001).

OBJECTIVE: To determine clinical features of horses with bacterial meningitis or brain abscesses secondary to infectious disease processes involving the head. DESIGN: Retrospective study. ANIMALS: 7 adult horses. PROCEDURE: Medical records of Tufts University, the University of Pennsylvania, and the Livestock Disease Diagnostic Center (Lexington, Ky) were reviewed to identify adult (> 12 months old) horses in which a postmortem diagnosis of bacterial meningitis or brain abscess had been made. Horses were included in the study if an intracranial infection was confirmed, the horse had a primary infectious disease process involving the head, and there were no signs of systemic infection. RESULTS: 23 adult horses with bacterial meningitis or a brain abscess were examined during the study period, but only 7 met the criteria for inclusion in the study. Primary sites of infection included the paranasal sinuses, nasal cavity, periocular tissues, and submandibular lymph nodes. Three horses died suddenly prior to hospitalization, and 1 horse was hospitalized but died 7 days after the onset of neurologic abnormalities. The remaining 3 horses were euthanatized because of a rapid deterioration in clinical status. CONCLUSIONS AND CLINICAL RELEVANCE: Although rare, fatal intracranial complications can develop in horses with infectious diseases involving the head.

Animals↗

PubMed2004

The pea gene LH encodes ent-kaurene oxidase.

The pea (Pisum sativum) homolog, PsKO1, of the Arabidopsis GA3 gene was isolated. It codes for a cytochrome P450 from the CYP701A subfamily and has ent-kaurene oxidase (KO) activity, catalyzing the three step oxidation of ent-kaurene to ent-kaurenoic acid in the gibberellin (GA) biosynthetic pathway when expressed in yeast (Saccharomyces cerevisiae). PsKO1 is encoded by the LH gene because in three independent mutant alleles, lh-1, lh-2, and lh-3, PsKO1 has altered sequence, and the lh-1 allele, when expressed in yeast, failed to metabolize ent-kaurene. The lh mutants of pea are GA deficient and have reduced internode elongation and root growth. One mutant (lh-2) also causes a large increase in seed abortion. PsKO1 (LH) is expressed in all tissues examined, including stems, roots, and seeds, and appears to be a single-copy gene. Differences in sensitivity to the GA synthesis inhibitor, paclobutrazol, between the mutants appear to result from the distinct nature of the genetic lesions. These differences may also explain the tissue-specific differences between the mutants.

Alternative Splicing↗

PubMed2004

Auxin from the developing inflorescence is required for the biosynthesis of active gibberellins in barley stems.

Multiple gibberellins (GAs) were quantified in the stems of intact, decapitated, and decapitated auxin-treated barley (Hordeum vulgare) plants. Removal of the developing inflorescence reduced the endogenous levels of indole-3-acetic acid (IAA), GA(1), and GA(3) and increased the level of GA(29) in internodal and nodal tissues below the site of excision. Application of IAA to the excised stump restored GA levels to normal in almost all cases. The conversion of [(14)C]GA(20) to bioactive [(14)C]GA(1) and of [(14)C]GA(5) to bioactive [(14)C]GA(3) was reduced by decapitation, and IAA application was able to restore conversion rates back to the levels found in intact plants. The amount of mRNA for the principal vegetative 3-oxidase (converting GA(20) to GA(1), and GA(5) to GA(3)) was decreased in decapitated plants and restored by IAA application. The results indicate that the inflorescence of barley is a source of IAA that is transported basipetally into the internodes and nodes where bioactive GA(1) and GA(3) are biosynthesized. Thus, IAA is required for normal GA biosynthesis in stems, acting at multiple steps in the latter part of the pathway.

Carbon Radioisotopes↗

PubMed2003

Pex11-related proteins in peroxisome dynamics: a role for the novel peroxin Pex27p in controlling peroxisome size and number in Saccharomyces cerevisiae.

Transcriptome profiling identified the gene PEX25 encoding Pex25p, a peroxisomal membrane peroxin required for the regulation of peroxisome size and maintenance in Saccharomyces cerevisiae. Pex25p is related to a protein of unknown function encoded by the open reading frame, YOR193w, of the S. cerevisiae genome. Yor193p is a peripheral peroxisomal membrane protein that exhibits high sequence similarity not only to Pex25p but also to the peroxisomal membrane peroxin Pex11p. Unlike Pex25p and Pex11p, Yor193p is constitutively expressed in wild-type cells grown in oleic acid-containing medium, the metabolism of which requires intact peroxisomes. Cells deleted for the YOR193w gene show a few enlarged peroxisomes. Peroxisomes are greatly enlarged in cells harboring double deletions of the YOR193w and PEX25 genes, the YOR193w and PEX11 genes, and the PEX25 and PEX11 genes. Yeast two-hybrid analyses showed that Yor193p interacts with Pex25p and itself, Pex25p interacts with Yor193p and itself, and Pex11p interacts only with itself. Overexpression of YOR193w, PEX25, or PEX11 led to peroxisome proliferation and the formation of small peroxisomes. Our data suggest a role for Yor193p, renamed Pex27p, in controlling peroxisome size and number in S. cerevisiae.

