A Synopsis of Proteins and Their Purification.

The goal of protein purification is to separate a specific protein from all other biomolecules. Classical chromatographic procedures have been designed to exploit particular distinguishing features of individual target proteins, such as size, shape, physicochemical properties, and binding affinity. Advances in molecular biology and bioinformatics have positively contributed at every level to the challenge of purifying individual proteins and more recently have led to the development of high-throughput proteomic platforms. In this chapter, a synopsis of advancements in the field of protein chromatography is presented, with reference to the principal tools and resources that are available to assist with protein purification strategies.

Poly-Histidine-Tagged Protein Purification Using Immobilized Metal Affinity Chromatography (IMAC).

His-tagging is the most widespread and versatile strategy used to purify recombinant proteins for biochemical and structural studies. Recombinant DNA methods are first used to engineer the addition of a short tract of poly-histidine tag (His-tag) to the N-terminus or C-terminus of a target protein. The His-tag is then exploited to enable purification of the "tagged" protein by immobilized metal affinity chromatography (IMAC). In this chapter, we describe efficient procedures for the isolation of highly purified His-tagged target proteins from an Escherichia coli host using IMAC in a bind-wash-elute strategy that can be performed under both native and denaturing conditions.

Tagging Recombinant Proteins to Enhance Solubility and Aid Purification.

Protein fusion technology has had a major impact on the efficient production and purification of individual recombinant proteins. The use of genetically engineered affinity and solubility-enhancing polypeptide "tags" has a long history, and there is a considerable repertoire of these that can be used to address issues related to the expression, stability, solubility, folding, and purification of their fusion partner. In the case of large-scale proteomic studies, the development of purification procedures tailored to individual proteins is not practicable, and affinity tags have become indispensable tools for structural and functional proteomic initiatives that involve the expression of many proteins in parallel. In this chapter, the rationale and applications of a range of established and more recently developed solubility-enhancing and affinity tags is described.

Protein Quantitation and Analysis of Purity.

The accurate quantitation of proteins and an analysis of their purity is essential in numerous areas of scientific research and is a critical factor in many clinical applications. The large number and variety of techniques employed for this purpose is therefore not surprising. The selection of a suitable assay is dependent on such factors as the level of sensitivity required, the presence of interfering agents, and the composition of the protein itself. In this chapter, protocols for the most commonly used protein determination methodologies are outlined, including an overview of the highly sensitive real-time quantitative immuno-polymerase chain reaction assay. In addition, an approach to validate the UV protein absorption assay is outlined, which can be applied to any procedure for method validation.

A TLR5 mono-agonist restores inhibited immune responses to Streptococcus pneumoniae during influenza virus infection in human monocytes.

Influenza A virus (IAV) predisposes individuals to often more severe secondary bacterial infections with Streptococcus pneumonia (S. pneumoniae). The outcomes of these infections may be made worse with the increase in antimicrobial resistance and a lack of new treatments to combat this. Th17 responses are crucial in clearing S. pneumoniae from the lung. We previously demonstrated that early IAV infection of human monocytes significantly reduced levels of S. pneumoniae-driven cytokines involved in the Th17 response. Here, we have further identified that IAV targets specific TLRs (TLR2, TLR4, TLR9) involved in sensing S. pneumoniae infection resulting, in a reduction in TLR agonist-induced IL-23 and TGF-ß. The effect of IAV is more profound on the TLR2 and TLR9 pathways. We have established that IAV-mediated inhibition of TLR9-induction is related to a downregulation of RORC, a Th17 specific transcription factor. Other studies using mouse models demonstrated that TLR5 agonism improved the efficacy of antibiotics in the treatment of IAV/S. pneumoniae co-infections. Therefore, we investigated if TLR5 agonism could restore inhibited Th17 responses in human monocytes. Levels of pneumococcus-driven cytokines, which had previously been inhibited by IAV were not reduced in the presence of the TLR5 mono-agonist, suggesting that such treatment may overcome IAV inhibition of Th17 responses. The importance of our research is in demonstrating the IAV directly targets S. pneumoniae-associated TLR pathways. Additionally, the IAV-inhibition of Th17 responses can be restored by TLR5 agonism, which indicates that there may be a different Th17 signalling pathway which is not affected by IAV infection.

Gene Expression Analysis by Reverse Transcription Quantitative PCR.

