Whole genome sequencing of marine organisms by Oxford Nanopore Technologies: Assessment and optimization of HMW-DNA extraction protocols

Marine habitats are Earth's largest aquatic ecosystems, yet little is known about marine organism's genomes. Molecular studies can unravel their genetics print, thus shedding light on specie's adaptation and speciation with precise authentication. However, extracting high molecular weight DNA from marine organisms and subsequent DNA library preparation for whole genome sequencing is challenging. The challenges can be explained by excessive metabolites secretion that co-precipitates with DNA and barricades their sequencing. In this work, we sought to resolve this issue by describing an optimized isolation method and comparing its performance with the most commonly reported protocols or commercial kits: SDS/phenol–chloroform method, Qiagen Genomic Tips kit, Qiagen DNeasy Plant mini kit, a modified protocol of Qiagen DNeasy Plant kit, Qiagen DNeasy Blood and Tissue kit, and Qiagen Qiamp DNA Stool mini kit. Our method proved to work significantly better for different marine species regardless of their shape, consistency, and sample preservation, improving Oxford Nanopore Technologies sequencing yield by 39 folds for Spirobranchus sp. and enabling generation of almost 10 GB data per flow cell/run for Chrysaora sp. and Palaemon sp. samples

Molecular investigation of waterborne protozoan contamination using marine Demospongiae

Sponges play important role within aquatic ecosystems due to their diverse abilities including filter-based feeding mechanisms. Hence, this study evaluated the potential use of sponges as ecological biomonitors for water safety surveillance, especially in the presence of Waterborne protozoan pathogens WBPP. Sponge specimens were collected from different Qatari marine ecosystems and subjected to gDNA extraction and real-time PCR using specific primer sets for the most common WBPP. Two sponges from the coastal marine ecosystems were found to be positive for Blastocystis sp., and one sponge was positive for Dientamoeba fragilis within offshore site. No Cryptosporidium spp., Giardia duodenalis, nor Toxoplasma gondii were detected. Further genotyping analysis revealed that the Blastocystis sp. positive samples were subtype ST3 (allele 34), which matched local clinical isolates and D. fragilis specimen was unambiguously clustering with Genotype 2. In conclusion, this study demonstrates the role of marine sponges as ecological biomonitors for WBPP screening and provide insights into these pathogens widespread and their potential transmission to marine and terrestrial organisms including human

Self-Mating in the Definitive Host Potentiates Clonal Outbreaks of the Apicomplexan Parasites Sarcocystis neurona and Toxoplasma gondii

Tissue-encysting coccidia, including Toxoplasma gondii and Sarcocystis neurona, are heterogamous parasites with sexual and asexual life stages in definitive and intermediate hosts, respectively. During its sexual life stage, T. gondii reproduces either by genetic out-crossing or via clonal amplification of a single strain through self-mating. Out-crossing has been experimentally verified as a potent mechanism capable of producing offspring possessing a range of adaptive and virulence potentials. In contrast, selfing and other life history traits, such as asexual expansion of tissue-cysts by oral transmission among intermediate hosts, have been proposed to explain the genetic basis for the clonal population structure of T. gondii. In this study, we investigated the contributing roles self-mating and sexual recombination play in nature to maintain clonal population structures and produce or expand parasite clones capable of causing disease epidemics for two tissue encysting parasites. We applied high-resolution genotyping against strains isolated from a T. gondii waterborne outbreak that caused symptomatic disease in 155 immune-competent people in Brazil and a S. neurona outbreak that resulted in a mass mortality event in Southern sea otters. In both cases, a single, genetically distinct clone was found infecting outbreak-exposed individuals. Furthermore, the T. gondii outbreak clone was one of several apparently recombinant progeny recovered from the local environment. Since oocysts or sporocysts were the infectious form implicated in each outbreak, the expansion of the epidemic clone can be explained by self-mating. The results also show that out-crossing preceded selfing to produce the virulent T. gondii clone. For the tissue encysting coccidia, self-mating exists as a key adaptation potentiating the epidemic expansion and transmission of newly emerged parasite clones that can profoundly shape parasite population genetic structures or cause devastating disease outbreaks

7th Drug hypersensitivity meeting: part two

No abstract availabl

Optimized DNA Extracting Method for Oxford Nanopore- Long reads Sequencing from Marine samples

