Randolph B Caldwell

Randolph B Caldwell
Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) | HZM · Research Unit Radiation Cytogenetics

MS Biotechnology

About

48
Publications
46,240
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3,886
Citations
Citations since 2016
22 Research Items
940 Citations
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2016201720182019202020212022050100150
2016201720182019202020212022050100150

Publications

Publications (48)
Article
Full-text available
Activation‐induced cytidine deaminase (AID) is required for the immunoglobulin diversification processes of somatic hypermutation, gene conversion and class‐switch recombination. The targeting of AID's deamination activity is thought to be a combination of cis‐ and trans‐acting elements, but has not been fully elucidated. Deletion analysis of putat...
Article
Full-text available
PC4 is an abundant single-strand DNA binding protein that has been implicated in transcription and DNA repair. Here, we show that PC4 is involved in the cellular DNA damage response. To elucidate the role, we used the DT40 chicken B cell model, which produces clustered DNA lesions at Ig loci via the action of activation-induced deaminase. Our resul...
Article
Full-text available
Histone demethylases have recently gained interest as potential targets in cancer treatment and several histone demethylases have been implicated in the DNA damage response. We investigated the effects of siRNA-mediated depletion of histone demethylase Jarid1A (KDM5A, RBP2), which demethylates transcription activating tri- and dimethylated lysine 4...
Data
Depletion of Jarid1A does not lead to strong induction of p21. Expression of p21 after depletion of Jarid1A in HeLa, MCF-7 and U2OS cells, 72 h after transfection with scr or Jarid1A siRNA. A representative sample and its quantitative evaluation are shown. Cont = untransfected control. (TIF)
Data
Depletion of Jarid1A does not affect anti-correlation of γH2AX and H3K4me3 or active RNA Pol II, respectively, after ion irradiation. HeLa cell transfected with scr or Jarid1A A1+A3 siRNAs were subject to ion microirradiation with single carbon ions applied in line patterns (lateral distance between single ion hits 1 μm, distance between “lines” 5...
Data
Early formation of γH2AX foci is not affected by depletion of Jarid1A. 72 h after transfection with scr or Jarid1A A1+A3 siRNA, HeLa cells were irradiated in a small angle configuration with 55 MeV carbon ions and fixed after 5 min (A) and 2 min (B), or irradiated with 5 Gy X-rays and fixed after 15 min (C). Indirect immunofluorescence was performe...
Data
Depletion of Jarid1A enhances radiosensitivity. Colony formation experiment with Hela cells transfected with JaridA1 siRNAs A1 or A3 or a combination thereof, as well as untransfected controls and cells transfected with scr siRNA. Cells were irradiated 72 h after siRNA transfection with 0 Gy, 2 Gy, 5 Gy or 10 Gy X-rays. Cells were incubated for 10...
Data
Background and residual 53BP1 and Rad51 foci are not affected by depletion of Jarid1A. Mean background frequency and number of residual 53BP1 and Rad51 foci (+/- SEM) were determined in at least 20 cells after 5 Gy X-irradiation. Cells were fixed before irradiation or at 24 h and 48 h after irradiation and indirect immunofluorescence was performed....
Data
Efficient down-regulation of Jarid1A is associated with a global increase of H3K4me3. (A) Decreased levels of Jarid1A in whole cell protein extracts of HeLa, MCF-7 and U2OS cells after siRNA transfection. Western blot images show levels of Jarid1A in untransfected cells (cont), in cells transfected with scrambled siRNA (scr) and in cells transfecte...
Data
MNase accessibility is not affected by Jarid1A depletion. Analysis of chromatin accessibility by MNase digestion of isolated nuclei. After different incubation periods with 0.5 u MNase, comparable amounts of partially digested DNA were loaded onto an agarose gel. The emerging ladder of mono- and oligonucleosomes is comparable in both samples indica...
Data
Comparison of relative band intensities corresponding to Jarid1A and Jarid1B proteins. Band intensities were normalized with respect to Tubulin loading control. Intensities in HeLa cells were set as 100%. All bands to be compared were on the same blot. Data are from 2 Western Blots. (DOCX)
Article
Full-text available
With rare exceptions, natural evolution is an extremely slow process. One particularly striking exception in the case of protein evolution is in the natural production of antibodies. Developing B cells activate and diversify their immunoglobulin (Ig) genes by recombination, gene conversion (GC) and somatic hypermutation (SHM). Iterative cycles of h...
Article
Endothelial cells are highly sensitive to high doses of ionizing radiation and the cellular response leads to acute damage of the endothelium. This chapter describes how to measure the effects of ionizing radiation on the proteome of endothelial cells, here showing analysis at 4 and 24 h after exposure. Two complementary proteomic strategies, namel...
Article
Full-text available
This work is part of the joint research project ‘radiation-induced DNA damage’ of the KVSF, a BMBF Initiative (maintenance of radiation biology expertise in Germany). The focus of the research is the mechanism of DNA repair, specifically damage repair aspects arising from radiation-induced reactive oxygen species production. The authors will system...
