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1.
Am J Psychiatry ; 180(12): 884-895, 2023 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-37849304

RESUMO

OBJECTIVE: Postpartum depression (PPD) is a common subtype of major depressive disorder (MDD) that is more heritable, yet is understudied in psychiatric genetics. The authors conducted meta-analyses of genome-wide association studies (GWASs) to investigate the genetic architecture of PPD. METHOD: Meta-analyses were conducted on 18 cohorts of European ancestry (17,339 PPD cases and 53,426 controls), one cohort of East Asian ancestry (975 cases and 3,780 controls), and one cohort of African ancestry (456 cases and 1,255 controls), totaling 18,770 PPD cases and 58,461 controls. Post-GWAS analyses included 1) single-nucleotide polymorphism (SNP)-based heritability ([Formula: see text]), 2) genetic correlations between PPD and other phenotypes, and 3) enrichment of the PPD GWAS findings in 27 human tissues and 265 cell types from the mouse central and peripheral nervous system. RESULTS: No SNP achieved genome-wide significance in the European or the trans-ancestry meta-analyses. The [Formula: see text] of PPD was 0.14 (SE=0.02). Significant genetic correlations were estimated for PPD with MDD, bipolar disorder, anxiety disorders, posttraumatic stress disorder, insomnia, age at menarche, and polycystic ovary syndrome. Cell-type enrichment analyses implicate inhibitory neurons in the thalamus and cholinergic neurons within septal nuclei of the hypothalamus, a pattern that differs from MDD. CONCLUSIONS: While more samples are needed to reach genome-wide levels of significance, the results presented confirm PPD as a polygenic and heritable phenotype. There is also evidence that despite a high correlation with MDD, PPD may have unique genetic components. Cell enrichment results suggest GABAergic neurons, which converge on a common mechanism with the only medication approved by the U.S. Food and Drug Administration for PPD (brexanolone).


Assuntos
Transtorno Bipolar , Depressão Pós-Parto , Transtorno Depressivo Maior , Feminino , Humanos , Animais , Camundongos , Transtorno Depressivo Maior/genética , Estudo de Associação Genômica Ampla , Depressão Pós-Parto/genética , Predisposição Genética para Doença , Transtorno Bipolar/genética , Polimorfismo de Nucleotídeo Único/genética
2.
Anal Chem ; 94(27): 9540-9547, 2022 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-35767427

RESUMO

Despite advances in proteomic technologies, clinical translation of plasma biomarkers remains low, partly due to a major bottleneck between the discovery of candidate biomarkers and costly clinical validation studies. Due to a dearth of multiplexable assays, generally only a few candidate biomarkers are tested, and the validation success rate is accordingly low. Previously, mass spectrometry-based approaches have been used to fill this gap but feature poor quantitative performance and were generally limited to hundreds of proteins. Here, we demonstrate the capability of an internal standard triggered-parallel reaction monitoring (IS-PRM) assay to greatly expand the numbers of candidates that can be tested with improved quantitative performance. The assay couples immunodepletion and fractionation with IS-PRM and was developed and implemented in human plasma to quantify 5176 peptides representing 1314 breast cancer biomarker candidates. Characterization of the IS-PRM assay demonstrated the precision (median % CV of 7.7%), linearity (median R2 > 0.999 over 4 orders of magnitude), and sensitivity (median LLOQ < 1 fmol, approximately) to enable rank-ordering of candidate biomarkers for validation studies. Using three plasma pools from breast cancer patients and three control pools, 893 proteins were quantified, of which 162 candidate biomarkers were verified in at least one of the cancer pools and 22 were verified in all three cancer pools. The assay greatly expands capabilities for quantification of large numbers of proteins and is well suited for prioritization of viable candidate biomarkers.


