Response of immune response genes to adjuvants poly [di(sodium carboxylatoethylphenoxy)phosphazene] (PCEP), CpG oligodeoxynucleotide and emulsigen at intradermal injection site in pigs

Understanding the mechanisms by which adjuvants mediate their effects provide critical information on how innate immunity influences the development of adaptive immunity. Despite being a critical vaccine component, the mechanisms by which adjuvants mediate their effects are not fully understood and this is especially true when they are used in large animals. This lack of understanding limits our ability to design effective vaccines. In the present study, we administered polyphosphazene (PCEP), CpG oligodeoxynucleotides (CpG), emulsigen or saline via an intradermal injection into pigs and assessed the impact on the expression of reported 'adjuvant response genes' over time. CpG induced a strong upregulation of the chemokine CXL10 several 'Interferon Response Genes', as well as TNFα, and IL-10, and a down-regulation of IL-17 genes. Emulsigen upregulated expression of chemokines CCL2 and CCL5, proinflammatory cytokines IL-6 and TNFα, as well as TLR9, and several IFN response genes. PCEP induced the expression of chemokine CCL2 and proinflammatory cytokine IL-6. These results suggest that emulsigen and CpG may promote recruitment of innate immune cells and Th1 type cytokine production but that PCEP may promote a Th-2 type immune response through the induction of IL-6, an inducer of B cell activity and differentiation.

Standard Information Models for Representing Adverse Sensitivity Information in Clinical Documents

BACKGROUND

Adverse sensitivity (e.g., allergy and intolerance) information is a critical component of any electronic health record system. While several standards exist for structured entry of adverse sensitivity information, many clinicians record this data as free text.

OBJECTIVES

This study aimed to 1) identify and compare the existing common adverse sensitivity information models, and 2) to evaluate the coverage of the adverse sensitivity information models for representing allergy information on a subset of inpatient and outpatient adverse sensitivity clinical notes.

METHODS

We compared four common adverse sensitivity information models: Health Level 7 Allergy and Intolerance Domain Analysis Model, HL7-DAM; the Fast Healthcare Interoperability Resources, FHIR; the Consolidated Continuity of Care Document, C-CDA; and OpenEHR, and evaluated their coverage on a corpus of inpatient and outpatient notes (n = 120).

RESULTS

We found that allergy specialists' notes had the highest frequency of adverse sensitivity attributes per note, whereas emergency department notes had the fewest attributes. Overall, the models had many similarities in the central attributes which covered between 75% and 95% of adverse sensitivity information contained within the notes. However, representations of some attributes (especially the value-sets) were not well aligned between the models, which is likely to present an obstacle for achieving data interoperability. Also, adverse sensitivity exceptions were not well represented among the information models.

CONCLUSIONS

Although we found that common adverse sensitivity models cover a significant portion of relevant information in the clinical notes, our results highlight areas needed to be reconciled between the standards for data interoperability.

Flow cytometry as an improved method for the titration of Chlamydiaceae and other intracellular bacteria

Chlamydiaceae is a family of intracellular bacteria causing a range of diverse pathological outcomes. The most devastating human diseases are ocular infections with C. trachomatis leading to blindness and genital infections causing pelvic inflammatory disease with long-term sequelae including infertility and chronic pelvic pain. In order to enable the comparison of experiments between laboratories investigating host-chlamydia interactions, the infectious titer has to be determined. Titer determination of chlamydia is most commonly performed via microscopy of host cells infected with a serial dilution of chlamydia. However, other methods including fluorescent ELISpot (Fluorospot) and DNA Chip Scanning Technology have also been proposed to enumerate chlamydia-infected cells. For viruses, flow cytometry has been suggested as a superior alternative to standard titration methods. In this study we compared the use of flow cytometry with microscopy and Fluorospot for the titration of C. suis as a representative of other intracellular bacteria. Titer determination via Fluorospot was unreliable, while titration via microscopy led to a linear read-out range of 16 - 64 dilutions and moderate reproducibility with acceptable standard deviations within and between investigators. In contrast, flow cytometry had a vast linear read-out range of 1,024 dilutions and the lowest standard deviations given a basic training in these methods. In addition, flow cytometry was faster and material costs were lower compared to microscopy. Flow cytometry offers a fast, cheap, precise, and reproducible alternative for the titration of intracellular bacteria like C. suis. © 2016 International Society for Advancement of Cytometry.

