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  1. Article ; Online: In silico SNP prediction of selected protein orthologues in insect models for Alzheimer's, Parkinson's, and Huntington’s diseases

    Eshraka A. Al-Ayari / Magdi G. Shehata / Mohamed EL-Hadidi / Mona G. Shaalan

    Scientific Reports, Vol 13, Iss 1, Pp 1-

    2023  Volume 15

    Abstract: Abstract Alzheimer's, Parkinson’s, and Huntington’s are the most common neurodegenerative diseases that are incurable and affect the elderly population. Discovery of effective treatments for these diseases is often difficult, expensive, and serendipitous. ...

    Abstract Abstract Alzheimer's, Parkinson’s, and Huntington’s are the most common neurodegenerative diseases that are incurable and affect the elderly population. Discovery of effective treatments for these diseases is often difficult, expensive, and serendipitous. Previous comparative studies on different model organisms have revealed that most animals share similar cellular and molecular characteristics. The meta-SNP tool includes four different integrated tools (SIFT, PANTHER, SNAP, and PhD-SNP) was used to identify non synonymous single nucleotide polymorphism (nsSNPs). Prediction of nsSNPs was conducted on three representative proteins for Alzheimer's, Parkinson’s, and Huntington’s diseases; APPl in Drosophila melanogaster, LRRK1 in Aedes aegypti, and VCPl in Tribolium castaneum. With the possibility of using insect models to investigate neurodegenerative diseases. We conclude from the protein comparative analysis between different insect models and nsSNP analyses that D. melanogaster is the best model for Alzheimer’s representing five nsSNPs of the 21 suggested mutations in the APPl protein. Aedes aegypti is the best model for Parkinson’s representing three nsSNPs in the LRRK1 protein. Tribolium castaneum is the best model for Huntington’s disease representing 13 SNPs of 37 suggested mutations in the VCPl protein. This study aimed to improve human neural health by identifying the best insect to model Alzheimer's, Parkinson’s, and Huntington’s.
    Keywords Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2023-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Soil biochar amendment affects the diversity of nosZ transcripts

    Johannes Harter / Mohamed El-Hadidi / Daniel H. Huson / Andreas Kappler / Sebastian Behrens

    Scientific Reports, Vol 7, Iss 1, Pp 1-

    Implications for N2O formation

    2017  Volume 14

    Abstract: Abstract Microbial nitrogen transformation processes such as denitrification represent major sources of the potent greenhouse gas nitrous oxide (N2O). Soil biochar amendment has been shown to significantly decrease N2O emissions in various soils. However, ...

    Abstract Abstract Microbial nitrogen transformation processes such as denitrification represent major sources of the potent greenhouse gas nitrous oxide (N2O). Soil biochar amendment has been shown to significantly decrease N2O emissions in various soils. However, the effect of biochar on the structure and function of microbial communities that actively perform nitrogen redox transformations has not been studied in detail yet. To analyse the community composition of actively denitrifying and N2O-reducing microbial communities, we collected RNA samples at different time points from a soil microcosm experiment conducted under denitrifying conditions and performed Illumina amplicon sequencing targeting nirK, typical nosZ and atypical nosZ mRNA transcripts. Within 10 days, biochar significantly increased the diversity of nirK and typical nosZ transcripts and resulted in taxonomic shifts among the typical nosZ-expressing microbial community. Furthermore, biochar addition led to a significant increase in transcript production among microbial species that are specialized on direct N2O reduction from the environment. Our results point towards a potential coupling of biochar-induced N2O emission reduction and an increase in microbial N2O reduction activity among specific groups of typical and atypical N2O reducers. However, experiments with other soils and biochars will be required to verify the transferability of these findings to other soil-biochar systems.
    Keywords Medicine ; R ; Science ; Q
    Subject code 660
    Language English
    Publishing date 2017-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Author Correction

    Reem Hassan / Marwa Tantawy / Nouran A. Gouda / Mariam G. Elzayat / Sara Gabra / Amena Nabih / Aya A. Diab / Mohamed El-Hadidi / Usama Bakry / Mohamed R. Shoeb / Mervat Elanany / Lobna Shalaby / Ahmed A. Sayed

    Scientific Reports, Vol 10, Iss 1, Pp 1-

    Genotypic characterization of multiple drug resistant Escherichia coli isolates from a pediatric cancer hospital in Egypt