Sustaining social and economic growth is impossible without a holistic environmental vision that places environmental preservation for Qatar's future generations at the forefront. According to the ministry of development and panning and statistics, the Qatar National Vision (QNV) 2030 aims to direct Qatar towards a balance between developmental needs and the protection of its natural environment, whether land, sea or air. As such, the QNV 2030 includes an emphasis on establishing an environmental institutions that can serve as the guardians of Qatar's environmental heritage. The QNV 2030 also emphasizes the importance of increasing citizens' awareness of their role in protecting the country's environment for their children and the nation's future generations. The State of Qatar has chosen to pursue the path of sustainable development, making it the focus of the Qatar National Development Strategy. Given the large-scale industrialization and the limited land availability, the urban environment will be crucial in maintaining native species. The presence of heavy petrochemical firms in Qatar necessitate stressing on researches related to biomonitoring of environmental ecosystem with the aim to understand and provide impactful solution for different environmental challenges affecting Qatari health, and damages local ecosystem. Due to the extreme temperatures and salinities in the gulf region, the national biodiversity has adapted to survive under extreme conditions. Furthermore, the barriers that isolates the ARABIAN GULF HAS CREATED AN ENVIRONMENT THAT IS RICH WITH ENDEMIC SPECIES THAT ARE SPECIFIC TO THE REGION. As such this project aimed to cover the gap in the genomic analysis of Qatar's rich environment. The goal was to decipher the genetic background of different animal species, marine and environmental species specific to the Qatari environmental landscape that has been previously been described by Qatar University's environmental science center. The study also deciphered the microflora in marine environment that is an important building block of the environment and an indicator of its richness. The outcomes from this study is to help in preservation of important species in Qatar and will guide the establishment of a national genomic habitat platform in Qatar

Molecular identification and characterization of Cryptosporidium spp. among pediatric and food-handlers subjects in Qatar

World Health Organization (WHO) has identified Cryptosporidium spp. as globally the most common diarrhea-causing protozoan. Its transmission occurs mainly through ingestion of water or food contaminated with the feces of an infected human or animal. Infected food handlers are also a major Cryptosporidium contamination risk. A wide diversity of Cryptosporidium spp. and subtypes infect humans and due to the host specificity of each species, the use of molecular techniques and genotyping of subject’s stool samples will help in identifying contamination source. Molecular prevalence was investigated using real-time PCR targeting a 214 base pairs fragment of 18s-rRNA. The analyzed populations consist of hospitalized diarrheic pediatrics and asymptomatic food handlers. The positive samples by RT-PCR were subjected to species identification by PCR-RFLP and GP60 gene sequencing. The parasite was detected by RT-PCR in 15% of the children and 4% of the food-handlers. Genotyping of Cryptosporidium spp. revealed a predominance of Cryptosporidium parvum. Sequence analysis of the GP60 locus in the present study has identified only C. parvum subtype family IId with mostly the IIdA20G1 subtype among the two populations. This study provides supplementary information for implementing prevention and control strategies to reduce the burden of these pediatric protozoan infections.This study was funded by the Qatar National Research Fund (QRNF) at Qatar Foundation through the National Priorities Research Program (Project No. NPRP8-1556-3-313)

Cross-cultural validation of the short form of the physical self-inventory (PSI-S).

The study examined the cross-cultural validity of the short form of the Physical Self-Inventory (PSI-S) among samples of adolescents speaking French, Dutch, Turkish, Italian, and Arab. A total of 4,867 adolescents (1,173 Belgian Flemish, 598 French, 1,222 Italian, 643 Turkish, 646 Kuwaiti, and 585 Tunisian) completed the original PSI-S version, and a revised version including a positively worded reformulation of the 3 negatively worded PSI-S items. The results supported the factor validity and reliability of revised PSI-S version across all cultural groups, and its superiority when compared to the original version. Compared with confirmatory factor analyses, relying on an exploratory structural equation modeling measurement model resulted in superior solution, and in more cleanly differentiated factors. PSI-S responses proved to be fully invariant across cultural groups, and presented no evidence of differential item functioning as a function of age, gender, body mass index (BMI), and sport involvement. However, the results revealed meaningful mean level differences as a function of gender, age, sport involvement, and BMI that were mostly consistent with the results from previous studies