Amino Acid Sequence↗

PubMed2002

Transcriptome profiling to identify genes involved in peroxisome assembly and function.

Yeast cells were induced to proliferate peroxisomes, and microarray transcriptional profiling was used to identify PEX genes encoding peroxins involved in peroxisome assembly and genes involved in peroxisome function. Clustering algorithms identified 224 genes with expression profiles similar to those of genes encoding peroxisomal proteins and genes involved in peroxisome biogenesis. Several previously uncharacterized genes were identified, two of which, YPL112c and YOR084w, encode proteins of the peroxisomal membrane and matrix, respectively. Ypl112p, renamed Pex25p, is a novel peroxin required for the regulation of peroxisome size and maintenance. These studies demonstrate the utility of comparative gene profiling as an alternative to functional assays to identify genes with roles in peroxisome biogenesis.

Gene Expression Profiling↗

PubMed2002

Control of gibberellin levels and gene expression during de-etiolation in pea.

Gibberellin A(1) (GA(1)) levels drop significantly in wild-type pea (Pisum sativum) plants within 4 h of exposure to red, blue, or far-red light. This response is controlled by phytochrome A (phyA) (and not phyB) and a blue light receptor. GA(8) levels are increased in response to 4 h of red light, whereas the levels of GA(19), GA(20), and GA(29) do not vary substantially. Red light appears to control GA(1) levels by down-regulating the expression of Mendel's LE (PsGA3ox1) gene that controls the conversion of GA(20) to GA(1), and by up-regulating PsGA2ox2, which codes for a GA 2-oxidase that converts GA(1) to GA(8). This occurs within 0.5 to 1 h of exposure to red light. Similar responses occur in blue light. The major GA 20-oxidase gene expressed in shoots, PsGA20ox1, does not show substantial light regulation, but does show up-regulation after 4 h of red light, probably as a result of feedback regulation. Expression of PsGA3ox1 shows a similar feedback response, whereas PsGA2ox2 shows a feed-forward response. These results add to our understanding of how light reduces shoot elongation during de-etiolation.

Gene Expression Regulation, Plant↗

PubMedDate not supplied

Splenic torsion in an alpaca.

OBJECTIVE: To describe the clinical signs, diagnostic evaluation and surgical management of an alpaca with splenic torsion. ANIMALS: Six-year-old female alpaca. RESULTS: Splenic torsion and uterine torsion were the inciting cause for persistent abdominal discomfort in this alpaca. Rectal examination, abdominocentesis, and transabdominal ultrasonographic findings were suggestive of a splenic lesion. Surgical management involved splenectomy of a necrotized spleen. CONCLUSIONS: Although rare in occurrence, splenic torsion should be considered as a potential cause of abdominal discomfort in alpacas. Splenectomy is a reasonable and successful method of treatment for a devitalized spleen secondary to splenic torsion in alpacas. CLINICAL RELEVANCE: Splenic torsion causes persistent abdominal discomfort in camelids and may be associated with uterine torsion. Rectal examination, transabdominal ultrasound and abdominocentesis are useful diagnostic tools to differentiate splenic torsion from other causes of abdominal discomfort. Splenectomy is an uncomplicated procedure in camelids and has a favorable prognosis.

Abdominal Pain↗

PubMedDate not supplied

Sternothyroideus myotomy, staphylectomy, and oral caudal soft palate photothermoplasty for treatment of dorsal displacement of the soft palate in 102 thoroughbred racehorses.

OBJECTIVE: To compare racing performance before and after sternothyroideus myotomy, staphylectomy, and oral caudal soft palate photothermoplasty in Thoroughbred racehorses with intermittent dorsal displacement of the soft palate (DDSP). STUDY DESIGN: Retrospective study. ANIMALS: Thoroughbred racehorses (n=102) with DDSP. METHODS: Retrieved data included signalment, primary complaint, and upper respiratory tract endoscopic finding. Lifetime race records were compared for earnings per start before and after surgery, days to 1st start, and races won postoperatively. RESULTS: Comparing mean earnings per start for 3 races before (2792 dollars) and after (3806 dollars) surgery, racing performance improved significantly after surgery in 63% (46/73) of horses that competed in at least 1 race before and after surgery (P=.02). Mean and median days to 1st start after surgery were 109 and 69 days, respectively. Of horses that raced postoperatively 65% (60/92) won at least 1 race, and 77% (71/92) raced in >5 races after surgery. CONCLUSIONS: Sternothyroideus myotomy, staphylectomy, and oral caudal soft palate photothermoplasty significantly improved racing performance in experienced Thoroughbred racehorses with performance limiting DDSP, and overall had a similar outcome to other reported surgical techniques for treatment of DDSP. Clinical Relevance-Sternothyroideus myotomy, staphylectomy, and oral caudal soft palate photothermoplasty should be considered as a surgical approach to correction of DDSP in Thoroughbred racehorses; however, it is possible that staphylectomy may not be necessary to achieve a desirable outcome.

Animals↗