Assuntos
Neoplasias da Mama , Proteômica , Biomarcadores/análise , Biomarcadores Tumorais , Neoplasias da Mama/diagnóstico , Feminino , Humanos , Espectrometria de Massas/métodos , Peptídeos/análise , Proteínas , Proteômica/métodos
3.
Plant Dis ; 106(11): 2788-2796, 2022 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-35442057

RESUMO

As molecular genetic techniques improve and sequence data becomes available for more fungal species, taxonomic classifications historically based upon growth morphology alone are being revisited and occasionally reclassified. Herein, we present such an instance for the fungal pathogen that causes dry berry disease of caneberries. The organism was previously described as the basidiomycete fungus Rhizoctonia rubi based upon the pathogen's production of Rhizoctonia-like angular branching hyphae. Utilizing molecular genetic techniques unavailable when the pathogen was first characterized in 1959, three housekeeping gene regions (ITS, ß-tubulin, and G3PDH) were sequenced across 13 contemporary dry berry isolates, as well as the original 1959 R. rubi type strain, CBS382.59. The resulting neighbor-joining, maximum likelihood, and Bayesian phylogenies for single and multilocus sequences provide strong evidence that the dry berry pathogen was misclassified. This data, in addition to revisiting in vivo macroscopic and microscopic growth morphology, again comparing contemporary dry berry isolates to the CBS382.59 type strain, suggests that the causal organism is a new species within the genus Monilinia that we propose be classified as Monilinia rubi. A transition from designation as a basidiomycete fungus to an ascomycete fungus could have implications on chemical management decisions, as well as the assumptions made about cell structure and the pathogen's putative life cycle.


Assuntos
Ascomicetos , Basidiomycota , Frutas/microbiologia , Teorema de Bayes , Ascomicetos/genética , Filogenia
4.
Neuropsychopharmacology ; 46(13): 2304-2311, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34588609

RESUMO

Studies in post-mortem human brain tissue have associated major depressive disorder (MDD) with cortical transcriptomic changes, whose potential in vivo impact remains unexplored. To address this translational gap, we recently developed a transcriptome-based polygenic risk score (T-PRS) based on common functional variants capturing 'depression-like' shifts in cortical gene expression. Here, we used a non-clinical sample of young adults (n = 482, Duke Neurogenetics Study: 53% women; aged 19.8 ± 1.2 years) to map T-PRS onto brain morphology measures, including Freesurfer-derived subcortical volume, cortical thickness, surface area, and local gyrification index, as well as broad MDD risk, indexed by self-reported family history of depression. We conducted side-by-side comparisons with a PRS independently derived from a Psychiatric Genomics Consortium (PGC) MDD GWAS (PGC-PRS), and sought to link T-PRS with diagnosis and symptom severity directly in PGC-MDD participants (n = 29,340, 59% women; 12,923 MDD cases, 16,417 controls). T-PRS was associated with smaller amygdala volume in women (t = -3.478, p = 0.001) and lower prefrontal gyrification across sexes. In men, T-PRS was associated with hypergyrification in temporal and occipital regions. Prefrontal hypogyrification mediated a male-specific indirect link between T-PRS and familial depression (b = 0.005, p = 0.029). PGC-PRS was similarly associated with lower amygdala volume and cortical gyrification; however, both effects were male-specific and hypogyrification emerged in distinct parietal and temporo-occipital regions, unassociated with familial depression. In PGC-MDD, T-PRS did not predict diagnosis (OR = 1.007, 95% CI = [0.997-1.018]) but correlated with symptom severity in men (rho = 0.175, p = 7.957 × 10-4) in one cohort (N = 762, 48% men). Depression-like shifts in cortical gene expression have sex-specific effects on brain morphology and may contribute to broad depression vulnerability in men.


Assuntos
Transtorno Depressivo Maior , Transcriptoma , Encéfalo/diagnóstico por imagem , Depressão/genética , Transtorno Depressivo Maior/genética , Feminino , Predisposição Genética para Doença , Humanos , Masculino , Herança Multifatorial , Adulto Jovem
5.
Front Immunol ; 12: 658372, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33986749

RESUMO

Conventional immunoprecipitation/mass spectroscopy identification of HLA-restricted peptides remains the purview of specializing laboratories, due to the complexity of the methodology, and requires computational post-analysis to assign peptides to individual alleles when using pan-HLA antibodies. We have addressed these limitations with ARTEMIS: a simple, robust, and flexible platform for peptide discovery across ligandomes, optionally including specific proteins-of-interest, that combines novel, secreted HLA-I discovery reagents spanning multiple alleles, optimized lentiviral transduction, and streamlined affinity-tag purification to improve upon conventional methods. This platform fills a middle ground between existing techniques: sensitive and adaptable, but easy and affordable enough to be widely employed by general laboratories. We used ARTEMIS to catalog allele-specific ligandomes from HEK293 cells for seven classical HLA alleles and compared results across replicates, against computational predictions, and against high-quality conventional datasets. We also applied ARTEMIS to identify potentially useful, novel HLA-restricted peptide targets from oncovirus oncoproteins and tumor-associated antigens.


