Bursaphelenchus xylophilus : opportunities in comparative genomics and molecular host–parasite interactions

Most Bursaphelenchus species are fungal feeding nematodes that colonize dead or dying trees. However, Bursaphelenchus xylophilus , the pine wood nematode, is also a pathogen of trees and is the causal agent of pine wilt disease. B. xylophilus is native to North America and here it causes little damage to trees. Where it is introduced to new regions it causes huge damage. The most severely affected areas are found in the Far East but more recently B. xylophilus has been introduced into Portugal and the potential for damage here is also high. As incidence and severity of pine wilt disease are linked to temperature we suggest that climate change is likely to exacerbate the problems caused by B. xylophilus and, in addition, will extend (northwards in Europe) the range in which pine wilt disease can occur. Here we review what is currently known about the interactions of B. xylophilus with its hosts, including recent developments in our understanding of the molecular biology of pathogenicity in the nematode. We also examine the potential developments that could be made by more widespread use of genomics tools to understand interactions between B. xylophilus , bacterial pathogens that have been implicated in disease and host trees.

Morphobiometric and molecular characterization of Bursaphelenchus Fuchs, 1937 (Nematoda: Aphelenchoididae) species associated with Pinus pinaster Ainton in Portugal

Abstract - The genus Bursaphelenchus comprises almost 100 species mainly from the northern hemisphere, with conifers as the most important hosts. Among the various nematode species, the pine wood nematode (PWN), Bursaphelenchus xylophilus, is the casual agent of pine wilt disease (PWD), and the most important forest pest for pines worldwide, classified as an A1 quarantine organism within the European Union. In 1999 this nematode was detected for the first time in Portugal and Europa associated with maritime pine, Pinus pinaster. Following detection, a national program denominated "Programa Nacional de Luta contra o Nemátodo da Madeira do Pinheiro" (PROLUNP) was created to, among other objectives, determine the distribution of the PWN and its associated vector(s) and host(s), and therefore intensive surveys covering the entire country were conducted with thousands of wood samples and suspected insects being analyzed. This thesis presents the listing, distribution, frequency and the insects associated with Bursaphelenchus species found associated with maritime pine in Portugal, identifying and characterizing the various species by morphological, biometrical and molecular biology (ITS-RFLP and rDNA sequencing analysis) techniques. To achieve the objectives, a total of 4813 maritime pine wood samples and 3294 insects from 22 species and six families were individually analyzed. A total of nine Bursaphelenchus species were found, namely: B. antoniae, B. hellenicus, B. leoni, B. mucronatus, B. pinasteri, B. sexdentati, B. teratospicularis, B. tusciae and B. xylophilus, all of them (with the exception of B. xylophilus) being new records for Portugal. Some of the species appear to have a widespread distribution, such as B. leoni, B. teratospicularis and B. tusciae while others were very rarely found and apparently have a localized distribution range within the country, namely B. antoniae and B. mucronatus. The majority of the species is characteristic of the Mediterranean region and can also be found in countries such as Spain, Italy and Greece, reflecting the affinity of our fauna with those locations. The association of B. hellenicus and B. tusciae with maritime pine is here reported for the first time. Six of the Bursaphelenchus species were also found associated with insects, mainly from the family Scolytidae (Coleoptera). Some of these interactions were described for the first time, namely: B. hellenicus with both Ips sexdentatus and Hylurgus ligniperda, B. sexdentati with both H. ligniperda and Orthotomicus erosus and B. tusciae with H. ligniperda. The exclusive association of B. xylophilus with the cerambycid Monochamus galloprovincialis was also confirmed. The nematode's dauer juveniles were usually found in low numbers in the insect vectors (ca 10-100 per insect), although for B. xylophilus a few thousand specimens per insect were sometimes found. The location of the dauer juveniles differed according to the species, although they were more common under the elytra and wings of the adult insects. A species new to science was detected and formally described as B. antoniae, associated with Hylobius sp. (Coleoptera; Curculionidae) beetles. Morphologically, this new species is very similar to B. hylobianum, although it's distinct ITS-RFLP molecular pattern (with only the enzyme Haelll producing comparable restriction bands) and the failure of hybridization supported the two species as distinct entities. Additional phylogenetic analysis of the 18S rDNA sequence further supported the taxonomical proximity of B. antoniae with B. hylobianum. Concerning the PWN, detailed studies on the development and morphology of B. xylophilus were conducted, and comparative measurements of field-collected and laboratory-maintained