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Gomez A, Gonzalez S, Oke A, Luo J, Duong JB, Esquerra RM, Zimmerman T, Capponi S, Fung JC, Nystul TG. A high-throughput method for quantifying Drosophila fecundity. bioRxiv 2024:2024.03.27.587093. [PMID: 38585877 PMCID: PMC10996622 DOI: 10.1101/2024.03.27.587093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Measurements of Drosophila fecundity are used in a wide variety of studies, such as investigations of stem cell biology, nutrition, behavior, and toxicology. In addition, because fecundity assays are performed on live flies, they are suitable for longitudinal studies such as investigations of aging or prolonged chemical exposure. However, standard Drosophila fecundity assays have been difficult to perform in a high-throughput manner because experimental factors such as the physiological state of the flies and environmental cues must be carefully controlled to achieve consistent results. In addition, exposing flies to a large number of different experimental conditions (such as chemical additives in the diet) and manually counting the number of eggs laid to determine the impact on fecundity is time-consuming. We have overcome these challenges by combining a new multiwell fly culture strategy with a novel 3D-printed fly transfer device to rapidly and accurately transfer flies from one plate to another; the RoboCam, a low-cost, custom built robotic camera to capture images of the wells automatically; and an image segmentation pipeline to automatically identify and quantify eggs. We show that this method is compatible with robust and consistent egg laying throughout the assay period; and demonstrate that the automated pipeline for quantifying fecundity is very accurate (r2 = 0.98 for the correlation between the automated egg counts and the ground truth) In addition, we show that this method can be used to efficiently detect the effects on fecundity induced by dietary exposure to chemicals. Taken together, this strategy substantially increases the efficiency and reproducibility of high throughput egg laying assays that require exposing flies to multiple different media conditions.
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Affiliation(s)
- Andreana Gomez
- University of California, San Francisco, Department of Anatomy
| | - Sergio Gonzalez
- San Francisco State University, Department of Biology
- Center for Cellular Construction, San Francisco, CA
| | - Ashwini Oke
- San Francisco State University, Department of Chemistry and Biochemistry; University of California, San Francisco, OB/GYN Department
- IBM Almaden Research Center, San Jose, CA; University of California, San Francisco, Center for Reproductive Sciences
| | - Jiayu Luo
- San Francisco State University, Department of Biology
- Center for Cellular Construction, San Francisco, CA
| | - Johnny B Duong
- Center for Cellular Construction, San Francisco, CA
- San Francisco State University, Department of Chemistry and Biochemistry; University of California, San Francisco, OB/GYN Department
| | - Raymond M Esquerra
- Center for Cellular Construction, San Francisco, CA
- San Francisco State University, Department of Chemistry and Biochemistry; University of California, San Francisco, OB/GYN Department
| | - Thomas Zimmerman
- Center for Cellular Construction, San Francisco, CA
- IBM Almaden Research Center, San Jose, CA; University of California, San Francisco, Center for Reproductive Sciences
| | - Sara Capponi
- Center for Cellular Construction, San Francisco, CA
- IBM Almaden Research Center, San Jose, CA; University of California, San Francisco, Center for Reproductive Sciences
| | - Jennifer C Fung
- San Francisco State University, Department of Chemistry and Biochemistry; University of California, San Francisco, OB/GYN Department
- IBM Almaden Research Center, San Jose, CA; University of California, San Francisco, Center for Reproductive Sciences
- University of California, San Francisco EaRTH Center
| | - Todd G Nystul
- University of California, San Francisco, Department of Anatomy
- San Francisco State University, Department of Chemistry and Biochemistry; University of California, San Francisco, OB/GYN Department
- IBM Almaden Research Center, San Jose, CA; University of California, San Francisco, Center for Reproductive Sciences
- University of California, San Francisco EaRTH Center
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2
