Pursuing Impactful Quantitative Proteomics Using QC-Channels in Every Spectrum and Trend-Design in Experiment.

False changes discovered by quantitative proteomics reduce the trust of biologists in proteomics and limit the applications of proteomics to unlock biological mechanisms, which suppresses the application of proteomics techniques in the pharmaceutical industry more than it does in academic research. To remove false changes that arise during LC-MS/MS data acquisition, we evaluated the contributions of peptide abundance and number of unique peptides on reproducibility. Lower abundance and only one unique peptide have a higher risk of generating a higher coefficient of variation (CV), resulting in less accurate quantification. However, the abundance of peptides in samples is not adjustable and discarding proteins quantified by only one unique peptide is not a choice either. Indeed, a large percentage of proteins are accurately quantified by only one unique peptide. Therefore, to improve the calculations of the CV, we leverage a new function in PEAKS called QC-channels which enables technical replicates of each spectrum to be evaluated prior to calculation of the CV. While the QC-channels function in PEAKS significantly reduced the false quantification, random false changes still exist due to known or unknown reasons. To address this challenge, we present the idea of Trend-design to track trend changes rather than changes from two points to remove false quantifications and reveal consequential changes responding to a treatment or condition. The idea was confirmed by molecules with different affinity and dose in the current study. The combination of QC-channels and Trend-design enables a more impactful quantitative proteomics to allow unlocking biological mechanisms using proteomics.

Multiple micronutrient deficiencies alter energy metabolism in host and gut microbiome in an early-life murine model.

Introduction: Micronutrients perform a wide range of physiological functions essential for growth and development. However, most people still need to meet the estimated average requirement worldwide. Globally, 2 billion people suffer from micronutrient deficiency, most of which are co-occurring deficiencies in children under age five. Despite decades of research, animal models studying multiple micronutrient deficiencies within the early-life period are lacking, which hinders our complete understanding of the long-term health implications and may contribute to the inefficacy of some nutritional interventions. Evidence supporting the Developmental Origins of Health and Disease (DOHaD) theory demonstrates that early-life nutritional deficiencies carry life-long consequences mediated through various mechanisms such as abnormal metabolic programming, stunting, altered body composition, and the gut microbiome. However, this is largely unexplored in the multiple micronutrient deficient host. Methods: we developed a preclinical model to examine undernutrition's metabolic and functional impact on the host and gut microbiome early in life. Three-week-old weanling C57BL/6N male mice were fed a low-micronutrient diet deficient in zinc, folate, iron, vitamin A, and vitamin B12 or a control diet for 4-weeks. Results: Our results showed that early-life multiple micronutrient deficiencies induced stunting, altered body composition, impaired glucose and insulin tolerance, and altered the levels of other micronutrients not depleted in the diet within the host. In addition, functional metagenomics profiling and a carbohydrate fermentation assay showed an increased microbial preference for simple sugars rather than complex ones, suggestive of a less developed microbiome in the low-micronutrient-fed mice. Moreover, we found that a zinc-only deficient diet was not sufficient to induce these phenotypes, further supporting the importance of studying co-occurring deficiencies. Discussion: Together, these findings highlight a previously unappreciated role of early-life multiple micronutrient deficiencies in shaping the metabolic phenome of the host and gut microbiome through altered glucose energy metabolism, which may have implications for metabolic disease later in life in micronutrient-deficient survivors.

Stability of vitamin C, color, and garlic aroma of garlic mashed potatoes in polymer packages processed with microwave-assisted thermal sterilization technology.

