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Article ; Online: PacBio-Based Protocol for Bacterial Genome Assembly.

Motyka-Pomagruk, Agata / Zoledowska, Sabina / Kabza, Michal / Lojkowska, Ewa

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2242, Page(s) 3–14

Abstract: Acquisition of high-quality bacterial genomes is fundamental, while having in mind investigation of subtitle intraspecies variation in addition to development of sensitive species-specific tools for detection and identification of the pathogens. In this ... ...

Abstract	Acquisition of high-quality bacterial genomes is fundamental, while having in mind investigation of subtitle intraspecies variation in addition to development of sensitive species-specific tools for detection and identification of the pathogens. In this view, Pacific Biosciences technology seems highly tempting taking into consideration over 10,000 bp length of the generated reads. In this work, we describe a bacterial genome assembly pipeline based on open-source software that might be handled also by non-bioinformaticians interested in transformation of sequencing data into reliable biological information. With the use of this method, we successfully closed six Dickeya solani genomes, while the assembly process was run just on a slightly improved desktop computer.
MeSH term(s)	DNA, Bacterial/genetics ; Databases, Genetic ; Dickeya/genetics ; Genome, Bacterial ; Genomics ; High-Throughput Nucleotide Sequencing ; Research Design ; Single Molecule Imaging ; Whole Genome Sequencing ; Workflow
Chemical Substances	DNA, Bacterial
Language	English
Publishing date	2021-05-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1099-2_1
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Article ; Online: The Impaired Wound Healing Process Is a Major Factor in Remodeling of the Corneal Epithelium in Adult and Adolescent Patients With Keratoconus.

Jaskiewicz, Katarzyna / Maleszka-Kurpiel, Magdalena / Matuszewska, Eliza / Kabza, Michal / Rydzanicz, Malgorzata / Malinowski, Robert / Ploski, Rafal / Matysiak, Jan / Gajecka, Marzena

Investigative ophthalmology & visual science

2023 Volume 64, Issue 2, Page(s) 22

Abstract: Purpose: Keratoconus (KTCN) is the most common corneal ectasia, characterized by pathological cone formation. Here, to provide an insight into the remodeling of the corneal epithelium (CE) during the course of the disease, we evaluated topographic ... ...

Abstract	Purpose: Keratoconus (KTCN) is the most common corneal ectasia, characterized by pathological cone formation. Here, to provide an insight into the remodeling of the corneal epithelium (CE) during the course of the disease, we evaluated topographic regions of the CE of adult and adolescent patients with KTCN. Methods: The CE samples from 17 adult and 6 adolescent patients with KTCN, and 5 control CE samples were obtained during the CXL and PRK procedures, respectively. Three topographic regions, central, middle, and peripheral, were separated toward RNA sequencing and MALDI-TOF/TOF Tandem Mass Spectrometry. Data from transcriptomic and proteomic investigations were consolidated with the morphological and clinical findings. Results: The critical elements of the wound healing process, epithelial-mesenchymal transition, cell-cell communications, and cell-extracellular matrix interactions were altered in the particular corneal topographic regions. Abnormalities in pathways of neutrophils degranulation, extracellular matrix processing, apical junctions, IL, and IFN signaling were revealed to cooperatively disorganize the epithelial healing. Deregulation of the epithelial healing, G2M checkpoints, apoptosis, and DNA repair pathways in the middle CE topographic region in KTCN explains the presence of morphological changes in the corresponding doughnut pattern (a thin cone center surrounded by a thickened annulus). Despite similar morphological characteristics of CE samples in adolescents and adults with KTCN, their transcriptomic features were different. Values of the posterior corneal elevation differentiated adults with KTCN from adolescents with KTCN and correlated with the expression of TCHP, SPATA13, CNOT3, WNK1, TGFB2, and KRT12 genes. Conclusions: Identified molecular, morphological, and clinical features indicate the effect of impaired wound healing on corneal remodeling in KTCN CE.
MeSH term(s)	Humans ; Adult ; Adolescent ; Epithelium, Corneal/metabolism ; Keratoconus/metabolism ; Proteomics ; Cornea/metabolism ; Wound Healing ; Cross-Linking Reagents ; Transcription Factors
Chemical Substances	Cross-Linking Reagents ; CNOT3 protein, human ; Transcription Factors
Language	English
Publishing date	2023-05-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	391794-0
ISSN	1552-5783 ; 0146-0404
ISSN (online)	1552-5783
ISSN	0146-0404
DOI	10.1167/iovs.64.2.22
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Article ; Online: Sequence variants contributing to dysregulated inflammatory responses across keratoconic cone surface in adolescent patients with keratoconus.

