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1.
J Econ Entomol ; 116(6): 2104-2115, 2023 12 11.
Article in English | MEDLINE | ID: mdl-37904544

ABSTRACT

Exclusion netting in some European and North American apple (Malus domestica Borkhausen, Rosaceae, Rosales) orchards has been documented to be an effective method of control for multiple insect pest species. By minimizing reliance on insecticides, these orchards have reduced costs, risks to the environment and non-target species, and reduced the risk of insecticide resistance. This study examined the use of commercially available hail netting (DrapeNet®; Prosser, WA) as a pest exclusion strategy under conditions in Minnesota, USA. In 2021 and 2022, we assessed the efficacy of hail netting as a tool for pest suppression in orchards by monitoring pest species in netted and open plots crossed with and without insecticide applications. Our findings show that both of the major pest species in Minnesota, the codling moth (Cydia pomonella L.; Lepidoptera: Tortricidae) and the apple maggot (Rhagoletis pomonella Walsh; Diptera: Tephritidae), were significantly reduced inside the netting compared to open plots by 94% and 96%, respectively. For a secondary pest, the red-banded leafroller (Argyrotaenia velutinana Walker; Lepidoptera: Tortricidae), moth populations were reduced by 56%. We also found that insecticide application alone did not significantly reduce pest pressure in these species. Additionally, we investigated the subsequent effects of hail netting on fruit quality and yield. The use of hail netting and insecticide application resulted in significantly higher proportions of high-quality fruit at harvest. However, netting did not significantly influence yield. These findings suggest that hail netting can be used to control Midwest apple insect pests with limited insecticide applications while maintaining high fruit quality.


Subject(s)
Insecticides , Malus , Moths , Tephritidae , Animals , Insecticides/pharmacology , Fruit , Minnesota , Insect Control/methods
2.
Expert Rev Neurother ; 23(10): 859-866, 2023.
Article in English | MEDLINE | ID: mdl-37646130

ABSTRACT

INTRODUCTION: Amyotrophic lateral sclerosis (ALS) is a progressive and incurable neurodegenerative disease. While pharmacotherapy options remain limited, the Food and Drug Administration (FDA) approved intravenous (IV) and oral edaravone for the treatment of ALS in 2017 and 2022, respectively. With the addition of oral edaravone, patients with ALS may exclusively use oral medications. AREAS COVERED: The authors performed a review of the published literature using the United States (US) National Library of Medicine's PubMed.gov resource to describe the pharmacokinetics, pharmacodynamics, safety, and efficacy of oral edaravone, as well as pertinent completed and ongoing clinical trials, including the oral edaravone clinical trial development program. The clinical profile of oral edaravone is also discussed. EXPERT OPINION: Edaravone has been shown to slow the rate of motor function deterioration experienced by patients with ALS. As the oral formulation has been approved, patients with ALS may use it alone or in combination with other approved therapeutics. Additional clinical trials and real-world evidence are ongoing to gain further understanding of the clinical profile of oral edaravone.


Subject(s)
Amyotrophic Lateral Sclerosis , Neurodegenerative Diseases , Humans , Edaravone/pharmacokinetics , Amyotrophic Lateral Sclerosis/drug therapy , Neurodegenerative Diseases/drug therapy , Free Radical Scavengers/pharmacology , Administration, Intravenous
3.
G3 (Bethesda) ; 13(4)2023 04 11.
Article in English | MEDLINE | ID: mdl-36861345

ABSTRACT

The cecidomyiid fly, soybean gall midge, Resseliella maxima Gagné, is a recently discovered insect that feeds on soybean plants in the Midwestern United States. R. maxima larvae feed on soybean stems that may induce plant death and can cause considerable yield losses, making it an important agricultural pest. From three pools of 50 adults each, we used long-read nanopore sequencing to assemble a R. maxima reference genome. The final genome assembly is 206 Mb with 64.88× coverage, consisting of 1,009 contigs with an N50 size of 714 kb. The assembly is high quality with a Benchmarking Universal Single-Copy Ortholog (BUSCO) score of 87.8%. Genome-wide GC level is 31.60%, and DNA methylation was measured at 1.07%. The R. maxima genome is comprised of 21.73% repetitive DNA, which is in line with other cecidomyiids. Protein prediction annotated 14,798 coding genes with 89.9% protein BUSCO score. Mitogenome analysis indicated that R. maxima assembly is a single circular contig of 15,301 bp and shares highest identity to the mitogenome of the Asian rice gall midge, Orseolia oryzae Wood-Mason. The R. maxima genome has one of the highest completeness levels for a cecidomyiid and will provide a resource for research focused on the biology, genetics, and evolution of cecidomyiids, as well as plant-insect interactions in this important agricultural pest.