The reverse transcription quantitative polymerase chain reaction (RT-qPCR) is a rapid detection technology that allows the amplification and quantification of specific RNA transcripts. RT-qPCR has increasingly been adopted for the detection and quantification of H. pylori across a range of sample types and applications. In addition, it is widely used to monitor host gene expression in cells and tissues in response to H. pylori infection . Outlined here is a two-step protocol that can be employed to analyze gene expression in H. pylori or H. pylori-infected samples.

A feasibility study of an exercise intervention to educate and promote health and well-being among medical students: the 'MED-WELL' programme.

BACKGROUND: Medical School programme workloads challenge the physical and mental health of students particularly in compressed graduate entry programmes. There is evidence that physical activity (PA) can improve holistic care and help maintain wellness among medical students. We tested the feasibility of introducing an exercise programme to the medical school curriculum which would educate and promote health and well-being among its students. METHODS: This study was conducted in a single graduate entry medical school at the University of Limerick (UL). The 'MED-WELL' programme was a six-week programme of 1 hour-long weekly sessions, each involving a different type of PA (45 min). These sessions were prefaced by an interactive lecture about how to incorporate exercise theory into daily medical practice (15 min). The study was conducted in a single graduate entry medical school at UL and involved year one and year two graduate entry medical students. Three parameters were used to test feasibility: 1. Recruitment and retention of participants, 2. Acceptability of the programme and 3. Efficacy in terms of health and well-being. The latter was assessed by administering questionnaires pre and post the intervention. The questionnaires used the following validated measurement scales: EQ-VAS; WHO-5 Well-Being Index; 3-item Loneliness Scale; Social Support Measure 3-item scale. Free text boxes also encouraged participants to discuss the merits of the programme. RESULTS: In total, 26% (74/286 students) participated in the programme. Of those who participated, 69 students (93%) attended one or more sessions of the programme and completed questionnaires at baseline and at follow-up. Significant improvements were seen in scores after the programme in the WHO-5 Well-Being Index which increased from 63.2 (95%CI: 48-78.4) to 67.5 (95%CI: 55.1-79.9); (P < 0.01), the sleep scale which increased from 3.1 (95%CI: 2.2-4.0) to 3.5 (95%CI: 2.5-4.5); (P < 0.001), and the loneliness scale which decreased from 4.1 (95%CI: 2.7-5.5) to 3.5 (95%CI: 2.5-4.5); (P < 0.005). Students level of PA during a typical week also increased from 3.7 (95%CI: 2.1-5.4) to 4.0 (95%CI, 3.5-4.5); (P < 0.05). CONCLUSION: This study has shown it is feasible to deliver this programme in a medical school's curriculum. The programme seems to be of benefit and is acceptable to students. Well-designed randomised controlled trials are needed to measure outcomes, durability of effect, and cost effectiveness.

Influenza infection directly alters innate IL-23 and IL-12p70 and subsequent IL-17A and IFN-γ responses to pneumococcus in vitro in human monocytes.

IMPORTANCE: Influenza virus is highly contagious and poses substantial public health problems due to its strong association with morbidity and mortality. Approximately 250,000-500,000 deaths are caused by seasonal influenza virus annually, and this figure increases during periods of pandemic infections. Most of these deaths are due to secondary bacterial pneumonia. Influenza-bacterial superinfection can result in hospitalisation and/or death of both patients with pre-existing lung disease or previously healthy individuals. The importance of our research is in determining that influenza and its component haemagglutinin has a direct effect on the classic pneumococcus induced pathways to IL-17A in our human ex vivo model. Our understanding of the mechanism which leaves people exposed to influenza infection during superinfection remain unresolved. This paper demonstrates that early infection of monocytes inhibits an arm of immunity crucial to bacterial clearance. Understanding this mechanism may provide alternative interventions in the case of superinfection with antimicrobial resistant strains of bacteria.

Evaluation of a coaching workshop for the management of veterinary nursing students' OSCE-associated test anxiety.

