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Analysis of human gene transcripts: Identification and characterisation based on homology and differential expression
KTH, Superseded Departments, Biotechnology.ORCID iD: 0000-0003-0996-1644
1998 (English)Doctoral thesis, comprehensive summary (Other scientific)
Place, publisher, year, edition, pages
Stockholm: KTH , 1998. , 68 p.
National Category
Industrial Biotechnology
Identifiers
URN: urn:nbn:se:kth:diva-2751ISBN: 91-7170-347-0 (print)OAI: oai:DiVA.org:kth-2751DiVA: diva2:8462
Public defence
1998-12-18, 00:00
Note
QC 20100615Available from: 2000-01-01 Created: 2000-01-01 Last updated: 2010-06-17Bibliographically approved
List of papers
1. FALL-39, a putative human peptide antibiotic, is cysteine-free and expressed in bone marrow and testis.
Open this publication in new window or tab >>FALL-39, a putative human peptide antibiotic, is cysteine-free and expressed in bone marrow and testis.
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1995 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 92, no 1, 195-9 p.Article in journal (Refereed) Published
Abstract [en]

PR-39, a proline/arginine-rich peptide antibiotic, has been purified from pig intestine and later shown to originate in the bone marrow. Intending to isolate a clone for a human counterpart to PR-39, we synthesized a PCR probe derived from the PR-39 gene. However, when this probe was used to screen a human bone marrow cDNA library, eight clones were obtained with information for another putative human peptide antibiotic, designated FALL-39 after the first four residues. FALL-39 is a 39-residue peptide lacking cysteine and tryptophan. All human peptide antibiotics previously isolated (or predicted) belong to the defensin family and contain three disulfide bridges. The clone for prepro-FALL-39 encodes a cathelin-like precursor protein with 170 amino acid residues. We have postulated a dibasic processing site for the mature FALL-39 and chemically synthesized the putative peptide. In basal medium E, synthetic FALL-39 was highly active against Escherichia coli and Bacillus megaterium. Residues 13-34 in FALL-39 can be predicted to form a perfect amphiphatic helix, and CD spectra showed that medium E induced 30% helix formation in FALL-39. RNA blot analyses disclosed that the gene for FALL-39 is expressed mainly in human bone marrow and testis.

National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-13359 (URN)7529412 (PubMedID)
Note
QC 20100615Available from: 2010-06-15 Created: 2010-06-15 Last updated: 2017-12-12Bibliographically approved
2. The human gene FALL39 and processing of the cathelin precursor to the antibacterial peptide LL-37 in granulocytes.
Open this publication in new window or tab >>The human gene FALL39 and processing of the cathelin precursor to the antibacterial peptide LL-37 in granulocytes.
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1996 (English)In: European Journal of Biochemistry, ISSN 0014-2956, E-ISSN 1432-1033, Vol. 238, no 2, 325-32 p.Article in journal (Refereed) Published
Abstract [en]

The peptide FA-LL-37, previously termed FALL-39, was originally predicted from on ORF of a cDNA clone isolated from a human bone marrow library. This peptide was synthesized and found to have antibacterial activity. We have now characterized and sequenced the complete gene for FA-LL-37, termed FALL39. It is a compact gene of 1963 bp with four exons. Exons 1-3 code for a signal sequence and the cathelin region. Exon 4 contains the information for the mature antibacterial peptide. Our results indicate that FALL39 is the only member of the cathelin gene family present in the human genome. Potential binding sites for acute-phase-response factors are identified in the promoter and in intron 2. A possible role for the cytokine interleukin-6 in the regulation of FALL 39 is discussed. Anti-(FA-LL-37) IgG located the peptide in granulocytes and we isolated the mature peptide from these cells after degranulation. Structural analysis determined the mature peptide to be LL-37. To obtain LL-37 for antibacterial assays, synthetic FA-LL-37 was degraded with dipeptidyl-peptidase I. This analysis showed that mature LL-37 is a potent antibacterial peptide.

