Malaria: therapy, genes and vaccines

Malaria kills over 3,000 children each day. Modern molecular and biochemical approaches are being used to help understand and control Plasmodium falciparum, the parasite that causes this deadly disease. New drugs are being invented for both chemoprophylaxis and therapeutic treatments and their use is discussed along side that of the more commonly used treatments. Classical genetic crosses coupled with molecular analysis of gene loci are use to explain the genetics behind the development of specific drug resistances that the parasites have naturally developed. Rapid advances in DNA sequencing techniques have allowed the compete sequencing of the P. falciparum and several other rodent malaria parasite genomes. Proteomics and computational analysis of these vast databanks are being used to model and investigate the three-dimensional structure of many key malaria proteins in an attempt to facilitate drug design. Recombinant protein expression in bacteria and yeast coupled with cGMP purification technologies and conditions have lead to the recent availability of several dozen malaria protein antigens for human-use Phase I and Phase II vaccine trials. Drug companies, private foundations, and key government agencies have contributed to the coordinated efforts needed to test these antigens, adjuvants and delivery methods in an effort to find an effective malaria vaccine that will prevent infection and disease.     

Applying negative rule mining to improve genome annotation

Background  

Unsupervised annotation of proteins by software pipelines suffers from very high error rates. Spurious functional assignments are usually caused by unwarranted homology-based transfer of information from existing database entries to the new target sequences. We have previously demonstrated that data mining in large sequence annotation databanks can help identify annotation items that are strongly associated with each other, and that exceptions from strong positive association rules often point to potential annotation errors. Here we investigate the applicability of negative association rule mining to revealing erroneously assigned annotation items.     

Neural network detects errors in the assignment of mRNA splice sites.

The use of databanks in genetic research assumes reliability of the information they contain. Currently, error-detection in the manually or electronically entered data contained in the nucleotide sequence databanks at EMBL, Heidelberg and GenBank at Los Alamos is limited. We have used a subset of sequences from these databanks to train neural networks to recognize pre-mRNA splicing signals in human genes. During the training on 33 human genes from the EMBL databank seven genes appeared to disturb the learning process. Subsequent investigation revealed discrepancies from the original published papers, for three genes. In four genes, we found wrongly assigned splicing frames of introns. We believe this to be a reflection of the fact that splicing frames cannot always be unambiguously assigned on the basis of experimental data. Thus incorrect assignment appear both due to mere typographical misprints as well as erroneous interpretation of experiments. Training on 241 human sequences from GenBank revealed nine new errors. We propose that such errors could be detected by computer algorithms designed to check the consistency of data prior to their incorporation in databanks.     

Cytochrome P450 Enzymes and Drug Metabolism—Basic Concepts and Methods of Assessment

1. The cytochrome P450 enzyme family is one of the major drug metabolizing systems in man.2. Factors such as age, gender, race, environment, and drug treatment may have considerable influence on the activity of these enzymes.3. There are now well-established in vitro techniques for assessing the role of specific cytochrome P450 enzymes in the metabolism of drugs, as well as the inhibitory or inducing effects of drugs on enzyme activity. In vitro data have been utilized to predict clinical outcomes (i.e., pharmacokinetic interactions), with close correlations between in vitro and in vivo data.4. This information can be of considerable practical assistance to clinicians, to help with rational prescribing or to prevent or minimize the potential for drug interactions.     

Wrapping SRS with CORBA: from textual data to distributed objects.

MOTIVATION: Biological data come in very different shapes. Databanks are maintained and used by distinct organizations. Text is the de facto Standard exchange format. The SRS system can integrate heterogeneous textual databanks but it was lacking a way to structure the extracted data. RESULTS: This paper presents a CORBA interface to the SRS system which manages databanks in a flat file format. SRS Object Servers are CORBA wrappers for SRS. They allow client applications (visualisation tools, data mining tools, etc.) to access and query SRS servers remotely through an Object Request Broker (ORB). They provide loader objects that contain the information extracted from the databanks by SRS. Loader objects are not hard-coded but generated in a flexible way by using loader specifications which allow SRS administrators to package data coming from distinct databanks. AVAILABILITY: The prototype may be available for beta-testing. Please contact the SRS group (http://srs.ebi.ac.uk).     

