Dual Fragmentation Isobaric Tags for Metabolomics

Isobaric tags typically leverage an a1 type fragmentation to produce constant mass reporter ions. While this motif allows for efficient reporter formation, isobaric tags lack structural diversity, which limits the number and type of isotopes that are synthetically available. Presented here are two examples of dual fragmentation isobaric tagging. The first example mimics the typical isobaric tag structure through trimethylamine neutral loss and cyclization. Subsequent fragmentation releases a constant mass reporter with high efficiency. This provides a route to create a variety of isobaric tags with regard to both the reporter and the balancer mass. The second example is a set of six-plex isobaric, thiol-reactive tags that produce constant mass reporters by a similar sequential fragmentation mechanism. A trimethylamine neutral loss allows for the incorporation of up to 13 total isotopes in the balancer region, while minimizing deuterium retention time shifts. A subsequent C-S bond cleavage produces a constant mass reporter in the low-mass region. The thiols investigated produced an average RSD of 14% and R² of 0.98 when analyzed as a six-plex injection. Thiol metabolism was disrupted using the glutamyl-cysteine synthetase inhibitor buthionine sulfoximine (BSO). Endothelial cells were incubated with BSO and showed significant decreases in glutathione and cysteinyl-glycine compared to control. Overall, a new method to generate constant mass reporters using a dual fragmentation scheme is presented.

Preservation of black grapes by isochoric freezing

Fruits are perishable. It's crucial to have an efficient preservation technique that may extend storage duration while maintaining the physical quality and nutritional values to avoid wastage. The majority of long-term storage solutions for fruits use refrigeration. In this study, we evaluate the potential of isochoric freezing as an alternative method of preservation for black grapes (Vitis vinifera L.). We compare the properties of black grapes preserved for 7 days in trehalose solution at -4 °C in isochoric conditions (average pressure 34.2 MPa) with those of fresh black grapes and with grapes preserved isobarically in four conditions (room temperature, in the fridge, in the freezer, and in a plastic bag filled with trehalose solution). The results indicate that grapes preserved by isochoric freezing at temperatures below the freezing point of water do not lose weight; on the contrary, they resulted in a very small (2%) weight gain. Freezing under isochoric conditions did not result in significant changes in terms of macroscopic appearance, colour, firmness, °Brix values, or pH. We consider that isochoric freezing has the potential to be used as a preservation method for grapes while maintaining physicochemical parameters similar to those of fresh fruits.

Procedures to Evaluate the Role of Heparan Sulfate on the Reactivity of Resistance and Conductance Arteries Ex Vivo

Evidence is emerging that disruption of the endothelial glycocalyx might contribute importantly to arterial dysfunction in the context of diabetes. One approach to assess the integrity of the endothelium and the vascular smooth muscle cell layer, in the absence of neural, humoral, and mechanical influences, is by measuring arterial vasomotion ex vivo. Here we describe a procedure to assess non-receptor-mediated vasoconstriction, receptor-mediated vasoconstriction, and endothelium-dependent and -independent vasodilation, in resistance and conductance arteries pressurized to 60 mmHg. In addition to evaluating vasoreactivity using isobaric approaches, the same experimental set-up can be used to initiate a pressure gradient across the artery such that intraluminal, flow-mediated vasodilation can be measured. After recording endothelium-dependent vasodilation using isobaric or flow-mediated approaches, identical interventions can be completed in the presence of enzymes that cleave biologically active heparan sulfates into inactive disaccharide and oligosaccharide fragments to assess the contribution from: (a) endothelial-derived substances (e.g., nitric oxide via nitric oxide synthase inhibition); or (b) important components of the glycocalyx (e.g., removal of heparan sulfate via heparitinase III treatment). Here, we show that acute disruption of a predominant glycosaminoglycan i.e., heparan sulfate impairs intraluminal flow-mediated vasodilation in murine resistance arteries.

Multiplexed proteome profiling of carbon source perturbations in two yeast species with SL-SP3-TMT

Saccharomyces cerevisiae and Schizosaccharomyces pombe are the most commonly studied yeast model systems, yet comparisons of global proteome remodeling between these yeast species are scarce. Here, we profile the proteomes of S. cerevisiae and S. pombe cultured with either glucose or pyruvate as the sole carbon source to define common and distinctive alterations in the protein landscape across species. In addition, we develop an updated streamlined-tandem mass tag (SL-TMT) strategy that substitutes chemical-based precipitation with more versatile bead-based protein aggregation method (SP3) prior to enzymatic digestion and TMT labeling. Our new workflow, SL-SP3-TMT, allow for near-complete proteome profiles in a single experiment for each species. The data reveal expected alterations in protein abundance and differences between species, highlighted complete canonical biochemical pathways, and provided insight into previously uncharacterized proteins. The techniques used herein, namely SL-SP3-TMT, can be applied to virtually any experiment aiming to study remodeling of the proteome using a high-throughput, comprehensive, yet streamlined mass spectrometry-based strategy. SIGNIFICANCE: Saccharomyces cerevisiae and Schizosaccharomyces pombe are single-celled eukaryotes that diverged from a common ancestor over a period of 100 million years, such that evolution has driven fundamental differences between the two species. Cellular metabolism and the regulation thereof are vital for living organisms. Here, we hypothesize that large scale proteomic alterations are prevalent upon the substitution of glucose with another carbon source, in this case pyruvate. To efficiently process our samples, we developed an updated streamlined-tandem mass tag (SL-TMT) strategy with more versatile bead-based protein aggregation. The data revealed expected alterations in protein abundance and illustrated differences between species. We highlighted complete canonical biochemical pathways and provided insight into previously uncharacterized proteins.