Article
Full-text available
Author Summary It remains an open question how AID-mediated gene diversification is targeted to the immunoglobulin loci. Here we define a cis-acting sequence, named DIVAC for diversification activator, which is required for hypermutation of the Ig light chain gene and sufficient to activate hypermutation at various non-Ig loci in the DT40 B cell li...
Data
(A) Targeting strategy of the GFP2 reporter into four different loci on chromosome 15. (B) Targeting strategy of the GFP2 reporter into the A-MYB, RAD52, BACH2, and BCL6 loci. The targeting strategies used for the insertions into the AID and the RMD1 loci were described previously [2],[29]. (1.87 MB EPS)
Data
Comparison of GFP gene expression levels analyzed by semi-quantitative RT-PCR of primary transfectants belonging to the stepwise deletions series of the ‘W’ fragment. (2.27 MB EPS)
Data
Green fluorescence decrease in individual primary transfectants. (A) GFP2 reporter in the vicinity of the IgL locus. (B) GFP2 reporter in non-Ig loci. (0.11 MB XLS)
Article
Full-text available
Genome-wide mutations and selection within a population are the basis of natural evolution. A similar process occurs during antibody affinity maturation when immunoglobulin genes are hypermutated and only those B cells which express antibodies of improved antigen-binding specificity are expanded. Protein evolution might be simulated in cell culture...
Article
Quidquid agis, prudenter agas et respice finem!-Whatever you do, do it wisely and consider the goal. In consideration of that sage advice, the chicken B-cell line DT40 is an excellent model cell system to study the function of vertebrate genes. In addition to being highly amenable to gene manipulations, the recent influx of genome and gene/protein...
Article
Full-text available
Protein optimization is a major focus of the biotech and pharmaceutical industry. Various in vitro technologies have been developed to accelerate protein evolution and to achieve protein optimization of functional characteristics such as substrate specificity, enzymatic activity and thermostability. The chicken B cell line DT40 diversifies its immu...
Article
The chicken B cell line DT40 is a tool that is uniquely situated to study the function of genes due to its high rate of homologous recombination. As any tool is only as good as the resources behind it, the recent boon and continuing output of available genomic information has only widened the possibilities for the DT40 community. Besides the releas...
Article
Nuclear and cytoplasmic proteins from DT40 B cells are extracted by serial fractionation in this protocol. The protein extracts are suitable for the detection of DNA-protein interaction, protein-protein interaction, DNase I footprinting analysis, and related techniques. This is a general protocol that was adapted as shown here to our use due to the...
Article
Full-text available
A large number of cDNA inserts were sequenced from a high-quality library of chicken bursal lymphocyte cDNAs. Comparisons to public gene databases indicate that the cDNA collection represents more than 2,000 new, full-length transcripts. This resource defines the structure and the coding potential of a large fraction of B-cell specific and housekee...
Article
Full-text available
The understanding of whole genome sequences in higher eukaryotes depends to a large degree on the reliable definition of transcription units including exon/intron structures, translated open reading frames (ORFs) and flanking untranslated regions. The best currently available chicken transcript catalog is the Ensembl build based on the mappings of...
Article
Full-text available
We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a n...
Article
Full-text available
We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a n...
Article
Full-text available
A simple and reliable method for precipitating protein from bacterial culture supernatants based on a pyrogallol red-molybdate-methanol (PRMM) protocol has been developed and applied for the analysis of proteins secreted by a bacterial type III secretion system. PRMM-based precipitation has been shown to be more efficient and robust than are conven...

Questions

Questions (5)
Question
I have received over a dozen repackaged/rebranded invites in the last two weeks, and they all seem to be suspect to say the least. There was a third that sent 3 or 4 emails, but that particular one (ap open access journals)biz is now being reported/blocked as a phishing site.
It must be profitable, as old ones hide behind new email addresses and new ones pop up regularly with "email lists" to spam.
@sajopensource.biz = scholarenajournals.org
@submitresearch.online = scholarena.com
Journal of Waste Management and Disposal
Journal of Food Technology and Food Chemistry
Journal of Nutrition and Obesity
Journal of Public Health and Disease Prevention
@researchinfotext.com = Created: 2019-08-06 10:21:36 UTC Mailing Address: Virginia, United States
Quarterly Journal of Pharmacology and Pharmaceutical Studies
Infotext Journal of Infectious Diseases and Therapy
COVID-19 Pandemic: Case Studies, Commentaries, and Opinions

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Projects (2)
Project
http://www.nature.com/articles/srep28890