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Scott A Harding

Publications and source records attributed to Scott A Harding.

14 recordsLinked to original sources
PubMed2026

Parent-of-origin effects on allelic expression bias in interspecific poplar hybrids.

In hybrid plants, phenotypic outcomes are governed by interactions between the two parental genomes. However, the mechanisms underlying the interplay of divergent regulatory networks from these genomes remain poorly understood. In this study, we compared gene-level and allele-specific expression patterns, as well as differentially enriched pathways between F₁ and complex backcross (CBC) lines derived from a natural interspecific hybrid population of Populus fremontii (Pf) and P. angustifolia (Pa). Metabolic differences between Pf and Pa which exhibit low and high levels respectively of phenylpropanoid-derived condensed tannins were leveraged. Using individualized transcriptome references, differential expression and clustering analyses revealed CBC-biased and F₁-biased expression for genes involved in phenylpropanoid metabolism and photosynthesis, respectively. Biased expression of these genes at the allele level was also observed in F1. At the whole-transcriptome level, Pa-biased genes predominated in F₁ hybrids, and Pa alleles displayed more conserved expression patterns than Pf alleles across examined samples. Further analyses indicated that allelic expression bias was significantly associated with parental origin, which could be driven by sequence variations in cis-regulatory elements and differences in CpG island length. Our findings demonstrate strong parent-of-origin effects on divergent regulatory networks governing gene expression in poplar hybrids and provide clues for strategic parental selection tailored to specific metabolic pathways of interest.

cis-regulation↗
PubMed2025

Tonoplast sucrose transporter SUT4-dependent sugar partitioning modulates phenological transitions and reproductive success in poplar.

Climate uncertainty is intensifying the need for greater plasticity in carbohydrate reserve utilization to support winter survival and spring growth in woody perennials. In poplar, the single-copy SUT4, which encodes a tonoplast-localized sucrose transporter, and the SUT5/SUT6 genome duplicates, which encode plasma membrane-localized transporters, are expressed year-round, with SUT4 showing the highest expression during cool seasons. Given its role in vacuolar sucrose efflux and winter-predominant expression, SUT4 may play a key role in modulating seasonal carbohydrate dynamics. While SUT4-knockdown and knockout effects have been studied under greenhouse conditions, their impact under field conditions remains unexplored. Here, we report a field-based study comparing CRISPR knockout mutants of winter-expressed SUT4 and SUT5/SUT6 in Populus tremula × alba. We show that sut4, but not sut5/6, mutants exhibited earlier autumn leaf senescence, delayed spring bud flush, reduced stem growth, and altered sugar partitioning in winter xylem and bark relative to controls. After 2 years in the field, all genotypes flowered before leaf flush in early spring; however, sut4 mutants produced sterile ovules despite developing normal-looking catkins. Metabolic profiling revealed disrupted sucrose and raffinose dynamics in elongating sut4 catkins. This was accompanied by transcriptomic signatures of elevated stress and downregulation of proanthocyanidin biosynthesis and circadian clock genes. These findings highlight the critical role of SUT4 in coordinating sugar allocation, stress responses, and seasonal development in poplar.

Populus↗
PubMed2006

Genome-wide analysis of the structural genes regulating defense phenylpropanoid metabolism in Populus.

Salicin-based phenolic glycosides, hydroxycinnamate derivatives and flavonoid-derived condensed tannins comprise up to one-third of Populus leaf dry mass. Genes regulating the abundance and chemical diversity of these substances have not been comprehensively analysed in tree species exhibiting this metabolically demanding level of phenolic metabolism. Here, shikimate-phenylpropanoid pathway genes thought to give rise to these phenolic products were annotated from the Populus genome, their expression assessed by semiquantitative or quantitative reverse transcription polymerase chain reaction (PCR), and metabolic evidence for function presented. Unlike Arabidopsis, Populus leaves accumulate an array of hydroxycinnamoyl-quinate esters, which is consistent with broadened function of the expanded hydroxycinnamoyl-CoA transferase gene family. Greater flavonoid pathway diversity is also represented, and flavonoid gene families are larger. Consistent with expanded pathway function, most of these genes were upregulated during wound-stimulated condensed tannin synthesis in leaves. The suite of Populus genes regulating phenylpropanoid product accumulation should have important application in managing phenolic carbon pools in relation to climate change and global carbon cycling.

