157 research outputs found
A needle in a haystack: tracing bivalve-associated viruses in high-throughput transcriptomic data
No full textBivalve mollusks thrive in environments rich in microorganisms, such as estuarine and coastal waters, and they tend to accumulate various particles, including viruses. However, the current knowledge on mollusk viruses is mainly centered on few pathogenic viruses, whereas a general view of bivalve-associated viromes is lacking. This study was designed to explore viral abundance and diversity in bivalve mollusks using transcriptomic datasets. Analyzing RNA-seq data of 58 bivalve species, we have reconstructed 26 nearly complete and over 413 partial RNA virus genomes. Although 96.4 % of the predicted viral proteins refer to new viruses, some sequences belong to viruses associated to bivalve species or other marine invertebrates. We considered short non-coding RNAs (sncRNA) and post-transcriptional modifications occurring specifically on viral RNAs as tools for virus host-assignment. We could not identify virus-derived small RNAs in sncRNA reads obtained from the oyster sample richest in viral reads. SNP analysis revealed 938 A-to-G substitutions occurring on the 26 identified RNA viruses, preferentially impacting the AA di-nucleotide motif. Under-representation analysis revealed that the AA motif is under-represented in these bivalve-associated viruses. These findings improve our understanding of bivalve viromes and set the stage for targeted investigations on the specificity and dynamics of identified viruses
Author response
No full textDetecting pathogens and mounting immune responses upon infection is crucial for animal health. However, these responses come at a high metabolic price (McKean and Lazzaro, 2011, Kominsky et al., 2010), and avoiding pathogens before infection may be advantageous. The bacterial endotoxins lipopolysaccharides (LPS) are important immune system infection cues (Abbas et al., 2014), but it remains unknown whether animals possess sensory mechanisms to detect them prior to infection. Here we show that Drosophila melanogaster display strong aversive responses to LPS and that gustatory neurons expressing Gr66a bitter receptors mediate avoidance of LPS in feeding and egg laying assays. We found the expression of the chemosensory cation channel dTRPA1 in these cells to be necessary and sufficient for LPS avoidance. Furthermore, LPS stimulates Drosophila neurons in a TRPA1-dependent manner and activates exogenous dTRPA1 channels in human cells. Our findings demonstrate that flies detect bacterial endotoxins via a gustatory pathway through TRPA1 activation as conserved molecular mechanism.sponsorship: Vlaams Instituut voor Biotechnologie Alessia Soldano Luis Franco Guangda Liu Natalia Mora Emre Yaksi Bassem A Hassanr Fonds Wetenschappelijk Onderzoek G.0702.12 Alessia Soldano Yeranddy A Alpizar Brett Boonen Alejandro Lopez-Requena Natalia Mora Thomas Voets Rudi Vennekens Bassem A Hassan Karel Talaverar Fonds Wetenschappelijk Onderzoek G.0077.15 Alessia Soldano Yeranddy A Alpizar Brett Boonen Alejandro Lopez-Requena Natalia Mora Thomas Voets Rudi Vennekens Bassem A Hassan Karel Talaverar Fonds Wetenschappelijk Onderzoek G.0680.10 Alessia Soldano Yeranddy A Alpizar Brett Boonen Alejandro Lopez-Requena Natalia Mora Thomas Voets Rudi Vennekens Bassem A Hassan Karel Talaverar Fonds Wetenschappelijk Onderzoek G.0681.10 Alessia Soldano Yeranddy A Alpizar Brett Boonen Alejandro Lopez-Requena Natalia Mora Thomas Voets Rudi Vennekens Bassem A Hassan Karel Talaverar Fonds Wetenschappelijk Onderzoek G.0503.12 Alessia Soldano Yeranddy A Alpizar Brett Boonen Alejandro Lopez-Requena Natalia Mora Thomas Voets Rudi Vennekens Bassem A Hassan Karel Talaverar Fonds Wetenschappelijk Onderzoek G.0654.15 Alessia Soldano Yeranddy A Alpizar Brett Boonen Alejandro Lopez-Requena Natalia Mora Thomas Voets Rudi Vennekens Bassem A