Aberrant transcript produced by a splice donor site deletion in the TECTA gene is associated with autosomal dominant deafness in a Brazilian family

We ascertained a Brazilian family with nine individuals affected by autosomal dominant nonsyndromic sensorineural hearing loss. The bilateral hearing loss affected mainly mid-high frequencies, was apparently stable with an early onset. Microsatellites close to the DFNA8/DFNA12 locus, which harbors the TECTA gene, showed significant multipoint lod scores (32) close to marker D11S4107. Sequencing of the exons and exon-intron boundaries of the TECTA gene in one affected subject revealed the deletion c.5383 + 5delGTGA in the 5' end of intron 16, that includes the last two bases of the donor splice site consensus sequence. This mutation segregates with deafness within the family. To date, 33 different TECTA mutations associated with autossomal dominant hearing loss have been described. Among them is the mutation reported herein, first described by Hildebrand et al. (2011) in a UK family. The audioprofiles from the UK and Brazilian families were similar. In order to investigate the transcripts produced by the mutated allele, we performed cDNA analysis of a lymphoblastoid cell line from an affected heterozygote with the c.5383 + 5delGTGA and a noncarrier from the same family. The analysis allowed us to identify an aberrant transcript with skipping of exon 16, without affecting the reading frame. One of the dominant TECTA mutations already described, a synonymous substitution in exon 16 (c.5331 G<A), was also shown to affect splicing resulting in an aberrant transcript lacking exon 16. Despite the difference in the DNA level, both the synonymous substitution in exon 16 (c.5331 G<A) and the mutation described herein affect splicing of exon 16, leading to its skipping. At the protein level they would have the same effect, an in-frame deletion of 37 amino-acids (p.S1758Y/G1759_N1795del) probably leading to an impaired function of the ZP domain. Thus, like the TECTA missense mutations associated with dominant hearing loss, the c5383 + 5delGTGA mutation does not have an inactivating effect on the protein. (C) 2012 Elsevier B.V. All rights reserved.

BF Integrase Genes of HIV-1 Circulating in Sao Paulo, Brazil, with a Recurrent Recombination Region

Although some studies have shown diversity in HIV integrase (IN) genes, none has focused particularly on the gene evolving in epidemics in the context of recombination. The IN gene in 157 HIV-1 integrase inhibitor-naive patients from the Sao Paulo State, Brazil, were sequenced tallying 128 of subtype B (23 of which were found in non-B genomes), 17 of subtype F (8 of which were found in recombinant genomes), 11 integrases were BF recombinants, and 1 from subtype C. Crucially, we found that 4 BF recombinant viruses shared a recurrent recombination breakpoint region between positions 4900 and 4924 (relative to the HXB2) that includes 2 gRNA loops, where the RT may stutter. Since these recombinants had independent phylogenetic origin, we argue that these results suggest a possible recombination hotspot not observed so far in BF CRF in particular, or in any other HIV-1 CRF in general. Additionally, 40% of the drug-naive and 45% of the drug-treated patients had at least 1 raltegravir (RAL) or elvitegravir (EVG) resistance-associated amino acid change, but no major resistance mutations were found, in line with other studies. Importantly, V151I was the most common minor resistance mutation among B, F and BF IN genes. Most codon sites of the IN genes had higher rates of synonymous substitutions (dS) indicative of a strong negative selection. Nevertheless, several codon sites mainly in the subtype B were found under positive selection. Consequently, we observed a higher genetic diversity in the B portions of the mosaics, possibly due to the more recent introduction of subtype F on top of an ongoing subtype B epidemics and a fast spread of subtype F alleles among the B population.

Nuculidae (Bivalvia) in the Cape Melville Formation, King George Island, Antarctica, with an overview of the bivalve fauna

Nuculid bivalves of the Cape Melville Formation (Early Miocene, King George Island) are reviewed. Ten bivalve taxa are listed from the formation in the families Nuculidae (two species), Sareptidae, Malletiidae, Limopsidae (two species), Limidae, Pectinidae, Hiatellidae, and Periplomatidae. The Nuculidae consist of two species of Leionucula Quenstedt, 1930. One of these, L. melvilleana n. sp., is described and the other consists of the two species named previously by Anelli et al. (2006), which are demonstrated to be synonymous and are assigned to the species Leionucula frigida (Anelli, Rocha-Campos, Santos, Perinotto & Quaglio 2006). This assemblage, dominated by protobranchs (89% of specimens), is a typical fauna of offshore soft substrates, with a few specimens transported from hard substrates nearby. The diversity of Nuculidae has decreased in the Antarctic region through the Cenozoic.

Analysis of energetically biased transcripts of viruses and transposable elements

RNA interference (RNAi) is a natural endogenous process by which double-stranded RNA molecules trigger potent and specific gene silencing in eukaryotic cells and is characterized by target RNA cleavage. In mammals, small interfering RNAs (siRNAs) are the trigger molecules of choice and constitute a new class of RNA-based antiviral agents. In an efficient RNAi response, the antisense strand of siRNAs must enter the RNA-induced silencing complex (RISC) in a process mediated by thermodynamic features. In this report, we hypothesize that silent mutations capable of inverting thermodynamic properties can promote resistance to siRNAs. Extensive computational analyses were used to assess whether continuous selective pressure that promotes such mutations could lead to the emergence of viral strains completely resistant to RNAi (i.e., prone to transfer only the sense strands to RISC). Based on our findings, we propose that, although synonymous mutations may produce functional resistance, this strategy cannot be systematically adopted by viruses since the longest RNAi-refractory sequence is only 10 nt long. This finding also suggests that all mRNAs display fluctuating thermodynamic landscapes and that, in terms of thermodynamic features, RNAi is a very efficient antiviral system since there will always be sites susceptible to siRNAs.