Bringing sequences to life: how bioinformatics corporealizes sequence data

Sequence databases have become more visible through the heavy publicity associated with the Human Genome Project. This paper looks at some of the emerging artefacts and systems developed to read, write, order and visualise sequence data and other kinds of biological data retrieved from databases and databanks such as GenBank. It argues that bioinformatics software can be regarded as a symptom of a broad and powerful transformation in biological knowledges and in the biopolitical constitution of living bodies. Two facets of this transformation are emphasised. Firstly, examining bioinformatics software might help us situate how sequence data is actually circulating, and to what ends. In particular, the paper looks at the significance of sequence comparison and protein folding problems. Secondly, an emerging nexus of property relations and intellectual work can be detected within the ordering of sequence data carried out bioinformatics.     

Structural proteomics in drug discovery

High-throughput, automated or semiautomated methodologies implemented by companies and structural genomics initiatives have accelerated the process of acquiring structural information for proteins via x-ray crystallography. This has enabled the application of structure-based drug design technologies to a variety of new structures that have potential pharmacologic relevance. Although there remain major challenges to applying these approaches more broadly to all classes of drug discovery targets, clearly the continued development and implementation of these structure-based drug design methodologies by the scientific community at large will help to address and provide solutions to these hurdles. The result will be a growing number of protein structures of important pharmacologic targets that will help to streamline the process of identification and optimization of lead compounds for drug development. These lead agonist and antagonist pharmacophores should, in turn, help to alleviate one of the current critical bottlenecks in the drug discovery process; that is, defining the functional relevance of potential novel targets to disease modification. The prospect of generating an increasing number of potential drug candidates will serve to highlight perhaps the most significant future bottleneck for drug development, the cost and complexity of the drug approval process.     

Structural proteomics in drug discovery

High-throughput, automated or semiautomated methodologies implemented by companies and structural genomics initiatives have accelerated the process of acquiring structural information for proteins via x-ray crystallography. This has enabled the application of structure-based drug design technologies to a variety of new structures that have potential pharmacologic relevance. Although there remain major challenges to applying these approaches more broadly to all classes of drug discovery targets, clearly the continued development and implementation of these structure-based drug design methodologies by the scientific community at large will help to address and provide solutions to these hurdles. The result will be a growing number of protein structures of important pharmacologic targets that will help to streamline the process of identification and optimization of lead compounds for drug development. These lead agonist and antagonist pharmacophores should, in turn, help to alleviate one of the current critical bottlenecks in the drug discovery process; that is, defining the functional relevance of potential novel targets to disease modification. The prospect of generating an increasing number of potential drug candidates will serve to highlight perhaps the most significant future bottleneck for drug development, the cost and complexity of the drug approval process.     

DNA fingerprinting in the criminal justice system: an overview

DNA fingerprinting is a powerful technology that has revolutionized forensic science. No two individuals can have an identical DNA pattern except identical twins. Such DNA-based technologies have enormous social implications and can help in the fight against crime. This technology has experienced many changes over time with many advancements occurring. DNA testing is a matter of serious concern as it involves ethical issues. This article describes various trends in DNA fingerprinting and the current technology used in DNA profiling, possible uses and misuses of DNA databanks and ethical issues involved in DNA testing. Limitations and problems prevailing in this field are highlighted.     

MyWEST: my Web Extraction Software Tool for effective mining of annotations from web-based databanks

MOTIVATION: High-throughput technologies create the necessity to mine large amounts of gene annotations from diverse databanks, and to integrate the resulting data. Most databanks can be interrogated only via Web, for a single gene at a time, and query results are generally available only in the HTML format. Although some databanks provide batch retrieval of data via FTP, this requires expertise and resources for locally reimplementing the databank. RESULTS: We developed MyWEST, a tool aimed at researchers without extensive informatics skills or resources, which exploits user-defined templates to easily mine selected annotations from different Web-interfaced databanks, and aggregates and structures results in an automatically updated database. Using microarray results from a model system of retinoic acid-induced differentiation, MyWEST effectively gathered relevant annotations from various biomolecular databanks, highlighted significant biological characteristics and supported a global approach to the understanding of complex cellular mechanisms. AVAILABILITY: MyWEST is freely available for non-profit use at http://www.medinfopoli.polimi.it/MyWEST/     

Novel putative drugs and key initiating genes for neurodegenerative disease determined using network-based genetic integrative analysis