Subject(s)
Diptera , Animals , Diptera/genetics , Glycine max/genetics , Genome , DNA , Larva
4.
bioRxiv ; 2023 Feb 12.
Article in English | MEDLINE | ID: mdl-36798210

ABSTRACT

The cecidomyiid fly, soybean gall midge, Resseliella maxima Gagné, is a recently discovered insect that feeds on soybean plants in the Midwest US. Resseliella maxima larvae feed on soybean stems which may induce plant death and can cause considerable yield losses, making it an important agricultural pest. From three pools of 50 adults each, we used long-read nanopore sequencing to assemble a R. maxima reference genome. The final genome assembly is 206 Mb with 64.88X coverage, consisting of 1009 contigs with an N50 size of 714 kb. The assembly is high quality with a BUSCO score of 87.8%. Genome-wide GC level is 31.60% and DNA methylation was measured at 1.07%. The R. maxima genome is comprised of 21.73% repetitive DNA, which is in line with other cecidomyiids. Protein prediction annotated 14,798 coding genes with 89.9% protein BUSCO score. Mitogenome analysis indicated that R. maxima assembly is a single circular contig of 15,301 bp and shares highest identity to the mitogenome of the Asian rice gall midge, Orseolia oryzae (Wood-Mason). The R. maxima genome has one of the highest completeness levels for a cecidomyiid and will provide a resource for research focused on the biology, genetics, and evolution of cecidomyiids, as well as plant-insect interactions in this important agricultural pest.

5.
Front Insect Sci ; 3: 1266426, 2023.
Article in English | MEDLINE | ID: mdl-38469531

ABSTRACT

Apple orchards are highly managed agricultural ecosystems where growers typically rely on insecticides to minimize the risk of pest-related fruit losses. Apple growers practicing integrated pest management require cost-effective alternatives to conventional insecticides for control of major pests such as codling moth (Cydia pomonella L.) and apple maggot (Rhagoletis pomonella Walsh). Exclusion netting has been shown to effectively control multiple insect pest species, limit fruit damage and reduce the use of insecticides while also conferring consumer and environmental benefits. In this study, partial budgeting was applied to explore the financial efficacy of using a hail netting (DrapeNet®) system as a sustainable pest management strategy for Midwest U.S. apple (Malus x domestica). The cost of the hail netting was compared to a common Midwest insecticide spray regimen for apples using yield and quality data from a field study at two Minnesota apple orchards in 2021-2022. The PB analysis indicated that the netting system was an economically competitive alternative to conventional insecticide applications. The economic results were robust across a range of apple prices and yields suggesting that Minnesota apple growers can benefit economically from the application of hail netting for sustainable pest management.

6.
Muscle Nerve ; 66(5): 593-602, 2022 11.
Article in English | MEDLINE | ID: mdl-36053970

ABSTRACT

INTRODUCTION/AIMS: In this study we examined the relationship between urate levels at baseline and functional change measured by the Amyotrophic Lateral Sclerosis Functional Rating Scale-Revised (ALSFRS-R) total score after edaravone treatment. METHODS: Data from the edaravone trials MCI186-16, MCI186-17, and MCI186-19 were analyzed, including the following treatment sequence groups: edaravone-edaravone (EE, n = 113); edaravone-placebo (EP, n = 45); and placebo-edaravone (PE, n = 146). Subgroups were defined as low baseline urate (below the median value of 4.8 mg/dL) and high baseline urate (≥4.8 mg/dL). The differences in ALSFRS-R total score change and urate change were evaluated using the mixed model for repeated measurement for overall population, by urate-level subgroup, and by trial. RESULTS: Compared with the PE group, the EE group showed a slower decline in ALSFRS-R score, regardless of the urate baseline level, and a slower decline in urate level in the higher baseline urate subgroup. Smaller changes in ALSFRS-R score and urate were observed in patients diagnosed with "probable, laboratory-supported ALS." There was a positive correlation between changes from baseline to cycle 12 in urate levels and ALSFRS-R score. DISCUSSION: Edaravone treatment in ALS patients diagnosed with "definite ALS" or "probable ALS" showed slowing of disease progression, regardless of baseline urate level. In addition, because edaravone treatment was associated with a slower decline in urate level in the higher baseline urate subgroup and urate-level changes were associated with changes in ALSFRS-R score, urate level, and/or change may be one indicator in predicting disease progression after edaravone administration.