The U.S. Army and NASA need ready-to-eat meals with extended shelf-life for military operations and future manned space missions. For traditional heat sterilization methods, aluminum foil laminated pouches are used to achieve a shelf-life of 3 to 5 years at room temperature. However, those packages are not suited for advanced thermal processing technologies based on microwave energy. This research investigated the effect of polymeric packaging materials on storage stability of garlic flavor, vitamin C, and color of garlic mashed potatoes processed with microwave-assisted thermal sterilization (MATS) technology. Three types of high-barrier metal oxide-coated polymer pouches were used for MATS process, designed to achieve lethality approximately F0 = 6 min. Aluminum foil-based pouches were used for retort process as control. Results demonstrated that both oxygen and water vapor barrier properties (oxygen transmission rate [OTR] and water vapor transmission rate [WVTR]) of the polymer pouches were affected by MATS processing. OTR increased by three to nine times, while WVTR increased by 5 to 20 times after processing. The MATS process resulted in 13% to 16% vitamin C loss, while retort process resulted in 18% loss in garlic mashed potato. The kinetics of vitamin C indicated that metal oxide-coated high-barrier packages (after processing OTR <0.1 cc/m2 .day; WVTR <1.0 g/m2 .day) could replace aluminum foil-based pouches for MATS processed shelf-stable ready-to-eat garlic mashed potatoes. PRACTICAL APPLICATION: Garlic mashed potatoes in polymer packages processed in a microwave-assisted thermal sterilization (MATS) system had better retention of vitamin C compared to samples packaged in aluminum laminated pouches and processed in retort. Polymer packages combined with MATS processing could potentially provide safe, better quality, and nutritious shelf-stable food products for military and space missions.

TGF-ß1-induced PAI-1 contributes to a profibrotic network in patients with eosinophilic esophagitis.

BACKGROUND: Eosinophilic esophagitis (EoE) is an allergic disease of increasing worldwide incidence. Complications are due to tissue remodeling and involve TGF-ß1-mediated fibrosis. Plasminogen activator inhibitor 1 (PAI-1/serpinE1) can be induced by TGF-ß1, but its role in EoE is not known. OBJECTIVE: We sought to understand the expression and role of PAI-1 in patients with EoE. METHODS: We used esophageal biopsy specimens and plasma samples from control subjects and patients with EoE, primary human esophageal epithelial cells, and fibroblasts from patients with EoE in immunohistochemistry, quantitative PCR, and immunoassay experiments to understand the induction of PAI-1 by TGF-ß1, the relationship between PAI-1 and esophageal fibrosis, and the role of PAI-1 in fibrotic gene expression. RESULTS: PAI-1 expression was significantly increased in epithelial cells of biopsy specimens from patients with active EoE compared with that seen in biopsy specimens from patients with inactive EoE or control subjects (P < .001). Treatment of primary esophageal epithelial cells with recombinant TGF-ß1 increased PAI-1 transcription, intracellular protein expression, and secretion. Esophageal PAI-1 expression correlated with basal zone hyperplasia, fibrosis, and markers of esophageal remodeling, including vimentin, TGF-ß1, collagen I, fibronectin, and matrix metalloproteases, and plasma PAI-1 levels correlated with plasma TGF-ß1 levels. PAI-1 inhibition significantly decreased baseline and TGF-ß1-induced fibrotic gene expression. CONCLUSIONS: PAI-1 expression is significantly increased in the epithelium in patients with EoE and reflects fibrosis, and its inhibition decreases TGF-ß1-induced gene expression. Epithelial PAI-1 might serve as a marker of EoE severity and form part of a TGF-ß1-induced profibrotic network.

Impact of post-rigor high pressure processing on the physicochemical and microbial shelf-life of cultured red abalone (Haliotis rufescens).

High pressure processing (HPP) of post-rigor abalone at 300MPa for 10min extended the refrigerated shelf-life to four times that of unprocessed controls. Shucked abalone meats were processed at 100 or 300MPa for 5 or 10min, and stored at 2°C for 35days. Treatments were analyzed for aerobic plate count (APC), total volatile base nitrogen (TVBN), K-value, biogenic amines, color, and texture. APC did not exceed 10(6) and TVBN levels remained below 35mg/100g for 35days for the 300MPa treatments. No biogenic amines were detected in the 300MPa treatments, but putrescine and cadaverine were detected in the control and 100MPa treatments. Color and texture were not affected by HPP or storage time. These results indicate that post-rigor processing at 300MPa for 10min can significantly increase refrigerated shelf-life of abalone without affecting chemical or physical quality characteristics important to consumers.

Human prion protein sequence elements impede cross-species chronic wasting disease transmission.

