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Slotkin RK, Vaughn M, Tanurdžic M, Borges F, Becker JD, Feijó JA, Martienssen RA. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 2009; 136:461-72. [PMID: 19203581 PMCID: PMC2661848 DOI: 10.1016/j.cell.2008.12.038] [Citation(s) in RCA: 749] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Revised: 09/15/2008] [Accepted: 12/11/2008] [Indexed: 10/21/2022]
Abstract
The mutagenic activity of transposable elements (TEs) is suppressed by epigenetic silencing and small interfering RNAs (siRNAs), especially in gametes that could transmit transposed elements to the next generation. In pollen from the model plant Arabidopsis, we show that TEs are unexpectedly reactivated and transpose, but only in the pollen vegetative nucleus, which accompanies the sperm cells but does not provide DNA to the fertilized zygote. TE expression coincides with downregulation of the heterochromatin remodeler decrease in DNA methylation 1 and of many TE siRNAs. However, 21 nucleotide siRNAs from Athila retrotransposons are generated and accumulate in pollen and sperm, suggesting that siRNA from TEs activated in the vegetative nucleus can target silencing in gametes. We propose a conserved role for reprogramming in germline companion cells, such as nurse cells in insects and vegetative nuclei in plants, to reveal intact TEs in the genome and regulate their activity in gametes.
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Research Support, N.I.H., Extramural |
16 |
749 |
2
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Vitaliano PP, Russo J, Carr JE, Maiuro RD, Becker J. The Ways of Coping Checklist: Revision and Psychometric Properties. MULTIVARIATE BEHAVIORAL RESEARCH 1985; 20:3-26. [PMID: 26776273 DOI: 10.1207/s15327906mbr2001_1] [Citation(s) in RCA: 593] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
This study examined the psychometric properties of the "original" seven factored scales derived by Aldwin et al. from Folkman and Lazarus' Ways of Coping Checklist (WCCL) versus a revised set of scales. Four psychometric properties were examined including the reproducibility of the factor structure of the original scales, the internal consistency reliabilities and intercorrelations of the original and the revised scales, the construct and concurrent validity of the scales, and their relationships to demographic factors. These properties were studied on three distressed samples: 83 psychiatric outpatients, 62 spouses of patients with Alzheimer's disease, and 425 medical students. The revised scales were consistently shown to be more reliable and to share substantially less variance than the original scales across all samples. In terms of construct validity, depression was positively related to the revised Wishful Thinking Scale and negatively related to the revised Problem-Focused Scale consistently across samples. Anxiety was also related to these scales, and in addition, it was positively related to the Seeks Social Support Scale across samples. The Mixed Scale was the only original scale that was consistently related to depression and anxiety across the three samples. Evidence for concurrent validity was provided by the fact that medical students in group therapy had significantly higher original and revised scale scores than students not participating in such groups. Both sets of scales were shown to be generally free of demographic biases.
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40 |
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3
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Becker J, Knackstedt R, Pöppelbuß J. Developing Maturity Models for IT Management. BUSINESS & INFORMATION SYSTEMS ENGINEERING 2009. [DOI: 10.1007/s12599-009-0044-5] [Citation(s) in RCA: 461] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16 |
461 |
4
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Calarco JP, Borges F, Donoghue MT, Van Ex F, Jullien PE, Lopes T, Gardner R, Berger F, Feijó JA, Becker JD, Martienssen RA. Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 2012; 151:194-205. [PMID: 23000270 PMCID: PMC3697483 DOI: 10.1016/j.cell.2012.09.001] [Citation(s) in RCA: 402] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 08/14/2012] [Accepted: 08/30/2012] [Indexed: 11/20/2022]
Abstract
Epigenetic inheritance is more widespread in plants than in mammals, in part because mammals erase epigenetic information by germline reprogramming. We sequenced the methylome of three haploid cell types from developing pollen: the sperm cell, the vegetative cell, and their precursor, the postmeiotic microspore, and found that unlike in mammals the plant germline retains CG and CHG DNA methylation. However, CHH methylation is lost from retrotransposons in microspores and sperm cells and restored by de novo DNA methyltransferase guided by 24 nt small interfering RNA, both in the vegetative nucleus and in the embryo after fertilization. In the vegetative nucleus, CG methylation is lost from targets of DEMETER (DME), REPRESSOR OF SILENCING 1 (ROS1), and their homologs, which include imprinted loci and recurrent epialleles that accumulate corresponding small RNA and are premethylated in sperm. Thus genome reprogramming in pollen contributes to epigenetic inheritance, transposon silencing, and imprinting, guided by small RNA.