Coumaric Acids↗
PubMed2005

Plasma TAFI and soluble CD40 ligand do not predict reperfusion following thrombolysis for acute myocardial infarction.

INTRODUCTION: Thrombolytic therapy fails to achieve reperfusion in almost a third of patients with acute myocardial infarction. Thrombin activatable fibrinolysis inhibitor (TAFI) and soluble CD40 ligand (sCD40L) are novel endogenous fibrinolytic and atherothrombotic factors that determine clot stability. We investigated whether admission plasma thrombin activatable fibrinolysis inhibitor (TAFI) and soluble CD40 ligand (sCD40L) concentrations predicted reperfusion following thrombolytic therapy in patients with acute myocardial infarction. MATERIALS AND METHODS: Prior to administration of thrombolytic therapy, venous blood was collected from 110 patients presenting with acute ST segment elevation myocardial infarction and plasma assayed for tissue plasminogen activator (t-PA) antigen and activity, plasminogen activator inhibitor type-1 antigen (PAI-1), TAFI antigen and activity, C-reactive protein (CRP) and sCD40L concentrations. Reperfusion was determined using continuous ST segment monitoring. RESULTS: Reperfusion occurred in 77 (70%) patients with a mean treatment to reperfusion time of 83 +/- 46 min. Peak creatine kinase was significantly lower in patients who reperfused (1578 +/- 1199 versus 2200 +/- 1744 U/L; P < 0.05) and correlated with time to reperfusion (r = 0.44 [95% CI: 0.23 - 0.61], P = 0.0001). There was a modest correlation between plasma TAFI antigen and activity (r = 0.3 [95% CI: 0.04 - 0.53]; P < 0.05). There were no significant associations between coronary reperfusion and plasma concentrations of t-PA, PAI-1, TAFI, CRP or sCD40L. CONCLUSIONS: Systemic plasma TAFI, sCD40L and CRP concentrations do not predict reperfusion in patients receiving thrombolytic therapy for acute ST elevation myocardial infarction.

Adult↗
PubMed2005

Functional genomics analysis of foliar condensed tannin and phenolic glycoside regulation in natural cottonwood hybrids.

Regulation of leaf condensed tannins (CT) and salicylate-derived phenolic glycosides (PG) in fast- and slow-growing cottonwood backcrosses was analyzed by metabolic profiling and cDNA microarray hybridization. Seven hybrid lines of Populus fremontii L. and P. angustifolia James exhibiting growth/CT-PG phenotypes ranging from fast/low (Lines 18 and 1979) to slow/high (Lines 1012 and RL2) and intermediate (Lines NUL, 3200 and RM5) were investigated. Methanol-extractable leaf metabolites were analyzed by gas chromatography-mass spectrometry, and the results evaluated by principal component analysis. The hybrid lines formed separate clusters based on their primary metabolite profiles, with cluster arrangement also reflecting differences in CT-PG phenotype. Nitrogen (N) supply was manipulated to alter CT-PG partitioning and to obtain molecular insights into how primary metabolism interfaces with CT-PG accumulation. Three backcross lines (RM5, 1012, 18) exhibiting differential CT-PG responses to a 10-day hydroponic N-deprivation treatment were chosen for metabolite and gene expression analyses. The fast- growing Line 18 showed a minimal CT-PG response to N deprivation, and a reduction in photosynthetic gene expression. Line 1012 exhibited a strong phenylpropanoid response to N deprivation, including a doubling in phenylalanine ammonia-lyase (PAL) gene expression, and a shift from CT accumulation in the absence of stress toward PG accumulation under N-deprivation conditions. Amino acid concentrations were depressed in Lines 18 and 1012, as was expression of nitrate-sensitive genes coding for transketolase (TK), and malate dehydrogenase (MDH). Genes associated with protein synthesis and fate were down-regulated in Line 1012 but not in Line 18. Line RM5 exhibited a comparatively large increase in CT in response to N deprivation, but did not sustain decreases in amino acid concentrations, or changes in PAL, TK or MDH gene expression. Molecular characterization of the variable CT-PG responses shows promise for the identification and future testing of candidate genes for CT-PG trait selection or manipulation.