populations demonstrated that nematodes from the second group displayed larger size in all morphometric parameters, which could derive from more adequate conditions of nourishment and/or temperature. Taxonomical studies on the development stages of B. xylophilus confirmed the existence of four propagative juvenile stages (J1,J2,J3 and J4), an adult stage with both sexes and two dispersal stages (jIII e jIV), with the measurements of the gonad length allowing the separation of the propagative stages. It is hoped that the acquired knowledge will be useful on future surveys of nematodes of the Bursaphelenchus genus collected from either wood material or insect vectors, and facilitate the correct distinction and identification of the various species which are now known to occur. ### Resumo - 0 género Bursaphelenchus compreende quase 100 espécies, distribuídas sobretudo nos países do hemisfério norte do globo terrestre. Embora algumas espécies já tenham sido detectadas em plantas herbáceas, os hospedeiros vegetais mais comuns deste género são as coníferas, particularmente pinheiros. 0 nemátode da madeira do pinheiro (NMP), Bursaphelenchus xylophilus, é considerado a espécie mais importante deste género uma vez que é o agente causal da doença da murchidão dos pinheiros ("pine wilt disease"). Originário dos Estados Unidos, onde não causa grande impacte, o NMP foi introduzido em alguns países da Ásia (China, Japão, Coreia e Taiwan) e mais recentemente na Europa (Portugal). Nestas regiões é responsável pela destruição de milhares de hectares de coníferas, assumindo uma elevada importância económica. Em Portugal, depois da sua detecção em 1999, associado a Pinus pinaster, foi implementado um programa nacional "Programa Nacional de Luta contra o Nemátodo da Madeira do Pinheiro" (PROLUNP) que permitiu determinar a área afectada pela praga (a sul do rio Tejo, península de Setúbal) bem como definir e implementar estratégias de controlo e prevenção da disseminação do NMP a outras zonas de Portugal. Recentemente, em Junho de 2008, foi confirmada a presença de B. xylophilus em outras regiões de Portugal levando as autoridades oficiais a definir todo o território continental como zona afectada e de restrição. As prospecções intensivas realizadas nos últimos anos incluíram a recolha e análise de milhares de amostras de madeira de pinheiro bem como de insectos associados ao pinheiro bravo conduzindo à identificação de várias espécies de Bursaphelenchus. Assim, os estudos conduzidos neste trabalho tiveram como objectivos efectuar uma caracterização morfológica, biométrica e molecular das espécies associadas a P. pinaster em Portugal bem como a sua distribuição geográfica e abundância. Os estudos biométricos foram realizados com populações extraídas directamente do meio natural. Foi ainda realizada uma pesquisa que permitiu identificar os insectos a que estão associadas essas espécies, os seus possíveis vectores. Foram analisadas no total 4813 amostras de P. pinaster e 3294 insectos (22 espécies pertencentes a seis famílias diferentes). Foram identificadas um total de nove espécies: B. antoniae n. sp., B. hellenicus, B. leoni, B. mucronatus, B. pinasteri, B. sexdentati, B. teratospicularis, B. tusciae e B. xylophilus. Foram realizados estudos morfológicos e biométricos de todas as espécies com excepção de B. mucronatus; o reduzido número de exemplares encontrados em apenas uma amostra foram utilizados para efectuar o diagnóstico molecular desta espécie (ITS-RFLP). Apesar de ter havido, sempre que possível, a confirmação molecular, na maioria dos casos a caracterização morfológica e biométrica permitiu a correcta identificação das espécies. Contudo, foi imprescindível a análise molecular em algumas amostras, nomeadamente para a identificação de B. xylophilus e B. sexdentati; dada a grande semelhança entre B. xylophilus e B. mucronatus e tendo sido encontradas algumas populações de B. xylophilus que possuíam fêmeas com cauda mucronada, foi necessária a realização da confirmação molecular. Com excepção de B. xylophilus, todas as outras espécies foram reportadas pela primeira vez em Portugal. Juntamente com B. xylophilus, B. pinasteri foi a espécie encontrada nas amostras de madeira de pinheiro com maior frequência. Algumas destas espécies como B. leoni, B. teratospicularis e B. tusciae foram reportadas em diferentes localidades do norte, centro e sul de Portugal, apresentando uma vasta distribuição geográfica; este resultado está em consonância com a forte associação destas espécies a climas mediterrânicos tal como acontece em Espanha, França, Itália e Grécia. Em oposição, espécies como B. antoniae e B. mucronatus foram encontradas apenas numa ocasião na região centro (Leiria) e norte (Figueira da Foz) do país, respectivamente. Bursaphelenchus mucronatus é igualmente pouco frequente em Espanha onde ocorre sobretudo na região norte, na Galiza. Esta espécie preferirá climas mais frios, ocorrendo com uma maior frequência nas regiões de latitude norte; esta análise é corroborada pela presença constante em países como Alemanha, Finlândia, França, Noruega, Rússia e Suécia. A nível mundial são descritas neste trabalho pela primeira vez as associações das espécies B. hellenicus e B. tusciae ao hospedeiro vegetal P. pinaster.