Assuntos
Mapeamento de Epitopos/métodos , Espectrometria de Massas/métodos , Peptídeos/química , Peptídeos/imunologia , Motivos de Aminoácidos , Sequência de Aminoácidos , Animais , Linhagem Celular , Antígenos de Histocompatibilidade Classe I/imunologia , Antígenos de Histocompatibilidade Classe II/imunologia , Humanos , Camundongos , Modelos Moleculares , Ligação Proteica , Reprodutibilidade dos Testes , Relação Estrutura-Atividade , Fluxo de Trabalho
6.
Biol Psychiatry ; 87(5): 419-430, 2020 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-31570195

RESUMO

BACKGROUND: The prevalence of depression is higher in individuals with autoimmune diseases, but the mechanisms underlying the observed comorbidities are unknown. Shared genetic etiology is a plausible explanation for the overlap, and in this study we tested whether genetic variation in the major histocompatibility complex (MHC), which is associated with risk for autoimmune diseases, is also associated with risk for depression. METHODS: We fine-mapped the classical MHC (chr6: 29.6-33.1 Mb), imputing 216 human leukocyte antigen (HLA) alleles and 4 complement component 4 (C4) haplotypes in studies from the Psychiatric Genomics Consortium Major Depressive Disorder Working Group and the UK Biobank. The total sample size was 45,149 depression cases and 86,698 controls. We tested for association between depression status and imputed MHC variants, applying both a region-wide significance threshold (3.9 × 10-6) and a candidate threshold (1.6 × 10-4). RESULTS: No HLA alleles or C4 haplotypes were associated with depression at the region-wide threshold. HLA-B*08:01 was associated with modest protection for depression at the candidate threshold for testing in HLA genes in the meta-analysis (odds ratio = 0.98, 95% confidence interval = 0.97-0.99). CONCLUSIONS: We found no evidence that an increased risk for depression was conferred by HLA alleles, which play a major role in the genetic susceptibility to autoimmune diseases, or C4 haplotypes, which are strongly associated with schizophrenia. These results suggest that any HLA or C4 variants associated with depression either are rare or have very modest effect sizes.


Assuntos
Transtorno Depressivo Maior , Alelos , Depressão , Transtorno Depressivo Maior/epidemiologia , Transtorno Depressivo Maior/genética , Predisposição Genética para Doença , Antígenos HLA , Haplótipos , Humanos , Complexo Principal de Histocompatibilidade
7.
Biol Psychiatry ; 86(2): 110-119, 2019 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-30686506

RESUMO

BACKGROUND: Genetic risk for bipolar disorder (BD) is conferred through many common alleles, while a role for rare copy number variants (CNVs) is less clear. Subtypes of BD including schizoaffective disorder bipolar type (SAB), bipolar I disorder (BD I), and bipolar II disorder (BD II) differ according to the prominence and timing of psychosis, mania, and depression. The genetic factors contributing to the combination of symptoms among these subtypes are poorly understood. METHODS: Rare large CNVs were analyzed in 6353 BD cases (3833 BD I [2676 with psychosis, 850 without psychosis, and 307 with unknown psychosis history], 1436 BD II, 579 SAB, and 505 BD not otherwise specified) and 8656 controls. CNV burden and a polygenic risk score (PRS) for schizophrenia were used to evaluate the relative contributions of rare and common variants to risk of BD, BD subtypes, and psychosis. RESULTS: CNV burden did not differ between BD and controls when treated as a single diagnostic entity. However, burden in SAB was increased relative to controls (p = .001), BD I (p = .0003), and BD II (p = .0007). Burden and schizophrenia PRSs were increased in SAB compared with BD I with psychosis (CNV p = .0007, PRS p = .004), and BD I without psychosis (CNV p = .0004, PRS p = 3.9 × 10-5). Within BD I, psychosis was associated with increased schizophrenia PRSs (p = .005) but not CNV burden. CONCLUSIONS: CNV burden in BD is limited to SAB. Rare and common genetic variants may contribute differently to risk for psychosis and perhaps other classes of psychiatric symptoms.


