Harnessing bioinformatics to discover new vaccines

Vaccine design is highly suited to the application of in silico techniques, for both the discovery and development of new and existing vaccines. Here, we discuss computational contributions to epitope mapping and reverse vaccinology, two techniques central to the new discipline of immunomics. Also discussed are methods to improve the efficiency of vaccination, such as codon optimization and adjuvant discovery in addition to the identification of allergenic proteins. We also review current software developed to facilitate vaccine design.

Quinols as novel therapeutic agents. 2.1 4-(1-arylsulfonylindol- 2-yl)-4-hydroxycyclohexa-2,5-dien-1-ones and related agents as potent and selective antitumor agents

A series of substituted 4-(1-arylsulfonylindol-2-yl)-4-hydroxycyclohexa-2, 5-dien-1-ones (indolylquinols) has been synthesized on the basis of the discovery of lead compound 1a and screened for antitumor activity. Synthesis of this novel series was accomplished via the "one-pot" addition of lithiated (arylsulfonyl)indoles to 4,4-dimethoxycyclohexa-2,5-dienone followed by deprotection under acidic conditions. Similar methodology gave rise to the related naphtho-, 1H-indole-, and benzimidazole-substituted quinols. A number of compounds in this new series were found to possess in vitro human tumor cell line activity substantially more potent than the recently reported antitumor 4-substituted 4-hydroxycyclohexa-2,5-dien-1-ones1 with similar patterns of selectivity against colon, renal, and breast cell lines. The most potent compound in the series in vitro, 4-(1-benzenesulfonyl-6-fluoro-1H-indol- 2-yl)-4-hydroxycyclohexa-2,5-dienone (1h), exhibits a mean GI50 value of 16 nM and a mean LC50 value of 2.24 μM in the NCI 60-cell-line screen, with LC50 activity in the HCT 116 human colon cancer cell line below 10 nM. The crystal structure of the unsubstituted indolylquinol 1a exhibits two independent molecules, both participating in intermolecular hydrogen bonds from quinol OH to carbonyl O, but one OH group also interacts intramolecularly with a sulfonyl O atom. This interaction, which strengthens upon ab initio optimization, may influence the chemical environment of the bioactive quinol moiety. In vivo, significant antitumor activity was recorded (day 28) in mice bearing subcutaneously implanted MDA-MB-435 xenografts, following intraperitoneal treatment of mice with compound 1a at 50 mg/kg.

To which extent can attention and/or modulation explains deficits in dyslexia?

This thesis investigates the visual deficits associated with developmental dyslexia, particularly that of visual attention. Visual attention has previously been investigated in a wide array of behavioural and psychophysical (amongst others) studies but not many have produced consistent findings. Attention processes are believed to play an integral part in depicting the overall "extent" of reading deficits in dyslexia, so it was of paramount importance to aim at such attention mechanisms in this research. The experiments in this thesis focused on signal enhancement and noise (distractor) exclusion. Given the flexibility of the visual search paradigms employed in this research, factors such as visual crowding and attention distribution was also investigated. The experiments systematically manipulated noise (by increasing distractor count, i.e. set-size), crowding (varying the spacing between distractors), attention allocation (use of peripheral cues to direct attention), and attention distribution (influence of one visual field over the other), all of which were tied to a critical factor, the "location/spatial/decisional uncertainty". Adults with dyslexia were: (i) able to modulate attention appropriately using peripheral pre-cues, (ii) severely affected by crowding, and (iii) unable to counteract increased set-sizes when post or un-cued, the latter signifying poor distractor (noise) suppression. By controlling for location uncertainty, the findings confirmed that adults with dyslexia were yet again affected by crowding and set-size, in addition to an asymmetric attention distribution. Confounding effects of ADHD symptoms did not explain a significant independent variance in performance, suggesting that the difficulty shown by adult dyslexics were not accounted for by co-morbid ADHD. Furthermore, the effects of crowding, set-size and asymmetric attention correlated significantly with literacy, but not ADHD measures. It is believed that a more diffuse and an asymmetric attention system (in dyslexia) to be the limiting factor concerning noise exclusion and attention distribution. The findings from this thesis add to the current understanding of the potential role of deficits in visual attention in dyslexia and in the literacy difficulties experienced by this population.