Jaskiewicz, Katarzyna / Maleszka-Kurpiel, Magdalena / Kabza, Michał / Karolak, Justyna A / Gajecka, Marzena

Frontiers in immunology

2023 Volume 14, Page(s) 1197054

Abstract: Background: Keratoconus (KTCN) is the most common corneal ectasia resulting in a conical shape of the cornea. Here, genomic variation in the corneal epithelium (CE) across the keratoconic cone surface in patients with KTCN and its relevance in the ... ...

Abstract	Background: Keratoconus (KTCN) is the most common corneal ectasia resulting in a conical shape of the cornea. Here, genomic variation in the corneal epithelium (CE) across the keratoconic cone surface in patients with KTCN and its relevance in the functioning of the immune system were assessed. Methods: Samples from four unrelated adolescent patients with KTCN and two control individuals were obtained during the CXL and PRK procedures, respectively. Three Results: First, pathway enrichment analysis of genes with identified coding variants pointed to "Antigen presentation" and "Interferon alpha/beta signaling" as the most overrepresented pathways, indicating the involvement of inflammatory responses in KTCN. Both coding and non-coding sequence variants were found in genes (or in their close proximity) linked to the previously revealed KTCN-specific cellular components, namely, "Actin cytoskeleton", "Extracellular matrix", "Collagen-containing extracellular matrix", "Focal adhesion", "Hippo signaling pathway", and "Wnt signaling" pathways. No genomic heterogeneity across the corneal surface was found comparing the assessed Conclusion: The identified genomic features indicate the involvement of innate and adaptive immune system responses in KTCN pathogenesis.
MeSH term(s)	Humans ; Adolescent ; Keratoconus/genetics ; Keratoconus/pathology ; Cornea/pathology ; Collagen/genetics ; Transcriptome ; Gene Expression Profiling
Chemical Substances	Collagen (9007-34-5)
Language	English
Publishing date	2023-07-06
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.2023.1197054
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Article ; Online: Influence of

Tomela, Katarzyna / Karolak, Justyna A / Ginter-Matuszewska, Barbara / Kabza, Michal / Gajecka, Marzena

Current issues in molecular biology

2021 Volume 43, Issue 1, Page(s) 276–285

Abstract: Dermal fibroblasts are responsible for the production of the extracellular matrix that undergoes significant changes during the skin aging process. These changes are partially controlled by the TGF-β signaling, which regulates tissue homeostasis ... ...