Assuntos
Transtorno Bipolar/genética , Variações do Número de Cópias de DNA/genética , Transtornos Psicóticos/genética , Transtorno Bipolar/psicologia , Estudos de Casos e Controles , Estudos de Coortes , Duplicação Gênica/genética , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Humanos , Herança Multifatorial , Transtornos Psicóticos/psicologia , Esquizofrenia/genética
8.
Mol Microbiol ; 110(1): 114-127, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-30039535

RESUMO

Chronic infection with Helicobacter pylori can lead to the development of gastric ulcers and stomach cancers. The helical cell shape of H. pylori promotes stomach colonization. Screens for loss of helical shape have identified several periplasmic peptidoglycan (PG) hydrolases and non-enzymatic putative scaffolding proteins, including Csd5. Both over and under expression of the PG hydrolases perturb helical shape, but the mechanism used to coordinate and localize their enzymatic activities is not known. Using immunoprecipitation and mass spectrometry we identified Csd5 interactions with cytosolic proteins CcmA, a bactofilin required for helical shape, and MurF, a PG precursor synthase, as well as the inner membrane spanning ATP synthase. A combination of Csd5 domain deletions, point mutations, and transmembrane domain chimeras revealed that the N-terminal transmembrane domain promotes MurF, CcmA, and ATP synthase interactions, while the C-terminal SH3 domain mediates PG binding. We conclude that Csd5 promotes helical shape as part of a membrane associated, multi-protein shape complex that includes interactions with the periplasmic cell wall, a PG precursor synthesis enzyme, the bacterial cytoskeleton, and ATP synthase.


Assuntos
Parede Celular/metabolismo , Citoesqueleto/metabolismo , Helicobacter pylori/citologia , Helicobacter pylori/enzimologia , N-Acetil-Muramil-L-Alanina Amidase/metabolismo , Peptídeo Sintases/metabolismo , Proteínas da Membrana Bacteriana Externa/química , Proteínas da Membrana Bacteriana Externa/genética , Proteínas da Membrana Bacteriana Externa/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Membrana Celular/metabolismo , Deleção de Genes , Helicobacter pylori/genética , ATPases Mitocondriais Próton-Translocadoras/química , ATPases Mitocondriais Próton-Translocadoras/genética , ATPases Mitocondriais Próton-Translocadoras/metabolismo , N-Acetil-Muramil-L-Alanina Amidase/química , N-Acetil-Muramil-L-Alanina Amidase/genética , Peptídeo Sintases/química , Peptídeo Sintases/genética , Periplasma/metabolismo , Análise de Sequência de Proteína
9.
mBio ; 9(2)2018 04 03.
Artigo em Inglês | MEDLINE | ID: mdl-29615499

RESUMO

Elongation factor P (EF-P) is a ubiquitous translation factor that facilitates translation of polyproline motifs. In order to perform this function, EF-P generally requires posttranslational modification (PTM) on a conserved residue. Although the position of the modification is highly conserved, the structure can vary widely between organisms. In Bacillus subtilis, EF-P is modified at Lys32 with a 5-aminopentanol moiety. Here, we use a forward genetic screen to identify genes involved in 5-aminopentanolylation. Tandem mass spectrometry analysis of the PTM mutant strains indicated that ynbB, gsaB, and ymfI are required for modification and that yaaO, yfkA, and ywlG influence the level of modification. Structural analyses also showed that EF-P can retain unique intermediate modifications, suggesting that 5-aminopentanol is likely directly assembled on EF-P through a novel modification pathway. Phenotypic characterization of these PTM mutants showed that each mutant does not strictly phenocopy the efp mutant, as has previously been observed in other organisms. Rather, each mutant displays phenotypic characteristics consistent with those of either the efp mutant or wild-type B. subtilis depending on the growth condition. In vivo polyproline reporter data indicate that the observed phenotypic differences result from variation in both the severity of polyproline translation defects and altered EF-P context dependence in each mutant. Together, these findings establish a new EF-P PTM pathway and also highlight a unique relationship between EF-P modification and polyproline context dependence.IMPORTANCE Despite the high level of conservation of EF-P, the posttranslational modification pathway that activates EF-P is highly divergent between species. Here, we have identified and characterized in B. subtilis a novel posttranslational modification pathway. This pathway not only broadens the scope of potential EF-P modification strategies, but it also indicates that EF-P modifications can be assembled directly on EF-P. Furthermore, characterization of these PTM mutants has established that an altered modification state can impact both the severity of polyproline translational defects and context dependence.