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Research Support, N.I.H., Extramural |
13 |
402 |
5
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Pina C, Pinto F, Feijó JA, Becker JD. Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation. PLANT PHYSIOLOGY 2005; 138:744-56. [PMID: 15908605 PMCID: PMC1150393 DOI: 10.1104/pp.104.057935] [Citation(s) in RCA: 372] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Upon germination, pollen forms a tube that elongates dramatically through female tissues to reach and fertilize ovules. While essential for the life cycle of higher plants, the genetic basis underlying most of the process is not well understood. We previously used a combination of flow cytometry sorting of viable hydrated pollen grains and GeneChip array analysis of one-third of the Arabidopsis (Arabidopsis thaliana) genome to define a first overview of the pollen transcriptome. We now extend that study to approximately 80% of the genome of Arabidopsis by using Affymetrix Arabidopsis ATH1 arrays and perform comparative analysis of gene family and gene ontology representation in the transcriptome of pollen and vegetative tissues. Pollen grains have a smaller and overall unique transcriptome (6,587 genes expressed) with greater proportions of selectively expressed (11%) and enriched (26%) genes than any vegetative tissue. Relative gene ontology category representations in pollen and vegetative tissues reveal a functional skew of the pollen transcriptome toward signaling, vesicle transport, and the cytoskeleton, suggestive of a commitment to germination and tube growth. Cell cycle analysis reveals an accumulation of G2/M-associated factors that may play a role in the first mitotic division of the zygote. Despite the relative underrepresentation of transcription-associated transcripts, nonclassical MADS box genes emerge as a class with putative unique roles in pollen. The singularity of gene expression control in mature pollen grains is further highlighted by the apparent absence of small RNA pathway components.
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research-article |
20 |
372 |
6
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Bayer P, Arndt A, Metzger S, Mahajan R, Melchior F, Jaenicke R, Becker J. Structure determination of the small ubiquitin-related modifier SUMO-1. J Mol Biol 1998; 280:275-86. [PMID: 9654451 DOI: 10.1006/jmbi.1998.1839] [Citation(s) in RCA: 308] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The recently discovered small ubiquitin-related modifier SUMO-1 belongs to the growing family of ubiquitin-related proteins involved in postranslational protein modification. Unlike ubiquitin, SUMO-1 does not appear to target proteins for degradation but seems to be involved in the modulation of protein-protein interactions. Independent studies demonstrate an essential function of SUMO-1 in the regulation of nucleo-cytoplasmic transport, and suggest a role in cell-cycle regulation and apoptosis. Here, we present the first three-dimensional structure of SUMO-1 solved by NMR. Although having only 18% amino acid sequence identity with ubiquitin, the overall structure closely resembles that of ubiquitin, featuring the betabetaalphabetabetaalphabeta fold of the ubiquitin protein family. In addition, the position of the two C-terminal Gly residues required for isopeptide bond formation is conserved between ubiquitin and SUMO-1. The most prominent feature of SUMO-1 is a long and highly flexible N terminus, which protrudes from the core of the protein and which is absent in ubiquitin. Furthermore, ubiquitin Lys48, required to generate ubiquitin polymers, is substituted in SUMO-1 by Gln69 at the same position, which provides an explanation of why SUMO-1 has not been observed to form polymers. Moreover, the hydrophobic core of SUMO-1 and ubiquitin is maintained by conserved hydrophobic residues, whereas the overall charge topology of SUMO-1 and ubiquitin differs significantly, suggesting specific modifying enzymes and target proteins for both proteins.