Host-symbiont interactions in the deep-sea vent mussel Bathymodiolus azoricus : a molecular approach

Tese de Doutoramento, Ciências do Mar, especialidade de Biologia Marinha, 19 de Dezembro de 2015, Universidade dos Açores.

Functional and molecular characterization of SR45, a plant-specific factor involved in sugar and stress signaling in Arabidopsis thaliana

Dissertation presented to obtain the Ph.D degree in Molecular Biology

A-kinase anchoring proteins: Molecular regulators of the cardiac stress response

In response to stress or injury the heart undergoes a pathological remodeling process, associated with hypertrophy, cardiomyocyte death and fibrosis, that ultimately causes cardiac dysfunction and heart failure. It has become increasingly clear that signaling events associated with these pathological cardiac remodeling events are regulated by scaffolding and anchoring proteins, which allow coordination of pathological signals in space and time. A-kinase anchoring proteins (AKAPs) constitute a family of functionally related proteins that organize multiprotein signaling complexes that tether the cAMP-dependent protein kinase (PKA) as well as other signaling enzymes to ensure integration and processing of multiple signaling pathways. This review will discuss the role of AKAPs in the cardiac response to stress. Particular emphasis will be given to the adaptative process associated with cardiac hypoxia as well as the remodeling events linked to cardiac hypertrophy and heart failure. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Cardiac Pathways of Differentiation, Metabolism and Contraction.

Microbial diagnosis of bloodstream infection: towards molecular diagnosis directly from blood.

When a bloodstream infection (BSI) is suspected, most of the laboratory results-biochemical and haematologic-are available within the first hours after hospital admission of the patient. This is not the case for diagnostic microbiology, which generally takes a longer time because blood culture, which is to date the reference standard for the documentation of the BSI microbial agents, relies on bacterial or fungal growth. The microbial diagnosis of BSI directly from blood has been proposed to speed the determination of the etiological agent but was limited by the very low number of circulating microbes during these paucibacterial infections. Thanks to recent advances in molecular biology, including the improvement of nucleic acid extraction and amplification, several PCR-based methods for the diagnosis of BSI directly from whole blood have emerged. In the present review, we discuss the advantages and limitations of these new molecular approaches, which at best complement the culture-based diagnosis of BSI.

“Development of lymphoid cell culture system from Penaeus monodon and molecular approaches for its transformation

Unveiling the molecular and regulatory mechanisms that prevent in vitro transformation in shrimp remains elusive in the development of continuous cell lines, with an arduous history of over 25 years (Jayesh et al., 2012). Despite presenting challenges to researchers in developing a cell line, the billion dollar aquaculture industry is under viral threat. In addition, the regulatory mechanisms that prevent in vitro transformation and carcinoma in shrimps might provide new leads for the development of anti-ageing and anti-cancer interventions in human (Vogt, 2011) and in higher vertebrates. This highlights the importance of developing shrimp cell lines, to bring out effective prophylactics against shrimp viruses and for understanding the mechanism that induce cancer and ageing in human.. Advances in molecular biology and various gene transfer technologies for immortalization of cells have resulted in the development of hundreds of cell lines from insects and mammals, but yet not a single cell line has been developed from shrimp and other marine invertebrates. With this backdrop, the research described in this thesis attempted to develop molecular tools for induced in vitro transformation in lymphoid cells from Penaeus monodon and for the development of continuous cell lines using conventional and novel technologies to address the problems at cellular and molecular level.

