Tandem Mass Tag Labeling to Identify Proteome Changes in Beef Longissimus Lumborum and Psoas Major Muscles During Early Postmortem Period

ObjectivesLongissimus lumborum (LL) and psoas major (PM) are important muscles in beef hindquarters that exhibit variation in meat quality attributes. Postmortem metabolism (muscle-to-meat conversion) affects biochemical properties of muscles and in turn influence the meat quality. Although previous research has indicated that variation in the proteome profile of LL and PM post-rigor influences meat quality attributes such as tenderness and color stability during retail display, limited research has examined the influence of early postmortem metabolism on meat quality. Tandem mass tag (TMT) labeling is a chemical labeling approach used for accurate mass spectrometry-based quantification and identification of biological macromolecules. Therefore, the objective of this study was to use TMT labeling to examine proteome profile variation between beef LL and PM during the early postmortem period.Materials and MethodsMuscle biopsy samples were collected from carcasses (n = 4) at 45 min, 12 h, and 36 h postmortem from a commercial beef processing facility. Samples were frozen immediately in liquid nitrogen and stored at –80°C until proteomic analysis. Proteome was analyzed using TMT label containing ten different isobaric compounds with the same mass and chemical structure composed of an amine-reactive NHS-ester group, a spacer arm, and a mass reporter. After labeling and peptide fractionation, all the samples were multiplexed and ran through the Orbitrap Velos mass spectrometer equipped with a Nanospray Flex ion source to identify differentially abundant proteins. The proteins exhibiting 1.5-fold or more intensity difference and a statistical difference (P < 0.05) between LL and PM or within the muscles during the postmortem were reported as differentially abundant.ResultsSeventy differentially abundant proteins (P < 0.05) were identified from three comparisons between the muscles (31 proteins in PM 45 min vs. LL 45 min, 41 proteins in PM 12 h vs. LL 12 h, 49 proteins in PM 36 h vs. LL 36 h). However, no difference (P > 0.05) in protein expression within a muscle was observed during these time points. The differentially abundant proteins were mainly involved in oxidative phosphorylation and ATP-related transport, tricarboxylic acid cycle, NADPH regeneration, fatty acid degradation, muscle contraction, calcium signaling, chaperone activity, oxygen transport, as well as degradation of the extracellular matrix. At early postmortem, overabundant anti-apoptotic proteins in LL could cause high metabolic stability, enhanced autophagy, and delayed apoptosis, while overabundant metabolic enzymes and pro-apoptotic proteins in PM could accelerate the reactive oxygen species generation and programmed cell death.ConclusionDifferentially abundant proteins between LL and PM during the early postmortem were primarily associated with cellular metabolism and programmed cell death. The greater oxidative and color stability in LL compared to PM could be related to the increased expression of anti-apoptotic proteins and the decreased expression of metabolic enzymes and proapoptotic proteins in LL.

Depletion and Bioaccumulation of Ractopamine Hydrochloride (RH) in the Gastrointestinal Tract of Bovine

ObjectivesDue to developing meat trade issues associated with use of the β-agonist ractopamine hydrochloride (RH) as a growth-promoting agent in livestock production, this project was developed to provide recommendations of best practices to beef cattle producers in the United States who intend to export to China. This study is critically important in better understanding the bioaccumulation and depletion of RH in live animals, and how this may relate to depletion in differing tissues on animal harvest.This study was designed to determine dose response and depletion curves in the lower gastrointestinal (GI) tract of fistulated (i.e., cannulated- both rumen and duodenal) steers either receiving or not receiving ractopamine hydrochloride as part of the daily ration. There were originally five steers in this study, but due to performance challenges and scarring issues, one animal was removed from the study for a total of four test subjects.Materials and MethodsIn the dose and depletion study, four steers (n = 2 not receiving RH and n = 2 receiving RH at the approved dosage) were assessed from –3 d (still receiving RH if on the RH treatment) to 13 d post-withdrawal to determine the amount of RH present and length of time required for RH to clear the GI tract should a contamination event of low levels occur. Residues were quantified using liquid chromatography mass spectrometry (LC-MS).ResultsFor the dose and depletion study, RH residues were quantified in rumen fluids, rumen solids, fecal material, and duodenal fluids. Overall, the RH present in the two control steers (which did not receive RH) declined from approximately 30 ppb in all matrices 3 d before withdrawal to below the limit of quantitation at the end of withdrawal. Furthermore, samples tended to be below the limit of quantitation by Day 4 post-withdrawal. The steers that received RH also exhibited a decline of RH throughout the withdrawal period for all matrices (e.g., 5800 ppb in rumen fluids at day –3 versus 1.81 ppb 13 d post-withdrawal).ConclusionThe dose and depletion study results suggest that RH declines rapidly in the lower GI of beef cattle, with levels below detection by day four. There are events in which RH declines and then spikes, so further research may be necessary to determine why this rapid increase occurs.

RAMClust: a novel feature clustering method enables spectral-matching-based annotation for metabolomics data

Metabolomic data are frequently acquired using chromatographically coupled mass spectrometry (MS) platforms. For such datasets, the first step in data analysis relies on feature detection, where a feature is defined by a mass and retention time. While a feature typically is derived from a single compound, a spectrum of mass signals is more a more-accurate representation of the mass spectrometric signal for a given metabolite. Here, we report a novel feature grouping method that operates in an unsupervised manner to group signals from MS data into spectra without relying on predictability of the in-source phenomenon. We additionally address a fundamental bottleneck in metabolomics, annotation of MS level signals, by incorporating indiscriminant MS/MS (idMS/MS) data implicitly: feature detection is performed on both MS and idMS/MS data, and feature-feature relationships are determined simultaneously from the MS and idMS/MS data. This approach facilitates identification of metabolites using in-source MS and/or idMS/MS spectra from a single experiment, reduces quantitative analytical variation compared to single-feature measures, and decreases false positive annotations of unpredictable phenomenon as novel compounds. This tool is released as a freely available R package, called RAMClustR, and is sufficiently versatile to group features from any chromatographic-spectrometric platform or feature-finding software.

Association of human immune response to Aedes aegypti salivary proteins with dengue disease severity

Dengue viruses (DENV; family Flaviviridae, genus Flavivirus) are transmitted by Aedes aegypti mosquitoes and can cause dengue fever (DF), a relatively benign disease, or more severe dengue haemorrhagic fever (DHF). Arthropod saliva contains proteins delivered into the bite wound that can modulate the host haemostatic and immune responses to facilitate the intake of a blood meal. The potential effects on DENV infection of previous exposure to Ae. aegypti salivary proteins have not been investigated. We collected Ae. aegypti saliva, concentrated the proteins and fractionated them by nondenaturing polyacrylamide gel electrophoresis (PAGE). By the use of immunoblots, we analysed reactivity with the mosquito salivary proteins (MSP) of sera from 96 Thai children diagnosed with secondary DENV infections leading either to DF or DHF, or with no DENV infection, and found that different proportions of each patient group had serum antibodies reactive to specific Ae. aegypti salivary proteins. Our results suggest that prior exposure to MSP might play a role in the outcome of DENV infection in humans.