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27 |
308 |
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Borges F, Gomes G, Gardner R, Moreno N, McCormick S, Feijó JA, Becker JD. Comparative transcriptomics of Arabidopsis sperm cells. PLANT PHYSIOLOGY 2008; 148:1168-81. [PMID: 18667720 PMCID: PMC2556834 DOI: 10.1104/pp.108.125229] [Citation(s) in RCA: 294] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Accepted: 07/27/2008] [Indexed: 05/19/2023]
Abstract
In flowering plants, the two sperm cells are embedded within the cytoplasm of the growing pollen tube and as such are passively transported to the embryo sac, wherein double fertilization occurs upon their release. Understanding the mechanisms and conditions by which male gametes mature and take part in fertilization are crucial goals in the study of plant reproduction. Studies of gene expression in male gametes of maize (Zea mays) and Plumbago and in lily (Lilium longiflorum) generative cells already showed that the previously held view of transcriptionally inert male gametes was not true, but genome-wide studies were lacking. Analyses in the model plant Arabidopsis (Arabidopsis thaliana) were hindered, because no method to isolate sperm cells was available. Here, we used fluorescence-activated cell sorting to isolate sperm cells from Arabidopsis, allowing GeneChip analysis of their transcriptome at a genome-wide level. Comparative analysis of the sperm cell transcriptome with those of representative sporophytic tissues and of pollen showed that sperm has a distinct and diverse transcriptional profile. Functional classifications of genes with enriched expression in sperm cells showed that DNA repair, ubiquitin-mediated proteolysis, and cell cycle progression are overrepresented Gene Ontology categories. Moreover, analysis of the small RNA and DNA methylation pathways suggests that distinct mechanisms might be involved in regulating the epigenetic state of the paternal genome. We identified numerous candidate genes whose involvement in sperm cell development and fertilization can now be directly tested in Arabidopsis. These results provide a roadmap to decipher the role of sperm-expressed proteins.
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Comparative Study |
17 |
294 |
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Becker JD, Boavida LC, Carneiro J, Haury M, Feijó JA. Transcriptional profiling of Arabidopsis tissues reveals the unique characteristics of the pollen transcriptome. PLANT PHYSIOLOGY 2003; 133:713-25. [PMID: 14500793 PMCID: PMC219046 DOI: 10.1104/pp.103.028241] [Citation(s) in RCA: 278] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2003] [Revised: 07/07/2003] [Accepted: 07/09/2003] [Indexed: 05/18/2023]
Abstract
Pollen tubes are a good model for the study of cell growth and morphogenesis because of their extreme elongation without cell division. Yet, knowledge about the genetic basis of pollen germination and tube growth is still lagging behind advances in pollen physiology and biochemistry. In an effort to reduce this gap, we have developed a new method to obtain highly purified, hydrated pollen grains of Arabidopsis through flowcytometric sorting, and we used GeneChips (Affymetrix, Santa Clara, CA; representing approximately 8,200 genes) to compare the transcriptional profile of sorted pollen with those of four vegetative tissues (seedlings, leaves, roots, and siliques). We present a new graphical tool allowing genomic scale visualization of the unique transcriptional profile of pollen. The 1,584 genes expressed in pollen showed a 90% overlap with genes expressed in these vegetative tissues, whereas one-third of the genes constitutively expressed in the vegetative tissues were not expressed in pollen. Among the 469 genes enriched in pollen, 162 were selectively expressed, and most of these had not been associated previously with pollen. Their functional classification reveals several new candidate genes, mainly in the categories of signal transduction and cell wall biosynthesis and regulation. Thus, the results presented improve our knowledge of the molecular mechanisms underlying pollen germination and tube growth and provide new directions for deciphering their genetic basis. Because pollen expresses about one-third of the number of genes expressed on average in other organs, it may constitute an ideal system to study fundamental mechanisms of cell biology and, by omission, of cell division.
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research-article |
22 |
278 |
9
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Renault L, Nassar N, Vetter I, Becker J, Klebe C, Roth M, Wittinghofer A. The 1.7 A crystal structure of the regulator of chromosome condensation (RCC1) reveals a seven-bladed propeller. Nature 1998; 392:97-101. [PMID: 9510255 DOI: 10.1038/32204] [Citation(s) in RCA: 225] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The gene encoding the regulator of chromosome condensation (RCC1) was cloned by virtue of its ability to complement the temperature-sensitive phenotype of the hamster cell line tsBN2, which undergoes premature chromosome condensation or arrest in the G1 phase of the cell cycle at non-permissive temperatures. RCC1 homologues have been identified in many eukaryotes, including budding and fission yeast. Mutations in the gene affect pre-messenger RNA processing and transport, mating, initiation of mitosis and chromatin decondensation, suggesting that RCC1 is important in the control of nucleo-cytoplasmic transport and the cell cycle. Biochemically, RCC1 is a guanine-nucleotide-exchange factor for the nuclear Ras homologue Ran; it increases the dissociation of Ran-bound GDP by 10(5)-fold. It may also bind to DNAvia a protein-protein complex. Here we show that the structure of human RCC1, solved to 1.7-A resolution by X-ray crystallography, consists of a seven-bladed propeller formed from internal repeats of 51-68 residues per blade. The sequence and structure of the repeats differ from those of WD40-domain proteins, which also form seven-bladed propellers and include the beta-subunits of G proteins. The nature of the structure explains the consequences of a wide range of known mutations. The region of the protein that is involved in guanine-nucleotide exchange is located opposite the region that is thought to be involved in chromosome binding.