Subject(s)
Amyotrophic Lateral Sclerosis , Humans , Disease Progression , Edaravone/therapeutic use , Free Radical Scavengers/therapeutic use , Uric Acid , Clinical Trials as Topic
7.
Muscle Nerve ; 66(5): 583-592, 2022 11.
Article in English | MEDLINE | ID: mdl-36054038

ABSTRACT

INTRODUCTION/AIMS: Edaravone in amyotrophic lateral sclerosis (ALS) was analyzed in two phase 3 studies (MCI186-16 and MCI186-19). Those trials enrolled patients with Japanese ALS severity grades 1 and 2 (less severe ALS), but many patients progressed to grades 3 and 4 during the double-blind treatment period. The placebo patients who initiated edaravone treatment in the open-label periods provided an opportunity to assess the effects of edaravone in more severe ALS. This study also assessed the association between ALS Functional Rating Scale-Revised (ALSFRS-R) slope and biomarker changes after open-label edaravone initiation. METHODS: Change in ALSFRS-R slope in placebo patients before and after initiating edaravone treatment was assessed using the random coefficient model. The association of ALSFRS-R change and blood marker changes was explored by the least absolute shrinkage and selection operator (LASSO) method of machine learning. RESULTS: Twenty-four percent of patients (35/146) in the placebo-edaravone group showed ≥25% slowing of decline in the ALSFRS-R slope. Within the 25% slower-decline group, 60% (21/35) had Japanese ALS severity grades 3 or 4 at the start of edaravone treatment. The LASSO model identified serum urate as associated with the percentage change in ALSFRS-R slope. The rate of decrease in urate was smaller in the 25% slower-decline group than in the non-25% slower-decline group during edaravone treatment. DISCUSSION: This post hoc analysis indicated that ALS patients, including those with advanced ALS severity grades, may receive benefit in the group of patients whose urate levels are stable during the course of the edaravone treatment.


Subject(s)
Amyotrophic Lateral Sclerosis , Edaravone , Uric Acid , Humans , Amyotrophic Lateral Sclerosis/drug therapy , Amyotrophic Lateral Sclerosis/physiopathology , Disease Progression , Edaravone/therapeutic use , Free Radical Scavengers/therapeutic use , Uric Acid/blood , Double-Blind Method , Clinical Trials, Phase III as Topic
8.
Neurol Clin Pract ; 11(4): e472-e479, 2021 Aug.
Article in English | MEDLINE | ID: mdl-34476128

ABSTRACT

OBJECTIVES: To identify putative biomarkers that may serve as quantifiable, biological, nonclinical measures of the pharmacodynamic effect of edaravone in amyotrophic lateral sclerosis (ALS) and to report real-world treatment outcomes. METHODS: This is a prospective, observational, longitudinal, multicenter (up to 40 sites) US study (Clinicaltrials.gov; NCT04259255) with at least 200 patients with ALS who will receive edaravone for 24 weeks (6 cycles; Food and Drug Administration-approved regimen). All participants must either be treatment naive for edaravone or be more than 1 month without receiving any edaravone dose before screening. Biomarker quantification and other assessments will be performed at baseline (before cycle 1) and during cycles 1, 3, and 6. Selected biomarkers of oxidative stress, inflammation, neuronal injury and death, and muscle injury, as well as biomarker discovery panels (EpiSwitch and SOMAscan), will be evaluated and, when feasible, compared with biobanked samples. Clinical efficacy assessments will include the ALS Functional Rating Scale-Revised, King's clinical staging, ALS Assessment Questionnaire-40, Appel ALS Score (Rating Scale), slow vital capacity, hand-held dynamometry and grip strength, and time to specified states of disease progression or death. DNA samples will also be collected for potential genomic evaluation. The predicted rates of progression and survival, and their potential correlations with biomarkers, will be evaluated. Adverse events related to the study will be reported. RESULTS: The study is estimated to be completed in 2022 with an interim analysis planned. CONCLUSIONS: Findings may help to further the understanding of the pharmacodynamic effect of edaravone, including changes in biomarkers, in response to treatment.

