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Article ; Online: Genomic Adaptations to an Endoparasitic Lifestyle in the Morphologically Atypical Crustacean Sacculina carcini (Cirripedia: Rhizocephala).

Martin, Sebastian / Lesny, Peter / Glenner, Henrik / Hecht, Jochen / Vilcinskas, Andreas / Bartolomaeus, Thomas / Podsiadlowski, Lars

Genome biology and evolution

2022 Volume 14, Issue 10

Abstract: The endoparasitic crustacean Sacculina carcini (Cirripedia: Rhizocephala) has a much simpler morphology than conventional filter-feeding barnacles, reflecting its parasitic lifestyle. To investigate the molecular basis of its refined developmental ... ...

Abstract	The endoparasitic crustacean Sacculina carcini (Cirripedia: Rhizocephala) has a much simpler morphology than conventional filter-feeding barnacles, reflecting its parasitic lifestyle. To investigate the molecular basis of its refined developmental program, we produced a draft genome sequence for comparison with the genomes of nonparasitic barnacles and characterized the transcriptomes of internal and external tissues. The comparison of clusters of orthologous genes revealed the depletion of multiple gene families but also several unanticipated expansions compared to non-parasitic crustaceans. Transcriptomic analyses comparing interna and externa tissues revealed an unexpected variation of gene expression between rootlets sampled around host midgut and thoracic ganglia. Genes associated with lipid uptake were strongly expressed by the internal tissues. We identified candidate genes probably involved in host manipulation (suppression of ecdysis and gonad development) including those encoding crustacean neurohormones and the juvenile hormone binding protein. The evolution of Rhizocephala therefore appears to have involved a rapid turnover of genes (losses and expansions) as well as the fine tuning of gene expression.
MeSH term(s)	Animals ; Thoracica/anatomy & histology ; Thoracica/genetics ; Acclimatization ; Genomics
Language	English
Publishing date	2022-10-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2495328-3
ISSN	1759-6653 ; 1759-6653
ISSN (online)	1759-6653
ISSN	1759-6653
DOI	10.1093/gbe/evac149
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Genomic Adaptations to an Endoparasitic Lifestyle in the Morphologically Atypical Crustacean Sacculina carcini (Cirripedia

Martín, Sebastián / Leśny, Peter / Glenner, Henrik / Hecht, Jochen / Vilcinskas, Andreas / Bartolomaeus, Thomas / Podsiadłowski, Lars

Rhizocephala)

2022

Abstract	The endoparasitic crustacean Sacculina carcini (Cirripedia: Rhizocephala) has a much simpler morphology than conventional filter-feeding barnacles, reflecting its parasitic lifestyle. To investigate the molecular basis of its refined developmental program, we produced a draft genome sequence for comparison with the genomes of nonparasitic barnacles and characterized the transcriptomes of internal and external tissues. The comparison of clusters of orthologous genes revealed the depletion of multiple gene families but also several unanticipated expansions compared to non-parasitic crustaceans. Transcriptomic analyses comparing interna and externa tissues revealed an unexpected variation of gene expression between rootlets sampled around host midgut and thoracic ganglia. Genes associated with lipid uptake were strongly expressed by the internal tissues. We identified candidate genes probably involved in host manipulation (suppression of ecdysis and gonad development) including those encoding crustacean neurohormones and the juvenile hormone binding protein. The evolution of Rhizocephala therefore appears to have involved a rapid turnover of genes (losses and expansions) as well as the fine tuning of gene expression. 14 10
Keywords	sacculina ; differential expression ; endoparasite ; genome ; rhizocephala
Subject code	570
Language	English
Publishing country	de
Document type	Article ; Online
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Article ; Online: Differential Diagnosis of Interstitial Allograft Rejection and BKV Nephropathy by T-cell Receptor Sequencing.

Stervbo, Ulrik / Nienen, Mikalai / Hecht, Jochen / Viebahn, Richard / Amann, Kerstin / Westhoff, Timm H / Babel, Nina

Transplantation

2020 Volume 104, Issue 4, Page(s) e107–e108

MeSH term(s)	BK Virus/immunology ; BK Virus/pathogenicity ; Diagnosis, Differential ; Genes, T-Cell Receptor ; Graft Rejection/diagnosis ; Graft Rejection/genetics ; Graft Rejection/immunology ; Graft Rejection/prevention & control ; High-Throughput Nucleotide Sequencing ; Humans ; Immunocompromised Host ; Immunosuppressive Agents/adverse effects ; Kidney Transplantation/adverse effects ; Male ; Opportunistic Infections/diagnosis ; Opportunistic Infections/genetics ; Opportunistic Infections/immunology ; Opportunistic Infections/virology ; Polyomavirus Infections/diagnosis ; Polyomavirus Infections/genetics ; Polyomavirus Infections/immunology ; Polyomavirus Infections/virology ; Predictive Value of Tests ; Sequence Analysis, DNA ; Treatment Outcome ; Tumor Virus Infections/diagnosis ; Tumor Virus Infections/genetics ; Tumor Virus Infections/immunology ; Tumor Virus Infections/virology ; Viral Load ; Young Adult
Chemical Substances	Immunosuppressive Agents
Language	English
Publishing date	2020-03-30
Publishing country	United States
Document type	Case Reports ; Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	208424-7
ISSN	1534-6080 ; 0041-1337
ISSN (online)	1534-6080
ISSN	0041-1337
DOI	10.1097/TP.0000000000003054
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Zs.A 488: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 509: Show issues