Data management challenges in analysis and synthesis in the ecosystem sciences

Open-data has created an unprecedented opportunity with new challenges for ecosystem scientists. Skills in data management are essential to acquire, manage, publish, access and re-use data. These skills span many disciplines and require trans-disciplinary collaboration. Science synthesis centres support analysis and synthesis through collaborative 'Working Groups' where domain specialists work together to synthesise existing information to provide insight into critical problems. The Australian Centre for Ecological Analysis and Synthesis (ACEAS) served a wide range of stakeholders, from scientists to policy-makers to managers. This paper investigates the level of sophistication in data management in the ecosystem science community through the lens of the ACEAS experience, and identifies the important factors required to enable us to benefit from this new data-world and produce innovative science. ACEAS promoted the analysis and synthesis of data to solve transdisciplinary questions, and promoted the publication of the synthesised data. To do so, it provided support in many of the key skillsets required. Analysis and synthesis in multi-disciplinary and multi-organisational teams, and publishing data were new for most. Data were difficult to discover and access, and to make ready for analysis, largely due to lack of metadata. Data use and publication were hampered by concerns about data ownership and a desire for data citation. A web portal was created to visualise geospatial datasets to maximise data interpretation. By the end of the experience there was a significant increase in appreciation of the importance of a Data Management Plan. It is extremely doubtful that the work would have occurred or data delivered without the support of the Synthesis centre, as few of the participants had the necessary networks or skills. It is argued that participation in the Centre provided an important learning opportunity, and has resulted in improved knowledge and understanding of good data management practices.

Gene of the month: PIK3CA

PIK3CA encodes the p110α catalytic subunit of phosphatidylinositol 3-kinase (PI3K) which through its role in the PI3K/Akt pathway is important for the regulation of important cellular functions such as proliferation, metabolism and protein synthesis, angiogenesis and apoptosis. Mutations in PIK3CA are known to be involved in a wide range of human cancers and mutant PIK3CA is thought to act as an oncogene. The specific PIK3CA inhibitor, NVP-BYL719, has displayed promising results in cancer therapy and is currently under clinical trials. Furthermore, PI3K regulates autophagy, a cellular process that recycles proteins and organelles through lysosomal degradation and has recently been recognised as an attractive therapeutic target due to its pro- and anti-cancer properties. Several studies have attempted to investigate the effects of combining the inhibition of both PI3K and autophagy in cancer therapy, and an in vivo model has demonstrated that the combined use of a concomitant PI3K and autophagy inhibitor induced apoptosis in glioma cells.

Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities

Background

In eukaryotes, ubiquitin-conjugation is an important mechanism underlying proteasome-mediated degradation of proteins, and as such, plays an essential role in the regulation of many cellular processes. In the ubiquitin-proteasome pathway, E3 ligases play important roles by recognizing a specific protein substrate and catalyzing the attachment of ubiquitin to a lysine (K) residue. As more and more experimental data on ubiquitin conjugation sites become available, it becomes possible to develop prediction models that can be scaled to big data. However, no development that focuses on the investigation of ubiquitinated substrate specificities has existed. Herein, we present an approach that exploits an iteratively statistical method to identify ubiquitin conjugation sites with substrate site specificities.

Results

In this investigation, totally 6259 experimentally validated ubiquitinated proteins were obtained from dbPTM. After having filtered out homologous fragments with 40% sequence identity, the training data set contained 2658 ubiquitination sites (positive data) and 5532 non-ubiquitinated sites (negative data). Due to the difficulty in characterizing the substrate site specificities of E3 ligases by conventional sequence logo analysis, a recursively statistical method has been applied to obtain significant conserved motifs. The profile hidden Markov model (profile HMM) was adopted to construct the predictive models learned from the identified substrate motifs. A five-fold cross validation was then used to evaluate the predictive model, achieving sensitivity, specificity, and accuracy of 73.07%, 65.46%, and 67.93%, respectively. Additionally, an independent testing set, completely blind to the training data of the predictive model, was used to demonstrate that the proposed method could provide a promising accuracy (76.13%) and outperform other ubiquitination site prediction tool.