Abstract	Dermal fibroblasts are responsible for the production of the extracellular matrix that undergoes significant changes during the skin aging process. These changes are partially controlled by the TGF-β signaling, which regulates tissue homeostasis dependently on several genes, including CTGF and DNA methyltransferases. To investigate the potential differences in the regulation of the TGF-β signaling and related molecular pathways at distinct developmental stages, we silenced the expression of
MeSH term(s)	Adult ; Age Factors ; Blotting, Western ; Cell Line ; Connective Tissue Growth Factor/genetics ; Connective Tissue Growth Factor/metabolism ; DNA (Cytosine-5-)-Methyltransferase 1/genetics ; DNA (Cytosine-5-)-Methyltransferase 1/metabolism ; DNA Methyltransferase 3A/genetics ; DNA Methyltransferase 3A/metabolism ; Fibroblasts/cytology ; Fibroblasts/metabolism ; Humans ; Infant, Newborn ; RNA Interference ; Receptor, Transforming Growth Factor-beta Type II/genetics ; Receptor, Transforming Growth Factor-beta Type II/metabolism ; Skin/cytology ; Transforming Growth Factor beta3/genetics ; Transforming Growth Factor beta3/metabolism
Chemical Substances	CCN2 protein, human ; DNMT3A protein, human ; TGFB3 protein, human ; Transforming Growth Factor beta3 ; Connective Tissue Growth Factor (139568-91-5) ; DNA (Cytosine-5-)-Methyltransferase 1 (EC 2.1.1.37) ; DNA Methyltransferase 3A (EC 2.1.1.37) ; DNMT1 protein, human (EC 2.1.1.37) ; Receptor, Transforming Growth Factor-beta Type II (EC 2.7.11.30) ; TGFBR2 protein, human (EC 2.7.11.30)
Language	English
Publishing date	2021-06-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2000024-8
ISSN	1467-3045 ; 1467-3037
ISSN (online)	1467-3045
ISSN	1467-3037
DOI	10.3390/cimb43010023
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Article: Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota.

Matysiak, Anna / Kabza, Michal / Karolak, Justyna A / Jaworska, Marcelina M / Rydzanicz, Malgorzata / Ploski, Rafal / Szaflik, Jacek P / Gajecka, Marzena

Pathogens (Basel, Switzerland)

2021 Volume 10, Issue 4

Abstract: The ocular microbiome composition has only been partially characterized. Here, we used RNA-sequencing (RNA-Seq) data to assess microbial diversity in human corneal tissue. Additionally, conjunctival swab samples were examined to characterize ocular ... ...

Abstract	The ocular microbiome composition has only been partially characterized. Here, we used RNA-sequencing (RNA-Seq) data to assess microbial diversity in human corneal tissue. Additionally, conjunctival swab samples were examined to characterize ocular surface microbiota. Short RNA-Seq reads, obtained from a previous transcriptome study of 50 corneal tissues, were mapped to the human reference genome GRCh38 to remove sequences of human origin. The unmapped reads were then used for taxonomic classification by comparing them with known bacterial, archaeal, and viral sequences from public databases. The components of microbial communities were identified and characterized using both conventional microbiology and polymerase chain reaction (PCR) techniques in 36 conjunctival swabs. The majority of ocular samples examined by conventional and molecular techniques showed very similar microbial taxonomic profiles, with most of the microorganisms being classified into
Language	English
Publishing date	2021-03-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens10040405
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Article ; Online: Influence of TGFBR2 , TGFB3 , DNMT1 , and DNMT3A Knockdowns on CTGF, TGFBR2, and DNMT3A in Neonatal and Adult Human Dermal Fibroblasts Cell Lines

Katarzyna Tomela / Justyna A. Karolak / Barbara Ginter-Matuszewska / Michal Kabza / Marzena Gajecka

Current Issues in Molecular Biology, Vol 43, Iss 23, Pp 276-

2021 Volume 285

Abstract	Dermal fibroblasts are responsible for the production of the extracellular matrix that undergoes significant changes during the skin aging process. These changes are partially controlled by the TGF-β signaling, which regulates tissue homeostasis dependently on several genes, including CTGF and DNA methyltransferases. To investigate the potential differences in the regulation of the TGF-β signaling and related molecular pathways at distinct developmental stages, we silenced the expression of TGFB1 , TGFB3 , TGFBR2 , CTGF , DNMT1 , and DNMT3A in the neonatal (HDF-N) and adult (HDF-A) human dermal fibroblasts using the RNAi method. Through Western blot, we analyzed the effects of the knockdowns of these genes on the level of the CTGF, TGFBR2, and DNMT3A proteins in both cell lines. In the in vitro assays, we observed that CTGF level was decreased after knockdown of DNMT1 in HDF-N but not in HDF-A. Similarly, the level of DNMT3A was decreased only in HDF-N after silencing of TGFBR2, TGFB3 , or DNMT1 . TGFBR2 level was lower in HDF-N after knockdown of TGFB3 , DNMT1 , or DNMT3A, but it was higher in HDF-A after TGFB1 silencing. The reduction of TGFBR2 after silencing of DNMT3A and vice versa in neonatal cells only suggests the developmental stage-specific interactions between these two genes. However, additional studies are needed to explain the dependencies between analyzed proteins.
Keywords	TGFB1 ; TGFB2 ; TGFB3 ; TGFBR2 ; CTGF ; DNMT3A ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota