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Ulaganathan G, Jiang H, Canio N, Oke A, Armstrong SS, Abrahamsson D, Varshavsky JR, Lam J, Cooper C, Robinson JF, Fung JC, Woodruff TJ, Allard P. Screening and characterization of 133 physiologically-relevant environmental chemicals for reproductive toxicity. bioRxiv 2024:2024.03.22.584808. [PMID: 38585844 PMCID: PMC10996516 DOI: 10.1101/2024.03.22.584808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Reproduction is a functional outcome that relies on complex cellular, tissue, and organ interactions that span the developmental period to adulthood. Thus, the assessment of its disruption by environmental chemicals is remarkably painstaking in conventional toxicological animal models and does not scale up to the number of chemicals present in our environment and requiring testing. We adapted a previously described low-throughput in vivo chromosome segregation assay using C. elegans predictive of reproductive toxicity and leveraged available public data sources (ToxCast, ICE) to screen and characterize 133 physiologically-relevant chemicals in a high-throughput manner. The screening outcome was further validated in a second, independent in vivo assay assessing embryonic viability. In total, 13 chemicals were classified as reproductive toxicants with the two most active chemicals belonging to the large family of Quaternary Ammonium Compounds (QACs) commonly used as disinfectants but with limited available reproductive toxicity data. We compared the results from the C. elegans assay with ToxCast in vitro data compiled from 700+ cell response assays and 300+ signaling pathways-based assays. We did not observe a difference in the bioactivity or in average potency (AC50) between the top and bottom chemicals. However, the intended target categories were significantly different between the classified chemicals with, in particular, an over-representation of steroid hormone targets for the high Z-score chemicals. Taken together, these results point to the value of in vivo models that scale to high-throughput level for reproductive toxicity assessment and to the need to prioritize the assessment of QACs impacts on reproduction.
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Marshall WF, Fung JC. Homologous chromosome recognition via nonspecific interactions. bioRxiv 2023:2023.06.09.544427. [PMID: 37333079 PMCID: PMC10274854 DOI: 10.1101/2023.06.09.544427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
In many organisms, most notably Drosophila, homologous chromosomes in somatic cells associate with each other, a phenomenon known as somatic homolog pairing. Unlike in meiosis, where homology is read out at the level of DNA sequence complementarity, somatic homolog pairing takes place without double strand breaks or strand invasion, thus requiring some other mechanism for homologs to recognize each other. Several studies have suggested a "specific button" model, in which a series of distinct regions in the genome, known as buttons, can associate with each other, presumably mediated by different proteins that bind to these different regions. Here we consider an alternative model, which we term the "button barcode" model, in which there is only one type of recognition site or adhesion button, present in many copies in the genome, each of which can associate with any of the others with equal affinity. An important component of this model is that the buttons are non-uniformly distributed, such that alignment of a chromosome with its correct homolog, compared with a non-homolog, is energetically favored; since to achieve nonhomologous alignment, chromosomes would be required to mechanically deform in order to bring their buttons into mutual register. We investigated several types of barcodes and examined their effect on pairing fidelity. We found that high fidelity homolog recognition can be achieved by arranging chromosome pairing buttons according to an actual industrial barcode used for warehouse sorting. By simulating randomly generated non-uniform button distributions, many highly effective button barcodes can be easily found, some of which achieve virtually perfect pairing fidelity. This model is consistent with existing literature on the effect of translocations of different sizes on homolog pairing. We conclude that a button barcode model can attain highly specific homolog recognition, comparable to that seen in actual cells undergoing somatic homolog pairing, without the need for specific interactions. This model may have implications for how meiotic pairing is achieved.