BACKGROUND: High stress levels amongst undergraduates (particularly in relation to assessment) and efforts to improve mental wellbeing have been increasingly reported in the veterinary educational literature. However reports to date have primarily focused on the experiences of students of veterinary medicine, rather than veterinary nursing students. METHODS: The purpose of this mixed method sequential explanatory study was to establish the "Big-five" personality traits and quantify the level of test anxiety associated with objective structured clinical examinations (OSCEs) amongst a cohort of 23 final year veterinary nursing students at an Irish third level college. The 12 item Brief FRIEDBEN Test Anxiety Scale (B-FTAS) and the 20 item mini International Personality Item Pool (mini-IPIP) were used to identify test anxiety levels and personality traits in this cohort. Focus groups were then employed to examine the effectiveness of a coaching intervention in ameliorating this test anxiety. RESULTS: The initial, quantitative, phase found these students to have higher levels of test anxiety than previously reported for undergraduates sitting written examinations. No association was found between test anxiety and neurotic personality traits in this student cohort. In the qualitative follow up phase the coaching intervention was reported to have been helpful in equipping the students to better manage test anxiety. The OSCE stressors identified in this study closely resembled those previously reported by nursing and midwifery students. CONCLUSIONS: The shared experience of the coaching intervention and formative OSCE was reported to have been helpful in empowering the students to manage assessment-associated anxiety. Implications and recommendations for educators were identified.

Haemagglutinin-neuraminidase from HPIV3 mediates human NK regulation of T cell proliferation via NKp44 and NKp46.

HPIV3 is a respiratory virus causing airway diseases, including pneumonia, croup, and bronchiolitis, during infancy and childhood. Currently there is no effective vaccine or anti-viral therapy for this virus. Studies have suggested that poor T cell proliferation following HPIV3 infection is responsible for impaired immunological memory associated with this virus. We have previously demonstrated that NK cells mediate regulation of T cell proliferation during HPIV3 infection. Here we add to these studies by demonstrating that the regulation of T cell proliferation during HPIV3 infection is mediated via NK receptors NKp44 and NKp46 and involves the surface glycoprotein haemagglutinin-neuraminidase but not the fusion protein of the virus. These studies extend our knowledge of the regulatory repertoire of NK cells and provide mechanistic insights which may explain reoccurring failures of vaccines against this virus.

A Synopsis of Proteins and Their Purification.

The isolation of a given protein, free of all other biomolecules, is the primary objective of any protein purification scheme. Classical chromatographic procedures have been designed to exploit particular distinguishing features of individual target proteins, such as size, physicochemical properties, and binding affinity. Advances in molecular biology and bioinformatics have positively contributed at every level to the challenge of purifying individual proteins and more recently have led to the development of high-throughput proteomic platforms. Here, a synopsis of developments in the field of protein chromatography is given, with reference to the principal tools and resources that are available to assist with protein purification processes.

Tagging Recombinant Proteins to Enhance Solubility and Aid Purification.

Protein fusion technology has had a major impact on the efficient production and purification of individual recombinant proteins. The use of genetically engineered affinity and solubility-enhancing polypeptide "tags" has increased greatly in recent years and there now exists a considerable repertoire of these that can be used to solve issues related to the expression, stability, solubility, folding, and purification of their fusion partner. In the case of large-scale proteomic studies, the development of purification procedures tailored to individual proteins is not practicable, and affinity tags have therefore become indispensable tools for structural and functional proteomic initiatives that involve the expression of many proteins in parallel. Here, the rationale and applications of a range of established and more recently developed solubility-enhancing and affinity tags is described.

Protein Quantitation and Analysis of Purity.

The accurate quantitation of proteins and an analysis of their purity are essential in numerous areas of scientific research, and is a critical factor in many clinical applications. The large number and variety of techniques employed for this purpose is therefore not surprising. The selection of a suitable assay is dependent on such factors as the level of sensitivity required, the presence of interfering agents, and the composition of the protein itself. Here, protocols for the most commonly used protein determination methodologies are outlined, as well as for the more recently adapted technique of quantitative immuno-Polymerase Chain Reaction.

Purification of Polyhistidine-Tagged Proteins.

His-tagging is the most widespread and versatile strategy used to purify recombinant proteins for biochemical and structural studies. Recombinant DNA methods are first used to engineer the addition of a short tract of poly-histidine tag (His-tag) to the N-terminus or C-terminus of a target protein. The His-tag is then exploited to enable purification of the "tagged" protein by Immobilized Metal Affinity Chromatography (IMAC). Here, we describe efficient procedures for the isolation of highly purified His-tagged target proteins from an E. coli host using IMAC.

