Maria Smith - Academia.edu (original) (raw)

Papers by Maria Smith

Frontiers in Microbiology, 2013

The Columbia River (CR) is a powerful economic and environmental driver in the US Pacific Northwe... more The Columbia River (CR) is a powerful economic and environmental driver in the US Pacific Northwest. To characterize the dominant microorganisms and metabolisms contributing to coastal biogeochemistry, microbial communities in the water column were analyzed from four diverse habitats: 1) an estuarine turbidity maximum (ETM); 2) a chlorophyll maximum of the river plume; 3) an upwelling-associated hypoxic zone; and 4) the deep ocean bottom. Three size fractions, 0.1-0.8, 0.8-3 and 3-200 m were collected for each habitat in August 2007, and used for DNA isolation and 454 sequencing, resulting in 12 metagenomes of >5 million reads (>1.6 Gbp). The 3-and 0.8-m metagenomes, representing particulate fractions, were taxonomically diverse across habitats. The 3-m size fractions contained a high abundance of eukaryota with diatoms dominating the hypoxic water and plume, while cryptophytes were more abundant in the ETM. The 0.1-m metagenomes represented mainly free-living bacteria and archaea. The most abundant archaeal hits were observed in the deep ocean and hypoxic water (19% of prokaryotic peptides in the 0.1-m metagenomes), and were homologous to Nitrosopumilus maritimus (ammonia-oxidizing Thaumarchaeota). Bacteria dominated metagenomes of all samples. In the euphotic zone (estuary, plume and hypoxic ocean), the most abundant bacterial taxa (≥40 % of 47 prokaryotic peptides) represented aerobic photoheterotrophs. In contrast, the low-oxygen, deep 48 water metagenome was enriched with sequences for strict and facultative anaerobes. 49 Interestingly, many of the same anaerobic bacterial families were enriched in the 3-μm size 50 fraction of the ETM (2-10X more abundant relative to the 0.1-m metagenome), indicating 51 possible formation of anoxic microniches within particles. Metabolic profiling supported this 52 conclusion. Results from this study provide a metagenome perspective on ecosystem-scale 53 metabolism in an upwelling-influenced river-dominated coastal margin. 54 55 Key words: metagenome analysis, Columbia River coastal margin, environmental water, 56 microbial communities, particle-attached and free-living microbes 57 58 Another major source of nutrients to the CRCM is the nearshore seasonal upwelling that is frequently observed in summer when northerly winds push the surface water away from the coastline (Kudela et al., 2005). This offshore moving water is replaced by cooler, saltier and nutrient-rich water upwelling from depths of 150 to 300m of the northward-flowing California Current Undercurrent (Roegner et al., 2011) to the upper euphotic water layers, resulting in increased primary production and phytoplankton blooms (Kudela et al., 2005). As a consequence, the decomposition of settling dead bloom biomass by aerobic heterotrophs leads to the formation of hypoxic zones with oxygen levels ≤ 2 mg L −1 (Rabalais et al., 2002; Roegner et al., 2011). Microbial communities in the CRCM have been evaluated primarily by sequencing of smallsubunit (SSU) ribosomal RNA (rRNA) genes (

Cancer research, Jan 15, 2003

Hepatocellular carcinoma (HCC) is a common primary cancer associated frequently with hepatitis C ... more Hepatocellular carcinoma (HCC) is a common primary cancer associated frequently with hepatitis C virus (HCV). To gain insight into the molecular mechanisms of hepatocarcinogenesis, and to identify potential HCC markers, we performed cDNA microarray analysis on surgical liver samples from 20 HCV-infected patients. RNA from individual tumors was compared with RNA isolated from adjacent nontumor tissue that was cirrhotic in all of the cases. Gene expression changes related to cirrhosis were filtered out using experiments in which pooled RNA from HCV-infected cirrhotic liver without tumors was compared with pooled RNA from normal liver. Expression of approximately 13,600 genes was analyzed using the advanced analysis tools of the Rosetta Resolver System. This analysis revealed a set of 50 potential HCC marker genes, which were up-regulated in the majority of the tumors analyzed, much more widely than common clinical markers such as cell proliferation-related genes. This HCC marker set c...