    2020  Volume 1

    Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    Abstract An amendment to this paper has been published and can be accessed via a link at the top of the paper.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2020-04-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Genotypic characterization of multiple drug resistant Escherichia coli isolates from a pediatric cancer hospital in Egypt

    Reem Hassan / Marwa Tantawy / Nouran A. Gouda / Mariam G. Elzayat / Sara Gabra / Amena Nabih / Aya A. Diab / Mohamed El-Hadidi / Usama Bakry / Mohamed R. Shoeb / Mervat Elanany / Lobna Shalaby / Ahmed A. Sayed

    Scientific Reports, Vol 10, Iss 1, Pp 1-

    2020  Volume 10

    Abstract: Abstract Infection with multiple drug resistant (MDR) Escherichia coli poses a life threat to immunocompromised pediatric cancer patients. Our aim is to genotypically characterize the plasmids harbored in MDR E. coli isolates recovered from bacteremic ... ...

    Abstract Abstract Infection with multiple drug resistant (MDR) Escherichia coli poses a life threat to immunocompromised pediatric cancer patients. Our aim is to genotypically characterize the plasmids harbored in MDR E. coli isolates recovered from bacteremic patients of Children’s Cancer Hospital in Egypt 57357 (CCHE 57357). In this study, 21 carbapenem-resistant E. coli (CRE) isolates were selected that exhibit Quinolones and Aminoglycosides resistance. Plasmid shot-gun sequencing was performed using Illumina next- generation sequencing platform. Isolates demonstrated resistant to all beta-lactams, carbapenems, aminoglycosides and quinolones. Of the 32 antimicrobial resistant genes identified that exceeded the analysis cutoff coverage, the highest represented genes were aph(6)-Id, sul2, aph(3″)-Ib, aph(3′)-Ia, sul1, dfrA12, TEM-220, NDM-11. Isolates employed a wide array of resistance mechanisms including antibiotic efflux, antibiotic inactivation, antibiotic target replacements and antibiotic target alteration. Sequenced isolates displayed diverse insertion sequences, including IS26, suggesting dynamic reshuffling of the harbored plasmids. Most isolates carried plasmids originating from other bacterial species suggesting a possible horizontal gene transfer. Only two isolates showed virulence factors with iroA gene cluster which was found in only one of them. Outside the realms of nosocomial infections among patients in hospitals, our results indicate a transfer of resistant genes and plasmids across different organisms.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2020-03-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: A simple statistical test of taxonomic or functional homogeneity using replicated microbiome sequencing samples

    Huson, Daniel H / Matthias Willmann / Mike Steel / Mohamed El-Hadidi / Silke Peter / Suparna Mitra

    Journal of biotechnology. 2016,

    2016  

    Abstract: One important question in microbiome analysis is how to assess the homogeneity of the microbial composition in a given environment, with respect to a given analysis method. Do different microbial samples taken from the same environment follow the same ... ...

    Abstract One important question in microbiome analysis is how to assess the homogeneity of the microbial composition in a given environment, with respect to a given analysis method. Do different microbial samples taken from the same environment follow the same taxonomic distribution of organisms, or the same distribution of functions? Here we provide a non-parametric statistical “triangulation test” to address this type of question. The test requires that multiple replicates are available for each of the biological samples, and it is based on three-way computational comparisons of samples. To illustrate the application of the test, we collected three biological samples taken from different locations in one piece of human stool, each represented by three replicates, and analyzed them using MEGAN. (Despite its name, the triangulation test does not require that the number of biological samples or replicates be three.) The triangulation test rejects the null hypothesis that the three biological samples exhibit the same distribution of taxa or function (error probability ≤0.05), indicating that the microbial composition of the investigated human stool is not homogenous on a macroscopic scale, suggesting that pooling material from multiple locations is a reasonable practice. We provide an implementation of the test in our open source program MEGAN Community Edition.
    Keywords feces ; microbiome ; probability ; statistical analysis
    Language English
    Size p. .
    Publishing place Elsevier B.V.
    Document type Article
    Note Pre-press version
    ZDB-ID 843647-2
    ISSN 1873-4863 ; 0168-1656 ; 1389-0352
    ISSN (online) 1873-4863
    ISSN 0168-1656 ; 1389-0352
    DOI 10.1016/j.jbiotec.2016.10.020
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Cologne/Königswinter