Assuntos
Bacillus subtilis/genética , Bacillus subtilis/metabolismo , Fatores de Alongamento de Peptídeos/metabolismo , Peptídeos/metabolismo , Biossíntese de Proteínas , Processamento de Proteína Pós-Traducional , Genes Bacterianos , Lisina/metabolismo , Redes e Vias Metabólicas/genética
11.
Mol Microbiol ; 106(2): 236-251, 2017 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-28787546

RESUMO

Translation elongation factor P (EF-P) in Bacillus subtilis is required for a form of surface migration called swarming motility. Furthermore, B. subtilis EF-P is post-translationally modified with a 5-aminopentanol group but the pathway necessary for the synthesis and ligation of the modification is unknown. Here we determine that the protein YmfI catalyzes the reduction of EF-P-5 aminopentanone to EF-P-5 aminopentanol. In the absence of YmfI, accumulation of 5-aminopentanonated EF-P is inhibitory to swarming motility. Suppressor mutations that enhanced swarming in the absence of YmfI were found at two positions on EF-P, including one that changed the conserved modification site (Lys 32) and abolished post-translational modification. Thus, while modification of EF-P is thought to be essential for EF-P activity, here we show that in some cases it can be dispensable. YmfI is the first protein identified in the pathway leading to EF-P modification in B. subtilis, and B. subtilis encodes the first EF-P ortholog that retains function in the absence of modification.


Assuntos
Oxirredutases do Álcool/metabolismo , Bacillus subtilis/metabolismo , Bacillus subtilis/genética , Ácidos Carboxílicos , Movimento Celular/genética , Fatores de Alongamento de Peptídeos/metabolismo , Processamento de Proteína Pós-Traducional
12.
Ecol Evol ; 6(4): 873-9, 2016 02.
Artigo em Inglês | MEDLINE | ID: mdl-26941933

RESUMO

Species distribution models are valuable tools in studies of biogeography, ecology, and climate change and have been used to inform conservation and ecosystem management. However, species distribution models typically incorporate only climatic variables and species presence data. Model development or validation rarely considers functional components of species traits or other types of biological data. We implemented a species distribution model (Maxent) to predict global climate habitat suitability for Grass Carp (Ctenopharyngodon idella). We then tested the relationship between the degree of climate habitat suitability predicted by Maxent and the individual growth rates of both wild (N = 17) and stocked (N = 51) Grass Carp populations using correlation analysis. The Grass Carp Maxent model accurately reflected the global occurrence data (AUC = 0.904). Observations of Grass Carp growth rate covered six continents and ranged from 0.19 to 20.1 g day(-1). Species distribution model predictions were correlated (r = 0.5, 95% CI (0.03, 0.79)) with observed growth rates for wild Grass Carp populations but were not correlated (r = -0.26, 95% CI (-0.5, 0.012)) with stocked populations. Further, a review of the literature indicates that the few studies for other species that have previously assessed the relationship between the degree of predicted climate habitat suitability and species functional traits have also discovered significant relationships. Thus, species distribution models may provide inferences beyond just where a species may occur, providing a useful tool to understand the linkage between species distributions and underlying biological mechanisms.

13.
Plant Dis ; 99(4): 527-534, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30699553

RESUMO

A severe outbreak of bacterial speck of tomato, caused by Pseudomonas syringae pv. tomato, occurred in central New York in 2009. Isolate 09150, collected from this outbreak and subsequently named NYS-T1, was found to be highly virulent on tomato. To better understand the relationship of 09150 to other P. syringae strains and develop a diagnostic assay for aggressive strains of this pathogen, the 09150 genome was sequenced. Genome comparison revealed it to be highly similar to a previously sequenced isolate, T1. Genetic factors linked to host interaction including type III effectors, toxin biosynthetic genes, and elicitors of host innate immunity were identified. Type III effector repertoires were compared with other strains in the high virulence T1-like subgroup and lower virulence DC3000/P. syringae pv. maculicola subgroup within P. syringae phylogenetic Group I. Primers for conventional PCR were developed using sequences for avrA, hopW, conserved in the former subgroup and hopN, present in the latter. These were tested on isolates in the two subgroups, other pseudomonads, and other bacterial pathogens of tomato. Primers developed for avaA and hopW were diagnostic for more virulent strains of P. syringae pv. tomato while primers for hopN were diagnostic for P. syringae pv. tomato DC3000 and related P. syringe pv. maculicola strains. Primers designed against hopR distinguished both of these P. syringae subgroups from other P. syringae strains.