In-vitro characterisation of a novel celecoxib microbead formulation for the treatment and prevention of colorectal cancer.

OBJECTIVES: Colorectal cancer (CRC) is a life-threatening disease that can develop as a consequence of a sustained chronic inflammatory pathology of the colon. Although not devoid of side effects, the anti-inflammatory drug celecoxib (CLX) has been shown to exert protective effects in CRC therapy. The purpose of this study was to develop and characterise a novel CLX microbead formulation suitable for use in the treatment and prevention of CRC, which has the potential to minimise the side effects associated with CLX. METHODS: The study involved the assessment of the effectiveness of CLX formulations in an in-vitro cell model (HT29 cells) and a comparison of these effects to that of the marketed CLX product, Celebrex. Liquid CLX formulations were developed as precursors to microbead formulations. The effect of liquid CLX formulations on HT29 cell viability (MTT and flow cytometry apoptotic assays) and motility (scratch wound assay) were assessed and compared with the effect of Celebrex. A correlation between the in-vitro dissolution performance of the formulations and the effect in the cell model was also explored. Liquid CLX formulations were translated into an optimised CLX microbead formulation, and a colonic targeted sustained release coat (Surelease) was applied to the beads with the aim of producing a formulation for a future in-vivo study to compare the effect of the coated CLX microbeads versus Celebrex in the attenuation of CRC tumours and inflammation in a CRC murine model. The production of CLX microbeads was scaled-up using vibrating-jet encapsulation technology to allow for the development of an optimised dissolution profile to enable colonic release. KEY FINDINGS: In-vitro cell viability and motility were shown to be significantly reduced after treatment with CLX liquid formulations relative to the control, whereas the results for treatment with Celebrex were comparable with the control. Dissolution experiments and correlation analysis demonstrated that the formulations that showed a greater extent of drug release had reduced cell viability and motility. The CLX liquid formulations were translated into colon-targeted CLX microbeads suitable for use in a future in-vivo mouse study. CONCLUSIONS: These results represent a significant step forward in the chemopreventative treatment of CRC using CLX, as the microbead formulation developed suggests the possibility of presenting CLX in a format that has the potential to minimise gastrointestinal and cardiovascular side effects.

Repression of the proapoptotic cellular BIK/NBK gene by Epstein-Barr virus antagonizes transforming growth factor ß1-induced B-cell apoptosis.

UNLABELLED: The Epstein-Barr virus (EBV) establishes a lifelong latent infection in humans. EBV infection of primary B cells causes cell activation and proliferation, a process driven by the viral latency III gene expression program, which includes EBV nuclear proteins (EBNAs), latent membrane proteins, and untranslated RNAs, including microRNAs. Some latently infected cells enter the long-lived memory B-cell compartment and express only EBNA1 transiently (Lat I) or no EBV protein at all (Lat 0). Targeting the molecular machinery that controls B-cell fate decisions, including the Bcl-2 family of apoptosis-regulating proteins, is crucial to the EBV cycle of infection. Here, we show that BIK (also known as NBK), which encodes a proapoptotic "sensitizer" protein, is repressed by the EBNA2-driven Lat III program but not the Lat I program. BIK repression occurred soon after infection of primary B cells by EBV but not by a recombinant EBV in which the EBNA2 gene had been knocked out. Ectopic BIK induced apoptosis in Lat III cells by a mechanism dependent on its BH3 domain and the activation of caspases. We show that EBNA2 represses BIK in EBV-negative B-cell lymphoma-derived cell lines and that this host-virus interaction can inhibit the proapoptotic effect of transforming growth factor ß1 (TGF-ß1), a key physiological mediator of B-cell homeostasis. Reduced levels of TGF-ß1-associated regulatory SMAD proteins were bound to the BIK promoter in response to EBV Lat III or ectopic EBNA2. These data are evidence of an additional mechanism used by EBV to promote B-cell survival, namely, the transcriptional repression of the BH3-only sensitizer BIK. IMPORTANCE: Over 90% of adult humans are infected with the Epstein-Barr virus (EBV). EBV establishes a lifelong silent infection, with its DNA residing in small numbers of blood B cells that are a reservoir from which low-level virus reactivation and shedding in saliva intermittently occur. Importantly, EBV DNA is found in some B-cell-derived tumors in which viral genes play a key role in tumor cell emergence and progression. Here, we report for the first time that EBV can shut off a B-cell gene called BIK. When activated by a molecular signal called transforming growth factor ß1 (TGF-ß1), BIK plays an important role in killing unwanted B cells, including those infected by viruses. We describe the key EBV-B-cell molecular interactions that lead to BIK shutoff. These findings further our knowledge of how EBV prevents the death of its host cell during infection. They are also relevant to certain posttransplant lymphomas where unregulated cell growth is caused by EBV genes.