Conclusion

A case study demonstrated the effectiveness of the characterized substrate motifs for identifying ubiquitination sites. The proposed method presents a practical means of preliminary analysis and greatly diminishes the total number of potential targets required for further experimental confirmation. This method may help unravel their mechanisms and roles in E3 recognition and ubiquitin-mediated protein degradation.

Implementing a bar-code assisted medication administration system: effects on the dispensing process and user perceptions

PURPOSE

We assessed the effects of a bar-code assisted medication administration system used without the support of computerised prescribing (stand-alone BCMA), on the dispensing process and its users.

METHODS

The stand-alone BCMA system was implemented in one ward of a teaching hospital. The number of dispensing steps, dispensing time and potential dispensing errors (PDEs) were directly observed one month before and eight months after the intervention. Attitudes of pharmacy and nursing staff were assessed using a questionnaire (Likert scale) and interviews.

RESULTS

Among 1291 and 471 drug items observed before and after the introduction of the technology respectively, the number of dispensing steps increased from five to eight and time (standard deviation) to dispense one drug item by one staff personnel increased from 0.8 (0.09) to 1.5 (0.12) min. Among 2828 and 471 drug items observed before and after the intervention respectively, the number of PDEs increased significantly (P<0.001). 'Procedural errors' and 'missing drug items' were the frequently observed PDEs in the after study. 'Perceived usefulness' and 'job relevance' of the technology decreased significantly (P=0.003 and P=0.004 respectively) among users who participated in the before (N=16) and after (N=16) questionnaires surveys. Among the interviewees, pharmacy staff felt that the system offered less benefit to the dispensing process (9/16). Nursing staff perceived the system as useful in improving the accuracy of drug administration (7/10).

CONCLUSION

Implementing a stand-alone BCMA system may slow down and complicate the dispensing process. Nursing staff believe the stand-alone BCMA system could improve the drug administration process but pharmacy staff believes the technology would be more helpful if supported by computerised prescribing. However, periodical assessments are needed to identify weaknesses in the process after implementation, and all users should be educated on the benefits of using this technology.

Queensland tick typhus: three cases with unusual clinical features

Queensland tick typhus (QTT), caused by Rickettsia australis, is usually a relatively mild illness but can occasionally be severe. We describe three cases of probable QTT with unusual clinical features, namely splenic infarction, fulminant myopericarditis and severe leukocytoclastic vasculitis. QTT may present with uncommon clinical features in addition to the more common manifestations. A high index of suspicion enables specific antibiotic therapy that may hasten recovery.

In vitro and ex vivo analyses of co-infections with swine influenza and porcine reproductive and respiratory syndrome viruses

Viral respiratory diseases remain problematic in swine. Among viruses, porcine reproductive and respiratory syndrome virus (PRRSV) and swine influenza virus (SIV), alone or in combination, are the two main known contributors to lung infectious diseases. Previous studies demonstrated that experimental dual infections of pigs with PRRSV followed by SIV can cause more severe disease than the single viral infections. However, our understanding of the impact of one virus on the other at the molecular level is still extremely limited. Thus, the aim of the current study was to determine the influence of dual infections, compared to single infections, in porcine alveolar macrophages (PAMs) and precision cut lung slices (PCLS). PAMs were isolated and PCLS were acquired from the lungs of healthy 8-week-old pigs. Then, PRRSV (ATCC VR-2385) and a local SIV strain of H1N1 subtype (A/Sw/Saskatchewan/18789/02) were applied simultaneously or with 3 h apart on PAMs and PCLS for a total of 18 h. Immuno-staining for both viruses and beta-tubulin, real-time quantitative PCR and ELISA assays targeting various genes (pathogen recognition receptors, interferons (IFN) type I, cytokines, and IFN-inducible genes) and proteins were performed to analyze the cell and the tissue responses. Interference caused by the first virus on replication of the second virus was observed, though limited. On the host side, a synergistic effect between PRRSV and SIV co-infections was observed for some transcripts such as TLR3, RIG-I, and IFNβ in PCLS. The PRRSV infection 3 h prior to SIV infection reduced the response to SIV while the SIV infection prior to PRRSV infection had limited impact on the second infection. This study is the first to show an impact of PRRSV/SIV co-infection and superinfections in the cellular and tissue immune response at the molecular level. It opens the door to further research in this exciting and intriguing field.