14.
Appl Environ Microbiol ; 80(16): 4814-20, 2014 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-24878603

RESUMO

In the United States, surface water is commonly used to irrigate a variety of produce crops and can harbor pathogens responsible for food-borne illnesses and plant diseases. Understanding when pathogens infest water sources is valuable information for produce growers to improve the food safety and production of these crops. In this study, prevalence data along with regression tree analyses were used to correlate water quality parameters (pH, temperature, turbidity), irrigation site properties (source, the presence of livestock or fowl nearby), and precipitation data to the presence and concentrations of Escherichia coli, Salmonella spp., and hymexazol-insensitive (HIS) oomycetes (Phytophthora and Pythium spp.) in New York State surface waters. A total of 123 samples from 18 sites across New York State were tested for E. coli and Salmonella spp., of which 33% and 43% were positive, respectively. Additionally, 210 samples from 38 sites were tested for HIS oomycetes, and 88% were found to be positive, with 10 species of Phytophthora and 11 species of Pythium being identified from the samples. Regression analysis found no strong correlations between water quality parameters, site factors, or precipitation to the presence or concentration of E. coli in irrigation sources. For Salmonella, precipitation (≤ 0.64 cm) 3 days before sampling was correlated to both presence and the highest counts. Analyses for oomycetes found creeks to have higher average counts than ponds, and higher turbidity levels were associated with higher oomycete counts. Overall, information gathered from this study can be used to better understand the food safety and plant pathogen risks of using surface water for irrigation.


Assuntos
Escherichia coli/isolamento & purificação , Água Doce/microbiologia , Frutas/microbiologia , Oomicetos/isolamento & purificação , Salmonella/isolamento & purificação , Verduras/microbiologia , Irrigação Agrícola , Produtos Agrícolas/crescimento & desenvolvimento , Produtos Agrícolas/microbiologia , Escherichia coli/classificação , Escherichia coli/genética , Escherichia coli/crescimento & desenvolvimento , Inocuidade dos Alimentos , Frutas/crescimento & desenvolvimento , New York , Oomicetos/classificação , Oomicetos/genética , Oomicetos/crescimento & desenvolvimento , Salmonella/classificação , Salmonella/genética , Salmonella/crescimento & desenvolvimento , Verduras/crescimento & desenvolvimento
15.
Appl Environ Microbiol ; 80(3): 849-54, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24242253

RESUMO

Fruit and vegetable growers continually battle plant diseases and food safety concerns. Surface water is commonly used in the production of fruits and vegetables and can harbor both human- and plant-pathogenic microorganisms that can contaminate crops when used for irrigation or other agricultural purposes. Treatment methods for surface water are currently limited, and there is a need for suitable treatment options. A liquid-processing unit that uses UV light for the decontamination of turbid juices was analyzed for its efficacy in the treatment of surface waters contaminated with bacterial or oomycete pathogens, i.e., Escherichia coli, Salmonella enterica, Listeria monocytogenes, Clavibacter michiganensis subsp. michiganensis, Pseudomonas syringae pv. tomato, and Phytophthora capsici. Five-strain cocktails of each pathogen, containing approximately 10(8) or 10(9) CFU/liter for bacteria or 10(4) or 10(5) zoospores/liter for Ph. capsici, were inoculated into aliquots of two turbid surface water irrigation sources and processed with the UV unit. Pathogens were enumerated before and after treatment. In general, as the turbidity of the water source increased, the effectiveness of the UV treatment decreased, but in all cases, 99.9% or higher inactivation was achieved. Log reductions ranged from 10.0 to 6.1 and from 5.0 to 4.2 for bacterial pathogens and Ph. capsici, respectively.