Chronic wasting disease (CWD) is a fatal prion disease of North American deer and elk and poses an unclear risk for transmission to humans. Human exposure to CWD occurs through hunting activities and consumption of venison from prion-infected animals. Although the amino acid residues of the prion protein (PrP) that prevent or permit human CWD infection are unknown, NMR-based structural studies suggest that the ß2-α2 loop (residues 165-175) may impact species barriers. Here we sought to define PrP sequence determinants that affect CWD transmission to humans. We engineered transgenic mice that express human PrP with four amino acid substitutions that result in expression of PrP with a ß2-α2 loop (residues 165-175) that exactly matches that of elk PrP. Compared with transgenic mice expressing unaltered human PrP, mice expressing the human-elk chimeric PrP were highly susceptible to elk and deer CWD prions but were concurrently less susceptible to human Creutzfeldt-Jakob disease prions. A systematic in vitro survey of amino acid differences between humans and cervids identified two additional residues that impacted CWD conversion of human PrP. This work identifies amino acids that constitute a substantial structural barrier for CWD transmission to humans and helps illuminate the molecular requirements for cross-species prion transmission.

MMPs-2 and -14 Are Elevated in Eosinophilic Esophagitis and Reduced Following Topical Corticosteroid Therapy.

OBJECTIVES: Eosinophilic esophagitis (EoE) is a chronic, antigen-mediated disease in children and adults associated with substantial esophageal remodeling and fibrosis. The expression of the remodeling-associated matrix metalloproteinases (MMPs) has not been previously detailed in EoE. METHODS: MMP-2 and -14 expression and cellular localization were assessed using real-time quantitative polymerase chain reaction and immunohistochemistry/immunofluorescence in EoE fibroblasts, active and inactive pediatric EoE biopsies, and nondiseased control biopsies. The effect of transforming growth factor (TGF)-ß1 treatment on MMP-2 expression in cultured esophageal epithelial (HET1A) cells was analyzed. RESULTS: MMP-2 and -14 mRNA were expressed in EoE fibroblasts and biopsies. Proliferating epithelial cells produced MMP-14 more abundantly in EoE than in controls (P < 0.001) and the degree of epithelial MMP-14 expression correlated positively with basal zone hyperplasia (r = 0.65, P = 0.002). EoE lamina propria had higher numbers of MMP-2- and -14-positive cells (906 ±â€Š167 and 701 ±â€Š93 cells/mm²) as compared with controls (258 ±â€Š93 cells/mm², P < 0.01 and 232 ±â€Š54 cells/mm², P < 0.01), and MMP-14 expression correlated with the severity of fibrosis. Following therapy with topical corticosteroids, MMP-14 and -2 were significantly diminished (P < 0.01). TGF-ß1 increased the expression and secretion of MMP-2 from esophageal epithelial HET1A cells. CONCLUSIONS: MMP-2 and -14 are elevated in pediatric patients with EoE and significantly decrease following topical corticosteroid therapy. TGF-ß1 increases MMP-2 in esophageal epithelial cells. This alludes to previously unappreciated role for MMPs in EoE-associated esophageal remodeling and a potential positive feedback loop via TGF-ß1.

Effects of rigor status during high-pressure processing on the physical qualities of farm-raised abalone (Haliotis rufescens).

High-pressure processing (HPP) is used to increase meat safety and shelf-life, with conflicting quality effects depending on rigor status during HPP. In the seafood industry, HPP is used to shuck and pasteurize oysters, but its use on abalones has only been minimally evaluated and the effect of rigor status during HPP on abalone quality has not been reported. Farm-raised abalones (Haliotis rufescens) were divided into 12 HPP treatments and 1 unprocessed control treatment. Treatments were processed pre-rigor or post-rigor at 2 pressures (100 and 300 MPa) and 3 processing times (1, 3, and 5 min). The control was analyzed post-rigor. Uniform plugs were cut from adductor and foot meat for texture profile analysis, shear force, and color analysis. Subsamples were used for scanning electron microscopy of muscle ultrastructure. Texture profile analysis revealed that post-rigor processed abalone was significantly (P < 0.05) less firm and chewy than pre-rigor processed irrespective of muscle type, processing time, or pressure. L values increased with pressure to 68.9 at 300 MPa for pre-rigor processed foot, 73.8 for post-rigor processed foot, 90.9 for pre-rigor processed adductor, and 89.0 for post-rigor processed adductor. Scanning electron microscopy images showed fraying of collagen fibers in processed adductor, but did not show pressure-induced compaction of the foot myofibrils. Post-rigor processed abalone meat was more tender than pre-rigor processed meat, and post-rigor processed foot meat was lighter in color than pre-rigor processed foot meat, suggesting that waiting for rigor to resolve prior to processing abalones may improve consumer perceptions of quality and market value.

