A variant in the gene FUT9 is associated with susceptibility to placental malaria infection

Malaria in pregnancy forms a substantial part of the worldwide burden of malaria, with an estimated annual death toll of up to 200,000 infants, as well as increased maternal morbidity and mortality. Studies of genetic susceptibility to malaria have so far focused on infant malaria, with only a few studies investigating the genetic basis of placental malaria, focusing only on a limited number of candidate genes. The aim of this study therefore was to identify novel host genetic factors involved in placental malaria infection. To this end we carried out a nested case-control study on 180 Mozambican pregnant women with placental malaria infection, and 180 controls within an intervention trial of malaria prevention. We genotyped 880 SNPs in a set of 64 functionally related genes involved in glycosylation and innate immunity. A SNP located in the gene FUT9, rs3811070, was significantly associated with placental malaria infection (OR = 2.31, permutation p-value = 0.028). Haplotypic analysis revealed a similarly strong association of a common haplotype of four SNPs including rs3811070. FUT9 codes for a fucosyl-transferase that is catalyzing the last step in the biosynthesis of the Lewis-x antigen, which forms part of the Lewis blood group-related antigens. These results therefore suggest an involvement of this antigen in the pathogenesis of placental malaria infection.

Analysis of the multi-copy gene family FAM90A as a copy number variant in different ethnic backgrounds

Copy number variants contribute extensively to inter-individual genomic differences, but little is known about their inter-population variability and diversity. In a previous study (Bosch et al., 2007; 16:2572-2582), we reported that the primate-specific gene family FAM90A, which accounts for as many as 25 members in the human reference assembly, has expanded the number of FAM90A clusters across the hominoid lineage. Here we examined the copy number variability of FAM90A genes in 260 HapMap samples of European, African, and Asian ancestry, and showed significant inter-population differences (p<0.0001). Based on the recent study of Stranger et al. (2007; 315:848-853), we also explored the correlation between copy number variability and expression levels of the FAM90A gene family. Despite the high genomic variability, we found a low correlation between FAM90A copy number and expression levels, which could be due to the action of independent trans-acting factors. Our results show that FAM90A is highly variable in copy number between individuals and between populations. However, this variability has little impact on gene expression levels, thus highlighting the importance of genomic variability for genes located in regions containing segmental duplications.

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.

Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are "genomic fossils" valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an important problem in computational genomics, and is also critical for obtaining an accurate picture of a genome's structure and function. However, no consensus computational scheme for defining and detecting pseudogenes has been developed thus far. As part of the ENCyclopedia Of DNA Elements (ENCODE) project, we have compared several distinct pseudogene annotation strategies and found that different approaches and parameters often resulted in rather distinct sets of pseudogenes. We subsequently developed a consensus approach for annotating pseudogenes (derived from protein coding genes) in the ENCODE regions, resulting in 201 pseudogenes, two-thirds of which originated from retrotransposition. A survey of orthologs for these pseudogenes in 28 vertebrate genomes showed that a significant fraction ( approximately 80%) of the processed pseudogenes are primate-specific sequences, highlighting the increasing retrotransposition activity in primates. Analysis of sequence conservation and variation also demonstrated that most pseudogenes evolve neutrally, and processed pseudogenes appear to have lost their coding potential immediately or soon after their emergence. In order to explore the functional implication of pseudogene prevalence, we have extensively examined the transcriptional activity of the ENCODE pseudogenes. We performed systematic series of pseudogene-specific RACE analyses. These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues.

The protective effect of the obesity-associated rs9939609 A variant in fat mass- and obesity-associated gene on depression.

Candidate gene and genome-wide association studies have not identified common variants, which are reliably associated with depression. The recent identification of obesity predisposing genes that are highly expressed in the brain raises the possibility of their genetic contribution to depression. As variation in the intron 1 of the fat mass- and obesity-associated (FTO) gene contributes to polygenic obesity, we assessed the possibility that FTO gene may contribute to depression in a cross-sectional multi-ethnic sample of 6561 depression cases and 21 932 controls selected from the EpiDREAM, INTERHEART, DeCC (depression case-control study) and Cohorte Lausannoise (CoLaus) studies. Major depression was defined according to DSM IV diagnostic criteria. Association analyses were performed under the additive genetic model. A meta-analysis of the four studies showed a significant inverse association between the obesity risk FTO rs9939609 A variant and depression (odds ratio=0.92 (0.89, 0.97), P=3 × 10(-4)) adjusted for age, sex, ethnicity/population structure and body-mass index (BMI) with no significant between-study heterogeneity (I(2)=0%, P=0.63). The FTO rs9939609 A variant was also associated with increased BMI in the four studies (β 0.30 (0.08, 0.51), P=0.0064) adjusted for age, sex and ethnicity/population structure. In conclusion, we provide the first evidence that the FTO rs9939609 A variant may be associated with a lower risk of depression independently of its effect on BMI. This study highlights the potential importance of obesity predisposing genes on depression.

The role of the pathologist in tissue banking: European Consensus Expert Group Report.