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27 |
225 |
10
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Moser M, Pscherer A, Roth C, Becker J, Mücher G, Zerres K, Dixkens C, Weis J, Guay-Woodford L, Buettner R, Fässler R. Enhanced apoptotic cell death of renal epithelial cells in mice lacking transcription factor AP-2beta. Genes Dev 1997; 11:1938-48. [PMID: 9271117 PMCID: PMC316415 DOI: 10.1101/gad.11.15.1938] [Citation(s) in RCA: 213] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Expression of AP-2 transcription factors has been detected previously in embryonic renal tissues. We show here that AP-2beta -/- mice complete embryonic development and die at postnatal days 1 and 2 because of polycystic kidney disease. Analyses of kidney development revealed that induction of epithelial conversion, mesenchyme condensation, and further glomerular and tubular differentiation occur normally in AP-2beta-deficient mice. At the end of embryonic development expression of bcl-X(L), bcl-w, and bcl-2 is down-regulated in parallel to massive apoptotic death of collecting duct and distal tubular epithelia. Addressing the molecular mechanism we show that transfection of AP-2 into cell lines in vitro strongly suppresses c-myc-induced apoptosis pointing to a function of AP-2 in programming cell survival during embryogenesis. The position of the human AP-2beta gene was identified at chromosome 6p12-p21.1, within a region that has been mapped for autosomal recessive polycystic kidney disease (ARPKD). Sequence analyses of ARPKD patients and linkage analyses using intragenic polymorphic markers indicate that the AP-2beta gene is located in close proximity to but distinct from the ARPKD gene.
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research-article |
28 |
213 |
11
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Becker J, Vos P, Kuiper M, Salamini F, Heun M. Combined mapping of AFLP and RFLP markers in barley. MOLECULAR & GENERAL GENETICS : MGG 1995; 249:65-73. [PMID: 8552035 DOI: 10.1007/bf00290237] [Citation(s) in RCA: 209] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
AFLP marker technology allows efficient DNA fingerprinting and the analysis of large numbers of polymorphic restriction fragments on polyacrylamide gels. Using the doubled haploids from the F1 of the cross Proctor x Nudinka, 118 AFLP markers were mapped onto a barley (Hordeum vulgare L.) RFLP map, also including five microsatellite and four protein marker loci. The AFLP markers mapped to all parts of the barley chromosomes and filled in the gaps on barley chromosomes 2L, 4L and 6 in which no RFLP loci had been mapped. Interestingly, the AFLP markers seldom interrupted RFLP clusters, but grouped next to them. The combined map covers 1873 cM, with a total of 282 markers. The merging of AFLP and RFLP markers increased the total map length; 402 cM were added to the map at the tips of chromosomes or in regions corresponding to earlier gaps. Another 375 cM resulted from mapping AFLP markers near to RFLP clusters or in between non-clustered RFLP markers.
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Comparative Study |
30 |
209 |
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Vitaliano PP, Maiuro RD, Russo J, Becker J. Raw versus relative scores in the assessment of coping strategies. J Behav Med 1987; 10:1-18. [PMID: 3585998 DOI: 10.1007/bf00845124] [Citation(s) in RCA: 201] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Raw scores (frequency of efforts) versus relative scores (percentage of efforts) were compared on the five scales of the revised Ways of Coping Checklist. It was hypothesized that, conditional on the source of and appraisal of a stressor, problem-focused coping should be inversely related and Wishful Thinking should be positively related to depression when relative scores were used but that raw problem-focused scores would be less clearly related to depression in such a way. It was further hypothesized that these relationships would hold for very diverse samples: psychiatric outpatients (n = 145), spouses of patients with Alzheimer's disease (n = 66), and medical students (n = 185). Given the maladaptive status of the psychiatric outpatients, it was hypothesized that they would report more emotion-focused strategies and less problem-focused coping than the nonclinical samples and that these differences would be better observed using relative rather than raw scores. The hypotheses were generally supported.