Long-term risk preference and suboptimal decision making following adolescent alcohol use.

Individuals who abused alcohol at an early age show decision-making impairments. However, the question of whether maladaptive choice constitutes a predisposing factor to, or a consequence resulting from, alcohol exposure remains open. To examine whether a causal link exists between voluntary alcohol consumption during adolescence and adult decision making the present studies used a rodent model. High levels of voluntary alcohol intake were promoted by providing adolescent rats with access to alcohol in a palatable gel matrix under nondeprivation conditions. A probability-discounting instrumental response task offered a choice between large but uncertain rewards and small but certain rewards to assess risk-based choice in adulthood either 3 weeks or 3 months following alcohol exposure. While control animals' performance on this task closely conformed to a predictive model of risk-neutral value matching, rats that consumed high levels of alcohol during adolescence violated this model, demonstrating greater risk preference. Evidence of significant risk bias was still present when choice was assessed 3 months following discontinuation of alcohol access. These findings provide evidence that adolescent alcohol exposure may lead to altered decision making during adulthood and this model offers a promising approach to the investigation of the neurobiological underpinnings of this link.

Anti-glomerular basement membrane disease in an HIV-infected patient.

Background A 55-year-old HIV-positive male presented with gross hematuria, proteinuria, acute azotemia, and recurrent left hip septic arthritis. Anti-glomerular basement membrane (anti-GBM) antibodies were present in the patient's serum, and eosinophils were noted in his urine. Renal biopsy revealed active crescents, with linear staining of the capillary wall for IgG consistent with anti-GBM nephritis. Investigations Physical examination, blood and urine analyses, chest X-ray, CT imaging of the abdomen and pelvis, renal ultrasound, and renal biopsy. Diagnosis Anti-GBM disease. Management Owing to the presence of active HIV infection and recurrent left hip septic arthritis, a novel approach to treatment was pursued in the hope of reducing infectious consequences. The patient received steroids, intravenous immunoglobulin, rituximab, and mycophenolate mofetil.

Isoelectric focusing technology quantifies protein signaling in 25 cells.

A previously undescribed isoelectric focusing technology allows cell signaling to be quantitatively assessed in <25 cells. High-resolution capillary isoelectric focusing allows isoforms and individual phosphorylation forms to be resolved, often to baseline, in a 400-nl capillary. Key to the method is photochemical capture of the resolved protein forms. Once immobilized, the proteins can be probed with specific antibodies flowed through the capillary. Antibodies bound to their targets are detected by chemiluminescence. Because chemiluminescent substrates are flowed through the capillary during detection, localized substrate depletion is overcome, giving excellent linearity of response across several orders of magnitude. By analyzing pan-specific antibody signals from individual resolved forms of a protein, each of these can be quantified, without the problems associated with using multiple antibodies with different binding avidities to detect individual protein forms.

Detection of DNA mutations associated with mitochondrial diseases by Agilent 2100 bioanalyzer.

BACKGROUND: Molecular analysis of mitochondrial DNA (mtDNA) has provided a final diagnosis for many of the mitochondrial diseases. We evaluated the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA) to determine whether the system could replace the conventional restriction fragment length polymorphism (RFLP) analysis by the agarose gel electrophoresis for the detection of the mtDNA mutation. METHODS: Three members of a family with MELAS syndrome and four members of a family with MERRF syndrome were recruited for this study. After PCR and restriction enzyme digestion, DNA fragments were separated on the Agilent 2100 bioanalyzer in conjunction with the DNA 500 and DNA 1000 Labchip kits and by electrophoresis on precast 3% agarose gels. RESULTS: The data generated by the DNA 500 and DNA 1000 assays using the Agilent 2100 bioanalyzer showed a lower percentage error and a better reproducibility as compared to those obtained by the conventional method. CONCLUSION: Based on the performance of the bioanalyzer, we suggest that this novel Labchip is adequate to replace the current RFLP analysis by the agarose gel electrophoresis for mtDNA mutation detection.