9.
J Pediatr ; 170: 295-300, 2016 Mar.
Article in English | MEDLINE | ID: mdl-26725208

ABSTRACT

OBJECTIVE: To describe opinions about suicide risk screening in a pediatric medical inpatient sample. STUDY DESIGN: As part of a larger instrument validation study, 200 pediatric medical inpatients (ages 10-21 years) were screened for suicide risk. Participants completed demographic self-report forms and were asked their opinions about suicide risk screening. Patient responses were recorded verbatim by trained research social workers. Qualitative data was analyzed using thematic analysis. RESULTS: The majority of adolescents who participated had not been previously asked about suicide (N = 101; 62.3%) and were supportive of suicide risk screening (81.0%). Five salient themes emerged from the qualitative analysis of patient opinions: prevention, elevated risk, emotional benefits, provider responsibility, and lack of harm in asking. CONCLUSIONS: The majority of youth screened for suicide risk on medical inpatient units were supportive of suicide risk screening. Opinion data have the potential to inform screening practices and assure clinicians that suicide risk screening will be acceptable to pediatric patients and their parents. Given the lack of screening in these patients' past experiences, the medical setting is a unique opportunity to capture youth at risk for suicide.


Subject(s)
Adolescent, Hospitalized/psychology , Child, Hospitalized/psychology , Inpatients/psychology , Mass Screening/psychology , Patient Acceptance of Health Care/psychology , Suicide Prevention , Adolescent , Boston , Child , Female , Humans , Male , Mass Screening/methods , Patient Acceptance of Health Care/statistics & numerical data , Qualitative Research , Suicide/psychology , Young Adult
10.
J Alzheimers Dis ; 47(3): 741-50, 2015.
Article in English | MEDLINE | ID: mdl-26401708

ABSTRACT

BACKGROUND: There is an urgent need to discover Alzheimer's disease (AD) biomarkers that are both easily measured and reliable. Research into blood-based biomarkers for AD using transcriptomics and proteomics has been an attractive and promising area of research. However, to date researchers have not looked into the possibility of AD medication being a confounding factor in these studies. OBJECTIVE: This study explored whether acetylcholinesterase inhibitors (AChEIs), the main class of AD medication, are a confounding factor in AD blood biomarker studies. METHODS: The most promising blood transcriptomic and proteomic biomarkers from two recent studies were analyzed to determine if they were differentially expressed between AD subjects on AChEIs and subjects that were not. RESULTS: None of the gene or protein biomarkers analyzed were found to be significantly altered between subjects in either group. CONCLUSION: This study found no evidence that AChEIs are a confounding factor in these published AD blood biomarker studies. Further work is needed to confirm that this is also the case for other proposed biomarkers.


Subject(s)
Alzheimer Disease/blood , Alzheimer Disease/drug therapy , Cholinesterase Inhibitors/therapeutic use , Nootropic Agents/therapeutic use , Aged , Alzheimer Disease/genetics , Apolipoprotein E4/genetics , Biomarkers/blood , Cholinesterase Inhibitors/adverse effects , Cognitive Dysfunction/blood , Cognitive Dysfunction/drug therapy , Cognitive Dysfunction/genetics , Cohort Studies , Female , Gene Expression/drug effects , Gene Expression/physiology , Humans , Male , Mental Status Schedule , Microarray Analysis , Nootropic Agents/adverse effects , Proteomics , Reproducibility of Results
11.
Proc Natl Acad Sci U S A ; 112(23): 7153-8, 2015 Jun 09.
Article in English | MEDLINE | ID: mdl-26039989

ABSTRACT

Serum biomarkers in Duchenne muscular dystrophy (DMD) may provide deeper insights into disease pathogenesis, suggest new therapeutic approaches, serve as acute read-outs of drug effects, and be useful as surrogate outcome measures to predict later clinical benefit. In this study a large-scale biomarker discovery was performed on serum samples from patients with DMD and age-matched healthy volunteers using a modified aptamer-based proteomics technology. Levels of 1,125 proteins were quantified in serum samples from two independent DMD cohorts: cohort 1 (The Parent Project Muscular Dystrophy-Cincinnati Children's Hospital Medical Center), 42 patients with DMD and 28 age-matched normal volunteers; and cohort 2 (The Cooperative International Neuromuscular Research Group, Duchenne Natural History Study), 51 patients with DMD and 17 age-matched normal volunteers. Forty-four proteins showed significant differences that were consistent in both cohorts when comparing DMD patients and healthy volunteers at a 1% false-discovery rate, a large number of significant protein changes for such a small study. These biomarkers can be classified by known cellular processes and by age-dependent changes in protein concentration. Our findings demonstrate both the utility of this unbiased biomarker discovery approach and suggest potential new diagnostic and therapeutic avenues for ameliorating the burden of DMD and, we hope, other rare and devastating diseases.


