ParMap, an Algorithm for the Identification of Complex Genomic Variations in Nextgen Sequencing Data

Next-generation sequencing produces high-throughput data, albeit with greater error and shorter reads than traditional Sanger sequencing methods. This complicates the detection of genomic variations, especially, small insertions and deletions. Here we describe ParMap, a statistical algorithm for the identification of complex genetic variants using partially mapped reads in nextgen sequencing data. We also report ParMap’s successful application to the mutation analysis of chromosome X exome-captured leukemia DNA samples

Arquitectura no convencional con objetos cotidianos

En el trabajo se contemplan diferentes respuestas arquitectónicas que investigan el upcycling o reutilización de objetos, proponiendo soluciones permanentes en construcción con aquellos elementos ajenos en primera instancia a la propia arquitectura. Para ello se expone la importancia de esta arquitectura innovadora y sostenible y se establecen las pautas de su viabilidad y estabilidad temporal.Se explora el amplio campo de opciones que ofrece el empleo de objetos cotidianos, creando resultados que llegan a ser muy diversos, dados los ámbitos de actuación, emplazamiento y por tanto el clima, situación económica, índice de material utilizado y tipo de material, dependiendo siempre de la mente creadora del arquitecto.<br /

Gastrointestinal parasites of free-range chickens : a worldwide issue

Gastrointestinal parasites with direct and/or indirect life cycles, namely Eimeria spp., Ascaridia galli, Heterakis gallinarum and Capillaria spp., are responsible for the most frequent and heavy economic losses in aviculture. The current review aimed to collect information about gastrointestinal parasites affecting poultry, as well as, research studies regarding parasitic diseases in free-range chicken production. From the references used in this review, 20% highlight research studies correlating prevalence of gastrointestinal parasites in free-range chickens and factors such as the production system, age and animal density, hygienic conditions and weather. Coccidiosis is responsible for the major economic losses in poultry farms. Diseases have different clinical signs and result in variable impacts on animals. Control programs include mainly vaccination, anti-coccidia and anthelminthic drugs, as well as, house cleaning and disinfection. This review concluded that coccidia and helminths are a global threat to free-range poultry production. More research in this area is necessary in order to understand the major factors influencing the prevalence of parasitic diseases in this type of poultry production. Also the search for new control strategies must be a priority, mainly using natural antiparasitic compounds and biological control approaches.info:eu-repo/semantics/publishedVersio

ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding

ChIP-on-chip technology provides a genome-scale view of transcription factor (TF)/target interactions and a systems level window into transcriptional regulatory networks. However, while many studies have used ChIP-on-chip data to effectively discover new TF targets, statistical methods have fallen short of developing an accurate model to disassociate signals caused by experimental noise from those caused by true biological variation, thus leveraging the technology to provide high confidence predictions of the full range of interactions

Acetylcholine Neurotransmitter Receptor Densities in the Striatum of Hemiparkinsonian Rats Following Botulinum Neurotoxin-A Injection

Cholinergic neurotransmission has a pivotal function in the caudate-putamen, and is highly associated with the pathophysiology of Parkinson's disease. Here, we investigated long-term changes in the densities of the muscarinic receptor subtypes M1, M2, M3 (mAchRs) and the nicotinic receptor subtype α4β2 (nAchRs) in the striatum of the 6-OHDA-induced hemiparkinsonian (hemi-PD) rat model using quantitative in vitro receptor autoradiography. Hemi-PD rats exhibited an ipsilateral decrease in striatal mAchR densities between 6 and 16%. Moreover, a massive and constant decrease in striatal nAchR density by 57% was found. A second goal of the study was to disclose receptor-related mechanisms for the positive motor effect of intrastriatally injected Botulinum neurotoxin-A (BoNT-A) in hemi-PD rats in the apomorphine rotation test. Therefore, the effect of intrastriatally injected BoNT-A in control and hemi-PD rats on mAchR and nAchR densities was analyzed and compared to control animals or vehicle-injected hemi-PD rats. BoNT-A administration slightly reduced interhemispheric differences of mAchR and nAchR densities in hemi-PD rats. Importantly, the BoNT-A effect on striatal nAchRs significantly correlated with behavioral testing after apomorphine application. This study gives novel insights of 6-OHDA-induced effects on striatal mAchR and nAchR densities, and partly explains the therapeutic effect of BoNT-A in hemi-PD rats on a cellular level

Long-term survey of Eimeria spp. prevalence and faecal shedding in a traditional Portuguese free-range broiler farm

