Integrated Microfluidics for Protein Modification Discovery

Protein post-translational modifications mediate dynamic cellular processes with broad implications in human disease pathogenesis. There is a large demand for high-throughput technologies supporting post-translational modifications research, and both mass spectrometry and protein arrays have been successfully utilized for this purpose. Protein arrays override the major limitation of target protein abundance inherently associated with MS analysis. This technology, however, is typically restricted to pre-purified proteins spotted in a fixed composition on chips with limited life-time and functionality. In addition, the chips are expensive and designed for a single use, making complex experiments cost-prohibitive. Combining microfluidics with in situ protein expression from a cDNA microarray addressed these limitations. Based on this approach, we introduce a modular integrated microfluidic platform for multiple post-translational modifications analysis of freshly synthesized protein arrays (IMPA). The system''s potency, specificity and flexibility are demonstrated for tyrosine phosphorylation and ubiquitination in quasicellular environments. Unlimited by design and protein composition, and relying on minute amounts of biological material and cost-effective technology, this unique approach is applicable for a broad range of basic, biomedical and biomarker research.Protein post-translational modifications (PTMs)¹ vastly diversify eukaryotic proteomes and are integrated in essentially all cellular processes (1). Proteomic approaches, such as mass spectrometry (MS), have been instrumental in monitoring global molecular dynamics for research and clinical applications (2–5). However, even in this modern era, large-scale analyses of PTMs by MS is challenging because of the limited number of modified peptides derived from proteins that, by themselves, may not be abundant. Moreover, comprehensive PTM analysis by MS often requires significant amounts of biological material that may not be available. PTM analysis using protein arrays can overcome these limitations because of the equimolar amount of the arrayed proteins (6, 7). Large-scale protein arrays have been successfully integrated into PTM research (8, 9). However, this technology relies on pre-purified proteins that are arrayed on a surface and thus, incompatible with biochemically challenging proteins, let alone insoluble proteins. Moreover, the production of recombinant protein arrays is impractical in-house. Therefore, such arrays cannot be used fresh, and they are inherently limited to certain designs, protein compositions, and model organisms of high commercial value. To overcome the abovementioned limitations, we designed a modular integrated microfluidic platform for PTM analysis (IMPA).     

Clinical Outcomes and Cost Effectiveness of Accelerated Diagnostic Protocol in a Chest Pain Center Compared with Routine Care of Patients with Chest Pain

Aims

The aim of this study was to compare in patients presenting with acute chest pain the clinical outcomes and cost-effectiveness of an accelerated diagnostic protocol utilizing contemporary technology in a chest pain unit versus routine care in an internal medicine department.

Methods and Results

Hospital and 90-day course were prospectively studied in 585 consecutive low-moderate risk acute chest pain patients, of whom 304 were investigated in a designated chest pain center using a pre-specified accelerated diagnostic protocol, while 281 underwent routine care in an internal medicine ward. Hospitalization was longer in the routine care compared with the accelerated diagnostic protocol group (p<0.001). During hospitalization, 298 accelerated diagnostic protocol patients (98%) vs. 57 (20%) routine care patients underwent non-invasive testing, (p<0.001). Throughout the 90-day follow-up, diagnostic imaging testing was performed in 125 (44%) and 26 (9%) patients in the routine care and accelerated diagnostic protocol patients, respectively (p<0.001). Ultimately, most patients in both groups had non-invasive imaging testing. Accelerated diagnostic protocol patients compared with those receiving routine care was associated with a lower incidence of readmissions for chest pain [8 (3%) vs. 24 (9%), p<0.01], and acute coronary syndromes [1 (0.3%) vs. 9 (3.2%), p<0.01], during the follow-up period. The accelerated diagnostic protocol remained a predictor of lower acute coronary syndromes and readmissions after propensity score analysis [OR = 0.28 (CI 95% 0.14–0.59)]. Cost per patient was similar in both groups [($2510 vs. $2703 for the accelerated diagnostic protocol and routine care group, respectively, (p = 0.9)].

Conclusion

An accelerated diagnostic protocol is clinically superior and as cost effective as routine in acute chest pain patients, and may save time and resources.     