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Book ; Online ; Thesis: Genexpressionsanalysen zum besseren Verständnis von Knochenheilung und -entwicklung

Hecht, Jochen [Verfasser]

2007

Author's details	vorgelegt von Jochen Hecht
Keywords	Medizin, Gesundheit ; Medicine, Health
Subject code	sg610
Language	German
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article ; Online: Y chromosome sequence and epigenomic reconstruction across human populations.

Esteller-Cucala, Paula / Palmada-Flores, Marc / Kuderna, Lukas F K / Fontsere, Claudia / Serres-Armero, Aitor / Dabad, Marc / Torralvo, María / Faella, Armida / Ferrández-Peral, Luis / Llovera, Laia / Fornas, Oscar / Julià, Eva / Ramírez, Erika / González, Irene / Hecht, Jochen / Lizano, Esther / Juan, David / Marquès-Bonet, Tomàs

Communications biology

2023 Volume 6, Issue 1, Page(s) 623

Abstract: Recent advances in long-read sequencing technologies have allowed the generation and curation of more complete genome assemblies, enabling the analysis of traditionally neglected chromosomes, such as the human Y chromosome (chrY). Native DNA was ... ...

Abstract	Recent advances in long-read sequencing technologies have allowed the generation and curation of more complete genome assemblies, enabling the analysis of traditionally neglected chromosomes, such as the human Y chromosome (chrY). Native DNA was sequenced on a MinION Oxford Nanopore Technologies sequencing device to generate genome assemblies for seven major chrY human haplogroups. We analyzed and compared the chrY enrichment of sequencing data obtained using two different selective sequencing approaches: adaptive sampling and flow cytometry chromosome sorting. We show that adaptive sampling can produce data to create assemblies comparable to chromosome sorting while being a less expensive and time-consuming technique. We also assessed haplogroup-specific structural variants, which would be otherwise difficult to study using short-read sequencing data only. Finally, we took advantage of this technology to detect and profile epigenetic modifications among the considered haplogroups. Altogether, we provide a framework to study complex genomic regions with a simple, fast, and affordable methodology that could be applied to larger population genomics datasets.
MeSH term(s)	Humans ; Sequence Analysis, DNA/methods ; Epigenomics ; High-Throughput Nucleotide Sequencing/methods ; Genomics/methods ; Y Chromosome
Language	English
Publishing date	2023-06-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-023-05004-9
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Article ; Online: In vitro and in vivo evidence that the switch from calcineurin to mTOR inhibitors may be a strategy for immunosuppression in Epstein-Barr virus-associated post-transplant lymphoproliferative disorder.

Thieme, Constantin J / Schulz, Malissa / Wehler, Patrizia / Anft, Moritz / Amini, Leila / Blàzquez-Navarro, Arturo / Stervbo, Ulrik / Hecht, Jochen / Nienen, Mikalai / Stittrich, Anna-Barbara / Choi, Mira / Zgoura, Panagiota / Viebahn, Richard / Schmueck-Henneresse, Michael / Reinke, Petra / Westhoff, Timm H / Roch, Toralf / Babel, Nina

Kidney international

2022 Volume 102, Issue 6, Page(s) 1392–1408

Abstract: Post-transplant lymphoproliferative disorder is a life-threatening complication of immunosuppression following transplantation mediated by failure of T cells to control Epstein-Barr virus (EBV)-infected and transformed B cells. Typically, a modification ... ...