Differential induction, isolation, physicochemical and molecular characterization of temperate phages of environmental Vibrio cholerae as evidence of phage mediated Horizontal Gene Transfer

The resurgence of the enteric pathogen Vibrio cholerae, the causative organism of epidemic cholera, remains a major health problem in many developing countries like India. The southern Indian state of Kerala is endemic to cholera. The outbreaks of cholera follow a seasonal pattern in regions of endemicity. Marine aquaculture settings and mangrove environments of Kerala serve as reservoirs for V. cholerae. The non-O1/non-O139 environmental isolates of V. cholerae with incomplete ‘virulence casette’ are to be dealt with caution as they constitute a major reservoir of diverse virulence genes in the marine environment and play a crucial role in pathogenicity and horizontal gene transfer. The genes coding cholera toxin are borne on, and can be infectiously transmitted by CTXΦ, a filamentous lysogenic vibriophages. Temperate phages can provide crucial virulence and fitness factors affecting cell metabolism, bacterial adhesion, colonization, immunity, antibiotic resistance and serum resistance. The present study was an attempt to screen the marine environments like aquafarms and mangroves of coastal areas of Alappuzha and Cochin, Kerala for the presence of lysogenic V. cholerae, to study their pathogenicity and also gene transfer potential. Phenotypic and molecular methods were used for identification of isolates as V. cholerae. The thirty one isolates which were Gram negative, oxidase positive, fermentative, with or without gas production on MOF media and which showed yellow coloured colonies on TCBS (Thiosulfate Citrate Bile salt Sucrose) agar were segregated as vibrios. Twenty two environmental V. cholerae strains of both O1 and non- O1/non-O139 serogroups on induction with mitomycin C showed the presence of lysogenic phages. They produced characteristic turbid plaques in double agar overlay assay using the indicator strain V. cholerae El Tor MAK 757. PCR based molecular typing with primers targeting specific conserved sequences in the bacterial genome, demonstrated genetic diversity among these lysogen containing non-O1 V. cholerae . Polymerase chain reaction was also employed as a rapid screening method to verify the presence of 9 virulence genes namely, ctxA, ctxB, ace, hlyA, toxR, zot,tcpA, ninT and nanH, using gene specific primers. The presence of tcpA gene in ALPVC3 was alarming, as it indicates the possibility of an epidemic by accepting the cholera. Differential induction studies used ΦALPVC3, ΦALPVC11, ΦALPVC12 and ΦEKM14, underlining the possibility of prophage induction in natural ecosystems, due to abiotic factors like antibiotics, pollutants, temperature and UV. The efficiency of induction of prophages varied considerably in response to the different induction agents. The growth curve of lysogenic V. cholerae used in the study drastically varied in the presence of strong prophage inducers like antibiotics and UV. Bacterial cell lysis was directly proportional to increase in phage number due to induction. Morphological characterization of vibriophages by Transmission Electron Microscopy revealed hexagonal heads for all the four phages. Vibriophage ΦALPVC3 exhibited isometric and contractile tails characteristic of family Myoviridae, while phages ΦALPVC11 and ΦALPVC12 demonstrated the typical hexagonal head and non-contractile tail of family Siphoviridae. ΦEKM14, the podophage was distinguished by short non-contractile tail and icosahedral head. This work demonstrated that environmental parameters can influence the viability and cell adsorption rates of V. cholerae phages. Adsorption studies showed 100% adsorption of ΦALPVC3 ΦALPVC11, ΦALPVC12 and ΦEKM14 after 25, 30, 40 and 35 minutes respectively. Exposure to high temperatures ranging from 50ºC to 100ºC drastically reduced phage viability. The optimum concentration of NaCl required for survival of vibriophages except ΦEKM14 was 0.5 M and that for ΦEKM14 was 1M NaCl. Survival of phage particles was maximum at pH 7-8. V. cholerae is assumed to have existed long before their human host and so the pathogenic clones may have evolved from aquatic forms which later colonized the human intestine by progressive acquisition of genes. This is supported by the fact that the vast majority of V. cholerae strains are still part of the natural aquatic environment. CTXΦ has played a critical role in the evolution of the pathogenicity of V. cholerae as it can transmit the ctxAB gene. The unusual transformation of V. cholerae strains associated with epidemics and the emergence of V. cholera O139 demonstrates the evolutionary success of the organism in attaining greater fitness. Genetic changes in pathogenic V. cholerae constitute a natural process for developing immunity within an endemically infected population. The alternative hosts and lysogenic environmental V. cholerae strains may potentially act as cofactors in promoting cholera phage ‘‘blooms’’ within aquatic environments, thereby influencing transmission of phage sensitive, pathogenic V. cholerae strains by aquatic vehicles. Differential induction of the phages is a clear indication of the impact of environmental pollution and global changes on phage induction. The development of molecular biology techniques offered an accessible gateway for investigating the molecular events leading to genetic diversity in the marine environment. Using nucleic acids as targets, the methods of fingerprinting like ERIC PCR and BOX PCR, revealed that the marine environment harbours potentially pathogenic group of bacteria with genetic diversity. The distribution of virulence associated genes in the environmental isolates of V. cholerae provides tangible material for further investigation. Nucleotide and protein sequence analysis alongwith protein structure prediction aids in better understanding of the variation inalleles of same gene in different ecological niche and its impact on the protein structure for attaining greater fitness of pathogens. The evidences of the co-evolution of virulence genes in toxigenic V. cholerae O1 from different lineages of environmental non-O1 strains is alarming. Transduction studies would indicate that the phenomenon of acquisition of these virulence genes by lateral gene transfer, although rare, is not quite uncommon amongst non-O1/non-O139 V. cholerae and it has a key role in diversification. All these considerations justify the need for an integrated approach towards the development of an effective surveillance system to monitor evolution of V. cholerae strains with epidemic potential. Results presented in this study, if considered together with the mechanism proposed as above, would strongly suggest that the bacteriophage also intervenes as a variable in shaping the cholera bacterium, which cannot be ignored and hinting at imminent future epidemics.