Effects of 1.8 GHz radiofrequency radiation on protein expression in human lens epithelial cells

OBJECTIVE

The aim of the present study was to observe the effects of 1.8 GHz radiofrequency (RF) radiation on the protein expression of human lens epithelial cells (hLECs) in vitro.

METHODS

The hLECs were exposed and sham-exposed to 1.8 GHz RF radiation (specific absorption rate (SAR) of 4 W/kg) for 2 h. After exposure, the proteins extracted from LECs were loaded on the Ettan MDLC system connected to the LTQ-Orbitrap MS for screening the candidate protein biomarkers induced by RF. The quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the levels of messenger RNA of candidate biomarkers. After the hLECs were exposed to 1.8 GHz RF (SAR of 2, 3 and 4 W/kg) for 2 h, the Western blot assay was utilized to measure the expression levels of the above-screened candidate protein biomarkers.

RESULTS

The results of shotgun proteomic analysis indicated that there were eight proteins with differential expression between exposure and sham exposure groups. The results of qRT-PCR showed that there were three genes with expressional differences (valosin containing protein (VCP), ubiquitin specific peptidase 35 (USP35) and signal recognition particle 68 kDa (SRP68)) between exposure and sham exposure groups. The results of Western blot assay exhibited that the expressional levels of VCP and USP35 proteins significantly increased and the expressional level of protein SRP68 significantly decreased in hLECs exposed to 1.8 GHz RF radiation (SAR of 3 and 4 W/kg) for 2 h when compared with the corresponding sham groups (p < 0.05).

CONCLUSION

The shotgun proteomics technique can be applied to screen the proteins with differential expression between hLECs exposed to 1.8 GHz RF and hLECs sham-exposed to 1.8 GHz RF, and three protein biomarkers associated with RF radiation were validated by Western blot assay.

Innovative therapy for Classic Galactosemia - tale of two HTS

Classic Galactosemia is an autosomal recessive disorder caused by the deficiency of galactose-1-phosphate uridylyltransferase (GALT), one of the key enzymes in the Leloir pathway of galactose metabolism. While the neonatal morbidity and mortality of the disease are now mostly prevented by newborn screening and galactose restriction, long-term outcome for older children and adults with this disorder remains unsatisfactory. The pathophysiology of Classic Galactosemia is complex, but there is convincing evidence that galactose-1-phosphate (gal-1P) accumulation is a major, if not the sole pathogenic factor. Galactokinase (GALK) inhibition will eliminate the accumulation of gal-1P from both dietary sources and endogenous production, and efforts toward identification of therapeutic small molecule GALK inhibitors are reviewed in detail. Experimental and computational high-throughput screenings of compound libraries to identify GALK inhibitors have been conducted, and subsequent studies aimed to characterize, prioritize, as well as to optimize the identified positives have been implemented to improve the potency of promising compounds. Although none of the identified GALK inhibitors inhibits glucokinase and hexokinase, some of them cross-inhibit other related enzymes in the GHMP small molecule kinase superfamily. While this finding may render the on-going hit-to-lead process more challenging, there is growing evidence that such cross-inhibition could also lead to advances in antimicrobial and anti-cancer therapies.