Abstract	Post-transplant lymphoproliferative disorder is a life-threatening complication of immunosuppression following transplantation mediated by failure of T cells to control Epstein-Barr virus (EBV)-infected and transformed B cells. Typically, a modification or reduction of immunosuppression is recommended, but insufficiently defined thus far. In order to help delineate this, we characterized EBV-antigen-specific T cells and lymphoblastoid cell lines from healthy donors and in patients with a kidney transplant in the absence or presence of the standard immunosuppressants tacrolimus, cyclosporin A, prednisolone, rapamycin, and mycophenolic acid. Phenotypes of lymphoblastoid cell-lines and T cells, T cell-receptor-repertoire diversity, and T-cell reactivity upon co-culture with autologous lymphoblastoid cell lines were analyzed. Rapamycin and mycophenolic acid inhibited lymphoblastoid cell-line proliferation. T cells treated with prednisolone and rapamycin showed nearly normal cytokine production. Proliferation and the viability of T cells were decreased by mycophenolic acid, while tacrolimus and cyclosporin A were strong suppressors of T-cell function including their killing activity. Overall, our study provides a basis for the clinical decision for the modification and reduction of immunosuppression and adds information to the complex balance of maintaining anti-viral immunity while preventing acute rejection. Thus, an immunosuppressive regime based on mTOR inhibition and reduced or withdrawn calcineurin inhibitors could be a promising strategy for patients with increased risk of or manifested EBV-associated post-transplant lymphoproliferative disorder.
MeSH term(s)	Humans ; Herpesvirus 4, Human ; Tacrolimus/pharmacology ; Tacrolimus/therapeutic use ; Calcineurin/genetics ; MTOR Inhibitors ; Cyclosporine/pharmacology ; Cyclosporine/therapeutic use ; Epstein-Barr Virus Infections/drug therapy ; Mycophenolic Acid/therapeutic use ; Lymphoproliferative Disorders/drug therapy ; Lymphoproliferative Disorders/etiology ; Lymphoproliferative Disorders/prevention & control ; Immunosuppression Therapy ; Immunosuppressive Agents/therapeutic use ; Sirolimus/pharmacology ; Sirolimus/therapeutic use ; Prednisolone/pharmacology ; Prednisolone/therapeutic use ; TOR Serine-Threonine Kinases
Chemical Substances	Tacrolimus (WM0HAQ4WNM) ; Calcineurin (EC 3.1.3.16) ; MTOR Inhibitors ; Cyclosporine (83HN0GTJ6D) ; Mycophenolic Acid (HU9DX48N0T) ; Immunosuppressive Agents ; Sirolimus (W36ZG6FT64) ; Prednisolone (9PHQ9Y1OLM) ; MTOR protein, human (EC 2.7.1.1) ; TOR Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2022-09-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	120573-0
ISSN	1523-1755 ; 0085-2538
ISSN (online)	1523-1755
ISSN	0085-2538
DOI	10.1016/j.kint.2022.08.025
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Zs.A 797: Show issues

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Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors.

Willis, Jesse R / Saus, Ester / Iraola-Guzmán, Susana / Ksiezopolska, Ewa / Cozzuto, Luca / Bejarano, Luis A / Andreu-Somavilla, Nuria / Alloza-Trabado, Miriam / Blanco, Andrea / Puig-Sola, Anna / Broglio, Elisabetta / Carolis, Carlo / Ponomarenko, Julia / Hecht, Jochen / Gabaldón, Toni

NPJ biofilms and microbiomes

2022 Volume 8, Issue 1, Page(s) 38

Abstract: The relevance of the human oral microbiome to our understanding of human health has grown in recent years as microbiome studies continue to develop. Given the links of the oral cavity with the digestive, respiratory and circulatory systems, the ... ...

Abstract	The relevance of the human oral microbiome to our understanding of human health has grown in recent years as microbiome studies continue to develop. Given the links of the oral cavity with the digestive, respiratory and circulatory systems, the composition of the oral microbiome is relevant beyond just oral health, impacting systemic processes across the body. However, we still have a very limited understanding about intrinsic and extrinsic factors that shape the composition of the healthy oral microbiome. Here, we followed a citizen-science approach to assess the relative impact on the oral microbiome of selected biological, social, and lifestyle factors in 1648 Spanish individuals. We found that the oral microbiome changes across age, with middle ages showing a more homogeneous composition, and older ages showing more diverse microbiomes with increased representation of typically low abundance taxa. By measuring differences within and between groups of individuals sharing a given parameter, we were able to assess the relative impact of different factors in driving specific microbial compositions. Chronic health disorders present in the analyzed population were the most impactful factors, followed by smoking and the presence of yeasts in the oral cavity. Finally, we corroborate findings in the literature that relatives tend to have more similar oral microbiomes, and show for the first time a similar effect for classmates. Multiple intrinsic and extrinsic factors jointly shape the oral microbiome. Comparative analysis of metabarcoding data from a large sample set allows us to disentangle the individual effects.
MeSH term(s)	Bacteria/genetics ; Humans ; Life Style ; Microbiota ; Middle Aged ; Mouth ; Spain
Language	English
Publishing date	2022-05-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2817021-0
ISSN	2055-5008 ; 2055-5008
ISSN (online)	2055-5008
ISSN	2055-5008
DOI	10.1038/s41522-022-00279-y
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Article ; Online: Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data.