Despite extensive studies on the roles of phytochrome in photostimulated seed germination, the me... more Despite extensive studies on the roles of phytochrome in photostimulated seed germination, the mechanisms downstream of the photoreceptor that promote germination are largely unknown. Previous studies have indicated that light-induced germination of Arabidopsis seeds is mediated by the hormone gibberellin (GA). Using RNA gel blot analyses, we studied the regulation of two Arabidopsis genes, GA4 and GA4H (for GA4 homolog), both of which encode GA 3 ␤ -hydroxylases that catalyze the final biosynthetic step to produce bioactive GAs. The newly isolated GA4H gene was expressed predominantly during seed germination. We show that expression of both GA4 and GA4H genes in imbibed seeds was induced within 1 hr after a brief red (R) light treatment. In the phytochrome B-deficient phyB-1 mutant, GA4H expression was not induced by R light, but GA4 expression still was, indicating that R light-induced GA4 and GA4H expression is mediated by different phytochromes. In contrast to the GA4 gene, the GA4H gene was not regulated by the feedback inhibition mechanism in germinating seeds. Our data demonstrate that expression of GA 3 ␤ -hydroxylase genes is elevated by R light, which may result in an increase in biosynthesis of active GAs to promote seed germination. Furthermore, our results suggest that each GA 3 ␤ -hydroxylase gene plays a unique physiological role during light-induced seed germination.

Virology, 2006

Gene expression profiling was performed on liver biopsies from 28 patients (12 HCV and 16 HCV/HIV... more Gene expression profiling was performed on liver biopsies from 28 patients (12 HCV and 16 HCV/HIV infected) in an attempt to understand the mechanisms of HCV liver disease in the presence and absence of HIV coinfection. The data were compared with clinical observations and a gene expression database obtained for transplant HCV-infected samples. This is the first report of functional genomics being used to compare intrahepatic gene expression profiles of HCV- and HCV/HIV-infected individuals. Significantly, the intrahepatic global gene expression profiles do not differ between HCV- and HCV/HIV-infected individuals. However, a subset of patients was identified who share a specific pattern of gene expression, termed the enhanced gene expression (EGE) pattern. Specifically, the EGE (+) patients show a dramatic decreased expression of multiple genes associated with the FAS-apoptosis pathway and increased expression of lymphocyte adhesion molecules and lymphocyte-specific genes. The EGE (+) patients also have partially impaired Type I and II IFN-mediated antiviral responses, including a lack of induction of the anti-fibrogenic cytokine IFN-gamma. Importantly, the pattern of gene expression observed in EGE (+) patients has similarities to patients who developed fibrosis within 1 year of receiving a liver transplant.

THE PLANT CELL ONLINE, 1998

PLoS Pathogens, 2006

The severe combined immunodeficiency disorder (SCID)-beige/albumin (Alb)-urokinase plasminogen ac... more The severe combined immunodeficiency disorder (SCID)-beige/albumin (Alb)-urokinase plasminogen activator (uPA) mouse containing a human-mouse chimeric liver is currently the only small animal model capable of supporting hepatitis C virus (HCV) infection. This model was utilized to characterize the host transcriptional response to HCV infection. The purpose of these studies was to investigate the genetic component of the host response to HCV infection and also to distinguish virus-induced gene expression changes from adaptive HCV-specific immune-mediated effects. Gene expression profiles from HCV-infected mice were also compared to those from HCV-infected patients. Analyses of the gene expression data demonstrate that host factors regulate the response to HCV infection, including the nature of the innate antiviral immune response. They also indicate that HCV mediates gene expression changes, including regulation of lipid metabolism genes, which have the potential to be directly cytopathic, indicating that liver pathology may not be exclusively mediated by HCV-specific adaptive immune responses. This effect appears to be inversely related to the activation of the innate antiviral immune response. In summary, the nature of the initial interferon response to HCV infection may determine the extent of viral-mediated effects on host gene expression. Citation: Walters KA, Joyce MA, Thompson JC, Smith MW, Yeh MM, et al. (2006) Host-specific response to HCV infection in the chimeric SCID-beige/Alb-uPA mouse model: Role of the innate antiviral immune response. PLoS Pathog 2(6): e59.