Identification of novel small molecule inhibitors of 4-diphosphocytidyl-2-C-methyl-D-erythritol (CDP-ME) kinase of Gram-negative bacteria

The biosyntheses of isoprenoids is essential for the survival in all living organisms, and requires one of the two biochemical pathways: (a) Mevalonate (MVA) Pathway or (b) Methylerythritol Phosphate (MEP) Pathway. The latter pathway, which is used by all Gram-negative bacteria, some Gram-positive bacteria and a few apicomplexan protozoa, provides an attractive target for the development of new antimicrobials because of its absence in humans. In this report, we describe two different approaches that we used to identify novel small molecule inhibitors of Escherichia coli and Yersinia pestis 4-diphosphocytidyl-2-C-methyl D-erythritol (CDP-ME) kinases, key enzymes of the MEP pathway encoded by the E. coli ispE and Y. pestisipk genes, respectively. In the first approach, we explored existing inhibitors of the GHMP kinases while in the second approach; we performed computational high-throughput screening of compound libraries by targeting the CDP-ME binding site of the two bacterial enzymes. From the first approach, we identified two compounds with 6-(benzylthio)-2-(2-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1,3-thiazine-5-carbonitrile and (Z)-3-methyl-4-((5-phenylfuran-2-yl)methylene)isoxazol-5(4H)-one scaffolds which inhibited E. coli CDP-ME kinase in vitro. We then performed substructure search and docking experiments based on these two scaffolds and identified twenty three analogs for structure-activity relationship (SAR) studies. Three new compounds from the isoxazol-5(4H)-one series have shown inhibitory activities against E. coli and Y. pestis CDP-ME kinases with the IC(50) values ranging from 7 to 13 μM. The second approach by computational high-throughput screening (HTS) of two million drug-like compounds yielded two compounds with benzenesulfonamide and acetamide moieties which, at a concentration of 20 μM, inhibited 80% and 65%, respectively, of control CDP-ME kinase activity.

Molecular and biochemical characterization of human galactokinase and its small molecule inhibitors

Human galactokinase (GALK) is the first enzyme in the Leloir pathway, converting α-d-galactose into galactose-1-phosphate (Gal-1-P). Recently, there is increasing interest in targeting GALK as a novel therapy to ameliorate the disease manifestations in patients with Classic Galactosemia as it would, in combination with (ga-)lactose restriction reduce accumulation of Gal-1-P, a cytotoxic agent. Previously, we identified 34 small molecule compounds that inhibited GALK in vitro using experimental high-throughput screening. In order to isolate useful lead compounds, we characterized these hits with regards to their kinase selectivity profiles, potency and capability to reduce Gal-1-P accumulation in patient cell lines, and their modes of action. We found that the majority of these compounds had IC(50)s ranging from 0.7μM to 33.3μM. When tested against other members of the GHMP kinase family, three compounds (1, 4, and 24) selectively inhibited GALK with high potency. Through alignment of GALK and mevalonate kinase (MVK) crystal structures, we identified that eight amino acid residues and an L1 loop were different within the ATP-binding pockets of these two closely related kinases. By site-directed mutagenesis experiments, we identified one amino acid residue required for the inhibitory function of two of the three selective compounds. Based on these results, we generated binding models of these two compounds using a high-precision docking program. Compounds 4 and 24 inhibited GALK in a mixed model, while compound 1 exhibited parabolic competitive inhibition. Most importantly, using cells from galactosemic patients we found that selected compounds lowered Gal-1-P concentrations.

Tapping mode microwave impedance microscopy

We report tapping mode microwave impedance imaging based on atomic force microscope platforms. The shielded cantilever probe is critical to localize the tip-sample interaction near the tip apex. The modulated tip-sample impedance can be accurately simulated by the finite-element analysis and the result agrees quantitatively to the experimental data on a series of thin-film dielectric samples. The tapping mode microwave imaging is also superior to the contact mode in that the thermal drift in a long time scale is totally eliminated and an absolute measurement on the dielectric properties is possible. We demonstrated tapping images on working nanodevices, and the data are consistent with the transport results.