Hansen, Peter / Gargano, Michael / Hecht, Jochen / Ibn-Salem, Jonas / Karlebach, Guy / Roehr, Johannes T / Robinson, Peter N

Genes

2019 Volume 10, Issue 7

Abstract: Hi-C, capture Hi-C (CHC) and Capture-C have contributed greatly to our present understanding of the three-dimensional organization of genomes in the context of transcriptional regulation by characterizing the roles of topological associated domains, ... ...

Abstract	Hi-C, capture Hi-C (CHC) and Capture-C have contributed greatly to our present understanding of the three-dimensional organization of genomes in the context of transcriptional regulation by characterizing the roles of topological associated domains, enhancer promoter loops and other three-dimensional genomic interactions. The analysis is based on counts of chimeric read pairs that map to interacting regions of the genome. However, the processing and quality control presents a number of unique challenges. We review here the experimental and computational foundations and explain how the characteristics of restriction digests, sonication fragments and read pairs can be exploited to distinguish technical artefacts from valid read pairs originating from true chromatin interactions.
MeSH term(s)	Chromatin/genetics ; Chromosome Mapping ; Computational Biology/methods ; Databases, Genetic ; Genome ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Humans ; Quality Control
Chemical Substances	Chromatin
Language	English
Publishing date	2019-07-18
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes10070548
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Article ; Online: BKV Clearance Time Correlates With Exhaustion State and T-Cell Receptor Repertoire Shape of BKV-Specific T-Cells in Renal Transplant Patients.

Stervbo, Ulrik / Nienen, Mikalai / Weist, Benjamin J D / Kuchenbecker, Leon / Hecht, Jochen / Wehler, Patrizia / Westhoff, Timm H / Reinke, Petra / Babel, Nina

Frontiers in immunology

2019 Volume 10, Page(s) 767

Abstract: Reactivation of the BK polyomavirus is known to lead to severe complications in kidney transplant patients. The current treatment strategy relies on decreasing the immunosuppression to allow the immune system to clear the virus. Recently, we demonstrated ...

Abstract	Reactivation of the BK polyomavirus is known to lead to severe complications in kidney transplant patients. The current treatment strategy relies on decreasing the immunosuppression to allow the immune system to clear the virus. Recently, we demonstrated a clear association between the resolution of BKV reactivation and reconstitution of BKV-specific CD4
MeSH term(s)	Adult ; Aged ; BK Virus/physiology ; CD4-Positive T-Lymphocytes/immunology ; Humans ; Immunocompromised Host/immunology ; Kidney Transplantation ; Male ; Middle Aged ; Polyomavirus Infections/immunology ; Tumor Virus Infections/immunology ; Virus Activation/immunology
Language	English
Publishing date	2019-04-10
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2019.00767
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Article ; Online: High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing

Bus Anja / Hecht Jochen / Huettel Bruno / Reinhardt Richard / Stich Benjamin

BMC Genomics, Vol 13, Iss 1, p

2012 Volume 281

Abstract: Abstract Background The complex genome of rapeseed ( Brassica napus ) is not well understood despite the economic importance of the species. Good knowledge of sequence variation is needed for genetics approaches and breeding purposes. We used a diversity ...

Abstract	Abstract Background The complex genome of rapeseed ( Brassica napus ) is not well understood despite the economic importance of the species. Good knowledge of sequence variation is needed for genetics approaches and breeding purposes. We used a diversity set of B. napus representing eight different germplasm types to sequence genome-wide distributed restriction-site associated DNA (RAD) fragments for polymorphism detection and genotyping. Results More than 113,000 RAD clusters with more than 20,000 single nucleotide polymorphisms (SNPs) and 125 insertions/deletions were detected and characterized. About one third of the RAD clusters and polymorphisms mapped to the Brassica rapa reference sequence. An even distribution of RAD clusters and polymorphisms was observed across the B. rapa chromosomes, which suggests that there might be an equal distribution over the Brassica oleracea chromosomes, too. The representation of Gene Ontology (GO) terms for unigenes with RAD clusters and polymorphisms revealed no signature of selection with respect to the distribution of polymorphisms within genes belonging to a specific GO category. Conclusions Considering the decreasing costs for next-generation sequencing, the results of our study suggest that RAD sequencing is not only a simple and cost-effective method for high-density polymorphism detection but also an alternative to SNP genotyping from transcriptome sequencing or SNP arrays, even for species with complex genomes such as B. napus .
Keywords	Brassica napus ; Restriction-site associated DNA ; Next-generation sequencing ; Single nucleotide polymorphism ; Genotyping by sequencing ; Genetic diversity ; Genetics ; QH426-470 ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Genetics ; DOAJ:Biology ; DOAJ:Biology and Life Sciences ; Biotechnology ; TP248.13-248.65
Subject code	616
Language	English
Publishing date	2012-06-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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