Assuntos
Irrigação Agrícola , Bactérias/efeitos da radiação , Desinfecção/métodos , Viabilidade Microbiana/efeitos da radiação , Oomicetos/efeitos da radiação , Raios Ultravioleta , Microbiologia da Água , Contagem de Colônia Microbiana , Membro 14 da Superfamília de Ligantes de Fatores de Necrose Tumoral
16.
J Proteome Res ; 12(10): 4351-65, 2013 Oct 04.
Artigo em Inglês | MEDLINE | ID: mdl-24004147

RESUMO

Plasma proteomic experiments performed rapidly and economically using several of the latest high-resolution mass spectrometers were compared. Four quantitative hyperfractionated plasma proteomics experiments were analyzed in replicates by two AB SCIEX TripleTOF 5600 and three Thermo Scientific Orbitrap (Elite/LTQ-Orbitrap Velos/Q Exactive) instruments. Each experiment compared two iTRAQ isobaric-labeled immunodepleted plasma proteomes, provided as 30 labeled peptide fractions, and 480 LC-MS/MS runs delivered >250 GB of data in 2 months. Several analysis algorithms were compared. At 1% false discovery rate, the relative comparative findings concluded that the Thermo Scientific Q Exactive Mass Spectrometer resulted in the highest number of identified proteins and unique sequences with iTRAQ quantitation. The confidence of iTRAQ fold-change for each protein is dependent on the overall ion statistics (Mascot Protein Score) attainable by each instrument. The benchmarking also suggested how to further improve the mass spectrometry parameters and HPLC conditions. Our findings highlight the special challenges presented by the low abundance peptide ions of iTRAQ plasma proteome because the dynamic range of plasma protein abundance is uniquely high compared with cell lysates, necessitating high instrument sensitivity.


Assuntos
Proteínas Sanguíneas/química , Espectrometria de Massas em Tandem/métodos , Proteínas Sanguíneas/isolamento & purificação , Proteínas Sanguíneas/metabolismo , Humanos , Imunoprecipitação , Mapeamento de Peptídeos , Proteômica , Padrões de Referência , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Espectrometria de Massas em Tandem/instrumentação , Espectrometria de Massas em Tandem/normas
17.
Am J Med Genet B Neuropsychiatr Genet ; 156B(8): 929-40, 2011 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-21960518

RESUMO

Genetic factors are likely to influence clinical variation in schizophrenia, but it is unclear which variables are most suitable as phenotypes and which molecular genetic loci are involved. We evaluated clinical variable phenotypes and applied suitable phenotypes in genome-wide covariate linkage analysis. We ascertained 170 affected relative pairs (168 sibling-pairs and two avuncular pairs) with DSM-IV schizophrenia or schizoaffective disorder from the United Kingdom. We defined psychotic symptom dimensions, age at onset (AAO), and illness course using the OPCRIT checklist. We evaluated phenotypes using within sibling-pair correlations and applied suitable phenotypes in multipoint covariate linkage analysis based on 372 microsatellite markers at ∼10 cM intervals. The statistical significance of linkage results was assessed by simulation. The positive and disorganized symptom dimensions, AAO, and illness course qualified as suitable phenotypes. There were no genome-wide significant linkage results. There was suggestive evidence of linkage for the positive dimension on chromosomes 2q32, 10q26, and 20q12; the disorganized dimension on 8p21 and 17q21; and illness course on 2q33 and 22q11. The linkage peak for disorganization on 17q21 remained suggestive after correction for multiple testing. To our knowledge, this is the first study to integrate phenotype evaluation and genome-wide covariate linkage analysis for symptom dimensions and illness history variables in sibling-pairs with schizophrenia. The significant within-pair correlations strengthen the evidence that some clinical variables within schizophrenia are suitable phenotypes for molecular genetic investigations. At present there are no genome-wide significant linkage results for these phenotypes, but a number of suggestive findings warrant further investigation.


Assuntos
Ligação Genética , Estudo de Associação Genômica Ampla , Transtornos Psicóticos/genética , Esquizofrenia/genética , Adulto , Idade de Início , Alelos , Mapeamento Cromossômico , Feminino , Predisposição Genética para Doença , Genoma Humano , Genótipo , Humanos , Masculino , Repetições de Microssatélites/genética , Pessoa de Meia-Idade , Fenótipo , Esquizofrenia/diagnóstico , Irmãos
18.
Nat Biotechnol ; 29(7): 625-34, 2011 Jun 19.
Artigo em Inglês | MEDLINE | ID: mdl-21685906

RESUMO

High-throughput technologies can now identify hundreds of candidate protein biomarkers for any disease with relative ease. However, because there are no assays for the majority of proteins and de novo immunoassay development is prohibitively expensive, few candidate biomarkers are tested in clinical studies. We tested whether the analytical performance of a biomarker identification pipeline based on targeted mass spectrometry would be sufficient for data-dependent prioritization of candidate biomarkers, de novo development of assays and multiplexed biomarker verification. We used a data-dependent triage process to prioritize a subset of putative plasma biomarkers from >1,000 candidates previously identified using a mouse model of breast cancer. Eighty-eight novel quantitative assays based on selected reaction monitoring mass spectrometry were developed, multiplexed and evaluated in 80 plasma samples. Thirty-six proteins were verified as being elevated in the plasma of tumor-bearing animals. The analytical performance of this pipeline suggests that it should support the use of an analogous approach with human samples.