Transcriptomic analysis of Saccharomyces cerevisiae physiology in the context of galactose assimilation perturbations

Despite being extensively studied in various organisms due to scientific, industrial and medical interest, the galactose assimilation function and regulation, and especially its interaction with other parts of cellular physiology, have not been fully elucidated yet. The post-genomic era holistic techniques ("omics") could assist towards this goal. In this paper, we holistically analyzed full-genome Saccharomyces cerevisiae transcriptional profiling data concerning its glucose- and galactose-grown wild-type (WT) physiology and its glucose-grown gal7-deficient (GAL7Delta) physiology, as these were obtained in the experiment described in Lai and Elsas (Biochem. Biophys. Res. Commun. 2000, 271, 392-400). The gal7 gene encodes for the second enzyme of the galactose assimilation, Leloir, pathway, and its deficiency in humans causes a potentially lethal disease, named "classic galactosemia". Analysis of the galactose-grown compared to the glucose-grown WT physiology indicated a significant increase in the transcriptional expression of the ribosomal machinery and decrease in the transcriptional activity of the fatty acids' beta-oxidation at the peroxisomes. Comparison of GAL7Delta to WT physiology in glucose indicated a significant transcriptional increase in the mitochondrial activity and the rate of catabolism of disaccharides, including sucrose, mannose and trehalose, towards amplified biosynthesis of the main cell wall components. Comparison with other physiological conditions indicated strong correlation between the glucose-grown GAL7Delta transcriptional physiology and the WT growth under glucose derepression conditions. Finally, the acquired results and the large number of still unknown genes that were related to the galactose assimilation regulation indicated the need for further, specifically designed, perturbations and integrated analyses of multiple levels of cellular function.

Modeling and characterization of a cantilever-based near-field scanning microwave impedance microscope

This paper presents a detailed modeling and characterization of a microfabricated cantilever-based scanning microwave probe with separated excitation and sensing electrodes. Using finite-element analysis, we model the tip-sample interaction as small impedance changes between the tip electrode and the ground at our working frequencies near 1 GHz. The equivalent lumped elements of the cantilever can be determined by transmission line simulation of the matching network, which routes the cantilever signals to 50 Omega feed lines. In the microwave electronics, the background common-mode signal is canceled before the amplifier stage so that high sensitivity (below 1 aF capacitance changes) is obtained. Experimental characterization of the microwave microscope was performed on ion-implanted Si wafers and patterned semiconductor samples. Pure electrical or topographical signals can be obtained from different reflection modes of the probe.

Expression and distribution of MMPs and TIMPs in human uveal melanoma

Matrix metalloproteinases (MMPs) and tissue inhibitors of MMPs (TIMPs) are involved in tumour invasion, metastasis and angiogenesis, and have been implicated as progression markers in uveal melanoma, although their topographical expression has not been fully described. In this study we compared the distribution and specificity of several classes of MMPs (MMP-1, -2, -9, -19, and MT1-MMP) and physiological MMP inhibitors (TIMP-2 and -3) in different regions of the tumour microenvironment and adjacent choroid in a series of primary uveal melanomas. Paraffin sections of untreated uveal melanomas (n=18, 3/18 spindle; 11/18 mixed, and 4/18 epithelioid) were examined for MMP-1 (collagenase 1), MMP-2 and MMP-9 (gelatinases A and B), MT1-MMP (membrane-type 1-MMP), MMP-19, TIMP-2 and TIMP-3 (tissue inhibitors of MMPs), using indirect peroxidase immunohistochemistry. The distribution and intensity of immunolabelling was graded semi-quantitatively (0-3) by 2 independent observers. Non-parametric analyses were used to test for associations between tumour cell type, and the average grade of MMP or TIMP expression. Immunostaining for MMP-1, -9, -19 and MT1-MMP was > or =Grade 2 in more than 70% of specimens, and a heterogeneous pattern of MMP-1, -9, MT1-MMP and TIMP-3 expression was observed. At the tumour-scleral interface (TSI), melanoma cells had a flattened morphology and a much reduced MMP and TIMP expression, with a high expression in tumour areas adjacent to the TSI. Tumour vasculature and stromal cells strongly expressed MMP-2. We also observed heterogeneous immunostaining of the vasculature by MMP-1, -9, MT1-MMP and TIMP-2 antibodies, and of the extravascular matrix by MMP-9 antibody. The distinct immunostaining patterns observed for MMPs and TIMPs within uveal melanoma are consistent with their involvement in tumour growth and angiogenesis. In particular, the heterogeneous expression within regions of the tumours, and the localized expression in vasculature and stromal cells emphasises the importance of the tumour microenvironment in the pathogenesis of uveal melanoma (and other tumours).