Gas Chromatography-Mass Spectrometry↗
PubMed2004

Metabolic profiling of the sink-to-source transition in developing leaves of quaking aspen.

Profiles of small polar metabolites from aspen (Populus tremuloides Michx.) leaves spanning the sink-to-source transition zone were compared. Approximately 25% of 250 to 300 routinely resolved peaks were identified, with carbohydrates, organic acids, and amino acids being most abundant. Two-thirds of identified metabolites exhibited greater than 4-fold changes in abundance during leaf ontogeny. In the context of photosynthetic and respiratory measurements, profile data yielded information consistent with expected developmental trends in carbon-heterotrophic and carbon-autotrophic metabolism. Suc concentration increased throughout leaf expansion, while hexose sugar concentrations peaked at mid-expansion and decreased sharply thereafter. Amino acid contents generally decreased during leaf expansion, but an early increase in Phe and a later one in Gly and Ser reflected growing commitments to secondary metabolism and photorespiration, respectively. The assimilation of nitrate and utilization of stored Asn appeared to be marked by sequential changes in malate concentration and Asn transaminase activity. Principal component and hierarchical clustering analysis facilitated the grouping of cell wall maturation (pectins, hemicelluloses, and oxalate) and membrane biogenesis markers in relation to developmental changes in carbon and nitrogen assimilation. Metabolite profiling will facilitate investigation of nitrogen use and cellular development in Populus sp. varying widely in their growth and pattern of carbon allocation during sink-to-source development and in response to stress.

Amino Acids↗
PubMed2004

Suppression subtractive hybridization-mediated transcriptome analysis from multiple tissues of aspen (Populus tremuloides) altered in phenylpropanoid metabolism.

A PCR-based suppression subtractive hybridization (SSH) technique was used to identify differentially expressed genes in developing tissues of control and transgenic aspen (Populus tremuloides Michx.) with down-regulated 4CL1 (4-coumarate:coenzyme A ligase) expression and enhanced growth. A total of 11,308 expressed sequence tags (ESTs) representing 5,028 non-redundant transcripts encoding 4,224 unique proteins was obtained from shoot apex, young stem, young leaf and root tip SSH libraries. Putative functions can be assigned to 60% of these transcripts. Approximately 14% of the ESTs are not represented among the 111,000 entries already present in Populus EST databases. In general, ESTs of the metabolism class occurred at a higher frequency in control- than transgenic-enriched libraries of all tissues, whereas protein synthesis and protein fate ESTs were over-represented in meristematic tissues of transgenics where 4CL1 was relatively strongly suppressed. Among all tissues, leaves yielded the highest percentage of ESTs with either unknown protein function or insignificant similarity to other protein/DNA/EST sequences in existing databases. Of particular interest was a large number of ESTs (16%) associated with signal transduction in transgenic leaves. Among these were several leucine-rich-repeat receptor-like protein kinases with markedly elevated expression in transgenic leaves. We also identified homologs of transposable elements that were up-regulated in transgenic tissues, providing the first experimental data for active expression of DNA mobile elements in long-lived tree species.

DNA Transposable Elements↗
PubMed2004

Expression of a glycine decarboxylase complex H-protein in non-photosynthetic tissues of Populus tremuloides.

The Gly decarboxylase complex (GDC) is abundant in mitochondria of C3 leaves and functions in photorespiratory carbon recovery. However, expression of GDC component proteins has generally been less evident in non-green tissues. Here we report an aspen (Populus tremuloides Michx.) PtgdcH1 gene, encoding a GDC subunit H-protein that is phylogenetically distinct from previously characterized photorespiratory H-proteins. Strong expression of PtgdcH1 in root tips and developing xylem suggests that GDC supports a very active C1 metabolism in non-photosynthetic tissues of aspen.

Amino Acid Oxidoreductases↗
PubMed2004

Effects of a brief course of azithromycin on soluble cell adhesion molecules and markers of inflammation in survivors of an acute coronary syndrome: A double-blind, randomized, placebo-controlled study.

