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First Insights into the Viral Communities of the Deep-sea Anoxic Brines of the Red Sea

Genomics, Proteomics & Bioinformatics 2015年第5期13卷 304-309页

作者： Andr Antunes Intikhab Alam marta filipa simoes Camille Daniels Ari J.S.Ferreira Rania Siam Hamza El-Dorry Vladimir B.Bajic Computational Bioscience Research Center (CBRC) ComputerElectrical and Mathematical Sciences and Engineering Division (CEMSE)King Abdullah University of Science and Technology (KAUST) Red Sea Research Center (RSRC) Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST) Biology Department American University in Cairo

The deep-sea brines of the Red Sea include some of the most extreme and unique envi- ronments on Earth. They combine high salinities with increases in temperature, heavy metals, hydrostatic pressure, and anoxic conditions, creating unique settings for thriving populations of novel extremophiles. Despite a recent increase of studies focusing on these unusual biotopes, their viral communities remain unexplored. The current survey explores four metagenomic datasets obtained from different brine-seawater interface samples, focusing specifically on the diversity of their viral communities. Data analysis confirmed that the particle-attached viral communities present in the brine-seawater interfaces were diverse and generally dominated by Candovirales, yet appearing distinct from sample to sample. With a level of caution, we report the unexpected finding of Phycodnaviridae, which infects algae and plants, and trace amounts of insect-infecting Iridoviridae. Results from Kebrit Deep revealed stratification in the viral communities present in the interface： the upper-interface was enriched with viruses associated with typical marine bacteria, while the lower-interface was enriched with haloviruses and halophages. These results provide first insights into the unexplored viral communities present in deep-sea brines of the Red Sea, represent- ing one of the first steps for ongoing and future sampling efforts and studies.

关键词： Viral diversity Metagenomics Brine-seawater interface Caudovirales Red Sea

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Soil and Rhizosphere Associated Fungi in Gray Mangroves(Avicennia marina) from the Red Sea—A Metagenomic Approach

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Genomics, Proteomics & Bioinformatics 2015年第5期13卷 310-320页

作者： marta filipa simoes Andr Antunes Cristiane A.Ottoni Mohammad Shoaib Amini Intikhab Alam Hanin Alzubaidy Noor-Azlin Mokhtar John A.C.Archer Vladimir B.Bajic Computational Bioscience Research Center (CBRC) ComputerElectrical and Mathematical Sciences and Engineering Division (CEMSE)King Abdullah University of Science and Technology (KAUST) Laboratório de Biotecnologia Industrial (LBI) Instituto de Pesquisas Tecnológicas do Estado de Sao Paulo (IPT)

Covering a quarter of the world＇s tropical coastlines and being one of the most threat- ened ecosystems, mangroves are among the major sources of terrestrial organic matter to oceans and harbor a wide microbial diversity. In order to protect, restore, and better understand these ecosystems, researchers have extensively studied their microbiology, yet few surveys have focused on their fungal communities, Our lack of knowledge is even more pronounced for specific fungal populations, such as the ones associated with the rhizosphere. Likewise, the Red Sea gray man- groves （Avicennia marina） remain poorly characterized, and understanding of their fungal commu- nities still relies on cultivation-dependent methods. In this study, we analyzed metagenomic datasets from gray mangrove rhizosphere and bulk soil samples collected in the Red Sea coast, to obtain a snapshot of their fungal communities. Our data indicated that Ascomycota was the dominant phylum （76%-85%）, while Basidiomycota was less abundant （14%-24~）, yet present in higher numbers than usually reported for such environments. Fungal communities were more stable within the rhizosphere than within the bulk soil, both at class and genus level. This finding is consistent with the intrinsic patchiness in soil sediments and with the selection of specific microbial commu- nities by plant roots. Our study indicates the presence of several species on this mycobiome that were not previously reported as mangrove-associated. In particular, we detected representatives of several commercially-used fungi, e.g., producers of secreted cellulases and anaerobic producers of cellulosomes. These results represent additional insights into the fungal community of the gray mangroves of the Red Sea, and show that they are significantly richer than previously reported.