Análisis de muestras de orina para la detección molecular de enfermedades infecciosas. Aplicación en la identificación de citomegalovirus humano

La implementación de metodologías de biología molecular como la reacción en cadena de la polimerasa (PCR), ha permitido la realización de diagnósticos sensibles y específicos para múltiples enfermedades, dentro de las cuales son de gran interés las infecciosas. Hasta hoy, los métodos de identificación se basan principalmente en cultivos y serología por su sensibilidad y especificidad, pero consumen tiempo y dinero. Las muestras de orina se han constituido en una alternativa no invasiva de obtención de ADN para la realización de análisis de biología molecular. Metodología: Implementación de una estrategia para la obtención de ADN a partir de muestras de orina. Las muestras fueron tomadas de niños de guardería, para documentar la presencia o no de inhibidores de PCR a través de la amplificación de genes de Citomegalovirus humano (CMVH). Resultados: En el 27,1% de las muestras analizadas se evidenció amplificación específica para CMVH, no se encontraron diferencias significativas en la presencia del virus en los tres estratos, pero sí en la intensidad de las bandas. Conclusión: Se verificó la ausencia de inhibidores de PCR mediante la amplificación del gen de la B-globina. Se estandarizó una metodología molecular para la identificación de CMVH, la cual puede ser aplicada

Electronic couplings and on-site energies for hole transfer in DNA: systematic quantum mechanical/molecular dynamic study