Subject(s)
Biomarkers/blood , Blood Proteins/metabolism , Muscular Dystrophy, Duchenne/blood , Adolescent , Adult , Case-Control Studies , Child , Child, Preschool , Cohort Studies , Humans , Male , Young Adult
12.
J Gerontol A Biol Sci Med Sci ; 70(7): 809-16, 2015 Jul.
Article in English | MEDLINE | ID: mdl-25123647

ABSTRACT

To elucidate the proteomic features of aging in plasma, the subproteome targeted by the SOMAscan assay was profiled in blood samples from 202 females from the TwinsUK cohort. Findings were replicated in 677 independent individuals from the AddNeuroMed, Alzheimer's Research UK, and Dementia Case Registry cohorts. Results were further validated using RNAseq data from whole blood in TwinsUK and the most significant proteins were tested for association with aging-related phenotypes after adjustment for age. Eleven proteins were associated with chronological age and were replicated at protein level in an independent population. These were further investigated at gene expression level in 384 females from the TwinsUK cohort. The two most strongly associated proteins were chordin-like protein 1 (meta-analysis ß [SE] = 0.013 [0.001], p = 3.66 × 10(-46)) and pleiotrophin (0.012 [0.005], p = 3.88 × 10(-41)). Chordin-like protein 1 was also significantly correlated with birthweight (0.06 [0.02], p = 0.005) and with the individual Framingham 10-years cardiovascular risk scores in TwinsUK (0.71 [0.18], p = 9.9 × 10(-5)). Pleiotrophin is a secreted growth factor with a plethora of functions in multiple tissues and known to be a marker for cardiovascular risk and osteoporosis. Our study highlights the importance of proteomics to identify some molecular mechanisms involved in human health and aging.


Subject(s)
Aging/blood , Proteomics , Registries , Adult , Aged , Aged, 80 and over , Biomarkers/blood , Carrier Proteins/blood , Cohort Studies , Cytokines/blood , Eye Proteins/blood , Female , Humans , Insulin-Like Growth Factor Binding Protein 6/blood , Male , Matrix Metalloproteinase 12/blood , Middle Aged , Nerve Tissue Proteins/blood , Phenotype , Twins , United Kingdom
13.
Alzheimers Dement ; 10(6): 724-34, 2014 Nov.
Article in English | MEDLINE | ID: mdl-24768341

ABSTRACT

Blood proteins and their complexes have become the focus of a great deal of interest in the context of their potential as biomarkers of Alzheimer's disease (AD). We used a SOMAscan assay for quantifying 1001 proteins in blood samples from 331 AD, 211 controls, and 149 mild cognitive impaired (MCI) subjects. The strongest associations of protein levels with AD outcomes were prostate-specific antigen complexed to α1-antichymotrypsin (AD diagnosis), pancreatic prohormone (AD diagnosis, left entorhinal cortex atrophy, and left hippocampus atrophy), clusterin (rate of cognitive decline), and fetuin B (left entorhinal atrophy). Multivariate analysis found that a subset of 13 proteins predicted AD with an accuracy of area under the curve of 0.70. Our replication of previous findings provides further evidence that levels of these proteins in plasma are truly associated with AD. The newly identified proteins could be potential biomarkers and are worthy of further investigation.