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201 |
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Becker J, Walter W, Yan W, Craig EA. Functional interaction of cytosolic hsp70 and a DnaJ-related protein, Ydj1p, in protein translocation in vivo. Mol Cell Biol 1996; 16:4378-86. [PMID: 8754838 PMCID: PMC231436 DOI: 10.1128/mcb.16.8.4378] [Citation(s) in RCA: 190] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
In order to analyze the in vivo role of the SSA class of cytosolic 70-kDa heat shock proteins (hsps) of Saccharomyces cerevisiae, we isolated a temperature-sensitive mutant of SSA1. The effect of a shift of mutant cells (ssa1ts ssa2 ssa3 ssa4) from the permissive temperature of 23 degrees C to the nonpermissive temperature of 37 degrees C on the processing of several precursor proteins translocated into the endoplasmic reticulum or mitochondria was assessed. Of three mitochondrial proteins tested, the processing of only one, the beta subunit of the F1F0 ATPase, was dramatically affected. Of six proteins destined for the endoplasmic reticulum, the translocation of only prepro-alpha-factor and proteinase A was inhibited. The processing of prepro-alpha-factor was inhibited within 2 min of the shift to 37 degrees C, suggesting a direct effect of the hsp70 defect on translocation. More than 50% of radiolabeled alpha-factor accumulated in the precursor form, with the remainder rapidly reaching the mature form. However, the translocation block was complete, as the precursor form could not be chased through the translocation pathway. Since DnaJ-related proteins are known to interact with hsp70s and strains containing conditional mutations in a dnaJ-related gene, YDJ1, are defective in translocation of prepro-alpha-factor, we looked for a genetic interaction between SSA genes and YDJ1 in vivo. We found that a deletion mutation of YDJ1 was synthetically lethal in a ssa1ts ssa2 ssa3 ssa4 background. In addition, a strain containing a single functional SSA gene, SSA1, and a deletion of YDJ1 accumulated the precursor form of alpha-factor. However, no genetic interaction was observed between a YDJ1 mutation and mutations in the SSB genes, which encode a second class of cytosolic hsp70 chaperones. These results are consistent with SSA proteins and Ydj1p acting together in the translocation process.
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research-article |
29 |
190 |
14
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Fiore J, Becker J, Coppel DB. Social network interactions: a buffer or a stress. AMERICAN JOURNAL OF COMMUNITY PSYCHOLOGY 1983; 11:423-439. [PMID: 6637903 DOI: 10.1007/bf00894057] [Citation(s) in RCA: 186] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Forty-four caregivers to spouses with a diagnosis of Alzheimer's disease provided a stressed subject population considered at high risk for depression. Unlike more typical unidirectional measures of perceived social support quality, subject ratings were elicited separately as to how helpful as well as how upsetting each network member was in five different support categories. Correlations between perceived network "upset" and depression (Beck Depression Inventory) were highly significant, while in no case did perceived "helpfulness" relate to depression. Using stepwise multiple regression, the set of five support category Upset ratings predicted depression better than did helpful/upset ratios, which in turn predicted depression better than the Helpfulness ratings as a group. The implications of these findings for the conceptualization of social support and its measurement are discussed.
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186 |
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Abstract
The Screen for Caregiver Burden (SCB) is a measure designed to identify distressing caregiver experiences rapidly. The 25-item SCB, created specifically for spouse caregivers of Alzheimer's care recipients, provides scores for objective burden (OB; number of potentially negative experiences) and subjective burden (SB; appraised distress in response to the experiences). Three separate studies (total N = 191) demonstrate the internal consistency, test-retest reliability, and validity (content, divergent, convergent, and criterion) of the scales. Finally, evidence suggests that changes in OB and SB over time are explained by changes in care-recipient functioning and caregiver distress.
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34 |
184 |
16
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Löning T, Ikenberg H, Becker J, Gissmann L, Hoepfer I, zur Hausen H. Analysis of oral papillomas, leukoplakias, and invasive carcinomas for human papillomavirus type related DNA. J Invest Dermatol 1985; 84:417-20. [PMID: 2987361 DOI: 10.1111/1523-1747.ep12265517] [Citation(s) in RCA: 183] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Five papillomas, five leukoplakias, and six carcinomas were investigated for the presence of papillomavirus group-specific antigens and viral DNA. Viral proteins were identified with genus-specific papillomavirus antibodies. Cloned human papillomavirus (HPV) 11 and 16 DNA were used as probes in Southern blot hybridization at conditions of different stringency in order to determine viral DNA. Four of five papillomas, four of five leukoplakias, and three of six carcinomas reacted with HPV DNA probes and revealed some stained cells after exposure to HPV antibodies. HPV type 16 was found in one carcinoma and HPV type 11 was demonstrated in another case of carcinoma.
