A pipeline to study structural interactions among Spodoptera frugiperda serine proteinases and plant proteinase inhibitors.

We propose here a computational biology pipeline to identify and analyze possible structural determinants that could explain some level of insensitivity by S. frugiperda serine proteinases (SPs) against plant PIs observed in a real time PCR experiment.GA 330

Allele-and parent-of-origin-specific effects on expression of the KCNJ11 gene: A candidate for meat tenderness in cattle

ABSTRACT. In contrast to the Mendelian inheritance model, parental alleles can contribute unequally to gene expression, which may result in phenotypic variance among individuals and bias in the predicted additive effect of molecular markers associated with production traits. Given the need to understand the effects of allelic variation and parentof-origin effects on the expression of genes with a commercial interest in cattle, we analyzed the expression of KCNJ11 (potassium inwardly rectifying channel, subfamily J, member 11), which was previously described as a functional candidate gene for meat tenderness. Allelespecific and parent-of-origin-dependent expression of this gene were assessed in bovine muscle using the rs379610823 single nucleotide polymorphism as a reference. Biallelic expression was observed; however, the T allele was expressed at significantly higher levels than the C allele. Furthermore, increased expression of KCNJ11 was found in animals harboring the maternal T allele. This study is the first to describe the differential allelic expression of bovine KCNJ11. Our findings are important for understanding the mechanisms that underlie the pattern of KCNJ11 expression and its potential impact on the phenotypic variation of meat tenderness in Nelore beef cattle. This reinforces the need for further investigation of allelic-and parent-oforigin expression deviation in genetic markers eligible for the selection of target traits

Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds

The relationships of passerines (such as the well-studied zebra finch) with non-passerine birds is one of the great enigmas of avian phylogenetic research, because decades of extensive morphological and molecular studies yielded highly inconsistent results between and within data sets. Here we show the first application of the virtually homoplasy-free retroposon insertions to this controversy. Our study examined ~200,000 retroposon-containing loci from various avian genomes and retrieved 51 markers resolving early bird phylogeny. Among these, we obtained statistically significant evidence that parrots are the closest and falcons the second-closest relatives of passerines, together constituting the Psittacopasserae and the Eufalconimorphae, respectively. Our new and robust phylogenetic framework has substantial implications for the interpretation of various conclusions drawn from passerines as model organisms. This includes insights of relevance to human neuroscience, as vocal learning (that is, birdsong) probably evolved in the psittacopasseran ancestor, >30 million years earlier than previously assumed

Massive-Scale RNA-Seq Analysis of Non Ribosomal Transcriptome in Human Trisomy 21

Hybridization- and tag-based technologies have been successfully used in Down syndrome to identify genes involved in various aspects of the pathogenesis. However, these technologies suffer from several limits and drawbacks and, to date, information about rare, even though relevant, RNA species such as long and small non-coding RNAs, is completely missing. Indeed, none of published works has still described the whole transcriptional landscape of Down syndrome. Although the recent advances in high-throughput RNA sequencing have revealed the complexity of transcriptomes, most of them rely on polyA enrichment protocols, able to detect only a small fraction of total RNA content. On the opposite end, massive-scale RNA sequencing on rRNA-depleted samples allows the survey of the complete set of coding and non-coding RNA species, now emerging as novel contributors to pathogenic mechanisms. Hence, in this work we analysed for the first time the complete transcriptome of human trisomic endothelial progenitor cells to an unprecedented level of resolution and sensitivity by RNA-sequencing. Our analysis allowed us to detect differential expression of even low expressed genes crucial for the pathogenesis, to disclose novel regions of active transcription outside yet annotated loci, and to investigate a plethora of non-polyadenilated long as well as short non coding RNAs. Novel splice isoforms for a large subset of crucial genes, and novel extended untranslated regions for known genes—possibly novel miRNA targets or regulatory sites for gene transcription—were also identified in this study. Coupling the rRNA depletion of samples, followed by high-throughput RNA-sequencing, to the easy availability of these cells renders this approach very feasible for transcriptome studies, offering the possibility of investigating in-depth blood-related pathological features of Down syndrome, as well as other genetic disorders

A model for teaching amplification, cloning and sequencing of DNA for undergraduate students

Abstract of the panel presented at the SBBq annual meeting (see attachament).</p

Detection of Babesia bovis and Babesia bigemina in Water Buffaloes (Bubalus bubalis) in Endemic Areas of São Paulo State, Brazil

Abstract Babesiosis is a tick-transmitted disease that causes severe economic losses to the cattle industry in Brazil. Water buffaloes (Bubalus bubalis) are often carriers of Babesia spp., but there are no studies that provide an accurate estimation of this infection in animals raised in regions of endemic stability. This study was conducted to investigate Babesia bovis and B. bigemina infections in 108 water buffaloes (50 calves and 58 adult females) located in areas of São Paulo state, where the animals were continuously exposed to Rhipicephalus microplus ticks. B. bovis and B. bigemina infections were screened by microscopic examination of blood smears, nested PCR (nPCR) and quantitative real-time PCR (qPCR), which were also used to estimate the number of copies (NC) of the cytochrome b (mt-cytB) gene in the blood samples. B. bigemina was found in blood smears of three calves from Alambari herd (all with less than 0.1% parasitemia). Molecular techniques were more sensitive than blood smears to diagnose piroplasms in water buffaloes: 20.37% and 100.00% for B. bovis-infected animals and 59.26% and 100.00% for B. bigemina-infected animals, respectively for nPCR and qPCR. The NC of mt-cytB gene of B. bovis and B. bigemina in blood samples re-* Corresponding author. T. A. Néo et al. 76 vealed significant effects (p &lt; 0.05) of herd-age, species and their interaction. The NC values were higher (p ≤ 0.05) for B. bigemina (2.80 ± 0.06) than for B. bovis (2.61 ± 0.05). Within each herd-age, differences between the species&apos; NC values were found only in Alambari calves, which showed significantly higher (p ≤ 0.05) NC of B. bigemina (3.48 ± 0.13). The calves and cows from Ibaté showed the lowest NC of B. bigemina (2.29 ± 0.13 and 2.63 ± 0.14) and B. bovis (2.54 ± 0.11 and 2.37 ± 0.12), respectively. These data suggest a high prevalence of B. bovis and B. bigemina infection in the buffalo population in endemic areas of São Paulo state