Improving T cell-induced response to subunit vaccines:opportunities for a proteomic systems approach

Prophylactic vaccines are an effective strategy to prevent development of many infectious diseases. With new and re-emerging infections posing increasing risks to food stocks and the health of the population in general, there is a need to improve the rationale of vaccine development. One key challenge lies in development of an effective T cell-induced response to subunit vaccines at specific sites and in different populations. Objectives: In this review, we consider how a proteomic systems-based approach can be used to identify putative novel vaccine targets, may be adopted to characterise subunit vaccines and adjuvants fully. Key findings: Despite the extensive potential for proteomics to aid our understanding of subunit vaccine nature, little work has been reported on identifying MHC 1-binding peptides for subunit vaccines generating T cell responses in the literature to date. Summary: In combination with predictive and structural biology approaches to mapping antigen presentation, proteomics offers a powerful and as yet un-tapped addition to the armoury of vaccine discovery to predict T-cell subset responses and improve vaccine design strategies.

Pichia pastoris regulates its gene-specific response to different carbon sources at the transcriptional, rather than the translational, level

Background: The methylotrophic, Crabtree-negative yeast Pichia pastoris is widely used as a heterologous protein production host. Strong inducible promoters derived from methanol utilization genes or constitutive glycolytic promoters are typically used to drive gene expression. Notably, genes involved in methanol utilization are not only repressed by the presence of glucose, but also by glycerol. This unusual regulatory behavior prompted us to study the regulation of carbon substrate utilization in different bioprocess conditions on a genome wide scale. Results: We performed microarray analysis on the total mRNA population as well as mRNA that had been fractionated according to ribosome occupancy. Translationally quiescent mRNAs were defined as being associated with single ribosomes (monosomes) and highly-translated mRNAs with multiple ribosomes (polysomes). We found that despite their lower growth rates, global translation was most active in methanol-grown P. pastoris cells, followed by excess glycerol- or glucose-grown cells. Transcript-specific translational responses were found to be minimal, while extensive transcriptional regulation was observed for cells grown on different carbon sources. Due to their respiratory metabolism, cells grown in excess glucose or glycerol had very similar expression profiles. Genes subject to glucose repression were mainly involved in the metabolism of alternative carbon sources including the control of glycerol uptake and metabolism. Peroxisomal and methanol utilization genes were confirmed to be subject to carbon substrate repression in excess glucose or glycerol, but were found to be strongly de-repressed in limiting glucose-conditions (as are often applied in fed batch cultivations) in addition to induction by methanol. Conclusions: P. pastoris cells grown in excess glycerol or glucose have similar transcript profiles in contrast to S. cerevisiae cells, in which the transcriptional response to these carbon sources is very different. The main response to different growth conditions in P. pastoris is transcriptional; translational regulation was not transcript-specific. The high proportion of mRNAs associated with polysomes in methanol-grown cells is a major finding of this study; it reveals that high productivity during methanol induction is directly linked to the growth condition and not only to promoter strength.