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Pollard MG, Rockmill B, Oke A, Anderson CM, Fung JC. Kinetic analysis of synaptonemal complex dynamics during meiosis of yeast Saccharomyces cerevisiae reveals biphasic growth and abortive disassembly. Front Cell Dev Biol 2023; 11:1098468. [PMID: 36814598 PMCID: PMC9939684 DOI: 10.3389/fcell.2023.1098468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/19/2023] [Indexed: 02/08/2023] Open
Abstract
The synaptonemal complex (SC) is a dynamic structure formed between chromosomes during meiosis which stabilizes and supports many essential meiotic processes such as pairing and recombination. In budding yeast, Zip1 is a functionally conserved element of the SC that is important for synapsis. Here, we directly measure the kinetics of Zip1-GFP assembly and disassembly in live cells of the yeast S. cerevisiae. The imaging of SC assembly in yeast is challenging due to the large number of chromosomes packed into a small nucleus. We employ a zip3Δ mutant in which only a few chromosomes undergo synapsis at any given time, initiating from a single site on each chromosome, thus allowing the assembly and disassembly kinetics of single SCs to be accurately monitored in living cells. SC assembly occurs with both monophasic and biphasic kinetics, in contrast to the strictly monophasic assembly seen in C. elegans. In wild-type cells, once maximal synapsis is achieved, programmed final disassembly rapidly follows, as Zip1 protein is actively degraded. In zip3Δ, this period is extended and final disassembly is prolonged. Besides final disassembly, we found novel disassembly events involving mostly short SCs that disappeared in advance of programmed final disassembly, which we termed "abortive disassembly." Abortive disassembly is distinct from final disassembly in that it occurs when Zip1 protein levels are still high, and exhibits a much slower rate of disassembly, suggesting a different mechanism for removal in the two types of disassembly. We speculate that abortive disassembly events represent defective or stalled SCs, possibly representing SC formation between non-homologs, that is then targeted for dissolution. These results reveal novel aspects of SC assembly and disassembly, potentially providing evidence of additional regulatory pathways controlling not just the assembly, but also the disassembly, of this complex cellular structure.
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Affiliation(s)
| | | | | | | | - Jennifer C. Fung
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center of Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
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Navarro EJ, Marshall WF, Fung JC. Modeling cell biological features of meiotic chromosome pairing to study interlock resolution. PLoS Comput Biol 2022; 18:e1010252. [PMID: 35696428 PMCID: PMC9232156 DOI: 10.1371/journal.pcbi.1010252] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 06/24/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
During meiosis, homologous chromosomes become associated side by side in a process known as homologous chromosome pairing. Pairing requires long range chromosome motion through a nucleus that is full of other chromosomes. It remains unclear how the cell manages to align each pair of chromosomes quickly while mitigating and resolving interlocks. Here, we use a coarse-grained molecular dynamics model to investigate how specific features of meiosis, including motor-driven telomere motion, nuclear envelope interactions, and increased nuclear size, affect the rate of pairing and the mitigation/resolution of interlocks. By creating in silico versions of three yeast strains and comparing the results of our model to experimental data, we find that a more distributed placement of pairing sites along the chromosome is necessary to replicate experimental findings. Active motion of the telomeric ends speeds up pairing only if binding sites are spread along the chromosome length. Adding a meiotic bouquet significantly speeds up pairing but does not significantly change the number of interlocks. An increase in nuclear size slows down pairing while greatly reducing the number of interlocks. Interestingly, active forces increase the number of interlocks, which raises the question: How do these interlocks resolve? Our model gives us detailed movies of interlock resolution events which we then analyze to build a step-by-step recipe for interlock resolution. In our model, interlocks must first translocate to the ends, where they are held in a quasi-stable state by a large number of paired sites on one side. To completely resolve an interlock, the telomeres of the involved chromosomes must come in close proximity so that the cooperativity of pairing coupled with random motion causes the telomeres to unwind. Together our results indicate that computational modeling of homolog pairing provides insight into the specific cell biological changes that occur during meiosis.