PLANT PHYSIOLOGY, 1998

The first step in gibberellin biosynthesis is catalyzed by copalyl diphosphate synthase (CPS) and... more The first step in gibberellin biosynthesis is catalyzed by copalyl diphosphate synthase (CPS) and ent-kaurene synthase. We have cloned from pumpkin (Cucurbita maxima L.) two cDNAs, CmCPS1 and CmCPS2, that each encode a CPS. Both recombinant fusion CmCPS proteins were active in vitro. CPS are translocated into plastids and processed by cleavage of transit peptides. For CmCPS1 and CmCPS2, the putative transit peptides cannot exceed the first 99 and 107 amino acids, respectively, because longer N-terminal deletions abolished activity. Levels of both CmCPS transcripts were strictly regulated in an organ-specific and developmental manner. Both transcripts were almost undetectable in leaves and were abundant in petioles. CmCPS1 transcript levels were high in young cotyledons and low in roots. In contrast, CmCPS2 transcripts were undetectable in cotyledons but present at significant levels in roots. In hypocotyls, apices, and petioles, CmCPS1 transcript levels decreased with age much more rapidly than those of CmCPS2. We speculate that CmCPS1 expression is correlated with the early stages of organ development, whereas CmCPS2 expression is correlated with subsequent growth. In contrast, C. maxima ent-kaurene synthase transcripts were detected in every organ at almost constant levels. Thus, ent-kaurene biosynthesis may be regulated through control of CPS expression.

Molecular and Cellular Biology, 2001

rRNAs are the central players in the reactions catalyzed by ribosomes, and the individual rRNAs a... more rRNAs are the central players in the reactions catalyzed by ribosomes, and the individual rRNAs are actively involved in different ribosome functions. Our previous demonstration that yeast 5S rRNA mutants (called mof9) can impact translational reading frame maintenance showed an unexpected function for this ubiquitous biomolecule. At the time, however, the highly repetitive nature of the genes encoding rRNAs precluded more detailed genetic and molecular analyses. A new genetic system allows all 5S rRNAs in the cell to be transcribed from a small, easily manipulated plasmid. The system is also amenable for the study of the other rRNAs, and provides an ideal genetic platform for detailed structural and functional studies. Saturation mutagenesis reveals regions of 5S rRNA that are required for cell viability, translational accuracy, and virus propagation. Unexpectedly, very few lethal alleles were identified, demonstrating the resilience of this molecule. Superimposition of genetic phenotypes on a physical map of 5S rRNA reveals the existence of phenotypic clusters of mutants, suggesting that specific regions of 5S rRNA are important for specific functions. Mapping these mutants onto the Haloarcula marismortui large subunit reveals that these clusters occur at important points of physical interaction between 5S rRNA and the different functional centers of the ribosome. Our analyses lead us to propose that one of the major functions of 5S rRNA may be to enhance translational fidelity by acting as a physical transducer of information between all of the different functional centers of the ribosome.

Journal of Virology, 2004

Recent outbreaks of West Nile Virus (WNV) have been associated with an increase in morbidity and ... more Recent outbreaks of West Nile Virus (WNV) have been associated with an increase in morbidity and mortality in humans, birds, and many other species. We have initiated studies to define the molecular mechanisms by which a recent pathogenic isolate of WNV evades the host cell innate antiviral response. Biochemical and microarray analyses demonstrated that WNV induced the expression of beta interferon (IFN-beta) and several IFN-stimulated genes late in infection of cultured human cells. The late expression of these antiviral genes was due to the delayed activation of the transcription factor IFN regulatory factor 3 (IRF-3). Despite this host response, WNV was still able to replicate efficiently. The effect of the IRF-3 pathway on WNV replication was assessed by examining virus replication and spread in cultures of wild-type or IRF-3-null mouse embryo fibroblasts. The absence of IRF-3 was marked by a significant increase in plaque size and a sustained production of infectious particles. Although the activation of the IRF-3 pathway was not sufficient to block virus replication, our results suggest that IRF-3 target genes function to constrain WNV infection and limit cell-to-cell virus spread.