Subject(s)
Alzheimer Disease/blood , Biomarkers/blood , Blood Proteins/metabolism , Magnetic Resonance Imaging , Proteomics , Aged , Aged, 80 and over , Atrophy/etiology , Brain/pathology , Cognitive Dysfunction/blood , Cohort Studies , Female , Humans , Logistic Models , Male , ROC Curve
14.
J Alzheimers Dis ; 38(3): 515-31, 2014.
Article in English | MEDLINE | ID: mdl-24121966

ABSTRACT

A blood-based protein biomarker, or set of protein biomarkers, that could predict onset and progression of Alzheimer's disease (AD) would have great utility; potentially clinically, but also for clinical trials and especially in the selection of subjects for preventative trials. We reviewed a comprehensive list of 21 published discovery or panel-based (> 100 proteins) blood proteomics studies of AD, which had identified a total of 163 candidate biomarkers. Few putative blood-based protein biomarkers replicate in independent studies but we found that some proteins do appear in multiple studies; for example, four candidate biomarkers are found to associate with AD-related phenotypes in five independent research cohorts in these 21 studies: α-1-antitrypsin, α-2-macroglobulin, apolipoprotein E, and complement C3. Using SomaLogic's SOMAscan proteomics technology, we were able to conduct a large-scale replication study for 94 of the 163 candidate biomarkers from these 21 published studies in plasma samples from 677 subjects from the AddNeuroMed (ANM) and the Alzheimer's Research UK/Maudsley BRC Dementia Case Registry at King's Health Partners (ARUK/DCR) research cohorts. Nine of the 94 previously reported candidates were found to associate with AD-related phenotypes (False Discovery Rate (FDR) q-value < 0.1). These proteins show sufficient replication to be considered for further investigation as a biomarker set. Overall, we show that there are some signs of a replicable signal in the range of proteins identified in previous studies and we are able to further replicate some of these. This suggests that AD pathology does affect the blood proteome with some consistency.


Subject(s)
Alzheimer Disease/blood , Alzheimer Disease/diagnosis , Biomarkers/blood , Blood Proteins/metabolism , Disease Progression , Humans , Proteome
15.
Hum Mol Genet ; 21(16): 3719-26, 2012 Aug 15.
Article in English | MEDLINE | ID: mdl-22595970

ABSTRACT

Proteins are central to almost all cellular processes, and dysregulation of expression and function is associated with a range of disorders. A number of studies in human have recently shown that genetic factors significantly contribute gene expression variation. In contrast, very little is known about the genetic basis of variation in protein abundance in man. Here, we assayed the abundance levels of proteins in plasma from 96 elderly Europeans using a new aptamer-based proteomic technology and performed genome-wide local (cis-) regulatory association analysis to identify protein quantitative trait loci (pQTL). We detected robust cis-associations for 60 proteins at a false discovery rate of 5%. The most highly significant single nucleotide polymorphism detected was rs7021589 (false discovery rate, 2.5 × 10(-12)), mapped within the gene coding sequence of Tenascin C (TNC). Importantly, we identified evidence of cis-regulatory variation for 20 previously disease-associated genes encoding protein, including variants with strong evidence of disease association show significant association with protein abundance levels. These results demonstrate that common genetic variants contribute to the differences in protein abundance levels in human plasma. Identification of pQTLs will significantly enhance our ability to discover and comprehend the biological and functional consequences of loci identified from genome-wide association study of complex traits. This is the first large-scale genetic association study of proteins in plasma measured using a novel, highly multiplexed slow off-rate modified aptamer (SOMAmer) proteomic platform.


Subject(s)
Blood Proteins/genetics , Polymorphism, Single Nucleotide , Regulatory Sequences, Nucleic Acid , Aged , Aged, 80 and over , Aptamers, Nucleotide , Female , Genetic Predisposition to Disease , Genome-Wide Association Study , Humans , Male , Middle Aged , Proteomics/methods , Quantitative Trait Loci
16.
Am J Pathol ; 180(2): 446-56, 2012 Feb.
Article in English | MEDLINE | ID: mdl-22122984

ABSTRACT

An important precondition for the successful development of diagnostic assays of cerebrospinal fluid (CSF) biomarkers of age-related neurodegenerative diseases is an understanding of the dynamic nature of the CSF proteome during the normal aging process. In this study, a novel proteomic technology was used to quantify hundreds of proteins simultaneously in the CSF from 90 cognitively normal adults 21 to 85 years of age. SomaLogic's highly multiplexed proteomic platform can measure more than 800 proteins simultaneously from small volumes of biological fluids using novel slow off-rate modified aptamer (SOMAmer) protein affinity reagents with sensitivity, specificity, and dynamic ranges that meet or exceed those of enzyme-linked immunosorbent assays. In the first application of this technology to CSF, we detected 248 proteins that possessed signals greater than twofold over background. Several novel correlations between detected protein concentrations and age were discovered that indicate that both inflammation and response to injury in the central nervous system may increase with age. Applying this powerful proteomic approach to CSF provides potential new insight into the aging of the human central nervous system that may have utility in discovering new disease-related changes in the CSF proteome.