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40 |
183 |
17
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Werner-Washburne M, Becker J, Kosic-Smithers J, Craig EA. Yeast Hsp70 RNA levels vary in response to the physiological status of the cell. J Bacteriol 1989; 171:2680-8. [PMID: 2651414 PMCID: PMC209952 DOI: 10.1128/jb.171.5.2680-2688.1989] [Citation(s) in RCA: 173] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Yeast Hsp70 genes constitute a multigene family in which at least five of the nine members are heat inducible. Hsp70 RNA levels also vary dramatically during stationary arrest and sporulation. During growth to stationary phase, SSB1-SSB2 and SSC1 RNAs decreased in abundance as cell density increased. In contrast, SSA1-SSA2 RNA levels increased before the diauxic shift and then decreased as cells approach stationary phase. SSA3 RNA was detected only after the diauxic shift and accumulated to high levels as cells entered stationary phase. This accumulation was reversed by addition of glucose. Studies with cyr1 mutants indicated that SSA3 RNA accumulation is stimulated by decreasing intracellular cyclic AMP concentrations. When cells were incubated in sporulation medium, most Hsp70 RNAs, with the exception of SSA1-SSA2 RNA, decreased in abundance. This finding contrasted with the SSA1-SSA2 pattern observed during growth to stationary phase. SSA3 RNA was not detected during growth in acetate-based medium but accumulated after several hours. SSA3 RNA accumulation was higher in sporulating cells than in nonsporulating cells and was reversed by addition of glucose.
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research-article |
36 |
173 |
18
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Borg M, Jacob Y, Susaki D, LeBlanc C, Buendía D, Axelsson E, Kawashima T, Voigt P, Boavida L, Becker J, Higashiyama T, Martienssen R, Berger F. Targeted reprogramming of H3K27me3 resets epigenetic memory in plant paternal chromatin. Nat Cell Biol 2020; 22:621-629. [PMID: 32393884 PMCID: PMC7116658 DOI: 10.1038/s41556-020-0515-y] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 03/31/2020] [Indexed: 12/22/2022]
Abstract
Epigenetic marks are reprogrammed in the gametes to reset genomic potential in the next generation. In mammals, paternal chromatin is extensively reprogrammed through the global erasure of DNA methylation and the exchange of histones with protamines1,2. Precisely how the paternal epigenome is reprogrammed in flowering plants has remained unclear since DNA is not demethylated and histones are retained in sperm3,4. Here, we describe a multi-layered mechanism by which H3K27me3 is globally lost from histone-based sperm chromatin in Arabidopsis. This mechanism involves the silencing of H3K27me3 writers, activity of H3K27me3 erasers and deposition of a sperm-specific histone, H3.10 (ref. 5), which we show is immune to lysine 27 methylation. The loss of H3K27me3 facilitates the transcription of genes essential for spermatogenesis and pre-configures sperm with a chromatin state that forecasts gene expression in the next generation. Thus, plants have evolved a specific mechanism to simultaneously differentiate male gametes and reprogram the paternal epigenome.
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Research Support, N.I.H., Extramural |
5 |
148 |
19
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Pagel MD, Erdly WW, Becker J. Social networks: We get by with (and in spite of) a little help from our friends. J Pers Soc Psychol 1987; 53:793-804. [PMID: 3681652 DOI: 10.1037/0022-3514.53.4.793] [Citation(s) in RCA: 140] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Studies of social support networks have almost exclusively measured only their positive aspects. In this research, we investigated both the helpful or positive and the upsetting or negative aspects of social networks in a longitudinal study of spouses caring for a husband or wife with Alzheimer's disease, a progressive senile dementia. Measures of helpful and upsetting aspects of the care givers' networks, derived from interviews and daily interaction ratings, were studied for their relations with overall network satisfaction and depression at an initial interview period (n = 68) and at a follow-up period about 10 months later (n = 38). Results from hierarchical multiple regression analyses, in which care givers' age and sex and a measure of the spouses' health status were controlled, showed that the care givers' degree of upset with their networks was strongly associated with lower network satisfaction and increased depression at both time periods. Helpful aspects bore little or no direct relation to either depression or network satisfaction. Helpful aspects of the network did, however, interact with network upset in predicting network satisfaction, and depression (combined probabilities test, p less than .05). Longitudinal predictions of follow-up depression, after age, sex, care givers' health status, and initial depression levels were controlled, showed that changes in upsetting aspects of one's network were predictive of changes in depression over time. We interpreted these results within an attributional framework that emphasizes the salience of upsetting events within a social network.
