Bioinformatics and the politics of innovation in the life sciences: Science and the state in the United Kingdom, China, and India

The governments of China, India, and the United Kingdom are unanimous in their belief that bioinformatics should supply the link between basic life sciences research and its translation into health benefits for the population and the economy. Yet at the same time, as ambitious states vying for position in the future global bioeconomy they differ considerably in the strategies adopted in pursuit of this goal. At the heart of these differences lies the interaction between epistemic change within the scientific community itself and the apparatus of the state. Drawing on desk-based research and thirty-two interviews with scientists and policy makers in the three countries, this article analyzes the politics that shape this interaction. From this analysis emerges an understanding of the variable capacities of different kinds of states and political systems to work with science in harnessing the potential of new epistemic territories in global life sciences innovation

Assets, Commodities and Biosocialities. Multiple Biovalues in Hybrid Biobanking Practices

This is the final version. Available on open access from STS Italia via the URL in this record.Biobanks are crucial institutions in the infrastructure of contemporary life sciences. They depend on the participation of donors who give tissues and data. Through their participa-tion, donors can build identities and form biosociality. Biobanks are key sites in the cur-rent bioeconomy, that enable the generation of value from those tissues and bioinfor-mation, transformed into assets or commodities. We define biobanks as hybrid zones of heterogeneous practices that blur the boundaries between institutional sectors and ways of producing economic values. On that basis we introduce a novel empirical, realist approach to the analysis of biobanking economies, explaining the different economic and social biovalues that emerge from the practices of valuing and interacting between the research-ers, biobank staff and donor participants in specific banking activities. We discuss why STS studies on biobanking should explore the concrete practices through which multiple biovalues as well as biosocialities are produced simultaneously and in configurations of mutual interdependence

Agro-ento bioinformation: towards the edge of reality

Information communication has advanced from the fundamental universe-bio-physicschemistry probes to exploration of bioprocessing tangibles and intangibles. Bounded by such information advancement frames, domains of agro-forestry and entomology, and medicine, have witnessed progression through evolution, revolution, and bioinformation in their knowledge contents. Integrated Pest Management (IPM) paradigms steered the course of agro-forest and medical-industries during the 1800 and 1900 eras. IPM Concept is a synthetic framework that results from evolution, revolution, and presently bioformation in domains of agro-medico-ecological and anthropo-ecological activities. A chronological history of pest management parallels the history of industrial revolution and highlights man's attempts at dealing and living with the environment, arthropods and other pestly species. A cycle of progression from using natural controls to made-made utilities and back to enhancing of natural processes is evident as one walks through time and space of history during the development of civilization. IPM success demands usage and stringent compliance with ecological imperatives, which need to be lucidly expressed as knowledge precepts. Biological knowledge is at the forefront of this usage, especially with the new millennium becoming the Age of Biology. Consequently, bioinformation is commencing to thrive as a global entity, which revolutionizes and drives societal progress. Bioinformation, in brief, comprises biology, information algorithms, information technology, and communication protocols. Thus biology becomes a domain of information science. Attributes of bioinformation can be defined through its primers and profiles. The primers, which entrain processes, both natural and man-induced, include mechanisms such as protocols, algorithms, visualisations, and structural and visual designs. The protocols range from the molecular levels to domains of larger dimensions such as those encompassing fraternities of politics and policies, and societal applications. These protocols, algorithms, and visualisations undergo dynamic incubation processes to produce the end product, which is bioinformation. Entomology is an inherent component of this bioinformation revolution. The information communication technology linkages are exemplified through simulation, modelling, and visualization explorations

Mining for single nucleotide polymorphisms and insertions / deletions in expressed sequence tag libraries of oil palm

The oil palm is a tropical oil bearing tree. Recently EST-derived SNPs and SSRs are a free by-product of the currently expanding EST (Expressed Sequence Tag) data bases. The development of high-throughput methods for the detection of SNPs (Single Nucleotide Polymorphism) and small indels (insertion / deletion) has led to a revolution in their use as molecular markers. Available (5452) Oil palm EST sequences were mined from dbEST of NCBI. CAP3 program was used to assemble EST sequences into contigs. Candidate SNPs and Indel polymorphisms were detected using the perl script auto_snip version 1.0 which has used 576 ESTs for detecting SNPs and Indel sites. We found 1180 SNP sites and 137 indel polymorphisms with frequency 1.36 SNPs / 100 bp. Among the six tissues from which the EST libraries had been generated, mesocarp had high frequency of 2.91 SNPs and indels per 100 bp whereas the zygotic embryos had lowest frequency of 0.15 per 100 bp. We also used the Shannon index to analyze the proportion of ten possible types of SNP/indels. ESTs from tissues of normal apex showed highest values of Shannon index (0.60) whereas abnormal apex had least value (0.02). The present report deals the use of Shannon index for comparing SNP/ indel frequencies mined from ESTlibraries and also confirm that the frequency of SNP occurrence in oil palm to use them as markers for genetic studies

Proteomic signature of periodontal disease in pregnancy: Predictive validity for adverse outcomes