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Affiliation(s)
- Erik J. Navarro
- Department of Obstetrics, Gynecology and Reproductive Sciences and Center of Reproductive Sciences, University of California, San Francisco, California, United States of America
| | - Wallace F. Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America
| | - Jennifer C. Fung
- Department of Obstetrics, Gynecology and Reproductive Sciences and Center of Reproductive Sciences, University of California, San Francisco, California, United States of America
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Houshdaran S, Oke AB, Fung JC, Vo KC, Nezhat C, Giudice LC. Steroid hormones regulate genome-wide epigenetic programming and gene transcription in human endometrial cells with marked aberrancies in endometriosis. PLoS Genet 2020; 16:e1008601. [PMID: 32555663 PMCID: PMC7299312 DOI: 10.1371/journal.pgen.1008601] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 01/09/2020] [Indexed: 01/03/2023] Open
Abstract
Programmed cellular responses to cycling ovarian-derived steroid hormones are central to normal endometrial function. Abnormalities therein, as in the estrogen-dependent, progesterone-"resistant" disorder, endometriosis, predispose to infertility and poor pregnancy outcomes. The endometrial stromal fibroblast (eSF) is a master regulator of pregnancy success. However, the complex hormone-epigenome-transcriptome interplay in eSF by each individual steroid hormone, estradiol (E2) and/or progesterone (P4), under physiologic and pathophysiologic conditions, is poorly understood and was investigated herein. Genome-wide analysis in normal, early and late stage eutopic eSF revealed: i) In contrast to P4, E2 extensively affected the eSF DNA methylome and transcriptome. Importantly, E2 resulted in a more open versus closed chromatin, confirmed by histone modification analysis. Combined E2 with P4 affected a totally different landscape than E2 or P4 alone. ii) P4 responses were aberrant in early and late stage endometriosis, and mapping differentially methylated CpG sites with progesterone receptor targets from the literature revealed different but not decreased P4-targets, leading to question the P4-"resistant" phenotype in endometriosis. Interestingly, an aberrant E2-response was noted in eSF from endometriosis women; iii) Steroid hormones affected specific genomic contexts and locations, significantly enriching enhancers and intergenic regions and minimally involving proximal promoters and CpG islands, regardless of hormone type and eSF disease state. iv) In eSF from women with endometriosis, aberrant hormone-induced methylation signatures were mainly due to existing DNA methylation marks prior to hormone treatments and involved known endometriosis genes and pathways. v) Distinct DNA methylation and transcriptomic signatures revealed early and late stage endometriosis comprise unique disease subtypes. Taken together, the data herein, for the first time, provide significant insight into the hormone-epigenome-transcriptome interplay of each steroid hormone in normal eSF, and aberrant E2 response, distinct disease subtypes, and pre-existing epigenetic aberrancies in the setting of endometriosis, provide mechanistic insights into how endometriosis affects endometrial function/dysfunction.
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Affiliation(s)
- Sahar Houshdaran
- University of California San Francisco, Dept. of Obstetrics, Gynecology and Reproductive Sciences, San Francisco, California, United States of America
| | - Ashwini B. Oke
- University of California San Francisco, Dept. of Obstetrics, Gynecology and Reproductive Sciences, San Francisco, California, United States of America
| | - Jennifer C. Fung
- University of California San Francisco, Dept. of Obstetrics, Gynecology and Reproductive Sciences, San Francisco, California, United States of America
| | - Kim Chi Vo
- University of California San Francisco, Dept. of Obstetrics, Gynecology and Reproductive Sciences, San Francisco, California, United States of America
| | - Camran Nezhat
- Camran Nezhat Institute, Palo Alto, California, United States of America
| | - Linda C. Giudice
- University of California San Francisco, Dept. of Obstetrics, Gynecology and Reproductive Sciences, San Francisco, California, United States of America
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Wild P, Susperregui A, Piazza I, Dörig C, Oke A, Arter M, Yamaguchi M, Hilditch AT, Vuina K, Chan KC, Gromova T, Haber JE, Fung JC, Picotti P, Matos J. Network Rewiring of Homologous Recombination Enzymes during Mitotic Proliferation and Meiosis. Mol Cell 2019; 75:859-874.e4. [PMID: 31351878 PMCID: PMC6715774 DOI: 10.1016/j.molcel.2019.06.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/24/2019] [Accepted: 06/18/2019] [Indexed: 02/06/2023]
Abstract
Homologous recombination (HR) is essential for high-fidelity DNA repair during mitotic proliferation and meiosis. Yet, context-specific modifications must tailor the recombination machinery to avoid (mitosis) or enforce (meiosis) the formation of reciprocal exchanges-crossovers-between recombining chromosomes. To obtain molecular insight into how crossover control is achieved, we affinity purified 7 DNA-processing enzymes that channel HR intermediates into crossovers or noncrossovers from vegetative cells or cells undergoing meiosis. Using mass spectrometry, we provide a global characterization of their composition and reveal mitosis- and meiosis-specific modules in the interaction networks. Functional analyses of meiosis-specific interactors of MutLγ-Exo1 identified Rtk1, Caf120, and Chd1 as regulators of crossing-over. Chd1, which transiently associates with Exo1 at the prophase-to-metaphase I transition, enables the formation of MutLγ-dependent crossovers through its conserved ability to bind and displace nucleosomes. Thus, rewiring of the HR network, coupled to chromatin remodeling, promotes context-specific control of the recombination outcome.
