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Identificazione di marcatori molecolari per la resistenza alla fotobatteriosi nell'orata di allevamento (Sparus aurata)
Full text linkFish photobacteriosis is an infectious disease that affects several fish species living in marine temperate waters. Its causative agent is the Gram-negative bacterium Photobacterium damselae subsp. piscicida (Phdp). Fish photobacteriosis represents a serious health problem for the majority of intensive sea bream hatcheries, with 90–100% mortality during disease outbreaks. Larvae and juveniles are the most susceptible stages. A potential strategy to prevent fish photobacteriosis is to select for animals that are genetically resistant to it. Resistance to Phdp infection has low medium hereditabilty (0.12-0.45) and it is costly to measure, thus the best option for selective breeding is marked assisted selection. Aim of this work is to identify genetic loci involved in disease resistance in the gilthead sea bream (Sparus aurata) through an integrated genomic approach.
A QTL analysis for resistance to photobacteriosis was carried out on an experimental population of 500 offspring, originating from eight sires and six dams in a single mass-spawning event and experimentally infected with Phdp. A total of 151 microsatellite loci were genotyped in the experimental population, and half-sib regression QTL analysis was carried out on two continuous traits, body length at time of death and survival, and for two binary traits, survival at day 7 and survival at day 15, when the highest peaks of mortality were observed. Two significant QTLs were detected for disease resistance. The first one was located on linkage group LG3 affecting late survival (survival at day 15). The second one, for overall survival, was located on LG21, which allowed us to highlight a potential marker (Id13) linked to disease resistance. A significant QTL was also found for body length at death on LG6 explaining 5-8% of the phenotypic variation.
Microarray-based experiments were used to analyse changes at the transcriptome level upon Phdp experimental infection in sea bream juvenile head kidney. An update of the oligo-DNA microarray developed by Ferraresso et al. (2008) was produced by adding 6,412 novel unique transcripts. Statistical analysis identified 293 transcripts significantly up-regulated and 123 transcripts down-regulated leading to an infection response mainly associated to the more immediate innate immune system. It was observed, however, a significant predominance of anti-inflammatory mediators/signals, which help controlling excessive collateral damage to host tissue and cells due to host response, but, in so doing, might also reduce the effectiveness of immune mechanisms responsible for the clearance of the pathogen. Independent testing of a selection of differentially expressed genes with real-time RT-PCR confirmed microarray results.
Differentially expressed genes based on microarray analysis were mapped onto the stickleback genome, to find a possible co-localization of the loci contributing to disease resistance or susceptibility. These genes, which putatively co-localize with genome-wide significant QTLs, represent a starting point to refine the candidate regions for the already identified QTLs and might constitute potential markers for the implementation of selective breeding programs for photobacteriosis resistance.La fotobatteriosiosi ittica, causata dal batterio Gram negativo Photobacterium damselae subsp. piscicida (Phdp), è una patologia infettiva che colpisce diverse specie di pesci che vivono in acque marine temperate. La fotobatteriosi rappresenta un reale problema sanitario per gran parte degli allevamenti intesivi di orata (Sparus aurata), con tassi di mortalità che possono raggiungere il 90-100%; gli stadi larvali e giovanili sono i più suscettibili all’infezione. Una possibile strategia per prevenire la patologia prevede la selezione di animali geneticamente resistenti a essa. La resistenza alla fotobatteriosi presenta un’ereditabilità medio bassa (0.12-0.45) e la sua stima risulta dispendiosa, di conseguenza, la strategia migliore per l’attuazione di programmi di miglioramento genetico per questo tratto è la selezione assistita da marcatori. Scopo di questo progetto è l’identificazione di loci genetici coinvolti nella determinazione della resistenza all’infezione in orata, mediante un approccio genomico integrato. Un’analisi di QTL per la resistenza alla fotobatteriosi è stata effettuata considerando una popolazione di 500 individui, generati da 8 maschi e 5 femmine, infettati sperimentalmente con Phdp e genotipizzati utilizzando 151 loci microsatelliti. I dati ottenuti sono stati elaborati attraverso un’analisi di regressione half-sib per due caratteri con distribuzione continua, la lunghezza al momento del decesso e la saprovvivenza, e per due caratteri binari, la sopravvivenza al giorno 7 e al giorno 15, associati ai maggiori picchi di mortalità. Per la resistenza alla fotobatteriosi sono stati identificati due QTL significativi. Il primo, coinvolto nella sopravvivenza al giorno 15, è stato associato al LG3. Il secondo, per la sopravvivenza al termine del challenge, è stato collocato nel LG21, per cui è stato possibile anche identificare un potenziale marcatore (Id13) associato alla