Hassan Karel Talaverar Fonds Wetenschappelijk Onderzoek G.0761.10N Alessia Soldano Yeranddy A Alpizar Brett Boonen Alejandro Lopez-Requena Natalia Mora Thomas Voets Rudi Vennekens Bassem A Hassan Karel Talaverar Fonds Wetenschappelijk Onderzoek G.0596.12 Alessia Soldano Yeranddy A Alpizar Brett Boonen Alejandro Lopez-Requena Natalia Mora Thomas Voets Rudi Vennekens Bassem A Hassan Karel Talaverar Fonds Wetenschappelijk Onderzoek G.0565.07 Alessia Soldano Yeranddy A Alpizar Brett Boonen Alejandro Lopez-Requena Natalia Mora Thomas Voets Rudi Vennekens Bassem A Hassan Karel Talaverar KU Leuven GOA/14/011 Alessia Soldano Yeranddy A Alpizar Brett Boonen Luis Franco Alejandro Lopez-Requena Guangda Liu Natalia Mora Emre Yaksi Thomas Voets Rudi Vennekens Bassem A Hassan Karel Talaverar European Commission IUAP P7/13 Alessia Soldano Yeranddy A Alpizar Brett Boonen Luis Franco Alejandro Lopez-Requena Guangda Liu Natalia Mora Emre Yaksi Thomas Voets Rudi Vennekensr KU Leuven OT/12/091 Alessia Soldano Yeranddy A Alpizar Brett Boonen Luis Franco Alejandro Lopez-Requena Guangda Liu Natalia Mora Emre Yaksi Thomas Voets Rudi Vennekens Bassem A Hassan Karel Talaverar KU Leuven PF-TRPLe Alessia Soldano Yeranddy A Alpizar Brett Boonen Luis Franco Alejandro Lopez-Requena Guangda Liu Natalia Mora Emre Yaksi Thomas Voets Rudi Vennekens Bassem A Hassan Karel Talavera (Vlaams Instituut voor Biotechnologie, Fonds Wetenschappelijk Onderzoek|G.0702.12, Fonds Wetenschappelijk Onderzoek|G.0077.15, Fonds Wetenschappelijk Onderzoek|G.0680.10, Fonds Wetenschappelijk Onderzoek|G.0681.10, Fonds Wetenschappelijk Onderzoek|G.0503.12, Fonds Wetenschappelijk Onderzoek|G.0654.15, Fonds Wetenschappelijk Onderzoek|G.0761.10N, Fonds Wetenschappelijk Onderzoek|G.0596.12, KU Leuven|GOA/14/011, KU Leuven|OT/12/091, European Commission|IUAP P7/13, KU Leuven PF-TRPLe)status: Publishe
The Impact of Environmental Factors on the Physiology of the Atlantic surfclam, Spisula solidissima
No full textThe Atlantic surfclam supports a multi-million dollar fishery in New York. Between 2002 and 2008, surfclam abundance in New York State waters along the south shore of Long Island has decreased by 63% in biomass and 75% in the total number of clams. Population age structure has drastically shifted since 2002 indicating the lack of recruitment. Only 3% of the population was made up of clams that were 6 years old and younger in 2006, compared to 21% in 2002. In 2008, 15% of the population was composed of clams less than 6 years in age. It is hypothesized that increased temperatures in recent years has caused stress in these animals, negatively impacting their physiology leading to a reduction in population size.Studies were conducted on surfclam energy balance, scope for growth and immune function to investigate the impact of temperature on the physiology of these animals. Results suggest energy reserves are used differently during warm and cooler years, which may impact survival and reproductive success. Further studies on scope for growth indicate an increased metabolic demand at 23øC compared to 19øC. Results also demonstrated a reduction in filtration rate at 23øC compared to 19øC which could cause an energetic imbalance during the critical period following spawning. Furthermore, short term energy usage was greater at 23øC, and data from immune defense studies imply surfclams are immuno-compromised at this temperature. These results strongly suggest that stressful summer temperatures negatively influence surfclam physiology.Advisor(s): Bassem Allam. Committee Member(s): Emmanuelle Pales Espinosa; Robert M. Cerrato; Kamazima M.M. Lwiza.Stony Brook University Libraries. SBU Graduate School in Department of Marine and Atmospheric Science. Lawrence Martin (Dean of Graduate School)
The Influence of Pallial Mucus from the Oyster, Crassostrea virginica, on the Virulence of its Pathogenic Alveolate, Perkinsus marinus.