A comparison of freezing-damage during isochoric and isobaric freezing of the potato

Background

Freezing is commonly used for food preservation. It is usually done under constant atmospheric pressure (isobaric). While extending the life of the produce, isobaric freezing has detrimental effects. It causes loss of food weight and changes in food quality. Using thermodynamic analysis, we have developed a theoretical model of the process of freezing in a constant volume system (isochoric). The mathematical model suggests that the detrimental effects associated with isobaric freezing may be reduced in an isochoric freezing system. To explore this hypothesis, we performed a preliminary study on the isochoric freezing of a produce with which our group has experience, the potato.

Method

Experiments were performed in an isochoric freezing device we designed. The device is robust and has no moving parts. For comparison, we used a geometrically identical isobaric freezing device. Following freezing and thawing, the samples were weighed, examined with colorimetry, and examined with microscopy.

Results

It was found that potatoes frozen to −5 °C in an isochoric system experienced no weight loss and limited enzymatic browning. In contrast the −5 °C isobaric frozen potato experienced substantial weight loss and substantial enzymatic browning. Microscopic analysis shows that the structural integrity of the potato is maintained after freezing in the isochoric system and impaired after freezing in the isobaric system.

Discussion

Tissue damage during isobaric freezing is caused by the increase in extracellular osmolality and the mechanical damage by ice crystals. Our thermodynamic analysis predicts that during isochoric freezing the intracellular osmolality remains comparable to the extracellular osmolality and that isochoric systems can be designed to eliminate the mechanical damage by ice. The results of this preliminary study seem to confirm the theoretical predictions.

Conclusion

This is a preliminary exploratory study on isochoric freezing of food. We have shown that the quality of a food product preserved by isochoric freezing is better than the quality of food preserved to the same temperature in isobaric conditions. Obviously, more extensive research remains to be done to extend this study to lower freezing temperatures and other food items.

Stable isotope labelling methods in mass spectrometry-based quantitative proteomics

Mass-spectrometry based proteomics has evolved as a promising technology over the last decade and is undergoing a dramatic development in a number of different areas, such as; mass spectrometric instrumentation, peptide identification algorithms and bioinformatic computational data analysis. The improved methodology allows quantitative measurement of relative or absolute protein amounts, which is essential for gaining insights into their functions and dynamics in biological systems. Several different strategies involving stable isotopes label (ICAT, ICPL, IDBEST, iTRAQ, TMT, IPTL, SILAC), label-free statistical assessment approaches (MRM, SWATH) and absolute quantification methods (AQUA) are possible, each having specific strengths and weaknesses. Inductively coupled plasma mass spectrometry (ICP-MS), which is still widely recognised as elemental detector, has recently emerged as a complementary technique to the previous methods. The new application area for ICP-MS is targeting the fast growing field of proteomics related research, allowing absolute protein quantification using suitable elemental based tags. This document describes the different stable isotope labelling methods which incorporate metabolic labelling in live cells, ICP-MS based detection and post-harvest chemical label tagging for protein quantification, in addition to summarising their pros and cons.

The effects of hyperbaric or isobaric bupivacaine on bispectral index in spinal anesthesia for cesarean section

BACKGROUND

Hyperbaric and isobaric bupivacaine has been shown to reduce bispectral index (BIS) during spinal anesthesia. The aim of this study was to compare the effect of isobaric bupivacaine and hyperbaric bupivacaine on the BIS during cesarean section with spinal anesthesia.

MATERIALS AND METHODS

In this double-blind randomized controlled clinical trial, 84 pregnant women with ASA (American Society of Anesthesiologists) class I or II were randomly assigned to receive isobaric or hyperbaric bupivacaine. BIS was measured using electro encephalography (EEG) and recorded at the baseline and 5th, 10th, 15th, 30th, 45th, 60th, 90th and 120th minutes after spinal injection. The heart rate (HR), mean arterial pressure (MAP), signal quality index (SQI), electromyography (EMG) and the temperature were also recorded during surgery.

RESULTS

From recruited subjects, 41 completed the study in each group and their data were analyzed. The BIS score began to reduce until 30(th) minute for isobaric bupivacaine and 45(th) minute for hyperbaric bupivacaine after spinal injection. The recorded BIS was not significantly different between two groups at all the time points. Difference of BIS from baseline was not significant between two groups at most time points except for the 45(th) minute after injection that it was 5.9 ± 9 vs. 2.7 ± 4.6 for hyperbaric and isobaric bupivacaine, respectively (p = 0.047). The changing trend was not significantly different between groups with hyperbaric and isobaric bupivacaine.

CONCLUSION

According to the present study, the BIS score during surgery began to decrease when the patients were injected spinally by both of these drugs. The greatest decrease from baseline BIS values occurred at 30 and 45 minutes after induction of spinal anesthesia. However, hyperbaric or isobaric bupivacaine did not have different effects on the BIS during spinal anesthesia.