Understanding the genetic causes of neurodegenerative disease (ND) can be useful for their prevention and treatment. Among the genetic variations responsible for ND, heritable germline variants have been discovered in genome-wide association studies (GWAS), and nonheritable somatic mutations have been discovered in sequencing projects. Distinguishing the important initiating genes in ND and comparing the importance of heritable and nonheritable genetic variants for treating ND are important challenges. In this study, we analysed GWAS results, somatic mutations and drug targets of ND from large databanks by performing directed network-based analysis considering a randomised network hypothesis testing procedure. A disease-associated biological network was created in the context of the functional interactome, and the nonrandom topological characteristics of directed-edge classes were interpreted. Hierarchical network analysis indicated that drug targets tend to lie upstream of somatic mutations and germline variants. Furthermore, using directed path length information and biological explanations, we provide information on the most important genes in these created node classes and their associated drugs. Finally, we identified nine germline variants overlapping with drug targets for ND, seven somatic mutations close to drug targets from the hierarchical network analysis and six crucial genes in controlling other genes from the network analysis. Based on these findings, some drugs have been proposed for treating ND via drug repurposing. Our results provide new insights into the therapeutic actionability of GWAS results and somatic mutations for ND. The interesting properties of each node class and the existing relationships between them can broaden our knowledge of ND.     

Re-assessing the ecology of rare flood-meadow violets (<Emphasis Type="Italic">Viola elatior,V. pumila</Emphasis> and<Emphasis Type="Italic">V. persicifolia</Emphasis>) with large phytosociological data sets

This study demonstrates how conventional ecological knowledge on species together with models resulting from functional traits can be tested and refined by tapping large data sources that have been made available through recent electronic compilations. The study is based on the comparison of three rare, closely related flood-meadow violet species, which have been supposed to have similar ecological behaviour and niche occupation. In contrast, the analysis of 335 Central European relevés using different methods of numerical ordination, classification and calibration revealed distinct differences in habitat preferences between the three species. Detrended correspondence analysis ordination, and multiple-response permutation procedures and TWINSPAN classification displayed the separation ofViola persicifolia fromV. elatior andV. pumila along a moisture and base-richness gradient, while the latter two differed mostly in terms of mowing compatibility. Although the three violets are considered to be weak competitors they may be found under nutrient-poor as well as nutrient-rich site conditions. The distribution of C-S-R strategy types in relevés supported the hypothesis that at more fertile sites the violets crucially depend on disturbance by management or flooding events that create gaps and weaken strong competitors, while at less productive sites they may persist for a long time even under fallow conditions. The S/R strategy is shared by all three violets. Problems and perspectives arising with the use of phytosociological databanks as a source of ecological information are discussed.     

Principle of codification for quick comparisons with the entire biomolecule databanks and associated programs in FORTRAN 77.

We propose a new method for homology search of nucleic acids or proteins in databanks. All the possible subsequences of a specific length in a sequence are converted into a code and stored in an indexed file (hash-coding). This preliminary work of codifying an entire bank is rather long but it enables an immediate access to all the sequence fragments of a given type. With our method a strict homology pattern of twenty nucleotides can be found for example in the Los Alamos bank (GENBANK) in less than 2 seconds. We can also use this data storage to considerably speed up the non-strict homology search programs and to write a program to help in the selection of nucleic acid hybridization probes.     

Fast analysis of genomic homologies: Primate immunodeficiency virus

We have recently published a new probabilistic algorithm which performs genomic comparisons on a huge scale. In the present paper it was applied to immunodeficiency viral sequences extracted from international gene databanks. During global sequence analysis of human (HIV I and HIV2) and simian viruses by means of dot-matrix representation, series of homology were obtained which permitted the definition of families of viruses overlapping the species divisions. Sequences of interest were characterized to the lexical base sentence through successive zoomings. Strain-to-strain comparison confirmed subfamily classifications and led, for example, to the identification of divergent LTR sequences. By way of example, we described the application of the algorithm to the ANT70C and MVP5180 HIV1-O viruses, for which the observed differences were shown to correspond to a deletion in the U3 region, situated between the LEF and NF-κB sites. It was of interest to consider these data in a tentative phylogenetic interpretation. Correspondence to: M.L.J. Moncany     

Amiodarone inhibits multiple drug resistance in yeast <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>

Amiodarone is a widely used antiarrhythmic drug. There is also evidence that amiodarone decreases multidrug resistance in human cell lines. In this paper, we have shown that amiodarone has similar effect on yeast, Saccharomyces cerevisiae, decreasing multiple drug resistance. Amiodarone stimulates the accumulation of ethidium bromide by inhibiting its efflux from the cells. The effect of amiodarone is much stronger on wild-type cells compared to the mutant with inactivated ABC-transporters. Interestingly, the action of amiodarone is additive with the one of chloroquine, a known inhibitor of ABC-transporters. We speculate that these findings could help in the development of antifungal drug mixes.     