Human tissue biobanking encompasses a wide range of activities and study designs and is critical for application of a wide range of new technologies (-"omics") to the discovery of molecular patterns of disease and for implementation of novel biomarkers into clinical trials. Pathology is the cornerstone of hospital-based tissue biobanking. Pathologists not only provide essential information identifying the specimen but also make decisions on what should be biobanked, making sure that the timing of all operations is consistent with both the requirements of clinical diagnosis and the optimal preservation of biological products. This document summarizes the conclusions of a Pathology Expert Group Meeting within the European Biological and Biomolecular Research Infrastructure (BBMRI) Program. These recommendations are aimed at providing guidance for pathologists as well as for institutions hosting biobanks on how to better integrate and support pathological activities within the framework of biobanks that fulfill international standards.

Review. Precision viticulture. Research topics, challenges and opportunities in site-specific vineyard management

Precision Viticulture (PV) is a concept that is beginning to have an impact on the wine-growing sector. Its practical implementation is dependant on various technological developments: crop sensors and yield monitors, local and remote sensors, Global Positioning Systems (GPS), VRA (Variable-Rate Application) equipment and machinery, Geographic Information Systems (GIS) and systems for data analysis and interpretation. This paper reviews a number of research lines related to PV. These areas of research have focused on four very specific fields: 1) quantification and evaluation of within-field variability, 2) delineation of zones of differential treatment at parcel level, based on the analysis and interpretation of this variability, 3) development of Variable-Rate Technologies (VRT) and, finally, 4) evaluation of the opportunities for site-specific vineyard management. Research in these fields should allow winegrowers and enologists to know and understand why yield variability exists within the same parcel, what the causes of this variability are, how the yield and its quality are interrelated and, if spatial variability exists, whether site-specific vineyard management is justifiable on a technical and economic basis.

A functional variant in the Stearoyl-CoA desaturase gene promoter enhances fatty acid desaturation in pork

There is growing public concern about reducing saturated fat intake. Stearoyl-CoA desaturase (SCD) is the lipogenic enzyme responsible for the biosynthesis of oleic acid (18:1) by desaturating stearic acid (18:0). Here we describe a total of 18 mutations in the promoter and 3′ non-coding region of the pig SCD gene and provide evidence that allele T at AY487830:g.2228T>C in the promoter region enhances fat desaturation (the ratio 18:1/18:0 in muscle increases from 3.78 to 4.43 in opposite homozygotes) without affecting fat content (18:0+18:1, intramuscular fat content, and backfat thickness). No mutations that could affect the functionality of the protein were found in the coding region. First, we proved in a purebred Duroc line that the C-T-A haplotype of the 3 single nucleotide polymorphisms (SNPs) (g.2108C>T; g.2228T>C; g.2281A>G) of the promoter region was additively associated to enhanced 18:1/18:0 both in muscle and subcutaneous fat, but not in liver. We show that this association was consistent over a 10-year period of overlapping generations and, in line with these results, that the C-T-A haplotype displayed greater SCD mRNA expression in muscle. The effect of this haplotype was validated both internally, by comparing opposite homozygote siblings, and externally, by using experimental Duroc-based crossbreds. Second, the g.2281A>G and the g.2108C>T SNPs were excluded as causative mutations using new and previously published data, restricting the causality to g.2228T>C SNP, the last source of genetic variation within the haplotype. This mutation is positioned in the core sequence of several putative transcription factor binding sites, so that there are several plausible mechanisms by which allele T enhances 18:1/18:0 and, consequently, the proportion of monounsaturated to saturated fat.

The role of Caulobacter crescentus XerC and XerD recombinases in site-specific recombination

XerC et XerD, deux recombinases impliquées dans la recombinaison site spécifique, résolvent les multimères d’ADN en monomères. Cette réaction se produit au niveau du site dif du chromosome, et nécessite le domaine C-terminale de la protéine de division cellulaire FtsK. Caulobacter crescentus est une bactérie aquatique de type Gram-négative qui se retrouve dans plusieurs environnements. Elle présente un cycle cellulaire asymétrique avec deux types de cellules distinctes. Cette propriété peut être utilisée pour synchroniser la croissance d’une population bactérienne pour permettre l’étude de l’expression de gènes à travers le temps et les liens entre le cycle cellulaire et le développement de la bactérie. La liaison à l’ADN et la capacité de former des complexes covalents (phosphotyrosyl) avec le site dif de C. crescentus (ccdif) ont été testé pour les recombinases de C. crescentus (ccXerC et ccXerD). Les deux recombinases ont eu une meilleure liaison au demi-site gauche de ccdif et sont incapable d’effectuer une liaison coopérative, contrairement à ce qui se produit au niveau du site dif de E. coli. La formation de complexes covalents a été testé en utilisant des «substrats suicides avec bris» marqués à la fluorescence ainsi que des protéines de fusion (marquées ou non à la fluorescence). Des complexes ADN-protéines résistants à la chaleur et au SDS ont été observé lors de la réaction de ccXerC et ccXerD de type sauvage avec ccdif, mais pas lors de la réaction de mutants avec le même ADN. Des complexes covalents phosphotyrosine sont formés de façon plus efficace sur les substrats suicides avec un bris au niveau du brin supérieur que ceux ayant un bris au niveau du brin inférieur. Dans les deux cas, c’est ccXerC qui est resté lié de façon covalente à l’ADN de ccdif.