Pharmacotherapies to manage diabesity:an update

Several pharmacotherapies have recently become available for addition to lifestyle measures to assist the management of coexistent type 2 diabetes and obesity. These are mostly administered as add-on to metformin or as alternative therapies if metformin is not appropriate. The sodium–glucose cotransporter 2 inhibitors (dapagliflozin, canagliflozin and empagliflozin) act by eliminating excess glucose in the urine. These agents provide a non-insulin-dependent mechanism to reduce hyperglycaemia and facilitate weight loss without causing frank hypoglycaemia. Their efficacy requires the individual to have adequate renal function. The glucagon-like peptide-1 (GLP-1) receptor agonists (exenatide, liraglutide, lixisenatide, dulaglutide and albiglutide [the last at the pre-launch stage at the time of writing]) are injected subcutaneously. Different members of the class offer different time courses for their onset and duration of action. Each potentiates insulin secretion and reduces glucagon secretion in a glucose-dependent manner to address prandial glycaemic excursions while avoiding interprandial hypoglycaemia. A satiety effect of these agents assists weight reduction, but delayed gastric emptying can cause initial nausea. The dipeptidyl peptidase-4 inhibitor class now comprises sitagliptin, vildagliptin, saxagliptin, linagliptin and alogliptin. These agents offer similar glucose-lowering efficacy without weight gain or hypoglycaemia by boosting the half-life of endogenous incretins, particularly GLP-1. A fixed-ratio injected combination of insulin degludec with liraglutide (IDegLira) has recently been launched and further agents to address hyperglycaemia and assist weight loss are advancing in development.

[Review of] Ivo Mijnssen, The Quest for an Ideal Youth in Putin’s Russia I. Back to Our Future! History, Modernity and Patriotism According to Nashi, 2005–2012. Soviet and Post-Soviet Politics and Society, Stuttgart: Ibidem Verlag, 2012, 202pp., e 34.90 p/b

THE YOUTH MOVEMENT NASHI (OURS) WAS FOUNDED IN THE SPRING of 2005 against the backdrop of Ukraine’s ‘Orange Revolution’. Its aim was to stabilise Russia’s political system and take back the streets from opposition demonstrators. Personally loyal to Putin and taking its ideological orientation from Surkov’s concept of ‘sovereign democracy’, Nashi has sought to turn the tide on ‘defeatism’ and develop Russian youth into a patriotic new elite that ‘believes in the future of Russia’ (p. 15). Combining a wealth of empirical detail and the application of insights from discourse theory, Ivo Mijnssen analyses the organisation’s development between 2005 and 2012. His analysis focuses on three key moments—the organisation’s foundation, the apogee of its mobilisation around the Bronze Soldier dispute with Estonia, and the 2010 Seliger youth camp—to help understand Nashi’s organisation, purpose and ideational outlook as well as the limitations and challenges it faces. As such,the book is insightful both for those with an interest in post-Soviet Russian youth culture, and for scholars seeking a rounded understanding of the Kremlin’s initiatives to return a sense of identity and purpose to Russian national life.The first chapter, ‘Background and Context’, outlines the conceptual toolkit provided by Ernesto Laclau and Chantal Mouffe to help make sense of developments on the terrain of identity politics. In their terms, since the collapse of the Soviet Union, Russia has experienced acute dislocation of its identity. With the tangible loss of great power status, Russian realities have become unfixed from a discourse enabling national life to be constructed, albeit inherently contingently, as meaningful. The lack of a Gramscian hegemonic discourse to provide a unifying national idea was securitised as an existential threat demanding special measures. Accordingly, the identification of those who are ‘notUs’ has been a recurrent theme of Nashi’s discourse and activity. With the victory in World War II held up as a foundational moment, a constitutive other is found in the notion of ‘unusual fascists’. This notion includes not just neo-Nazis, but reflects a chain of equivalence that expands to include a range of perceived enemies of Putin’s consolidation project such as oligarchs and pro-Western liberals.The empirical background is provided by the second chapter, ‘Russia’s Youth, the Orange Revolution, and Nashi’, which traces the emergence of Nashi amid the climate of political instability of 2004 and 2005. A particularly note-worthy aspect of Mijnssen’s work is the inclusion of citations from his interviews with Nashicommissars; the youth movement’s cadres. Although relatively few in number, such insider conversations provide insight into the ethos of Nashi’s organisation and the outlook of those who have pledged their involvement. Besides the discussion of Nashi’s manifesto, the reader thus gains insight into the motivations of some participants and behind-the-scenes details of Nashi’s activities in response to the perceived threat of anti-government protests. The third chapter, ‘Nashi’s Bronze Soldier’, charts Nashi’s role in elevating the removal of a World War II monument from downtown Tallinn into an international dispute over the interpretation of history. The events subsequent to this securitisation of memory are charted in detail, concluding that Nashi’s activities were ultimately unsuccessful as their demands received little official support.The fourth chapter, ‘Seliger: The Foundry of Modernisation’, presents a distinctive feature of Mijnssen’s study, namely his ethnographic account as a participant observer in the Youth International Forum at Seliger. In the early years of the camp (2005–2007), Russian participants received extensive training, including master classes in ‘methods of forestalling mass unrest’ (p. 131), and the camp served to foster a sense of group identity and purpose among activists. After 2009 the event was no longer officially run as a Nashi camp, and its role became that of a forum for the exchange of ideas about innovation, although camp spirit remained a central feature. In 2010 the camp welcomed international attendees for the first time. As one of about 700 international participants in that year the author provides a fascinating account based on fieldwork diaries.Despite the polemical nature of the topic, Mijnssen’s analysis remains even-handed, exemplified in his balanced assessment of the Seliger experience. While he details the frustrations and disappointments of the international participants with regard to the unaccustomed strict camp discipline, organisational and communication failures, and the controlled format of many discussions,he does not neglect to note the camp’s successes in generating a gratifying collective dynamic between the participants, even among the international attendees who spent only a week there.In addition to the useful bibliography, the book is back-ended by two appendices, which provide the reader with important Russian-language primary source materials. The first is Nashi’s ‘Unusual Fascism’ (Neobyknovennyi fashizm) brochure, and the second is the booklet entitled ‘Some Uncomfortable Questions to the Russian Authorities’ (Neskol’ko neudobnykh voprosov rossiiskoivlasti) which was provided to the Seliger 2010 instructors to guide them in responding to probing questions from foreign participants. Given that these are not readily publicly available even now, they constitute a useful resource from the historical perspective.