Hoc protein regulates the biological effects of T4 phage in mammals

We previously investigated the biological, non-antibacterial effects of bacteriophage T4 in mammals (binding to cancer cells in vitro and attenuating tumour growth and metastases in vivo); we selected the phage mutant HAP1 that was significantly more effective than T4. In this study we describe a non-sense mutation in the hoc gene that differentiates bacteriophage HAP1 and its parental strain T4. We found no substantial effects of the mutation on the mutant morphology, and its effects on electrophoretic mobility and hydrodynamic size were moderate. Only the high ionic strength of the environment resulted in a size difference of about 10 nm between T4 and HAP1. We compared the antimetastatic activity of the T2 phage, which does not express protein Hoc, with those of T4 and HAP1 (B16 melanoma lung colonies). We found that HAP1 and T2 decreased metastases with equal effect, more strongly than did T4. We also investigated concentrations of T4 and HAP1 in the murine blood, tumour (B16), spleen, liver, or muscle. We found that HAP1 was rapidly cleared from the organism, most probably by the liver. Although HAP1 was previously defined to bind cancer cells more effectively (than T4), its rapid elimination precluded its higher concentration in tumours. Maria Zembala and Janusz Boratynski contributed equally to this work.     

Estimation of bacteriological spoilage of pork cutlets by electronic nose

The utility of chemosensor array (EN) signals of head-space volatiles of aerobically stored pork cutlets as a non-invasive technique for monitoring their microbiological load was studied during storage at 4, 8 and 12 degrees C, respectively. The bacteriological quality of the meat samples was determined by standard total aerobic plate counts (TAPC) and colony count of selectively estimated Pseudomonas (PS) spp., the predominant aerobic spoilage bacteria. Statistical analysis of the electronic nose measurements were principal component analysis (PCA), and canonical discriminant analysis (CDA). Partial least squares (PLS) regression was used to model correlation between microbial loads and EN signal responses, the degree of bacteriological spoilage, independently of the temperature of the refrigerated storage. Sensor selection techniques were applied to reduce the dimensionality and more robust calibration models were computed by determining few individual sensors having the smallest cross correlations and highest correlations with the reference data. Correlations between the predicted and "real" values were given on cross-validated data from both data reduced models and for full calibrations using the 23 sensor elements. At the same time, sensorial quality of the raw cutlets was noted subjectively on faultiness of the odour and colour, and drip formation of the samples. These preliminary studies indicated that the electronic nose technique has a potential to detect bacteriological spoilage earlier or at the same time as olfactory quality deterioration.     

Impact of the belowground herbivore and potential biological control agent, Ceutorhynchus scrobicollis, on Alliaria petiolata performance

We studied the influence of the root-crown weevil Ceutorhynchus scrobicollis on its host plant Alliaria petiolata, a European biennial herb that is currently invading much of temperate North America. Varying timing of attack and herbivore densities in a common garden allowed to assess seasonality of plant response, density-dependence of impact, and the effect of intraspecific competition on C. scrobicollis recruitment (number of F₁ generation adults emerged). Data collected in the common garden were compared with data collected at field sites. C. scrobicollis is a common weevil in Europe, frequently attaining high attack levels on its host plant. In the common garden, weevil attack decreased plant survival by up to 43%, reduced plant height by 54%, increased the number of shoots by up to four–fold and delayed seed ripening, but had no significant negative effect on seed production. Plants infested in spring allocated less biomass to aboveground plant parts, and remained smaller than plants attacked in autumn, indicating that the latter were able to partly compensate for weevil attack. Increasing weevil density rarely had an effect on A. petiolata performance, and did not increase F₁ recruitment, suggesting strong intraspecific competition. At field sites, C. scrobicollis attack is spread over a long time period, which probably alleviates intraspecific competition. In summary, attack by the root-crown feeding weevil, C. scrobicollis, can substantially reduce growth and survival of A. petiolata. If introduced as a biological control agent into North America, C. scrobicollis is likely to decrease the fitness and competitive superiority of A. petiolata.