Subject(s)
Aging/metabolism , Aptamers, Nucleotide/metabolism , Cerebrospinal Fluid Proteins/analysis , Protein Array Analysis/methods , Proteome/metabolism , Adult , Aged , Aged, 80 and over , Aging/genetics , Biomarkers/cerebrospinal fluid , Female , Humans , Male , Middle Aged , Proteome/genetics , Young Adult
17.
PLoS One ; 5(12): e15004, 2010 Dec 07.
Article in English | MEDLINE | ID: mdl-21165148

ABSTRACT

BACKGROUND: The interrogation of proteomes ("proteomics") in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology and medicine. METHODOLOGY/PRINCIPAL FINDINGS: We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes (15 µL of serum or plasma). Our current assay measures 813 proteins with low limits of detection (1 pM median), 7 logs of overall dynamic range (~100 fM-1 µM), and 5% median coefficient of variation. This technology is enabled by a new generation of aptamers that contain chemically modified nucleotides, which greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the aptamers are selected. Proteins in complex matrices such as plasma are measured with a process that transforms a signature of protein concentrations into a corresponding signature of DNA aptamer concentrations, which is quantified on a DNA microarray. Our assay takes advantage of the dual nature of aptamers as both folded protein-binding entities with defined shapes and unique nucleotide sequences recognizable by specific hybridization probes. To demonstrate the utility of our proteomics biomarker discovery technology, we applied it to a clinical study of chronic kidney disease (CKD). We identified two well known CKD biomarkers as well as an additional 58 potential CKD biomarkers. These results demonstrate the potential utility of our technology to rapidly discover unique protein signatures characteristic of various disease states. CONCLUSIONS/SIGNIFICANCE: We describe a versatile and powerful tool that allows large-scale comparison of proteome profiles among discrete populations. This unbiased and highly multiplexed search engine will enable the discovery of novel biomarkers in a manner that is unencumbered by our incomplete knowledge of biology, thereby helping to advance the next generation of evidence-based medicine.


Subject(s)
Aptamers, Nucleotide , Biomarkers/metabolism , Proteomics/methods , Aged , Evidence-Based Medicine , Female , Gene Library , Genetic Techniques , Glomerular Filtration Rate , Humans , Kidney Failure, Chronic/metabolism , Kinetics , Male , Mass Spectrometry/methods , Middle Aged , Nucleic Acid Hybridization , Oligonucleotide Array Sequence Analysis , Proteome , Reproducibility of Results
18.
Free Radic Biol Med ; 40(2): 341-7, 2006 Jan 15.
Article in English | MEDLINE | ID: mdl-16413416

ABSTRACT

A composition consisting of extracts of five widely studied medicinal plants (Protandim) was administered to healthy human subjects ranging in age from 20 to 78 years. Individual ingredients were selected on the basis of published findings of induction of superoxide dismutase (SOD) and/or catalase in rodents in vivo, combined with evidence of decreasing lipid peroxidation. Each ingredient was present at a dosage sufficiently low to avoid any accompanying unwanted pharmacological effects. Blood was analyzed before supplementation and after 30 and 120 days of supplementation (675 mg/day). Erythrocytes were assayed for SOD and catalase, and plasma was assayed for lipid peroxidation products as thiobarbituric acid-reacting substances (TBARS), as well as uric acid, C-reactive protein, and cholesterol (total, LDL, and HDL). Before supplementation, TBARS showed a strong age-dependent increase. After 30 days of supplementation, TBARS declined by an average of 40% (p = 0.0001) and the age-dependent increase was eliminated. By 120 days, erythrocyte SOD increased by 30% (p < 0.01) and catalase by 54% (p < 0.002). We conclude that modest induction of the catalytic antioxidants SOD and catalase may be a much more effective approach than supplementation with antioxidants (such as vitamins C and E) that can, at best, stoichiometrically scavenge a very small fraction of total oxidant production.