Hepatology, 2003

performed to identify a gene expression signature of liver disease. The expression levels of appr... more performed to identify a gene expression signature of liver disease. The expression levels of approximately 13,600 genes were analyzed using surgical material and core biopsy specimens from HCV-infected cirrhotic liver explants in comparison with reference samples of normal nondiseased liver. In addition, normal liver samples were compared with each other to determine normal physiologic variation in gene expression. A set of genes, including some associated with stress, acute-phase immune response, and hepatic stellate cell activation, had variable expression levels in normal livers. These genes were subtracted from the sets of genes differentially expressed in cirrhotic livers. To exclude cancer-related genes from our marker sets, we subtracted genes that also were expressed differentially in hepatocellular carcinomas.

Gastroenterology, 2006

Liver transplant recipients infected with hepatitis C virus (HCV) develop recurrent hepatitis soo... more Liver transplant recipients infected with hepatitis C virus (HCV) develop recurrent hepatitis soon after transplantation and, in some cases, progress to fibrosis within the first 2 years. Our goals were to identify molecular processes influencing the liver disease progression and to find potential gene markers of early fibrosis. We performed gene expression profiling on serial liver biopsy specimens obtained from 13 (11 infected and 2 uninfected) transplant recipients within the first year after transplantation at 0, 3, 6, and 12 months. The data were compared with clinical observations and with a gene expression database obtained for 55 nontransplant HCV-infected and uninfected liver samples. We identified several specific gene expression patterns. The first pattern was unique for the transplant recipients regardless of their infection status. The corresponding genes encoded stress response proteins and blood proteins involved in coagulation that were differentially expressed in response to posttransplantation graft recovery. The second pattern was specific to HCV-infected samples and included up-regulation of genes encoding components of the interferon-mediated antiviral response and immune system (antigen presentation, cytotoxic response). This up-regulation pattern was absent or suppressed in the patients who developed early fibrosis, indicating that the disease progression might result from an impaired liver response to infection. Finally, we identified gene expression patterns that were specific for 12-month biopsy specimens in all 4 HCV-infected patients who developed early fibrosis. The identified gene expression patterns may prove useful for diagnostic and prognostic applications in HCV-infected patients, including predicting early progression to fibrosis.

Many model systems of human viral disease involve human-mouse chimeric tissue. One such system is... more Many model systems of human viral disease involve human-mouse chimeric tissue. One such system is the recently developed SCID-beige/Alb-uPA mouse model of hepatitis C virus (HCV) infection which involves a human-mouse chimeric liver. The use of functional genomics to study HCV infection in these chimeric tissues is complicated by the potential cross-hybridization of mouse mRNA on human oligonucleotide microarrays. To identify genes affected by mouse liver mRNA hybridization, mRNA from identical human liver samples labeled with either Cy3 or Cy5 was compared in the presence and absence of known amounts of mouse liver mRNA labeled in only one dye. The results indicate that hybridization of mouse mRNA to the corresponding human gene probe on Agilent Human 22 K oligonucleotide microarray does occur. The number of genes affected by such cross-hybridization was subsequently reduced to approximately 300 genes both by increasing the hybridization temperature and using liver samples which contain at least 80% human tissue. In addition, Real Time quantitative RT-PCR using human specific probes was shown to be a valid method to verify the expression level in human cells of known cross-hybridizing genes. The identification of genes affected by cross-hybridization of mouse liver RNA on human oligonucleotide microarrays makes it feasible to use functional genomics approaches to study the chimeric SCID-beige/Alb-uPA mouse model of HCV infection. This approach used to study cross-species hybridization on oligonucleotide microarrays can be adapted to other chimeric systems of viral disease to facilitate selective analysis of human gene expression.