In free-range broiler production, animals are highly exposed to gastrointestinal parasitism, namely by coccidia, due to their long contact with the outdoor environment. Also, the prevalence of gastrointestinal parasites in extensive poultry production, is frequently influenced by biotic and abiotic factors. The current national pioneer long-term survey aimed to assess the prevalence and faecal shedding of Eimeria spp. oocysts in a traditional Portuguese free-range broiler farm, on different production conditions. Between July 2018 and March 2019, a total of 350 faecal samples were collected from different groups of free-range broilers at the fattening phase, in a poultry farm located in North-western Lisbon district, Portugal. Quantitative and qualitative coprological techniques were performed, aiming to quantify the Eimeria spp. prevalence and faecal shedding level. Coccidia prevalence was higher in Summer and Autumn groups (72% and 80%, respectively), although faecal shedding levels were higher in the Autumn and Winter groups (1191 and 1562 Oocysts Per Gram, OPG). Animals showed clinical signs of coccidiosis during the survey, especially in Autumn’s 1st sampling, in which 42% of the faecal samples had blood. The lack of sanitary depopulations, length of the fattening phase (1 month), short pre-patent period of coccidia, exposure to different environmental conditions and irregular drug treatments with amprolium, were key factors responsible for the different parasitic scenarios observed during this survey.info:eu-repo/semantics/publishedVersio

CUTLL1, a novel human T-cell lymphoma cell line with t(7;9) rearrangement, aberrant NOTCH1 activation and high sensitivity to c-secretase inhibitors

Activating mutations in NOTCH1 are present in over 50% of human T-cell lymphoblastic leukemia (T-ALL) samples and inhibition of NOTCH1 signaling with c-secretase inhibitors (GSI) has emerged as a potential therapeutic strategy for the treatment of this disease. Here, we report a new human T-cell lymphoma line CUTLL1, which expresses high levels of activated NOTCH1 and is extremely sensitive to c-secretase inhibitors treatment. CUTLL1 cells harbor a t(7;9)(q34;q34) translocation which induces the expression of a TCRB-NOTCH1 fusion transcript encoding a membrane-bound truncated form of the NOTCH1 receptor. GSI treatment of CUTLL1 cells blocked NOTCH1 processing and caused rapid clearance of activated intracellular NOTCH1. Loss of NOTCH1 activity induced a gene expression signature characterized by the downregulation of NOTCH1 target genes such as HES1 and NOTCH3. In contrast with most human T-ALL cell lines with activating mutations in NOTCH1, CUTLL1 cells showed a robust cellular phenotype upon GSI treatment characterized by G1 cell cycle arrest and increased apoptosis. These results show that the CUTLL1 cell line has a strong dependence on NOTCH1 signaling for proliferation and survival and supports that T-ALL patients whose tumors harbor t(7;9) should be included in clinical trials testing the therapeutic efficacy NOTCH1 inhibition with GSIs. Leukemia (2006) 20, 1279–1287. doi:10.1038/sj.leu.2404258; published online 11 May 200

ParMap, an algorithm for the identification of small genomic insertions and deletions in nextgen sequencing data

<p>Abstract</p> <p>Background</p> <p>Next-generation sequencing produces high-throughput data, albeit with greater error and shorter reads than traditional Sanger sequencing methods. This complicates the detection of genomic variations, especially, small insertions and deletions.</p> <p>Findings</p> <p>Here we describe ParMap, a statistical algorithm for the identification of complex genetic variants, such as small insertion and deletions, using partially mapped reads in nextgen sequencing data.</p> <p>Conclusions</p> <p>We report ParMap's successful application to the mutation analysis of chromosome X exome-captured leukemia DNA samples.</p

The BCL2A1 gene as a pre–T cell receptor–induced regulator of thymocyte survival

The pre–T cell receptor (TCR) is expressed early during T cell development and imposes a tight selection for differentiating T cell progenitors. Pre-TCR–expressing cells are selected to survive and differentiate further, whereas pre-TCR− cells are “negatively” selected to die. The mechanisms of pre-TCR–mediated survival are poorly understood. Here, we describe the induction of the antiapoptotic gene BCL2A1 (A1) as a potential mechanism regulating inhibition of pre–T cell death. We characterize in detail the signaling pathway involved in A1 induction and show that A1 expression can induce pre–T cell survival by inhibiting activation of caspase-3. Moreover, we show that in vitro “knockdown” of A1 expression can compromise survival even in the presence of a functional pre-TCR. Finally, we suggest that pre-TCR–induced A1 overexpression can contribute to T cell leukemia in both mice and humans