resistenza alla patologia. Per la lunghezza al momento del decesso è stato individuato un QTL significativo nel LG6, in grado di spiegare il 5-8% della varianza fenotipica. La tecnologia microarray è stata impiegata per analizzare i cambiamenti a livello trascrizionale nel rene cefalico di orate sottoposte a un’infezione sperimentale con Phdp. La piattaforma microarray a oligonucleotidi, sviluppata da Ferraresso e colleghi (2008), è stata aggiornata aggiungendo 6412 nuovi trascritti unici. Le analisi statistiche dei dati di espressione hanno identificato 293 trascritti significativamente sovraespressi e 123 trascritti significativamente sottoespressi, associati a una risposta all’infezione che coinvolge principalmente i più immediati meccanismi del sistema immunitario innato. È stata rilevata, inoltre, una significativa predominanza di molecole antinfiammatorie che aiutano a controllare gli eccessivi danni collaterali ai tessuti dovuti alla risposta dell’ospite, ma così facendo, porterebbero anche a una riduzione dell’efficacia dei meccanismi immunitari responsabili dell’eliminazione del patogeno. I saggi di espressione in Real time RT-PCR hanno confermato i risultati di microarray. I geni differenzialmente espressi sono stati localizzati nel genoma di Gasterosteus aculeatus, per trovare una possibile co-localizzazione dei loci che contribuiscono alla resistenza all’infezione o alla suscettibilità. Questi geni, che apparentemente si collocano nelle stesse regioni dei QTL significativi, rappresentano un punto di partenza per raffinare la localizzazione dei QTL qui identificati e potrebbero raprresentare dei potenziali marcatori per la selezione di linee di animali maggiormente resistenti alla fotobatterios
Evaluation of real-time PCR assays for detection and quantification of fraudulent addition of bovine milk to caprine and ovine milk for cheese manufacture
No full textMany typical Italian cheeses made from ovine milk are certified as Protected Designation of Origin (PDO). Because caprine and ovine milk production is limited, the fraudulent addition of cows' milk is widespread. In addition, some compounds in bovine milk have high allergenic potential; therefore, such fraud also has implications for Consumer health. In this study, a real-time polymerase chain reaction (real-time PCR) test was developed to detect and quantify cow's milk in caprine and ovine cheeses, based on two target genes. The mitochondrial Cytochrome b gene (Cytb) of Has taurus was used to detect and quantify bovine DNA. The nuclear gene myostatin (Myo), nuclear ribosomal gene 18S, or mitochondrial gene 16S were used alternatively as universal reference markets. Caprine (n = 30) and ovine (it = 51) cheese samples were purchased and analyzed and most were shown to be contaminated by bovine milk. Pairwise analysis of quantification data using a Spearmann Rank Correlation test demonstrated a highly significant correlation between data obtained with the different reference assays
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
High mortality of juvenile gilthead sea bream (Sparus aurata) from photobacteriosis is associated with alternative macrophage activation and anti-inflammatory response: Results of gene expression profiling of early responses in the head kidney
No full textThe halophilic bacterium Photobacterium damselae subsp. piscicida (Phdp) represents a substantial health problem for several fish species in aquaculture. Bacteria that reside free and inside phagocytes cause acute and chronic forms of photobacteriosis. Infections of juveniles rapidly kill up to 90-100% fish. Factors underlying failure of the immune protection against bacteria remain largely unknown. The reported study used a transcriptomic approach to address this issue. juvenile sea breams (0.5 g) were challenged by immersion in salt water containing 2.89 x 10(8) CFU of a virulent Phdp and the head kidney was sampled after 24- and 48-h. Analyses were performed using the second version of a 44 k oligonucleotide DNA microarray that represents 19,734 sea bream unique transcripts and covers diverse immune pathways. Expression changes of selected immune genes were validated with qPCR. Results suggested rapid recognition of the pathogen, as testified by up-regulation of lectins and antibacterial proteins (bactericidal permeability-increasing protein lectins, lysozyme, intracellular and extracellular proteases), chemokines and chemokine receptors. Increased expression of proteins involved in iron and heme metabolism also could be a response against bacteria that are dependent on iron. However, negative regulators of immune/inflammatory response were preponderant among the up-regulated genes. A remarkable finding was the increased expression of IL-10 in concert with up-regulation of arginase I and II and proteins of the polyamine biosynthesis pathway that diverts the arginine flux from the production of reactive nitrogen species. Such expression changes are characteristic for alternatively activated macrophages that do not develop acute inflammatory responses. Immune suppression can be induced by the host to reduce tissue damages or by the pathogen to evade host response. (C) 2013 Elsevier Ltd. All rights reserved
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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