BACKGROUND: The anti-chlamydial antibiotic, azithromycin, may improve outcome in patients who survive an acute coronary syndrome. The mechanisms are, however, poorly understood. The aims of this study were to define any relationship between Chlamydia pneumoniae seropositivity and levels of specific markers of endothelial activation (soluble cell adhesion molecules) and more general markers of inflammation (C-reactive protein [CRP] and interleukin-6 [IL-6]) and to assess whether azithromycin had any effect on such markers. METHODS: Patients who survived an acute coronary syndrome were randomized to receive treatment with azithromycin (n = 72) or placebo (n = 69) for 5 days. Before therapy, C pneumoniae IgA and IgG titers were checked, with serum levels of soluble intercellular adhesion molecule-1 (sICAM-1), soluble vascular cell adhesion molecule-1, soluble E-selectin (sE-selectin), soluble P-selectin, high-sensitivity CRP, and IL-6. They were rechecked 3 months later. RESULTS: There were no significant correlations between C pneumoniae titers and levels of CRP, IL-6, or soluble cell adhesion molecules. However, azithromycin treatment significantly reduced mean sICAM-1 levels (P =.006). This effect was more marked in patients with elevated titers of C pneumoniae IgA and IgG. Soluble E-selectin levels were also reduced in patients who were seropositive, but no effects were seen on other endothelial or inflammatory markers. CONCLUSIONS: After an acute coronary syndrome, a 5-day course of azithromycin reduces levels of sICAM-1, a marker of endothelial cell activation. Although these data suggest a potentially beneficial role for azithromycin, they should be interpreted with caution.

Aged↗
PubMed2003

Prophylaxis of contrast-induced nephropathy in patients undergoing coronary angiography.

Contrast-induced nephropathy (CIN) is a common complication of cardiac catheterization, reported to result in a 15% incidence of acute renal failure. Convincing evidence supports the prophylactic use of prehydration and low volumes of contrast medium. Recently, the antioxidant acetylcysteine has been shown to have a potential preventive role. The aim of this study was to examine the hypothesis that acetylcysteine prevents CIN. Patients undergoing cardiac catheterization with a serum creatinine >/= 1.5 mg/dl were prospectively randomized to receive acetylcysteine or placebo. A total of five doses of acetylcysteine 600 mg b.i.d. or placebo was administered, commencing on the day of the procedure. All patients were prehydrated with 0.45% saline and during the catheterization a nonionic low-osmolality contrast medium was used. Serum creatinine and urea were measured at 24, 48, and 72 hr postprocedure. A total of 43 patients were studied. There was no significant difference between the groups in terms of baseline characteristics, including baseline renal function. No adverse events were experienced with acetylcysteine treatment. Serum creatinine levels at 48 and 72 hr remained largely unchanged in the acetylcysteine group but continued to rise at 48 and 72 hr in the placebo group. By 72 hr, the incidence of CIN, defined as a 25% increase in baseline creatinine, was significantly lower in the acetylcysteine arm compared to placebo (5% for acetylcysteine vs. 32% for placebo; P = 0.046). In patients with mild to moderate renal impairment undergoing cardiac catheterization, prophylactic treatment with oral acetylcysteine reduces the incidence of contrast-induced nephropathy.

Acetylcysteine↗
PubMed2002

Acute coronary syndrome is a common clinical presentation of in-stent restenosis.

Coronary stents have been the major advancement in percutaneous coronary intervention in the last decade and are used in 60% to 80% of patients. However, in-stent restenosis continues to be a problem, occurring in 20% to 30% of cases. The clinical presentation of patients who develop restenosis after stenting has not been well characterized. In this study we compared the clinical presentation of in-stent restenosis with that of restenosis without stenting. Of 739 patients who underwent percutaneous coronary intervention and had repeat catheterization between October 1, 1997, and June 30, 2000, 262 consecutive patients with recurrent ischemia and restenosis were identified: 191 patients with (group A) and 71 without (Group B) stenting. Patients who underwent interventions in bypass grafts and those who developed early acute stent thrombosis were excluded from the study. Recurrent clinical ischemia occurred at a mean of 5.5 months in group A and 6.5 months in group B (p = 0.24). Rest angina (Braunwald class II and III) was more frequent in group A (48% vs 32%, p = 0.032). Acute coronary syndromes, the combination of rest angina, and acute myocardial infarction were also more frequent in group A (68% vs 46%, p = 0.03). Patients in group A were more likely to have angiographically visible thrombus than those in group B (9% vs 0%, p = 0.02). Thus, acute coronary syndromes are a common clinical presentation of restenosis among patients whose follow-up angiogram is obtained for clinical reasons, and occur more frequently in patients with in-stent restenosis than in those with restenosis without stenting.