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Affiliation(s)
- Philipp Wild
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Aitor Susperregui
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Ilaria Piazza
- Institute of Molecular Systems Biology, HPM-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Christian Dörig
- Institute of Molecular Systems Biology, HPM-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Ashwini Oke
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Meret Arter
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Miyuki Yamaguchi
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, USA
| | - Alexander T Hilditch
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Karla Vuina
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Ki Choi Chan
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Tatiana Gromova
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, USA
| | - Jennifer C Fung
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Paola Picotti
- Institute of Molecular Systems Biology, HPM-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Joao Matos
- Institute of Biochemistry, HPM D6.5-ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.
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8
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Marshall WF, Fung JC. Modeling meiotic chromosome pairing: a tug of war between telomere forces and a pairing-based Brownian ratchet leads to increased pairing fidelity. Phys Biol 2019; 16:046005. [PMID: 30943453 DOI: 10.1088/1478-3975/ab15a7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Meiotic homolog pairing involves associations between homologous DNA regions scattered along the length of a chromosome. When homologs associate, they tend to do so by a processive zippering process, which apparently results from avidity effects. Using a computational model, we show that this avidity-driven processive zippering reduces the selectivity of pairing. When active random forces are applied to telomeres, this drop in selectivity is eliminated in a force-dependent manner. Further simulations suggest that active telomere forces are engaged in a tug-of-war against zippering, which can be interpreted as a Brownian ratchet with a stall force that depends on the dissociation constant of pairing. When perfectly homologous regions of high affinity compete with homeologous regions of lower affinity, the affinity difference can be amplified through this tug of war effect provided the telomere force acts in a range that is strong enough to oppose zippering of homeologs while still permitting zippering of correct homologs. The degree of unzippering depends on the radius of the nucleus, such that complete unzippering of homeologous regions can only take place if the nucleus is large enough to pull the two chromosomes completely apart. A picture of meiotic pairing thus emerges that is fundamentally mechanical in nature, possibly explaining the purpose of active telomere forces, increased nuclear diameter, and the presence of 'Maverick' chromosomes in meiosis.
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Affiliation(s)
- Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, United States of America. Center for Cellular Construction, University of California San Francisco, San Francisco, CA, United States of America
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9
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Arter M, Hurtado-Nieves V, Oke A, Zhuge T, Wettstein R, Fung JC, Blanco MG, Matos J. Regulated Crossing-Over Requires Inactivation of Yen1/GEN1 Resolvase during Meiotic Prophase I. Dev Cell 2018; 45:785-800.e6. [PMID: 29920281 DOI: 10.1016/j.devcel.2018.05.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 03/30/2018] [Accepted: 05/16/2018] [Indexed: 01/27/2023]
Abstract
During meiosis, crossover recombination promotes the establishment of physical connections between homologous chromosomes, enabling their bipolar segregation. To ensure that persistent recombination intermediates are disengaged prior to the completion of meiosis, the Yen1(GEN1) resolvase is strictly activated at the onset of anaphase II. Whether controlled activation of Yen1 is important for meiotic crossing-over is unknown. Here, we show that CDK-mediated phosphorylation of Yen1 averts its pervasive recruitment to recombination intermediates during prophase I. Yen1 mutants that are refractory to phosphorylation resolve DNA joint molecules prematurely and form crossovers independently of MutLγ, the central crossover resolvase during meiosis. Despite bypassing the requirement for MutLγ in joint molecule processing and promoting crossover-specific resolution, unrestrained Yen1 impairs the spatial distribution of crossover events, genome-wide. Thus, active suppression of Yen1 function, and by inference also of Mus81-Mms4(EME1) and Slx1-Slx4(BTBD12) resolvases, avoids precocious resolution of recombination intermediates to enable meiotic crossover patterning.
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Affiliation(s)
- Meret Arter
- Institute of Biochemistry, HPM D6.5 - ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Vanesa Hurtado-Nieves
- Departamento de Bioquímica e Bioloxía Molecular, CIMUS, Universidade de Santiago de Compostela - IDIS, 15706 Santiago de Compostela, Spain
| | - Ashwini Oke
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, CA, USA
| | - Tangna Zhuge
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, CA, USA
| | - Rahel Wettstein
- Institute of Biochemistry, HPM D6.5 - ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Jennifer C Fung
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, CA, USA
| | - Miguel G Blanco
- Departamento de Bioquímica e Bioloxía Molecular, CIMUS, Universidade de Santiago de Compostela - IDIS, 15706 Santiago de Compostela, Spain.
| | - Joao Matos
- Institute of Biochemistry, HPM D6.5 - ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.