Pharmacokinetic de-risking tools for selection of monoclonal antibody lead candidates

Pharmacokinetic studies play an important role in all stages of drug discovery and development. Recent advancements in the tools for discovery and optimization of therapeutic proteins have created an abundance of candidates that may fulfill target product profile criteria. Implementing a set of in silico, small scale in vitro and in vivo tools can help to identify a clinical lead molecule with promising properties at the early stages of drug discovery, thus reducing the labor and cost in advancing multiple candidates toward clinical development. In this review, we describe tools that should be considered during drug discovery, and discuss approaches that could be included in the pharmacokinetic screening part of the lead candidate generation process to de-risk unexpected pharmacokinetic behaviors of Fc-based therapeutic proteins, with an emphasis on monoclonal antibodies.     

Quality control in databanks for molecular biology

Using a scientific measurement without an estimate of its error is like lending money to a stranger. Given the explosion in nucleic acid and protein sequence and structural data, what risks are the scientific and medical communities running in using these databases. Is there an ‘ombudsman’ who speaks for the users of the data? CODATA, the Committee on Data for Science and Technology of the International Council of Scientific Unions was established to improve the quality, reliability, processing, management, and accessibility of data for science and technology. The CODATA Task Group on Biological Macromolecules has surveyed quality control procedures of archival databanks in molecular biology. Our role is ‘to advise, to be consulted, and to warn.’ This report describes the kinds and extents of errors that may appear in nucleic acid and protein databases, and presents an agenda for future work to improve the quality of these databases. The results of the survey appear on the web http://www.codata.org/codata/tgreports/tg_reps.html . BioEssays 22:1024–1034, 2000. © 2000 John Wiley & Sons, Inc.     

What constitutes fair shared decision-making in global health research collaborations?

Funders (located primarily in high-income countries) and high-income country researchers have historically dominated decision-making within global health research collaborations: from setting agendas and research design to determining how data are collected and analysed and what happens with findings and outputs. The ethical principle of shared decision-making has been proposed as a way to help address these imbalances within collaborations and to reduce semicolonial and exploitative forms of global health research. It is important to be clear about what shared decision-making means in order to ensure that it is not done in a tokenistic, shallow way. Thus far, the principle’s content has not been examined and articulated in detail. This paper aims to start the process of delineating a concept of fair shared decision-making as a minimum standard for global health research. Using two hypothetical case examples, the paper will demonstrate that global health research practice is often inconsistent with ideal shared decision-making. In such instances, it can be difficult to decide whether shared decision-making within collaborations is fair. The paper describes how the two cases do not meet criteria for unfair or non-ideal shared decision-making, despite having potentially morally troubling features. The nuances of these examples of research practice help to generate clearer ideas about how to judge fairness in shared decision-making. The paper concludes by presenting ideas about when soft power can be fairly employed between high-income-country and low- and middle-income-country partners and what fair compromise agreements may look like in shared decision-making.     

Cultural values and other perceived benefits of organized activities: A qualitative analysis of Mexican-origin parents’ perspectives in Arizona

The limited understanding on why Latino parents endorse organized activities is problematic given that these beliefs can help elucidate why they overcome barriers to support their children’s participation. In this study, we analyzed interviews from a diverse group of 34 Mexican-origin parents who resided in Arizona. Results of the study indicate that although organized activities were perceived as contexts that can help youth gain skills reflecting mainstream American values (e.g., school engagement, interpersonal skills), parents also thought that activities promoted positive behaviors associated with their ethnic culture based on traditional values related to respeto, familism, and religiosity. The implications of this study suggest that understanding Mexican-origin parents’ perspectives can help organized activity leaders design programs that fully address the benefits that families seek from organized activities.