Assuntos
Biomarcadores Tumorais/sangue , Análise Química do Sangue/métodos , Espectrometria de Massas/métodos , Proteínas de Neoplasias/sangue , Neoplasias Experimentais/sangue , Mapeamento de Peptídeos/métodos , Proteoma/análise , Animais , Camundongos , Proteômica/métodos
19.
J Am Soc Echocardiogr ; 23(1): 38-42, 2010 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-20122493

RESUMO

BACKGROUND: Pediatric patients may need sedation for a transthoracic echocardiogram. Due to the unpredictability and safety concerns with chloral hydrate, we offered mask anesthesia as an alternate strategy. METHODS: A retrospective chart review of 507 pediatric patients sedated for transthoracic echocardiography was conducted to compare the use of oral chloral hydrate (n = 297) with the face mask administration of sevoflurane anesthesia (n = 210). RESULTS: Anesthesia had a shorter time from administration of sedation to hospital discharge (112 vs 155 minutes), largely because of a shorter, more predictable, and less variable time to achieve satisfactory study conditions. Using anesthesia, an average 43-minute difference would allow for an additional procedure using the same resources. Anesthesia was not associated with sedation failure (0% vs 6%), and the duration of examination was shorter (40 vs 46 minutes). There were no significant adverse events in either cohort. CONCLUSION: Anesthesia, although more costly, is balanced by more the efficient use of hospital and parental resources, with greater family and staff satisfaction.


Assuntos
Anestésicos Inalatórios/administração & dosagem , Hidrato de Cloral/administração & dosagem , Efeitos Colaterais e Reações Adversas Relacionados a Medicamentos/epidemiologia , Ecocardiografia/efeitos dos fármacos , Cardiopatias/diagnóstico por imagem , Cardiopatias/epidemiologia , Pentobarbital/administração & dosagem , Administração por Inalação , Administração Oral , Pré-Escolar , Comorbidade , Sedação Consciente/estatística & dados numéricos , Ecocardiografia/estatística & dados numéricos , Feminino , Humanos , Incidência , Lactente , Masculino , Pennsylvania/epidemiologia , Reprodutibilidade dos Testes , Estudos Retrospectivos , Medição de Risco/métodos , Fatores de Risco , Sensibilidade e Especificidade
20.
Mov Disord ; 25(1): 91-6, 2010 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-19908314

RESUMO

The aim of this study was to assess the criterion validity of three self-report measures of depression in a sample of patients with Huntington's disease (HD). Fifty patients with HD completed the Beck Depression Inventory-II (BDI-II), the Hospital Anxiety and Depression Scale (HADS), and the Depression Intensity Scale Circles (DISCs). Current psychiatric status was assessed using the schedules for clinical assessment in neuropsychiatry (SCAN), and ICD-10 diagnosis was used as the gold standard. Receiver operating characteristics (ROC) curves were obtained and the sensitivity, specificity, positive, and negative predictive values were calculated for different cut-off scores on each rating scale. Twelve patients (24%) met ICD-10 criteria for depressive disorder. The depression sub-scale of the HADS (HADS-D) at an optimal cut-off of 6/7 was found to discriminate maximally between depressed and nondepressed patients in this population. The DISCs at a cut-off of 1/2 also performed well at detecting possible "cases" of depression, whereas the BDI-II performed the least satisfactorily of all scales. The HADS-D and DISCs are good screening measures for depression in the HD population and the DISCs may be particularly useful in those patients with more severe communicative and cognitive deficits.


Assuntos
Depressão/diagnóstico , Depressão/etiologia , Doença de Huntington/complicações , Escalas de Graduação Psiquiátrica , Autoimagem , Adulto , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Curva ROC , Reprodutibilidade dos Testes , Índice de Gravidade de Doença
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