Syntaxin-4 is essential for IgE secretion by plasma cells.

The humoral immune system provides a crucial first defense against the invasion of microbial pathogens via the secretion of antigen specific immunoglobulins (Ig). The secretion of Ig is carried out by terminally differentiated B-lymphocytes called plasma cells. Despite the key role of plasma cells in the immune response, the mechanisms by which they constitutively traffic large volumes of Ig out of the cell is poorly understood. The involvement of Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins in the regulation of protein trafficking from cells has been well documented. Syntaxin-4, a member of the Qa SNARE syntaxin family has been implicated in fusion events at the plasma membrane in a number of cells in the immune system. In this work we show that knock-down of syntaxin-4 in the multiple myeloma U266 human plasma cell line results in a loss of IgE secretion and accumulation of IgE within the cells. Furthermore, we show that IgE co-localises with syntaxin-4 in U266 plasma cells suggesting direct involvement in secretion at the plasma membrane. This study demonstrates that syntaxin-4 plays a critical role in the secretion of IgE from plasma cells and sheds some light on the mechanisms by which these cells constitutively traffic vesicles to the surface for secretion. An understanding of this machinery may be beneficial in identifying potential therapeutic targets in multiple myeloma and autoimmune disease where over-production of Ig leads to severe pathology in patients.

Functional consequence of positive selection revealed through rational mutagenesis of human myeloperoxidase.

Myeloperoxidase (MPO) is a member of the mammalian heme peroxidase (MHP) multigene family. Whereas all MHPs oxidize specific halides to generate the corresponding hypohalous acid, MPO is unique in its capacity to oxidize chloride at physiologic pH to produce hypochlorous acid (HOCl), a potent microbicide that contributes to neutrophil-mediated host defense against infection. We have previously resolved the evolutionary relationships in this functionally diverse multigene family and predicted in silico that positive Darwinian selection played a major role in the observed functional diversities (Loughran NB, O'Connor B, O'Fagain C, O'Connell MJ. 2008. The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions. BMC Evol Biol. 8:101). In this work, we have replaced positively selected residues asparagine 496 (N496), tyrosine 500 (Y500), and leucine 504 (L504) with the amino acids present in the ancestral MHP and have examined the effects on the structure, biosynthesis, and activity of MPO. Analysis in silico predicted that N496F, Y500F, or L504T would perturb hydrogen bonding in the heme pocket of MPO and thus disrupt the structural integrity of the enzyme. Biosynthesis of the mutants stably expressed in human embryonic kidney 293 cells yielded apoproMPO, the heme-free, enzymatically inactive precursor of MPO, that failed to undergo normal maturation or proteolytic processing. As a consequence of the maturational arrest at the apoproMPO stage of development, cells expressing MPO with mutations N496F, Y500F, L504T, individually or in combination, lacked normal peroxidase or chlorinating activity. Taken together, our data provide further support for the in silico predictions of positive selection and highlight the correlation between positive selection and functional divergence. Our data demonstrate that directly probing the functional importance of positive selection can provide important insights into understanding protein evolution.

New approaches in the detection of calcium-containing microcrystals in synovial fluid.

BACKGROUND: The presence of calcium phosphate crystals such as basic calcium phosphate and calcium pyrophosphate dihydrate in intra-articular fluid is linked to a number of destructive arthropathies and detection of these deposits is often pivotal for early diagnosis and appropriate management of such disease. RESULTS: We describe the use of a calcium-sensitive dye, Fluo-4, to selectively label calcium-containing mineral deposits in synovial fluid, which can then be easily visualized using a standard fluorescence microscope. Furthermore, we have combined the fluorescent properties of the tagged crystals with flow cytometry as a fast and semi-quantitative method of detection. CONCLUSION: Dot-plots were used to quantify differences between various types of arthropathies and confirmed by visual observation of the crystals under a fluorescence microscope.