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10
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Fung JC. Kinetochores: Importance of Being Fashionably Late. Cell Syst 2017; 4:585-586. [PMID: 28662384 DOI: 10.1016/j.cels.2017.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A model explains how a critical delay before microtubules detach from kinetochores during cell division might be achieved.
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Affiliation(s)
- Jennifer C Fung
- Department of Obstetrics, Gynecology, and Reproductive Science and the Center of Reproductive Science, University of California, San Francisco, San Francisco, CA 94143-2240, USA.
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11
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Abstract
Tracking biological events in living cells provides kinetic information about biological processes that can be missed in more traditional methods using fixed samples at designated time intervals. Here we describe a methodology for in vivo fluorescence microscopy of yeast cells undergoing meiosis. This method allows tracking of individual cells over extended periods of time through every stage of the meiotic transformation while minimizing phototoxicity and sustaining conditions that support meiotic growth.
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Affiliation(s)
- Michael G Pollard
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center of Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
| | - Jennifer C Fung
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center of Reproductive Sciences, University of California, San Francisco, CA, 94143, USA.
- Fung Lab, University of California, San Francisco, GH N416, 600 16th St., San Francisco, CA, 94158, USA.
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12
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Marshall WF, Fung JC. Modeling meiotic chromosome pairing: nuclear envelope attachment, telomere-led active random motion, and anomalous diffusion. Phys Biol 2016; 13:026003. [PMID: 27046097 DOI: 10.1088/1478-3975/13/2/026003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The recognition and pairing of homologous chromosomes during meiosis is a complex physical and molecular process involving a combination of polymer dynamics and molecular recognition events. Two highly conserved features of meiotic chromosome behavior are the attachment of telomeres to the nuclear envelope and the active random motion of telomeres driven by their interaction with cytoskeletal motor proteins. Both of these features have been proposed to facilitate the process of homolog pairing, but exactly what role these features play in meiosis remains poorly understood. Here we investigate the roles of active motion and nuclear envelope tethering using a Brownian dynamics simulation in which meiotic chromosomes are represented by a Rouse polymer model subjected to tethering and active forces at the telomeres. We find that tethering telomeres to the nuclear envelope slows down pairing relative to the rates achieved by unattached chromosomes, but that randomly directed active forces applied to the telomeres speed up pairing dramatically in a manner that depends on the statistical properties of the telomere force fluctuations. The increased rate of initial pairing cannot be explained by stretching out of the chromosome conformation but instead seems to correlate with anomalous diffusion of sub-telomeric regions.
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Affiliation(s)
- Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California San Francisco, USA
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13
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Sousa Martins JP, Liu X, Oke A, Arora R, Franciosi F, Viville S, Laird DJ, Fung JC, Conti M. DAZL and CPEB1 regulate mRNA translation synergistically during oocyte maturation. Development 2016. [DOI: 10.1242/dev.137653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Sousa Martins JP, Liu X, Oke A, Arora R, Franciosi F, Viville S, Laird DJ, Fung JC, Conti M. DAZL and CPEB1 regulate mRNA translation synergistically during oocyte maturation. J Cell Sci 2016; 129:1271-82. [PMID: 26826184 DOI: 10.1242/jcs.179218] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 01/27/2016] [Indexed: 01/23/2023] Open
Abstract
Meiotic progression requires exquisitely coordinated translation of maternal messenger (m)RNA that has accumulated during oocyte growth. A major regulator of this program is the cytoplasmic polyadenylation element binding protein 1 (CPEB1). However, the temporal pattern of translation at different meiotic stages indicates the function of additional RNA binding proteins (RBPs). Here, we report that deleted in azoospermia-like (DAZL) cooperates with CPEB1 to regulate maternal mRNA translation. Using a strategy that monitors ribosome loading onto endogenous mRNAs and a prototypic translation target, we show that ribosome loading is induced in a DAZL- and CPEB1-dependent manner, as the oocyte reenters meiosis. Depletion of the two RBPs from oocytes and mutagenesis of the 3' untranslated regions (UTRs) demonstrate that both RBPs interact with the Tex19.1 3' UTR and cooperate in translation activation of this mRNA. We observed a synergism between DAZL and cytoplasmic polyadenylation elements (CPEs) in the translation pattern of maternal mRNAs when using a genome-wide analysis. Mechanistically, the number of DAZL proteins loaded onto the mRNA and the characteristics of the CPE might define the degree of cooperation between the two RBPs in activating translation and meiotic progression.