Anna Matysiak / Michal Kabza / Justyna A. Karolak / Marcelina M. Jaworska / Malgorzata Rydzanicz / Rafal Ploski / Jacek P. Szaflik / Marzena Gajecka

Pathogens, Vol 10, Iss 405, p

2021 Volume 405

Abstract	The ocular microbiome composition has only been partially characterized. Here, we used RNA-sequencing (RNA-Seq) data to assess microbial diversity in human corneal tissue. Additionally, conjunctival swab samples were examined to characterize ocular surface microbiota. Short RNA-Seq reads, obtained from a previous transcriptome study of 50 corneal tissues, were mapped to the human reference genome GRCh38 to remove sequences of human origin. The unmapped reads were then used for taxonomic classification by comparing them with known bacterial, archaeal, and viral sequences from public databases. The components of microbial communities were identified and characterized using both conventional microbiology and polymerase chain reaction (PCR) techniques in 36 conjunctival swabs. The majority of ocular samples examined by conventional and molecular techniques showed very similar microbial taxonomic profiles, with most of the microorganisms being classified into Proteobacteria , Firmicutes , and Actinobacteria phyla. Only 50% of conjunctival samples exhibited bacterial growth. The PCR detection provided a broader overview of positive results for conjunctival materials. The RNA-Seq assessment revealed significant variability of the corneal microbial communities, including fastidious bacteria and viruses. The use of the combined techniques allowed for a comprehensive characterization of the eye microbiome’s elements, especially in aspects of microbiota diversity.
Keywords	cornea ; eye microbiome ; corneal microbiota ; conjunctival microbiota ; RNA-Seq ; host–pathogen interactions ; Medicine ; R
Subject code	500
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: RetrogeneDB-a database of plant and animal retrocopies.

Rosikiewicz, Wojciech / Kabza, Michal / Kosinski, Jan G / Ciomborowska-Basheer, Joanna / Kubiak, Magdalena R / Makalowska, Izabela

Database : the journal of biological databases and curation

2017 Volume 2017

Abstract: Database url: http://yeti.amu.edu.pl/retrogenedb.: Secondary database url: http://rhesus.amu.edu.pl/retrogenedb. ...

Abstract	Database url: http://yeti.amu.edu.pl/retrogenedb. Secondary database url: http://rhesus.amu.edu.pl/retrogenedb.
MeSH term(s)	Animals ; Databases, Genetic ; Eukaryota/genetics ; Expressed Sequence Tags ; Genome/genetics ; Phylogeny ; Plants/genetics ; RNA/genetics ; Sequence Analysis, RNA ; User-Computer Interface
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2017--01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2496706-3
ISSN	1758-0463 ; 1758-0463
ISSN (online)	1758-0463
ISSN	1758-0463
DOI	10.1093/database/bax038
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Article ; Online: Multiple Differentially Methylated Regions Specific to Keratoconus Explain Known Keratoconus Linkage Loci.

Kabza, Michal / Karolak, Justyna A / Rydzanicz, Malgorzata / Udziela, Monika / Gasperowicz, Piotr / Ploski, Rafal / Szaflik, Jacek P / Gajecka, Marzena

Investigative ophthalmology & visual science

2019 Volume 60, Issue 5, Page(s) 1501–1509

Abstract: Purpose: Keratoconus (KTCN) is a complex eye disorder resulting in loss of visual function. Its development is affected by genetic and environmental components. The aim of this study was to unravel the role of epigenetic factors in KTCN.: Methods: To ...