The electron hole transfer (HT) properties of DNA are substantially affected by thermal fluctuations of the π stack structure. Depending on the mutual position of neighboring nucleobases, electronic coupling V may change by several orders of magnitude. In the present paper, we report the results of systematic QM/molecular dynamic (MD) calculations of the electronic couplings and on-site energies for the hole transfer. Based on 15 ns MD trajectories for several DNA oligomers, we calculate the average coupling squares 〈 V2 〉 and the energies of basepair triplets X G+ Y and X A+ Y, where X, Y=G, A, T, and C. For each of the 32 systems, 15 000 conformations separated by 1 ps are considered. The three-state generalized Mulliken-Hush method is used to derive electronic couplings for HT between neighboring basepairs. The adiabatic energies and dipole moment matrix elements are computed within the INDO/S method. We compare the rms values of V with the couplings estimated for the idealized B -DNA structure and show that in several important cases the couplings calculated for the idealized B -DNA structure are considerably underestimated. The rms values for intrastrand couplings G-G, A-A, G-A, and A-G are found to be similar, ∼0.07 eV, while the interstrand couplings are quite different. The energies of hole states G+ and A+ in the stack depend on the nature of the neighboring pairs. The X G+ Y are by 0.5 eV more stable than X A+ Y. The thermal fluctuations of the DNA structure facilitate the HT process from guanine to adenine. The tabulated couplings and on-site energies can be used as reference parameters in theoretical and computational studies of HT processes in DNA

Dynamic load balancing for the distributed mining of molecular structures

In molecular biology, it is often desirable to find common properties in large numbers of drug candidates. One family of methods stems from the data mining community, where algorithms to find frequent graphs have received increasing attention over the past years. However, the computational complexity of the underlying problem and the large amount of data to be explored essentially render sequential algorithms useless. In this paper, we present a distributed approach to the frequent subgraph mining problem to discover interesting patterns in molecular compounds. This problem is characterized by a highly irregular search tree, whereby no reliable workload prediction is available. We describe the three main aspects of the proposed distributed algorithm, namely, a dynamic partitioning of the search space, a distribution process based on a peer-to-peer communication framework, and a novel receiverinitiated load balancing algorithm. The effectiveness of the distributed method has been evaluated on the well-known National Cancer Institute’s HIV-screening data set, where we were able to show close-to linear speedup in a network of workstations. The proposed approach also allows for dynamic resource aggregation in a non dedicated computational environment. These features make it suitable for large-scale, multi-domain, heterogeneous environments, such as computational grids.

Molecular comparisons of the Culex pipiens (L.) complex esterase gene amplicons

The amplification of carboxylesterase genes is a mechanism of organophosphate resistance in Culex mosquitoes. Amplified carboxylesterase genes from an insecticide resistant Culex pipiens strain collected in Cyprus were analysed and compared to other Culex amplified carboxylesterase alleles. A 12 kb section of genomic DNA containing two gene loci coding for carboxylesterase alleles A5 and B5 was cloned and sequenced. A comparison between this amplicon and one from a strain with co-amplified carboxylesterase alleles A2 and B2 revealed a number of differences. The intergenic spacer was 3.7 kb in length in the A5-B5 amplicon (2.7 kb in A2-B2) and contained putative Juan and transposable elements upstream of B5. A fragment of a gene with high homology to aldehyde oxidase was also present immediately downstream of A5. The comparison revealed no differences that would explain the successful spread of the A2-B2 amplicon worldwide whilst the A5-B5 amplicon is restricted to the Mediterranean. (C) 2004 Elsevier Ltd. All rights reserved.

Longitudinal selenium status in healthy British adults: assessment using biochemical and molecular biomarkers