Aged↗
PubMed2002

Differential expression of two distinct phenylalanine ammonia-lyase genes in condensed tannin-accumulating and lignifying cells of quaking aspen.

Lignins, along with condensed tannins (CTs) and salicylate-derived phenolic glycosides, constitute potentially large phenylpropanoid carbon sinks in tissues of quaking aspen (Populus tremuloides Michx.). Metabolic commitment to each of these sinks varies during development and adaptation, and depends on L-phenylalanine ammonia-lyase (PAL), an enzyme catalyzing the deamination of L-phenylalanine to initiate phenylpropanoid metabolism. In Populus spp., PAL is encoded by multiple genes whose expression has been associated with lignification in primary and secondary tissues. We now report cloning two differentially expressed PAL cDNAs that exhibit distinct spatial associations with CT and lignin biosynthesis in developing shoot and root tissues of aspen. PtPAL1 was expressed in certain CT-accumulating, non-lignifying cells of stems, leaves, and roots, and the pattern of PtPAL1 expression varied coordinately with that of CT accumulation along the primary to secondary growth transition in stems. PtPAL2 was expressed in heavily lignified structural cells of shoots, but was also expressed in non-lignifying cells of root tips. Evidence of a role for Pt4CL2, encoding 4-coumarate:coenzyme A ligase, in determining CT sink strength was gained from cellular co-expression analysis with PAL1 and CTs, and from experiments in which leaf wounding increased PAL1 and 4CL2 expression as well as the relative allocation of carbon to CT with respect to phenolic glycoside, the dominant phenolic sink in aspen leaves. Leaf wounding also increased PAL2 and lignin pathway gene expression, but to a smaller extent. The absence of PAL2 in most CT-accumulating cells provides in situ support for the idea that PAL isoforms function in specific metabolic milieus.

Arabidopsis Proteins↗
PubMed2002

Differential substrate inhibition couples kinetically distinct 4-coumarate:coenzyme a ligases with spatially distinct metabolic roles in quaking aspen.

4-Coumarate:coenzyme A ligase (4CL) activates hydroxycinnamates for entry into phenylpropanoid branchways that support various metabolic activities, including lignification and flavonoid biosynthesis. However, it is not clear whether and how 4CL proteins with their broad substrate specificities fulfill the specific hydroxycinnamate requirements of the branchways they supply. Two tissue-specific 4CLs, Pt4CL1 and Pt4CL2, have previously been cloned from quaking aspen (Populus tremuloides Michx.), but whether they are catalytically adapted for the distinctive metabolic roles they are thought to support is not apparent from published biochemical data. Therefore, single- and mixed-substrate assays were conducted to determine whether the 4CLs from aspen exhibit clear catalytic identities under certain metabolic circumstances. Recombinant Pt4CL1 and Pt4CL2 exhibited the expected preference for p-coumarate in single-substrate assays, but strong competitive inhibition favored utilization of caffeate and p-coumarate, respectively, in mixed-substrate assays. The Pt4CL1 product, caffeoyl-CoA, predominated in mixed-substrate assays with xylem extract, and this was consistent with the near absence of Pt4CL2 expression in xylem tissue as determined by in situ hybridization. It is interesting that the Pt4CL2 product p-coumaroyl-CoA predominated in assays with developing leaf extract, although in situ hybridization revealed that both genes were coexpressed. The xylem extract and recombinant 4CL1 data allow us to advance a mechanism by which 4CL1 can selectively utilize caffeate for the support of monolignol biosynthesis in maturing xylem and phloem fibers. Loblolly pine (Pinus taeda), in contrast, possesses a single 4CL protein exhibiting broad substrate specificity in mixed-substrate assays. We discuss these 4CL differences in terms of the contrasts in lignification between angiosperm trees and their gymnosperm progenitors.

Acyl Coenzyme A↗