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Affiliation(s)
- Joao P Sousa Martins
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Xueqing Liu
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Ashwini Oke
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
| | - Ripla Arora
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Federica Franciosi
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA Reproductive and Developmental Biology Laboratory, Department of Health, Animal Science and Food Safety, Università degli Studi di Milano, 20133, Milano, Italy
| | - Stephan Viville
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale INSERM U964, Centre National de Recherche Scientifique CNRS UMR 1704, Université de Strasbourg, Illkirch 67404, France Centre Hospitalier Universitaire, Strasbourg F-67000, France
| | - Diana J Laird
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Jennifer C Fung
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
| | - Marco Conti
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA 94143, USA Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
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15
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Anderson CM, Oke A, Yam P, Zhuge T, Fung JC. Reduced Crossover Interference and Increased ZMM-Independent Recombination in the Absence of Tel1/ATM. PLoS Genet 2015; 11:e1005478. [PMID: 26305689 PMCID: PMC4549261 DOI: 10.1371/journal.pgen.1005478] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 07/31/2015] [Indexed: 11/18/2022] Open
Abstract
Meiotic recombination involves the repair of double-strand break (DSB) precursors as crossovers (COs) or noncrossovers (NCOs). The proper number and distribution of COs is critical for successful chromosome segregation and formation of viable gametes. In budding yeast the majority of COs occurs through a pathway dependent on the ZMM proteins (Zip2-Zip3-Zip4-Spo16, Msh4-Msh5, Mer3), which form foci at CO-committed sites. Here we show that the DNA-damage-response kinase Tel1/ATM limits ZMM-independent recombination. By whole-genome mapping of recombination products, we find that lack of Tel1 results in higher recombination and reduced CO interference. Yet the number of Zip3 foci in tel1Δ cells is similar to wild type, and these foci show normal interference. Analysis of recombination in a tel1Δ zip3Δ double mutant indicates that COs are less dependent on Zip3 in the absence of Tel1. Together these results reveal that in the absence of Tel1, a significant proportion of COs occurs through a non-ZMM-dependent pathway, contributing to a CO landscape with poor interference. We also see a significant change in the distribution of all detectable recombination products in the absence of Tel1, Sgs1, Zip3, or Msh4, providing evidence for altered DSB distribution. These results support the previous finding that DSB interference depends on Tel1, and further suggest an additional level of DSB interference created through local repression of DSBs around CO-designated sites.
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Affiliation(s)
- Carol M. Anderson
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Ashwini Oke
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Phoebe Yam
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Tangna Zhuge
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Jennifer C. Fung
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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16
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Faire M, Skillern A, Arora R, Nguyen DH, Wang J, Chamberlain C, German MS, Fung JC, Laird DJ. Follicle dynamics and global organization in the intact mouse ovary. Dev Biol 2015; 403:69-79. [PMID: 25889274 DOI: 10.1016/j.ydbio.2015.04.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 03/23/2015] [Accepted: 04/08/2015] [Indexed: 10/23/2022]
Abstract
Quantitative analysis of tissues and organs can reveal large-scale patterning as well as the impact of perturbations and aging on biological architecture. Here we develop tools for imaging of single cells in intact organs and computational approaches to assess spatial relationships in 3D. In the mouse ovary, we use nuclear volume of the oocyte to read out quiescence or growth of oocyte-somatic cell units known as follicles. This in-ovary quantification of non-growing follicle dynamics from neonate to adult fits a mathematical function, which corroborates the model of fixed oocyte reserve. Mapping approaches show that radial organization of folliculogenesis established in the newborn ovary is preserved through adulthood. By contrast, inter-follicle clustering increases during aging with different dynamics depending on size. These broadly applicable tools can reveal high dimensional phenotypes and age-related architectural changes in other organs. In the adult mouse pancreas, we find stochastic radial organization of the islets of Langerhans but evidence for localized interactions among the smallest islets.