Investigating the utility of clinical assessments to predict success with presbyopic contact lens correction

PURPOSE: To determine the utility of a range of clinical and non-clinical indicators to aid the initial selection of the optimum presbyopic contact lens. In addition, to assess whether lens preference was influenced by the visual performance compared to the other designs trialled (intra-subject) or compared to participants who preferred other designs (inter-subject). METHODS: A double-masked randomised crossover trial of Air Optix Aqua multifocal, PureVision 2 for Presbyopia, Acuvue OASYS for Presbyopia, Biofinity multifocal and monovision was conducted on 35 presbyopes (54.3±6.2years). Participant lifestyle, personality, pupil characteristics and aberrometry were assessed prior to lens fitting. After 4 weeks of wear, high and low contrast visual acuity (VA) under photopic and mesopic conditions, reading speed, Near Activity Visual Questionnaire (NAVQ) rating, subjective quality-of-vision scoring, defocus curves, stereopsis, halometry, aberrometry and ocular physiology were quantified. RESULTS: After trialling all the lenses, preference was mixed (n=12 Biofinity, n=10 monovision, n=7 Purevision, n=4 Air Optix Aqua, n=2 Oasys). Lens preference was not dependent on personality (F=1.182, p=0.323) or the hours spent working at near (p=0.535) or intermediate (p=0.759) distances. No intersubject or strong intrasubject relationships emerged between lens preference and reading speed, NAVQ rating, halo size, aberrometry or ocular physiology (p>0.05). CONCLUSIONS: Participant lifestyle and personality, ocular optics, contact lens visual performance and ocular physiology provided poor indicators of the preferred lens type after 4 weeks of wear. This is confounded by the wide range of task visual demands of presbyopes and the limited optical differences between current multifocal contact lens designs.