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  1. Article ; Online: Eurasian back-migration into Northeast Africa was a complex and multifaceted process.

    Hammarén, Rickard / Goldstein, Steven T / Schlebusch, Carina M

    PloS one

    2023  Volume 18, Issue 11, Page(s) e0290423

    Abstract: Recent studies have identified Northeast Africa as an important area for human movements during the Holocene. Eurasian populations have moved back into Northeastern Africa and contributed to the genetic composition of its people. By gathering the largest ...

    Abstract Recent studies have identified Northeast Africa as an important area for human movements during the Holocene. Eurasian populations have moved back into Northeastern Africa and contributed to the genetic composition of its people. By gathering the largest reference dataset to date of Northeast, North, and East African as well as Middle Eastern populations, we give new depth to our knowledge of Northeast African demographic history. By employing local ancestry methods, we isolated the Non-African parts of modern-day Northeast African genomes and identified the best putative source populations. Egyptians and Sudanese Copts bore most similarities to Levantine populations whilst other populations in the region generally had predominantly genetic contributions from the Arabian peninsula rather than Levantine populations for their Non-African genetic component. We also date admixture events and investigated which factors influenced the date of admixture and find that major linguistic families were associated with the date of Eurasian admixture. Taken as a whole we detect complex patterns of admixture and diverse origins of Eurasian admixture in Northeast African populations of today.
    MeSH term(s) Humans ; Africa ; Arabia ; Black People/genetics ; Egypt ; Genetics, Population ; White People/genetics ; Human Migration
    Language English
    Publishing date 2023-11-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0290423
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: FARAO: the flexible all-round annotation organizer.

    Hammarén, Rickard / Pal, Chandan / Bengtsson-Palme, Johan

    Bioinformatics (Oxford, England)

    2016  Volume 32, Issue 23, Page(s) 3664–3666

    Abstract: With decreasing costs of generating DNA sequence data, genome and metagenome projects have become accessible to a wider scientific community. However, to extract meaningful information and visualize the data remain challenging. We here introduce FARAO, a ...

    Abstract With decreasing costs of generating DNA sequence data, genome and metagenome projects have become accessible to a wider scientific community. However, to extract meaningful information and visualize the data remain challenging. We here introduce FARAO, a highly scalable software for organization, visualization and integration of annotation and read coverage data that can also combine output data from several bioinformatics tools. The capabilities of FARAO can greatly aid analyses of genomic and metagenomic datasets.
    Availability and implementation: FARAO is implemented in Perl and is supported under Unix-like operative systems, including Linux and macOS. The Perl source code is freely available for download under the MIT License from http://microbiology.se/software/farao/ CONTACT: johan.bengtsson-palme@microbiology.seSupplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Computational Biology/methods ; Genome ; Genomics ; Metagenomics ; Programming Languages ; Software
    Language English
    Publishing date 2016-12-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btw499
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: FARAO: the flexible all-round annotation organizer

    Hammarén, Rickard / Pal, Chandan / Bengtsson-Palme, Johan

    Bioinformatics. 2016 Dec. 01, v. 32, no. 23

    2016  

    Abstract: Summary: With decreasing costs of generating DNA sequence data, genome and metagenome projects have become accessible to a wider scientific community. However, to extract meaningful information and visualize the data remain challenging. We here introduce ...

    Abstract Summary: With decreasing costs of generating DNA sequence data, genome and metagenome projects have become accessible to a wider scientific community. However, to extract meaningful information and visualize the data remain challenging. We here introduce FARAO, a highly scalable software for organization, visualization and integration of annotation and read coverage data that can also combine output data from several bioinformatics tools. The capabilities of FARAO can greatly aid analyses of genomic and metagenomic datasets. Availability and Implementation: FARAO is implemented in Perl and is supported under Unix-like operative systems, including Linux and macOS. The Perl source code is freely available for download under the MIT License from http://microbiology.se/software/farao/. Contact: johan.bengtsson-palme@microbiology.se Supplementary information: Supplementary data are available at Bioinformatics online.
    Keywords DNA ; bioinformatics ; computer software ; data collection ; genome ; metagenomics ; nucleotide sequences
    Language English
    Dates of publication 2016-1201
    Size p. 3664-3666.
    Publishing place Oxford University Press
    Document type Article
    ZDB-ID 1468345-3
    ISSN 1460-2059 ; 1367-4803
    ISSN (online) 1460-2059
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btw499
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: The genetic legacy of the expansion of Bantu-speaking peoples in Africa.

    Fortes-Lima, Cesar A / Burgarella, Concetta / Hammarén, Rickard / Eriksson, Anders / Vicente, Mário / Jolly, Cecile / Semo, Armando / Gunnink, Hilde / Pacchiarotti, Sara / Mundeke, Leon / Matonda, Igor / Muluwa, Joseph Koni / Coutros, Peter / Nyambe, Terry S / Cikomola, Justin Cirhuza / Coetzee, Vinet / de Castro, Minique / Ebbesen, Peter / Delanghe, Joris /
    Stoneking, Mark / Barham, Lawrence / Lombard, Marlize / Meyer, Anja / Steyn, Maryna / Malmström, Helena / Rocha, Jorge / Soodyall, Himla / Pakendorf, Brigitte / Bostoen, Koen / Schlebusch, Carina M

    Nature

    2023  Volume 625, Issue 7995, Page(s) 540–547

    Abstract: The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the ... ...