No full textPerkinsus marinus, a protistan parasite of the Eastern oyster (Crassostrea virginica), has been a contributing factor to the severe decline of farmed and wild oysters on the East Coast of the United States and the Gulf of Mexico. Recent findings suggest that the pallial organs (mantle, gills) of the Eastern oyster are an important portal of entry for the parasite. In this case, the first contact P. marinus has with its host takes place in mucus covering the mantle and gill tissue. This study consisted of several experiments to investigate the effect of oyster pallial mucus on the growth, expression of virulence genes (pmSOD1, pmSOD2 and pmSUB), protease production and infectivity of P. marinus. In each experiment, P. marinus grown in pallial mucus (mantle, gill or both) was compared to P. marinus grown in media supplemented with seawater (control) and other experimental media such as oyster plasma or digestive extracts since the digestive tract is traditionally considered as the main portal of entry for the parasite. P. marinus grown in media supplemented with mantle mucus showed a significantly higher growth rate than cultures added with other supplemental extracts, while cultures grown in gill mucus promoted a higher protease production. No differences were noted in the expression of virulence-related genes between cultures supplemented with mantle or gill mucus as compared to those added with seawater, however those grown in digestive extract or plasma showed a down-regulation compared to control (seawater) cultures. Lastly, challenge experiments showed that parasite cultures grown in pallial mucus caused severe early mortality of oysters coupled with high infection intensities, whereas oysters injected with cultures grown in seawater showed minimal mortalities and no mortalities were found in oysters injected with cultures supplemented with digestive extract during the four week experiment. These results demonstrate that oyster mucus plays a significant role in the pathogenesis of P. marinus by enhancing the proliferation and the infectivity of this devastating parasite.Advisor(s): Bassem Allam. Committee Member(s): Mark Fast; Emmanuelle Pales Espinosa.Stony Brook University Libraries. SBU Graduate School in Department of Marine and Atmospheric Science. Lawrence Martin (Dean of Graduate School)
Les plages de Beyrouth : privatisation et communautarisation d’espaces publics
No full textBeirut beaches appeared on the western side of the city, which was once the most cosmopolitan district. The author describes these public spaces and the way of life prior to the war. He also considers the main evolutions that took place through the war period.El-Jisr Bassem. Les plages de Beyrouth : privatisation et communautarisation d’espaces publics. In: Reconstruire Beyrouth. Les paris sur le possible
Investigation of factors involved in the interaction between Quahog Parasite Unknown (QPX) and its host, the hard clam Mercenaria mercenaria
No full textQPX (Quahog parasite unknown) is a protistan parasite affecting the hard clam Mercenaria mercenaria along the Northeastern coast of the United States. The geographic distribution and occurrence of disease epizootics suggests the involvement of environmental parameters and host genotype in disease development. Field investigations and laboratory transmission studies revealed some variations in the susceptibility of different hard clam stocks to QPX infection. Histological observations demonstrated that clams mount marked inflammatory responses against the infection that can sometimes lead to the healing of infected individuals. This study investigated host-pathogen interactions in QPX disease by studying individual components of the tripartite interaction: The pathogen, the host and the environment. Methods were developed to investigate virulence factors of the parasite QPX. Constitutive defense factors and immune response to QPX challenge in hard clams exhibiting different susceptibility to the parasite were also assessed using cellular, biochemical and molecular approaches. Finally, integrative approaches were used to determine the effect of environmental parameters (temperature, salinity, dissolved oxygen) on constitutive and QPX-induced clam defenses as well as on QPX itself. Results demonstrated that QPX produces virulence factors that are cytotoxic to M. mercenaria hemocytes. QPX cytotoxicity appears to be induced by clam factors and QPX extracellular products modulated host response against the parasite. In vitro growth of QPX was significantly reduced at temperatures above and below optimal levels ranging from 20 øC to 23 øC. QPX appeared to tolerate a wide range of salinities (22 to 37 psu) and parasite growth was only significantly affected at very low salinity (15 psu). Different QPX isolates displayed various levels of cytotoxicity against clam hemocytes and had different temperature optima supporting previous studies suggesting the existence of different QPX strains. This study also demonstrated the presence of constitutive compounds in clam tissues that significantly inhibited (mantle, gills) or stimulated (adductor muscle) QPX growth in vitro. Difference in anti-QPX activity was also observed in plasma from different clam populations and was associated to their respective susceptibility to QPX. Molecular investigations of clam response to QPX led to the identification of several stress- and defense-related genes such as ferritin, metallothionein, defensins, lectins and a thioester-containing protein (or TEP). Components of signaling pathways (such