The rate of preterm birth is a public health concern worldwide because it is increasing and efforts to prevent it have failed. We report a Clinically Relevant Complex Systematic Review (CSCSR) designed to identify and evaluate the best available evidence in support of the association between periodontal status in women and pregnancy outcome of preterm low birth weight. We hypothesize that the traditional limits of research synthesis must be expanded to incorporate a translational component. As a proof-of-concept model, we propose that this CSCSR can yield greater validity of efficacy and effectiveness through supplementing its recommendations with data of the proteomic signature of periodontal disease in pregnancy, which can contribute to addressing specifically the predictive validity for adverse outcomes. For this CRCSR, systematic reviews were identified through The National Library of MedicinePubmed, The Cochrane library, CINAHL, Google Scholar, Web of Science, and the American Dental Association web library. Independent reviewers quantified the relevance and quality of this literature with R-AMSTAR. Homogeneity and inter-rater reliability testing were supplemented with acceptable sampling analysis. Research synthesis outcomes were analyzed qualitatively toward a Bayesian inference, and converge to demonstrate a definite association between maternal periodontal disease and pregnancy outcome. This CRCSR limits heterogeneity in terms of periodontal disease, outcome measure, selection bias, uncontrolled confounders and effect modifiers. Taken together, the translational CRCSR model we propose suggests that further research is advocated to explore the fundamental mechanisms underlying this association, from a molecular and proteomic perspective

Archives, promises, values: forensic infrastructures in times of austerity

This article analyses the role of infrastructures in the ‘bioinformational turn’ in forensic science and examines processes through which evidence is constituted, validated, or challenged in and through domains of expertise that engage different techniques, data, objects and knowledges through infrastructural arrangements. While the digitisation of the infrastructures that underpin forensic service delivery promised connectivity, prosperity and wellbeing, in reality it also brought forward new levels of risk and vulnerability, generating new tensions and frictions in the body politic. As genetic science reaches post-archival horizons through new genetic sequencing technologies, forensic science in postarchival times raises questions concerning the differential impact of the fragmentation of analytical and archival infrastructures and increasingly asynchronous bureaucracies whose role is displaced by the relative autonomy of datasets and computational architectures that elude governance oversight and citizens’ scrutiny

Infrastructuring educational genomics:Associations, architectures and apparatuses

Technoscientific transformations in molecular genomics have begun to influence knowledge production in education. Interdisciplinary scientific consortia are seeking to identify ‘genetic influences’ on ‘educationally relevant’ traits, behaviors, and outcomes. This article examines the emerging ‘knowledge infrastructure’ of educational genomics, attending to the assembly and choreography of organizational associations, epistemic architecture, and technoscientific apparatuses implicated in the generation of genomic understandings from masses of bioinformation. As an infrastructure of datafied knowledge production, educational genomics is embedded in data-centered epistemologies and practices which recast educational problems in terms of molecular genetic associations—insights about which are deemed discoverable from digital bioinformation and potentially open to genetically informed interventions in policy and practice. While scientists claim to be ‘opening the black box of the genome’ and its association with educational outcomes, we open the black box of educational genomics itself as a source of emerging scientific authority. Data-intensive educational genomics does not straightforwardly ‘discover’ the biological bases of educationally relevant behaviors and outcomes. Rather, this knowledge infrastructure is also an experimental ‘ontological infrastructure’ supporting particular ways of knowing, understanding, explaining, and intervening in education, and recasting the human subjects of education as being surveyable and predictable through the algorithmic processing of bioinformation

Antigenic variability in Neuraminidase protein of Influenza A/H3N2 vaccine strains (1968 – 2009)

Antigenic drift and shift involving the surface proteins of Influenza virus gave rise to new strains that caused epidemics affecting millions of people worldwide over the last hundred years. Variations in the membrane proteins like Hemagglutinin (HA) and Neuraminidase (NA) necessitates new vaccine strains to be updated frequently and poses challenge to effective vaccine design. Though the HA protein, the primary target of the human immune system, has been well studied, reports on the antigenic variability in the other membrane protein NA are sparse. In this paper we investigate the molecular basis of antigenic drift in the NA protein of the Influenza A/H3N2 vaccine strains between 1968 and 2009 and proceed to establish correlation between antigenic drift and antigen-antibody interactions. Sequence alignments and phylogenetic analyses were carried out and the antigenic variability was evaluated in terms of antigenic distance. To study the effects of antigenic drift on the protein structures, 3D structure of NA from various strains were predicted. Also, rigid body docking protocol has been used to study the interactions between these NA proteins and antibody Mem5, a 1998 antibody

Multimedia-based Medicinal Plants Sustainability Management System

Medicinal plants are increasingly recognized worldwide as an alternative source of efficacious and inexpensive medications to synthetic chemo-therapeutic compound. Rapid declining wild stocks of medicinal plants accompanied by adulteration and species substitutions reduce their efficacy, quality and safety. Consequently, the low accessibility to and non-affordability of orthodox medicine costs by rural dwellers to be healthy and economically productive further threaten their life expectancy. Finding comprehensive information on medicinal plants of conservation concern at a global level has been difficult. This has created a gap between computing technologies’ promises and expectations in the healing process under complementary and alternative medicine. This paper presents the design and implementation of a Multimedia-based Medicinal Plants Sustainability Management System addressing these concerns. Medicinal plants’ details for designing the system were collected through semi-structured interviews and databases. Unified Modelling Language, Microsoft-Visual-Studio.Net, C#3.0, Microsoft-Jet-Engine4.0, MySQL, Loquendo Multilingual Text-to-Speech Software, YouTube, and VLC Media Player were used. Keywords: Complementary and Alternative Medicine, conservation, extinction, medicinal plant, multimedia, phytoconstituents, rural dweller