    Abstract The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent
    MeSH term(s) Humans ; Africa, Western ; Datasets as Topic ; Democratic Republic of the Congo ; DNA, Ancient/analysis ; Emigration and Immigration/history ; Founder Effect ; Gene Flow/genetics ; Genetic Variation/genetics ; Genetics, Population ; History, Ancient ; Language/history ; Linguistics/history ; Zambia ; Geographic Mapping
    Chemical Substances DNA, Ancient
    Language English
    Publishing date 2023-11-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-023-06770-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.MG 9: Show issues
    Zs.MO 244: Show issues

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  5. Article: Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics

    Bengtsson-Palme, Johan / Hammarén, Rickard / Pal, Chandan / Östman, Marcus / Björlenius, Berndt / Flach, Carl-Fredrik / Fick, Jerker / Kristiansson, Erik / Tysklind, Mats / Larsson, D.G. Joakim

    Science of the total environment. 2016,

    2016  

    Abstract: Sewage treatment plants (STPs) have repeatedly been suggested as “hotspots” for the emergence and dissemination of antibiotic-resistant bacteria. A critical question still unanswered is if selection pressures within STPs, caused by residual antibiotics ... ...

    Abstract Sewage treatment plants (STPs) have repeatedly been suggested as “hotspots” for the emergence and dissemination of antibiotic-resistant bacteria. A critical question still unanswered is if selection pressures within STPs, caused by residual antibiotics or other co-selective agents, are sufficient to specifically promote resistance. To address this, we employed shotgun metagenomic sequencing of samples from different steps of the treatment process in three Swedish STPs. In parallel, concentrations of selected antibiotics, biocides and metals were analyzed. We found that concentrations of tetracycline and ciprofloxacin in the influent were above predicted concentrations for resistance selection, however, there was no consistent enrichment of resistance genes to any particular class of antibiotics in the STPs, neither for biocide and metal resistance genes. The most substantial change of the bacterial communities compared to human feces occurred already in the sewage pipes, manifested by a strong shift from obligate to facultative anaerobes. Through the treatment process, resistance genes against antibiotics, biocides and metals were not reduced to the same extent as fecal bacteria. The OXA-48 gene was consistently enriched in surplus and digested sludge. We find this worrying as OXA-48, still rare in Swedish clinical isolates, provides resistance to carbapenems, one of our most critically important classes of antibiotics. Taken together, metagenomics analyses did not provide clear support for specific antibiotic resistance selection. However, stronger selective forces affecting gross taxonomic composition, and with that resistance gene abundances, limit interpretability. Comprehensive analyses of resistant/non-resistant strains within relevant species are therefore warranted.
    Keywords anaerobes ; antibiotic resistance ; bacteria ; bacterial communities ; biocides ; carbapenems ; ciprofloxacin ; feces ; genes ; humans ; metagenomics ; metal tolerance ; metals ; pipes ; sewage ; sewage treatment ; sludge ; tetracycline
    Language English
    Size p. .
    Publishing place Elsevier B.V.
    Document type Article
    Note Pre-press version
    ZDB-ID 121506-1
    ISSN 1879-1026 ; 0048-9697
    ISSN (online) 1879-1026
    ISSN 0048-9697
    DOI 10.1016/j.scitotenv.2016.06.228
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    Zs.A 949: Show issues Location:
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  6. Article ; Online: Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics.

    Bengtsson-Palme, Johan / Hammarén, Rickard / Pal, Chandan / Östman, Marcus / Björlenius, Berndt / Flach, Carl-Fredrik / Fick, Jerker / Kristiansson, Erik / Tysklind, Mats / Larsson, D G Joakim

    The Science of the total environment

    2016  Volume 572, Page(s) 697–712

    Abstract: Sewage treatment plants (STPs) have repeatedly been suggested as "hotspots" for the emergence and dissemination of antibiotic-resistant bacteria. A critical question still unanswered is if selection pressures within STPs, caused by residual antibiotics ... ...

    Abstract Sewage treatment plants (STPs) have repeatedly been suggested as "hotspots" for the emergence and dissemination of antibiotic-resistant bacteria. A critical question still unanswered is if selection pressures within STPs, caused by residual antibiotics or other co-selective agents, are sufficient to specifically promote resistance. To address this, we employed shotgun metagenomic sequencing of samples from different steps of the treatment process in three Swedish STPs. In parallel, concentrations of selected antibiotics, biocides and metals were analyzed. We found that concentrations of tetracycline and ciprofloxacin in the influent were above predicted concentrations for resistance selection, however, there was no consistent enrichment of resistance genes to any particular class of antibiotics in the STPs, neither for biocide and metal resistance genes. The most substantial change of the bacterial communities compared to human feces occurred already in the sewage pipes, manifested by a strong shift from obligate to facultative anaerobes. Through the treatment process, resistance genes against antibiotics, biocides and metals were not reduced to the same extent as fecal bacteria. The OXA-48 gene was consistently enriched in surplus and digested sludge. We find this worrying as OXA-48, still rare in Swedish clinical isolates, provides resistance to carbapenems, one of our most critically important classes of antibiotics. Taken together, metagenomics analyses did not provide clear support for specific antibiotic resistance selection. However, stronger selective forces affecting gross taxonomic composition, and with that resistance gene abundances, limit interpretability. Comprehensive analyses of resistant/non-resistant strains within relevant species are therefore warranted.
    Language English
    Publishing date 2016-12-01
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 121506-1
    ISSN 1879-1026 ; 0048-9697
    ISSN (online) 1879-1026
    ISSN 0048-9697
    DOI 10.1016/j.scitotenv.2016.06.228
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 949: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
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