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  6. Article: Biochar affects community composition of nitrous oxide reducers in a field experiment

    Krause, Hans-Martin / Roman Hüppi / Jens Leifeld / Mohamed El-Hadidi / Johannes Harter / Andreas Kappler / Martin Hartmann / Sebastian Behrens / Paul Mäder / Andreas Gattinger

    Elsevier Ltd Soil biology & biochemistry. 2018 Apr., v. 119

    2018  

    Abstract: N2O is a major greenhouse gas and the majority of anthropogenic N2O emissions originate from agriculturally managed soils. Therefore, developing N2O mitigation strategies is a key challenge for the agricultural sector and biochar soil treatment is one ... ...

    Abstract N2O is a major greenhouse gas and the majority of anthropogenic N2O emissions originate from agriculturally managed soils. Therefore, developing N2O mitigation strategies is a key challenge for the agricultural sector and biochar soil treatment is one reported option. Biochar's capacity to increase soil pH and to foster activity of specialized N2O reducers has been proposed as possible mechanisms for N2O mitigation. An experiment was undertaken to investigate whether changes in the community composition of N2O reducers was observed under field conditions after biochar application. The study objective was to assess the abundance and taxonomic composition of the functional marker genes nosZ and nosZ –II across a vegetation period of Zea mays L. after biochar or lime addition compared to an untreated control. After fertilization, biochar amendment resulted in a significant increase of nosZ gene copy numbers compared to the control and the lime treatment. Simultaneously a shift in community composition of nosZ-II bearing bacteria was observed in the biochar treatment that went beyond the sole liming effect. This study broadens our understanding of the functional impact of biochar on N2O emissions and emphasizes the possibility to shape the functioning of the N2O reducing microbial community through the addition of biochar at a field scale.
    Keywords Zea mays ; agricultural industry ; bacteria ; biochar ; community structure ; field experimentation ; gene dosage ; genetic markers ; greenhouse gas emissions ; greenhouse gases ; microbial communities ; nitrous oxide ; soil pH ; soil treatment ; taxonomy ; vegetation
    Language English
    Dates of publication 2018-04
    Size p. 143-151.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 280810-9
    ISSN 0038-0717
    ISSN 0038-0717
    DOI 10.1016/j.soilbio.2018.01.018
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 2637: Show issues

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  7. Article ; Online: MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.

    Daniel H Huson / Sina Beier / Isabell Flade / Anna Górska / Mohamed El-Hadidi / Suparna Mitra / Hans-Joachim Ruscheweyh / Rewati Tappu

    PLoS Computational Biology, Vol 12, Iss 6, p e

    2016  Volume 1004957

    Abstract: There is increasing interest in employing shotgun sequencing, rather than amplicon sequencing, to analyze microbiome samples. Typical projects may involve hundreds of samples and billions of sequencing reads. The comparison of such samples against a ... ...

    Abstract There is increasing interest in employing shotgun sequencing, rather than amplicon sequencing, to analyze microbiome samples. Typical projects may involve hundreds of samples and billions of sequencing reads. The comparison of such samples against a protein reference database generates billions of alignments and the analysis of such data is computationally challenging. To address this, we have substantially rewritten and extended our widely-used microbiome analysis tool MEGAN so as to facilitate the interactive analysis of the taxonomic and functional content of very large microbiome datasets. Other new features include a functional classifier called InterPro2GO, gene-centric read assembly, principal coordinate analysis of taxonomy and function, and support for metadata. The new program is called MEGAN Community Edition (CE) and is open source. By integrating MEGAN CE with our high-throughput DNA-to-protein alignment tool DIAMOND and by providing a new program MeganServer that allows access to metagenome analysis files hosted on a server, we provide a straightforward, yet powerful and complete pipeline for the analysis of metagenome shotgun sequences. We illustrate how to perform a full-scale computational analysis of a metagenomic sequencing project, involving 12 samples and 800 million reads, in less than three days on a single server. All source code is available here: https://github.com/danielhuson/megan-ce.
    Keywords Biology (General) ; QH301-705.5
    Subject code 004
    Language English
    Publishing date 2016-06-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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