Discrete wavelet transform de-noising in eukaryotic gene splicing

This paper compares the most common digital signal processing methods of exon prediction in eukaryotes, and also proposes a technique for noise suppression in exon prediction. The specimen used here which has relevance in medical research, has been taken from the public genomic database - GenBank.Here exon prediction has been done using the digital signal processing methods viz. binary method, EIIP (electron-ion interaction psuedopotential) method and filter methods. Under filter method two filter designs, and two approaches using these two designs have been tried. The discrete wavelet transform has been used for de-noising of the exon plots.Results of exon prediction based on the methods mentioned above, which give values closest to the ones found in the NCBI database are given here. The exon plot de-noised using discrete wavelet transform is also given.Alterations to the proven methods as done by the authors, improves performance of exon prediction algorithms. Also it has been proven that the discrete wavelet transform is an effective tool for de-noising which can be used with exon prediction algorithms

The rise and evolution of the cambial variant in Bignonieae (Bignoniaceae)

Cambial variants represent a form of secondary growth that creates great stem anatomical diversity in lianas. Despite the importance of cambial variants, nothing is known about the developmental mechanisms that may have led to the current diversity seen in these stems. Here, a thorough anatomical analysis of all genera along the phylogeny of Bignonieae (Bignoniaceae) was carried out in order to detect when in their ontogeny and phylogeny there were shifts leading to different stem anatomical patterns. We found that all species depart from a common developmental basis, with a continuous, regularly growing cambium. Initial development is then followed by the modification of four equidistant portions of the cambium that reduce the production of xylem and increase the production of phloem, the former with much larger sieve tubes and an extended lifespan. In most species, the formerly continuous cambium becomes disjunct, with cambial portions within phloem wedges and cambial portions between them. Other anatomical modifications such as the formation of multiples of four phloem wedges, multiple-dissected phloem wedges, and included phloem wedges take place thereafter. The fact that each novel trait raised on the ontogenetic trajectory appeared in subsequently more recent ancestors on the phylogeny suggests a recapitulatory history. This recapitulation is, however, caused by the terminal addition of evolutionary novelties rather than a truly heterochronic process. Truly heterochronic processes were only found in shrubby species, which resemble juveniles of their ancestors, as a result of a decelerated phloem formation by the variant cambia. In addition, the modular evolution of phloem and xylem in Bignonieae seems to indicate that stem anatomical modifications in this group occurred at the level of cambial initials.

First detection of the equine herpesvirus 1 neuropathogenic variant in Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

First defection of the equine herpesvirus 1 neuropathogenic variant in Brazil

This report describes the first detection of an equine herpesvirus 1 (EHV-1) neuropathogenic variant (G 2254/D 752) in Brazil from a case of fatal equine herpesvirus myeloencephalopathy (EHM) in a mare. The results of nucleotide sequencing of the EHV-1 ORF30 gene showed that two other Brazilian EHV-1 isolates from EHM cases are representatives of the non-neuropathogenic variant (A 2254/N 752), suggesting that other unidentified factors are probably also involved in the neuropathogenicity of EHV-1 in horses. These findings will contribute to the epidemiological knowledge of EHV-1 infection in Brazil.

Influenza among the elderly in the Americas: A consensus statement

Influenza exacts a heavy burden on the elderly, a segment of the population that is estimated to experience rapid growth in the near future. In the past decade most developed and several developing countries have recommended influenza vaccination for those > 65 years of age. The World Health Organization (WHO) set a goal of 75% influenza vaccination coverage among the elderly by 2010, but it was not achieved. In 2011, the Technical Advisory Group at the Pan American Health Organization, Regional Office of WHO for the Americas, reiterated the influenza vaccine recommendation for older adults. Relatively little information has been compiled on the immunological aspect of aging or on reducing its impact, information particularly relevant for clinicians and gerontologist with firsthand experience confronting its effects. To fill this data gap, in 2012 the Americas Health Foundation (Washington, D.C., United States) and the nonprofit, Fighting Infectious Diseases in Emerging Countries (Miami, Florida, United States), convened a panel of Latin American clinicians and gerontologists with expertise in influenza to discuss key issues and develop a consensus statement. The major recommendations were to improve influenza surveillance throughout Latin America so that its impact can be quantified; and to conduct laboratory confirmation of influenza for all patients who have flu-like symptoms and are frail, immunosuppressed, have comorbidities, are respiratory compromised, or have been admitted to a hospital. The panel also noted that: since evidence for antivirals in the elderly is unclear, their use should be handled on a case-by-case basis; despite decreased immunological response, influenza vaccination in older adults is still crucial; indirect immunization strategies should be encouraged; and traditional infection control measures are essential in long-term care facilities.