National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-13360 (URN)8681941 (PubMedID)
Note
QC 20100615Available from: 2010-06-15 Created: 2010-06-15 Last updated: 2017-12-12Bibliographically approved
3. Solid-phase method for differential display of genes expressed in hematopoietic stem cells.
Open this publication in new window or tab >>Solid-phase method for differential display of genes expressed in hematopoietic stem cells.
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1996 (English)In: BioTechniques, ISSN 0736-6205, E-ISSN 1940-9818, Vol. 21, no 1, 114-21 p.Article in journal (Refereed) Published
Abstract [en]

A solid-phase differential display method was designed to analyze differential gene expression in samples with low amounts of mRNA. The principle was based on using a biotinylated probe to capture the mRNA and priming both the first-strand synthesis and the subsequent polymerase chain reaction step. Coupling the mRNA to a solid phase during the procedure simplified the purification steps, limited sample loss and enabled rapid handling of mRNA. DNA contamination was also minimized when the mRNA was bound to a solid phase. Optimization of the differential display method was achieved by analyzing both the enzymatic conditions and the required cell amounts. The approach was used for the characterization of genes expressed in the most immature hematopoietic progenitor cells (CD34+CD38-). The majority of the differentially expressed fragments represented previously uncharacterized sequences.

National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-13361 (URN)8816245 (PubMedID)
Note
QC 20100615Available from: 2010-06-15 Created: 2010-06-15 Last updated: 2017-12-12Bibliographically approved
4. Cloning and characterization of ZNF189, a novel human Krüppel-like zinc finger gene localized to chromosome 9q22-q31.
Open this publication in new window or tab >>Cloning and characterization of ZNF189, a novel human Krüppel-like zinc finger gene localized to chromosome 9q22-q31.
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1998 (English)In: Genomics, ISSN 0888-7543, E-ISSN 1089-8646, Vol. 50, no 2, 213-21 p.Article in journal (Refereed) Published
Abstract [en]

A 3-kb-long cDNA encoding a Krüppel-like human zinc finger protein was isolated and mapped to chromosome 9q22-q31. The ZNF189 gene encodes a protein with 16 zinc fingers at its C-terminus and belongs to the Krüppel-associated box (KRAB)-containing group of zinc finger proteins. Four differently spliced cDNA transcripts, differing at the 5' coding region where a KRAB A repressor domain is encoded, were isolated. In addition, Northern blot analysis indicates the presence of two additional unidentified splice variants. Comparison of cDNA and genomic sequences shows that the ZNF189 gene spans approximately 11 kb and is organized into at least four exons, the large 3'-end exon coding for the complete zinc finger domain and the 3' untranslated region. ZNF189 is expressed in all tissues and cell types currently investigated, at varying levels, but with a tissue- or cell-type-restricted expression pattern for the different splice variants. ZNF189 is conserved in the genome of several mammalian species. Direct sequencing of the ZNF189 gene in microdissected tumor biopsies of sporadic basal cell carcinoma and squamous cell carcinoma reveals no mutations in the coding sequence or at exon/intron boundaries.

National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-13362 (URN)10.1006/geno.1998.5309 (DOI)9653648 (PubMedID)
Note
QC 20100615Available from: 2010-06-15 Created: 2010-06-15 Last updated: 2017-12-14Bibliographically approved
5. Direct sequencing of the ZNF 189 gene promotor reveals artifact hot spot mutations.
Open this publication in new window or tab >>Direct sequencing of the ZNF 189 gene promotor reveals artifact hot spot mutations.
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(English)Manuscript (preprint) (Other academic)
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-13364 (URN)
Note
QC 20100615Available from: 2010-06-15 Created: 2010-06-15 Last updated: 2010-06-17Bibliographically approved
6. A cDNA RDA protocol using solid-phase technology suited for analysis in small tissue samples.
Open this publication in new window or tab >>A cDNA RDA protocol using solid-phase technology suited for analysis in small tissue samples.
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2000 (English)In: Biomolecular Engineering, ISSN 1389-0344, E-ISSN 1878-559X, Vol. 17, no 1, 1-9 p.Article in journal (Refereed) Published
Abstract [en]

cDNA representational difference analysis (cDNA RDA) is a PCR-based subtractive enrichment procedure for the cloning of differentially expressed genes. In this study, we have further developed the procedure to take advantage of solid-phase technology, and to facilitate the use of RDA when starting material is limited. Several parameters of the PCR-based generation of cDNA representations were investigated, and a solid-phase based purification step was introduced to simplify removal of digested adapter-ends and uncleaved fragments. The use of magnetic particles increased the speed of the method, and also eliminated the risk of carry-over contamination between iterative steps of subtraction and PCR amplification. The modified protocol was evaluated in monitoring differences in gene expression in (i) a rat system consisting of livers with and without growth hormone treatment, and in (ii) a human system consisting of normal colon and colon cancer.

National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-13363 (URN)11042471 (PubMedID)
Note
QC 20100615Available from: 2010-06-15 Created: 2010-06-15 Last updated: 2017-12-12Bibliographically approved

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