Subject(s)
Antioxidants/therapeutic use , Catalase/metabolism , Drugs, Chinese Herbal/administration & dosage , Gene Expression Regulation/drug effects , Superoxide Dismutase/metabolism , Adult , Age Factors , Aged , Antioxidants/administration & dosage , Ascorbic Acid/administration & dosage , Ascorbic Acid/therapeutic use , C-Reactive Protein/drug effects , C-Reactive Protein/metabolism , Catalase/blood , Catalase/drug effects , Dose-Response Relationship, Drug , Drugs, Chinese Herbal/adverse effects , Drugs, Chinese Herbal/toxicity , Female , Humans , Lipids/physiology , Male , Middle Aged , Reference Values , Superoxide Dismutase/blood , Superoxide Dismutase/drug effects , Thiobarbituric Acid Reactive Substances/metabolism , Time Factors , Uric Acid/blood , Uric Acid/metabolism , Vitamin A/administration & dosage , Vitamin A/therapeutic use
19.
Biomed Pharmacother ; 59(4): 149-57, 2005 May.
Article in English | MEDLINE | ID: mdl-15862708

ABSTRACT

Every transplant is a reperfused organ and, therefore, undergoes some degree of oxidative damage. Postischemic reperfusion injury results in non-specific free radical-mediated acute endothelial damage, cell death and organ failure. The endothelium is a key site of injury from reactive oxygen species (ROS), and the endothelial cell dysfunction is central to the pathogenesis of arteriosclerosis. Accelerated arteriosclerosis, secondary to chronic allograft rejection, is a major long-term complication of heart transplantation. Therefore, preservation methods that would decrease injury during reperfusion are very important. We have developed a unique preservation solution, with a multifaceted approach, which best preserves the organ from ROS for an extended period of time before transplantation. The advantages of extending this period of preservation include an expansion of the donor pool, by permitting more distant procurement, the ability to perform detailed tissue typing, therefore, improves histocompatibility match and a reduction in emergency surgery as a result of graft rejection.


Subject(s)
Free Radical Scavengers/metabolism , Heart Arrest, Induced/methods , Heart Transplantation/methods , Organ Preservation Solutions , Organ Preservation/methods , Oxidative Stress , Reactive Oxygen Species/adverse effects , Reperfusion Injury/enzymology , Superoxide Dismutase/metabolism , Animals , Humans , Rabbits , Reactive Oxygen Species/metabolism , Reperfusion Injury/prevention & control
20.
J Heart Lung Transplant ; 21(12): 1296-303, 2002 Dec.
Article in English | MEDLINE | ID: mdl-12490275

ABSTRACT

BACKGROUND: The plasma membranes of endothelial cells are sites of physiologic injury caused by superoxide attack, whether the radicals are generated within the cell (i.e., from enzymatic sources such as xanthine oxidase or from ischemically injured mitochondria) or are generated within the interstitial spaces by activated neutrophils or macrophages. An extracellular superoxide dismutase (ECSOD) electrostatically bound to endothelial surfaces partially protects against this oxidative attack. To provide a therapeutic equivalent of this ECSOD activity, we evaluated the product of a fusion gene encoding a chimeric manganese SOD (chimeric-SOD) and the carboxyl-terminal 26-amino acid basic "tail" from ECSOD with high affinity for heparin-like proteoglycans on cell surfaces. METHODS: We tested the chimeric-SOD in isolated rabbit hearts during warm and cold ischemia. RESULTS: When perfused through an isolated rabbit heart, chimeric-SOD bound to endothelial surfaces and was displaced by a bolus dose of heparin. In an established model of no-flow ischemia followed by reperfusion of the isolated rabbit heart, the chimeric-SOD was as protective as native Mn-SOD or Cu,Zn-SOD, but at doses nearly 2 orders of magnitude lower. In a rabbit-heart preservation model, the chimeric-SOD provided better recovery of function after 4 hours of cold ischemia than did University of Wisconsin cardioplegia solution. CONCLUSION: This chimeric-SOD can bind to cell surfaces and may aid in preventing superoxide-mediated endothelial damage and may function as a rational therapeutic agent for treating free-radical-mediated diseases.


Subject(s)
Heparin/pharmacology , Myocardial Reperfusion Injury/prevention & control , Recombinant Fusion Proteins/drug effects , Superoxide Dismutase/pharmacology , Analysis of Variance , Animals , Disease Models, Animal , Endothelium, Vascular/drug effects , Endothelium, Vascular/physiology , Female , Humans , Male , Myocardial Contraction/drug effects , Myocardial Contraction/physiology , Myocardial Reperfusion Injury/physiopathology , Probability , Protein Binding/drug effects , Rabbits , Recombinant Fusion Proteins/physiology , Sensitivity and Specificity
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