Childbirth experience according to a group of Brazilian primiparas

Objective: to understand the meaning of the childbirth experience for Brazilian primiparas in the postpartum period. Design: a qualitative approach using semi-structured interviews. Content analysis was used to derive the two themes that emerged from the discourses. Setting: participants were recruited at four primary-level health-care units in Ribeirao Preto, Brazil. After providing written informed consent, an appointment was made for an interview at the participants' homes. Participants: 20 primiparas in the postpartum period, aged 15-26 years old, who attended the health-care units to vaccinate their infants and test for phenylketonuria. Findings: two thematic categories emerged from the interviews: the meaning attributed to childbirth (with four subcategories) and perceptions of care. Among the participants, the childbirth experience was marked by the 'fear of death' and 'losing the child'. The pain of giving birth was expected, and the moment of childbirth was associated with pain of high intensity. Key conclusions: childbirth is considered synonymous with physical and emotional suffering, pain, fear and risk of death. Implications for practice: this research indicates the need to break the current mechanistic model of care on which health professionals' actions are based. Care during childbirth must be guided by the foundation that women are the subjects of childbirth actions, in an attempt to emphasise actions that grant them with the autonomy and empowerment needed to experience the situation. (C) 2011 Elsevier Ltd. All rights reserved.

On some species of Taeniotes Audinet-Serville, 1835 (Coleoptera: Cerambycidae: Lamiinae)

Taeniotes farinosus (Linnaeus, 1758) is a species that has been confused with other species during the past two centuries. In this work we demonstrate that Taeniotes farinosus sensu auctorum is not the species described by Linnaeus and designate a lectotype to establish its identity. Taeniotes pulverulentus (Olivier, 1790), currently synonymous with T. farinosus, is revalidated. Taeniotes guttullaris Schwarzer, 1929 and T parafarinosus Breuning, 1971 are junior synonyms of T. pulverulentus; Lamia subocellata Olivier, 1792 (= Taeniotes subocellatus) is a junior synonym of Cerambyx farinosus (= T farinosus). Additionally we monnei, a new species from Brazil and Argentina, is described and figured. Taeniotes peruanus provide annotated bibliographic references to T. farinosus and T pulverulentus. Taeniotes Breuning 1971 is figured for the first time.

Avian coronavirus Spike Glycoprotein Ectodomain Shows a Low Codon Adaptation to Gallus gallus with Virus-Exclusive Codons in Strategic Amino Acids Positions

This is a study on the Avian coronavirus IBV and chicken host-relationship from the codon usage point of view based on fifty-nine non-redundant IBV S1 sequences (nt 1-507) from strains detected worldwide and chicken tissue-specific protein genes sequences from IBV-replicating sites. The effective number of codons (ENC) values ranged from 36 to 47.8, indicating a high-to-moderate codon usage bias. The highest IBV codon adaptation index (CAI) value was 0.7, indicating a distant virus versus host synonymous codons usage. The ENC x GC3 % curve indicates that both mutational pressure and natural selection are the driving forces on codon usage pattern in S1. The low CAI values agree with a low S protein expression and considering that S protein is a determinant for attachment and neutralization, this could be a further mechanism besides mRNA transcription attenuation for a low expression of this protein leading to an immune camouflage.

Processes Mapping in Cotton Culture to Traceability Creation

Traceability is a concept that arose from the need for monitoring of production processes, this concept is usually used in sectors related to food production or activities involving some kind of direct risk to people. Agribusiness in the cotton industry does not have a comprehensive infrastructure for all stages of the processes involved in production. Map and define the data to enable traceability of products is synonymous to delegate responsibilities for all involved in the production, the collection of aggregate data on cotton production is done in stages and specific pre-defined since the choice of the variety through the processing, the scope of this article specifically addresses the production of lint cotton. The paper presents a proposal based on service oriented architecture (SOA) for data integration processes in the cotton industry, this proposal provide support for the implementation of platform independent solutions.

Dengue virus type 3 adaptive changes during epidemics in São Jose de Rio Preto, Brazil, 2006–2007

Global dengue virus spread in tropical and sub-tropical regions has become a major international public health concern. It is evident that DENV genetic diversity plays a significant role in the immunopathology of the disease and that the identification of polymorphisms associated with adaptive responses is important for vaccine development. The investigation of naturally occurring genomic variants may play an important role in the comprehension of different adaptive strategies used by these mutants to evade the human immune system. In order to elucidate this role we sequenced the complete polyprotein-coding region of thirty-three DENV-3 isolates to characterize variants circulating under high endemicity in the city of São José de Rio Preto, Brazil, during the onset of the 2006-07 epidemic. By inferring the evolutionary history on a local-scale and estimating rates of synonymous (dS) and nonsynonimous (dN) substitutions, we have documented at least two different introductions of DENV-3 into the city and detected 10 polymorphic codon sites under significant positive selection (dN/dS > 1) and 8 under significant purifying selection (dN/dS < 1). We found several polymorphic amino acid coding sites in the envelope (15), NS1 (17), NS2A (11), and NS5 (24) genes, which suggests that these genes may be experiencing relatively recent adaptive changes. Furthermore, some polymorphisms correlated with changes in the immunogenicity of several epitopes. Our study highlights the existence of significant and informative DENV variability at the spatio-temporal scale of an urban outbreak.