关键词： Fungal diversity Ascomycota Basidiomycota Red Sea Metagenomics Bioinformatics

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Protected Areas, Subsistence Farming Systems and Nature Conservation

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Journal of Agricultural Science and Technology(A) 2012年第3期2卷 402-411页

作者： Luis Tiberio filipa Manso Ana marta-Costa Carlos Fonseca Aurora Monzon Department of Economics Sociology and Management University of Tr6s-os-Montes and Alto Douro Vila Real 5000-660 Portugal

The preservation of the traditional subsistence farming systems and the conservation of natural values （habitats, fauna and flora）, in articulation with local development, was the key issues in this paper. The farmers have been able to manage the systems so as to cope with adverse conditions, but their future is quite uncertain. The methodology included：（1） field observation visits and cartographic information analysis of land use; （2） structured interviews with animal production and agro-forestry specialists; and （3） meetings with the participation of stakeholders. The paper concludes that depopulation is responsible for the increasing decline of agriculture and livestock. The decrease in agricultural activity in general and the consequent practices and traditional systems of agriculture causes changes in the landscape and has negative effects on nature conservation and biodiversity. Thus, we believe that the preservation and development of traditional economic activities linked to agriculture, agro-forestry and food processing are essential to maintain the typical landscape and to preserve natural values of Montemuro Site. The paper shows that in mountain areas, particularly those classified as nature network sites, farming, economic development and nature conservation are not antagonistic objectives.

关键词： Farming systems protected areas nature conservation biodiversity local development.

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CTNS Molecular Genetics Profile in a Portuguese Cystinosis Population

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Open Journal of Genetics 2018年第4期8卷 91-100页

作者： filipa Ferreira Ines Leal David Sousa Teresa Costa Conceicao Mota Ana marta Gomes Daniela Lopes Maria do Carmo Macario Isabel Tavares Helena Pinto Joao Paulo Oliveira Rita Magrico Celia Carmona Sonia Ramos Raquel Neiva Ana Marcao Laura Vilarinho Newborn Screening Metabolism and Genetics UnitHuman Genetics DepartmentNational Institute of Health Dr Ricardo JorgePortoPortugal Centro Hospitalar Lisboa Norte Hospital de Santa MariaLisboaPortugal Centro Hospitalar Universitario do Porto PortoPortugal Centro Hospitalar Vila Nova de Gaia EspinhoPortugal Centro Hospitalar Universitario de Coimbra CHUCCoimbraPortugal Servico de Genetica Medica Centro Hospitalar de Sao JoaoPortoPortugal Unidade de Genetica Faculdade de Medicina da Universidade do PortoPortoPortugal I3S—Instituto de Investigacao e Inovacao em Saude PortoPortugal Servico de Nefrologia do Hospital Garcia de Orta AlmadaPortugal Research and Development Unit Department of Human GeneticsNational Institute of Health Dr Ricardo JorgePortoPortugal

Background: Cystinosis is a multisystemic autosomal recessive deficiency of the lysosomal membrane transporter protein (cystinosin) caused by mutations in CTNS gene. Objective: This study summarizes the Portuguese experience in the diagnosis and management of patients with this rare disease over the past few years and reports recurrent mutations in the CTNS gene. Methods: Unrelated patients from different pediatric and adult hospitals all over Portugal with non-nephrotic proteinuria, hypercalciuria, hypokalemia impaired proximal reabsorption of amino acids, glycosuria and hypophosphatemia, suggestive of a Fanconi syndrome and ocular problems, were studied. Intra-leukocyte cystine levels were determined and molecular analysis was performed, to determine the presence or absence of the 57-kb deletion in CTNS, followed by direct sequencing of the coding exons of CTNS. Results: From 1998 to 2017, twenty-one cystinotic patients were biochemically diagnosed. From the remaining seventeen (four deceased), eleven were studied for CTNS gene. Five out of eleven patients were homozygous for the 57-kb deletion (10/22;45.5%), and other five were compound heterozygous for this variant (15/22;68.2%). The other mutations found were p.Q128X (c.721 C>T;2/22), p.S139F (c.755 C>T;4/22) and c.18-21delGACT (p.T7FfsX7;1/22). All of these seventeen cystinotic patients are in treatment. Approximately 84% are adults, 16% are young children, and 54.5% are kidney transplant recipient. Conclusions: The authors would like to emphasize the importance of first screening for the 57-kb deletion since it is very common in our population. This genetic study is the first in our country and it could be the basis for future genetic counseling in Portuguese population.

关键词： Cystinosis CTNS Gene Mutational Spectrum Kidney Failure 57-kb Deletion

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