as NF-kB) were also characterized and their transcriptional regulation was correlated to the abundance of some humoral transcripts. Further investigation of the modulation of hemolymph parameters and transcriptional regulation of ferritin and metallothionein during bacterial and QPX challenge indicated difference in clam response according to the challenge. Similarly, comparison of host response among QPX-resistant and. susceptible clam broodstocks exhibited significant difference. Effective response of resistant clams against QPX led to the elimination of the parasite and the restoration of constitutive defense status whereas susceptible clams exhibited a strong modulation characterized by an acute phase response but appeared less effective to eliminate QPX after 28 days. Finally, results demonstrated significant effect of temperature and salinity on clam constitutive defenses and also on host. pathogen interaction and QPX disease dynamics. For instance, low temperature (13 øC) impeded clam defenses causing QPX disease development whereas changes in hemolymph parameters among QPX-infected clams maintained at 21 øC were related to significant healing processes. Higher QPX-associated mortality was also observed in infected clams maintained at high salinity (30 psu) compared to 15 psu. Overall, this study provided essential insights on QPX virulence, M. mercenaria defenses and effects of environmental parameters on host. pathogen interactions and provided perspectives for the remediation of QPX disease. The results not only improved our knowledge of cellular and molecular pathways involved during QPX disease, but also generated important information on M. mercenaria defenses, and enhanced our understanding of invertebrate immunity in general. Generated molecular information significantly enhanced public databases and allowed the development of new tools for the investigation of M. mercenaria transcriptome.Advisor(s): Bassem Allam. Committee Member(s): Anne E. McElroy; Jackie L. Collier; Mark D. Fast; Susan E. Ford; Arnaud TanguyStony Brook University Libraries. SBU Graduate School in Department of Marine and Atmospheric Science. Lawrence Martin (Dean of Graduate School)
Academic freedom at Palestinian universities : a human rights report
No full textBassem Eid traces the history of Palestinian Universities over three
periods - the Israeli occupation early 1970s until the Intifada, the
Intifada and its aftermath and the current era. The author examines
the serious problems and restrictions faced by University students
and intellectuals. He denounces a series of human rights violations
particularly the rights of freedom of expression and association. Such
violations include deportations, violence against students, arrests and
detentions without formal charges and unfair dismissal of professors
who spoke their minds. These human rights violations are not solely
a result of Israeli oppression but also a result of the interference of
the Palestinian Authority. The author probes into the University
Security Administration and the presence of undercover agents
within the universities, who monitor and report the activities of
individuals, are associated with the Islamic bloc or who criticise the
Palestinian Authority.peer-reviewe
Characterization of Cuticular and Hemolymph Associated Defense Parameters in Shell Diseased Lobsters
No full textStony Brook University Libraries.
Department of
Lawrence Martin (Dean of Graduate School), Anne McElroy – Thesis Advisor
Associate Professor
School of Marine and Atmospheric Sciences, Bassem Allam – Thesis Advisor
Assistant Professor
School of Marine and Atmospheric Sciences, Mark Fast
Assistant Professor
School of Marine and Atmospheric Sciences
Seawater carbonate chemistry and larval viability, size, development, and shell mineralization of the eastern oyster (Crassostrea virginica)
No full textCalcifying marine organisms, including the eastern oyster (Crassostrea virginica), are vulnerable to ocean acidification (OA) because it is more difficult to precipitate calcium carbonate (CaCO3). Previous investigations of the molecular mechanisms associated with resilience to OA in C. virginica demonstrated significant differences in single nucleotide polymorphism and gene expression profiles among oysters reared under ambient and OA conditions. Converged evidence generated by both of these approaches highlighted the role of genes related to biomineralization, including perlucins. Here, gene silencing via RNA interference (RNAi) was used to evaluate the protective role of a perlucin gene under OA stress. Larvae were exposed to short dicer-substrate small interfering RNA (DsiRNA-perlucin) to silence the target gene or to one of two control treatments (control DsiRNA or seawater) before cultivation under OA (pH ~7.3) or ambient (pH ~8.2) conditions. Two transfection experiments were performed in parallel, one during fertilization and one during early larval development (6 h post-fertilization), before larval viability, size, development, and shell mineralization were monitored. Silenced oysters under acidification stress were the smallest, had shell abnormalities, and had significantly reduced shell mineralization, thereby suggesting that perlucin significantly helps larvae mitigate the effects of OA
Corrections to “D2D-V2X-SDN: Taxonomy and Architecture Towards 5G Mobile Communication”
No full textIn the above article [1], the following author bios must be updated as their posts and positions were upgraded, and the profile picture of Bassem F. Felemban was previously incorrect.Scopu
- …