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38 |
140 |
20
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Hogekamp C, Arndt D, Pereira PA, Becker JD, Hohnjec N, Küster H. Laser microdissection unravels cell-type-specific transcription in arbuscular mycorrhizal roots, including CAAT-box transcription factor gene expression correlating with fungal contact and spread. PLANT PHYSIOLOGY 2011; 157:2023-43. [PMID: 22034628 PMCID: PMC3327204 DOI: 10.1104/pp.111.186635] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 10/26/2011] [Indexed: 05/20/2023]
Abstract
Arbuscular mycorrhizae (AM) are the most widespread symbioses on Earth, promoting nutrient supply of most terrestrial plant species. To unravel gene expression in defined stages of Medicago truncatula root colonization by AM fungi, we here combined genome-wide transcriptome profiling based on whole mycorrhizal roots with real-time reverse transcription-PCR experiments that relied on characteristic cell types obtained via laser microdissection. Our genome-wide approach delivered a core set of 512 genes significantly activated by the two mycorrhizal fungi Glomus intraradices and Glomus mossae. Focusing on 62 of these genes being related to membrane transport, signaling, and transcriptional regulation, we distinguished whether they are activated in arbuscule-containing or the neighboring cortical cells harboring fungal hyphae. In addition, cortical cells from nonmycorrhizal roots served as a reference for gene expression under noncolonized conditions. Our analysis identified 25 novel arbuscule-specific genes and 37 genes expressed both in the arbuscule-containing and the adjacent cortical cells colonized by fungal hyphae. Among the AM-induced genes specifying transcriptional regulators were two members encoding CAAT-box binding transcription factors (CBFs), designated MtCbf1 and MtCbf2. Promoter analyses demonstrated that both genes were already activated by the first physical contact between the symbionts. Subsequently, and corresponding to our cell-type expression patterns, they were progressively up-regulated in those cortical areas colonized by fungal hyphae, including the arbuscule-containing cells. The encoded CBFs thus represent excellent candidates for regulators that mediate a sequential reprogramming of root tissues during the establishment of an AM symbiosis.
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Ortiz-Ramírez C, Hernandez-Coronado M, Thamm A, Catarino B, Wang M, Dolan L, Feijó JA, Becker JD. A Transcriptome Atlas of Physcomitrella patens Provides Insights into the Evolution and Development of Land Plants. MOLECULAR PLANT 2016; 9:205-220. [PMID: 26687813 DOI: 10.1016/j.molp.2015.12.002] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/28/2015] [Accepted: 12/01/2015] [Indexed: 05/08/2023]
Abstract
Identifying the genetic mechanisms that underpin the evolution of new organ and tissue systems is an aim of evolutionary developmental biology. Comparative functional genetic studies between angiosperms and bryophytes can define those genetic changes that were responsible for developmental innovations. Here, we report the generation of a transcriptome atlas covering most phases in the life cycle of the model bryophyte Physcomitrella patens, including detailed sporophyte developmental progression. We identified a comprehensive set of sporophyte-specific transcription factors, and found that many of these genes have homologs in angiosperms that function in developmental processes such as flowering and shoot branching. Deletion of the PpTCP5 transcription factor results in development of supernumerary sporangia attached to a single seta, suggesting that it negatively regulates branching in the moss sporophyte. Given that TCP genes repress branching in angiosperms, we suggest that this activity is ancient. Finally, comparison of P. patens and Arabidopsis thaliana transcriptomes led us to the identification of a conserved core of transcription factors expressed in tip-growing cells. We identified modifications in the expression patterns of these genes that could account for developmental differences between P. patens tip-growing cells and A. thaliana pollen tubes and root hairs.