Abstract	Purpose: Keratoconus (KTCN) is a complex eye disorder resulting in loss of visual function. Its development is affected by genetic and environmental components. The aim of this study was to unravel the role of epigenetic factors in KTCN. Methods: To verify if DNA methylation may play a role in KTCN development, reduced representation bisulfite sequencing of five KTCN and five non-KTCN human corneas was performed. Results: Multiple KTCN-specific differentially methylated regions were detected and many of them overlap previously identified KTCN linkage loci (3p14.3, 5q35.2, 13q32.3, 15q24.1, and 20p13) and chromosome arms that have been linked to KTCN (2q, 4q, 5p, 9p, 14q, and 17q). Reanalysis of the previously described RNA sequencing dataset of 25 KTCN and 25 non-KTCN human corneas revealed that 12 genes downregulated in KTCN and 6 upregulated genes overlapped or were located in the near vicinity of the identified differentially methylated regions. Particularly interesting were the DNA methylation changes in WNT3 and WNT5A encoding Wnt ligands, as they provide a potential explanation for the Wnt signaling pathway dysregulation observed in KTCN. Conclusions: We presented the results of data analysis from the first study of DNA methylation changes in human KTCN corneas compared to non-KTCN samples. We were able to identify genomic regions with distinct patterns of DNA hypo- and hypermethylation and link them to previously found KTCN susceptibility loci as well as transcriptomic disruption of Wnt signaling pathway observed in KTCN.
MeSH term(s)	Adult ; DNA Methylation/genetics ; Epigenesis, Genetic ; Female ; Genetic Linkage ; Genetic Predisposition to Disease ; Humans ; Keratoconus/genetics ; Keratoconus/surgery ; Keratoplasty, Penetrating ; Male ; Polymerase Chain Reaction ; Wnt-5a Protein/genetics ; Wnt3 Protein/genetics ; Young Adult
Chemical Substances	WNT3 protein, human ; WNT5A protein, human ; Wnt-5a Protein ; Wnt3 Protein
Language	English
Publishing date	2019-04-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	391794-0
ISSN	1552-5783 ; 0146-0404
ISSN (online)	1552-5783
ISSN	0146-0404
DOI	10.1167/iovs.18-25916
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Article: Characterization of Ocular Surface Microbial Profiles Revealed Discrepancies between Conjunctival and Corneal Microbiota

Matysiak, Anna / Kabza, Michal / Karolak, Justyna A / Jaworska, Marcelina M / Rydzanicz, Malgorzata / Ploski, Rafal / Szaflik, Jacek P / Gajecka, Marzena

Pathogens. 2021 Mar. 30, v. 10, no. 4

2021

Abstract	The ocular microbiome composition has only been partially characterized. Here, we used RNA-sequencing (RNA-Seq) data to assess microbial diversity in human corneal tissue. Additionally, conjunctival swab samples were examined to characterize ocular surface microbiota. Short RNA-Seq reads, obtained from a previous transcriptome study of 50 corneal tissues, were mapped to the human reference genome GRCh38 to remove sequences of human origin. The unmapped reads were then used for taxonomic classification by comparing them with known bacterial, archaeal, and viral sequences from public databases. The components of microbial communities were identified and characterized using both conventional microbiology and polymerase chain reaction (PCR) techniques in 36 conjunctival swabs. The majority of ocular samples examined by conventional and molecular techniques showed very similar microbial taxonomic profiles, with most of the microorganisms being classified into Proteobacteria, Firmicutes, and Actinobacteria phyla. Only 50% of conjunctival samples exhibited bacterial growth. The PCR detection provided a broader overview of positive results for conjunctival materials. The RNA-Seq assessment revealed significant variability of the corneal microbial communities, including fastidious bacteria and viruses. The use of the combined techniques allowed for a comprehensive characterization of the eye microbiome’s elements, especially in aspects of microbiota diversity.
Keywords	Actinobacteria ; Archaea ; Firmicutes ; Proteobacteria ; bacterial growth ; cornea ; genome ; humans ; microbiome ; polymerase chain reaction ; sequence analysis ; transcriptome
Language	English
Dates of publication	2021-0330
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens10040405
Database	NAL-Catalogue (AGRICOLA)

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