Human selenium (Se) requirements are currently based on biochemical markers of Se status. In rats, tissue glutathione peroxidase-1 (Gpx1) mRNA levels can be used effectively to determine Se requirements; blood Gpx1 mRNA levels decrease in Se-deficient rats, so molecular biology-based markers have potential for human nutrition assessment. To study the efficacy of molecular biology markers for assessing Se status in humans, we conducted a longitudinal study on 39 subjects (age 45 +/- 11) in Reading, UK. Diet diaries (5 day) and blood were obtained from each subject at 2, 8, 17 and 23 weeks, and plasma Se, glutathione peroxidase (Gpx3) enzyme activity, and selenoprotein mRNA levels were determined. There were no significant longitudinal effects on Se biomarkers. Se intake averaged 48 +/- 14 mu g/d. Plasma Se concentrations averaged 1.13 +/- 0.16 mu mol/l. Plasma Se v. energy-corrected Se intake (ng Se/kJ/d) was significantly correlated, but neither Gpx3 activity v. Se intake (ng Se/kJ/d) nor Gpx3 activity v. plasma Se was significantly correlated. Collectively, this indicates that subjects were on the plateaus of the response curves. Selenoprotein mRNAs were quantitated in total RNA isolated from whole blood, but mRNA levels for Gpx1, selenoprotein H, and selenoprotein W (all highly regulated by Se in rodents), as well selenoprotein P, Gpx3, and phospholipid hydroperoxide glutathione peroxidase were also not significantly correlated with plasma Se. Thus selenoprotein molecular biomarkers, as well as traditional biochemical markers, are unable to further distinguish differences in Se status in these Se replete subjects. The efficacy of molecular biomarkers to detect Se deficiency needs to be tested in Se-deficient populations.

SARS coronavirus unique domain: three-domain molecular architecture in solution and RNA binding

Nonstructural protein 3 of the severe acute respiratory syndrome (SARS) coronavirus includes a "SARS-unique domain" (SUD) consisting of three globular domains separated by short linker peptide segments. This work reports NMR structure determinations of the C-terminal domain (SUD-C) and a two-domain construct (SUD-MC) containing the middle domain (SUD-M) and the C-terminal domain, and NMR data on the conformational states of the N-terminal domain (SUD-N) and the SUD-NM two-domain construct. Both SUD-N and SUD-NM are monomeric and globular in solution; in SUD-NM, there is high mobility in the two-residue interdomain linking sequence, with no preferred relative orientation of the two domains. SUD-C adopts a frataxin like fold and has structural similarity to DNA-binding domains of DNA-modifying enzymes. The structures of both SUD-M (previously determined) and SUD-C (from the present study) are maintained in SUD-MC, where the two domains are flexibly linked. Gel-shift experiments showed that both SUD-C and SUD-MC bind to single-stranded RNA and recognize purine bases more strongly than pyrimidine bases, whereby SUD-MC binds to a more restricted set of purine-containing RNA sequences than SUD-M. NMR chemical shift perturbation experiments with observations of (15)N-labeled proteins further resulted in delineation of RNA binding sites (i.e., in SUD-M, a positively charged surface area with a pronounced cavity, and in SUD-C, several residues of an anti-parallel beta-sheet). Overall, the present data provide evidence for molecular mechanisms involving the concerted actions of SUD-M and SUD-C, which result in specific RNA binding that might be unique to the SUD and, thus, to the SARS coronavirus.

Application of molecular biological methods for studying probiotics and the gut flora

Increasingly, the microbiological scientific community is relying on molecular biology to define the complexity of the gut flora and to distinguish one organism from the next. This is particularly pertinent in the field of probiotics, and probiotic therapy, where identifying probiotics from the commensal flora is often warranted. Current techniques, including genetic fingerprinting, gene sequencing, oligonucleotide probes and specific primer selection, discriminate closely related bacteria with varying degrees of success. Additional molecular methods being employed to determine the constituents of complex microbiota in this area of research are community analysis, denaturing gradient gel electrophoresis (DGGE)/temperature gradient gel electrophoresis (TGGE), fluorescent in situ hybridisation (FISH) and probe grids. Certain approaches enable specific aetiological agents to be monitored, whereas others allow the effects of dietary intervention on bacterial populations to be studied. Other approaches demonstrate diversity, but may not always enable quantification of the population. At the heart of current molecular methods is sequence information gathered from culturable organisms. However, the diversity and novelty identified when applying these methods to the gut microflora demonstrates how little is known about this ecosystem. Of greater concern is the inherent bias associated with some molecular methods. As we understand more of the complexity and dynamics of this diverse microbiota we will be in a position to develop more robust molecular-based technologies to examine it. In addition to identification of the microbiota and discrimination of probiotic strains from commensal organisms, the future of molecular biology in the field of probiotics and the gut flora will, no doubt, stretch to investigations of functionality and activity of the microflora, and/or specific fractions. The quest will be to demonstrate the roles of probiotic strains in vivo and not simply their presence or absence.