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Gratacós E, Carreras E, Becker J, Lewi L, Enríquez G, Perapoch J, Higueras T, Cabero L, Deprest J. Prevalence of neurological damage in monochorionic twins with selective intrauterine growth restriction and intermittent absent or reversed end-diastolic umbilical artery flow. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2004; 24:159-163. [PMID: 15287053 DOI: 10.1002/uog.1105] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
OBJECTIVE To assess the incidence of parenchymal lesions on early and late neonatal brain scans and its association with the presence or absence of intermittent absent or reversed end-diastolic umbilical artery flow velocity (A/REDV) in monochorionic twins complicated by selective intrauterine growth restriction (IUGR), as compared to dichorionic twins and monochorionic twins without selective IUGR. METHODS This was a prospective cohort study involving 42 monochorionic twins diagnosed with selective IUGR and managed expectantly. The presence or absence of intermittent A/REDV was recorded in all cases. This study group was compared to dichorionic twins (n = 29) and monochorionic twins without selective IUGR (n = 32) delivered at 26-34 weeks during the study period. All infants underwent an early neonatal brain scan (at or before the fourth day of postnatal life) and at least one follow-up scan during the first 28 days of postnatal life. Perinatal outcome and the incidence of neurological damage were compared between the study groups. RESULTS The incidence of intrauterine fetal death (IUD) and periventricular leukomalacia was significantly increased in monochorionic twins complicated with selective IUGR, as compared with the other study groups. Intermittent A/REDV was observed in 22/42 (52.4%) twin pairs, and was always present in the growth-restricted twin. The incidence of IUD (overall 9/44 (20.5%) vs. 0/40, P < 0.001; smaller twin 6/22 (27.3%) vs. 0/20, P < 0.05) and parenchymal brain damage (overall 7/35 (20.0%) vs. 2/40 (5.0%), P = 0.07; larger twin 7/19 (36.8%) vs. 1/20 (5.0%), P < 0.05) was significantly higher in pregnancies with intermittent A/REDV than in those without intermittent A/REDV. Brain damage usually occurred in the larger twin, irrespective of whether the smaller twin was liveborn or not. CONCLUSIONS The presence of intermittent A/REDV in monochorionic twins with selective IUGR identifies a subgroup with an elevated risk of intrauterine demise of the smaller twin and neurological damage in the larger twin; this latter finding is not restricted to cases with IUD of the cotwin.
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Schwarz F, Bieling K, Latz T, Nuesry E, Becker J. Healing of intrabony peri-implantitis defects following application of a nanocrystalline hydroxyapatite (Ostimtm) or a bovine-derived xenograft (Bio-Osstm) in combination with a collagen membrane (Bio-Gidetm). A case series. J Clin Periodontol 2006; 33:491-9. [PMID: 16820037 DOI: 10.1111/j.1600-051x.2006.00936.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVES The aim of the present case series was to evaluate the healing of intrabony peri-implantitis defects following application of a nanocrystalline hydroxyapatite (NHA) or a bovine-derived xenograft in combination with a collagen membrane (BDX+BG). MATERIAL AND METHODS Twenty-two patients having moderate peri-implantitis (n=22 intrabony defects) were randomly treated with (i) access flap surgery (AFS) and the application of NHA, or with AFS and the application of BDX+BG. Clinical parameters were recorded at baseline and after 6 months of non-submerged healing. RESULTS Post-operative wound healing revealed that NHA compromized initial adhesion of the mucoperiosteal flaps in all patients. At 6 months after therapy, NHA showed a reduction in the mean PD from 7.0+/-0.6 to 4.9+/-0.6 mm and a change in the mean clinical attachment loss (CAL) from 7.5+/-0.8 to 5.7+/-1.0 mm. In the BDX+BC group, the mean PD was reduced from 7.1+/-0.8 to 4.5+/-0.7 mm and the mean CAL changed from 7.5+/-1.0 to 5.2+/-0.8 mm. CONCLUSION Within the limits of the present case series, it can be concluded that at 6 months after surgery both therapies resulted in clinically important PD reductions and CAL gains.
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Russo J, Vitaliano PP, Brewer DD, Katon W, Becker J. Psychiatric disorders in spouse caregivers of care recipients with Alzheimer's disease and matched controls: a diathesis-stress model of psychopathology. JOURNAL OF ABNORMAL PSYCHOLOGY 1995; 104:197-204. [PMID: 7897043 DOI: 10.1037/0021-843x.104.1.197] [Citation(s) in RCA: 117] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
To test a diathesis-stress model of psychopathology, the authors examined the rates of current and lifetime psychiatric disorders in 82 spouse caregivers of Alzheimer's disease (AD) patients and 86 demographically matched controls. Caregivers and controls did not differ in the prevalence of disorders before the onset of care recipients' AD (or during a similar time period for the controls); caregivers experienced more depressive-anxiety disorders after the onset of patient's AD than controls. This study strongly supported the 3 key components of a diathesis-stress interaction. First, caregivers with a psychiatric history prior to the onset of patient's AD were more likely than caregivers with no history to receive a diagnosis after the onset of AD. Second, a similar relationship existed for controls. Finally, caregivers with a psychiatric history were more likely to experience a recurrence after the onset of AD than controls with a psychiatric history. These findings indicate that the diathesis of psychiatric history and the stress of caregiving interact, resulting in the observed group differences in the prevalence of psychiatric disorders.
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Breuker D, Matzner M, Delfmann P, Becker J. Comprehensible Predictive Models for Business Processes. MIS QUART 2016. [DOI: 10.25300/misq/2016/40.4.10] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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