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Affiliation(s)
- Mehlika Faire
- Department of Ob/Gyn and Reproductive Sciences, Center for Reproductive Sciences, Eli and Edythe Broad, Center for Regeneration Medicine & Stem Cell Research, United States
| | - Amanda Skillern
- Department of Ob/Gyn and Reproductive Sciences, Center for Reproductive Sciences, Eli and Edythe Broad, Center for Regeneration Medicine & Stem Cell Research, United States
| | - Ripla Arora
- Department of Ob/Gyn and Reproductive Sciences, Center for Reproductive Sciences, Eli and Edythe Broad, Center for Regeneration Medicine & Stem Cell Research, United States
| | - Daniel H Nguyen
- Department of Ob/Gyn and Reproductive Sciences, Center for Reproductive Sciences, Eli and Edythe Broad, Center for Regeneration Medicine & Stem Cell Research, United States
| | - Jason Wang
- Diabetes Center UCSF, 35 Medical Center Way, San Francisco, CA 94043, United States
| | - Chester Chamberlain
- Diabetes Center UCSF, 35 Medical Center Way, San Francisco, CA 94043, United States
| | - Michael S German
- Diabetes Center UCSF, 35 Medical Center Way, San Francisco, CA 94043, United States
| | - Jennifer C Fung
- Department of Ob/Gyn and Reproductive Sciences, Center for Reproductive Sciences, Eli and Edythe Broad, Center for Regeneration Medicine & Stem Cell Research, United States
| | - Diana J Laird
- Department of Ob/Gyn and Reproductive Sciences, Center for Reproductive Sciences, Eli and Edythe Broad, Center for Regeneration Medicine & Stem Cell Research, United States.
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17
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Oke A, Anderson CM, Yam P, Fung JC. Controlling meiotic recombinational repair - specifying the roles of ZMMs, Sgs1 and Mus81/Mms4 in crossover formation. PLoS Genet 2014; 10:e1004690. [PMID: 25329811 PMCID: PMC4199502 DOI: 10.1371/journal.pgen.1004690] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 08/19/2014] [Indexed: 11/19/2022] Open
Abstract
Crossovers (COs) play a critical role in ensuring proper alignment and segregation of homologous chromosomes during meiosis. How the cell balances recombination between CO vs. noncrossover (NCO) outcomes is not completely understood. Further lacking is what constrains the extent of DNA repair such that multiple events do not arise from a single double-strand break (DSB). Here, by interpreting signatures that result from recombination genome-wide, we find that synaptonemal complex proteins promote crossing over in distinct ways. Our results suggest that Zip3 (RNF212) promotes biased cutting of the double Holliday-junction (dHJ) intermediate whereas surprisingly Msh4 does not. Moreover, detailed examination of conversion tracts in sgs1 and mms4-md mutants reveal distinct aberrant recombination events involving multiple chromatid invasions. In sgs1 mutants, these multiple invasions are generally multichromatid involving 3-4 chromatids; in mms4-md mutants the multiple invasions preferentially resolve into one or two chromatids. Our analysis suggests that Mus81/Mms4 (Eme1), rather than just being a minor resolvase for COs is crucial for both COs and NCOs in preventing chromosome entanglements by removing 3'- flaps to promote second-end capture. Together our results force a reevaluation of how key recombination enzymes collaborate to specify the outcome of meiotic DNA repair.
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Affiliation(s)
- Ashwini Oke
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center of Reproductive Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Carol M. Anderson
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center of Reproductive Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Phoebe Yam
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center of Reproductive Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Jennifer C. Fung
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center of Reproductive Sciences, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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18
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Liu Y, Gaines WA, Callender T, Busygina V, Oke A, Sung P, Fung JC, Hollingsworth NM. Down-regulation of Rad51 activity during meiosis in yeast prevents competition with Dmc1 for repair of double-strand breaks. PLoS Genet 2014; 10:e1004005. [PMID: 24465215 PMCID: PMC3900393 DOI: 10.1371/journal.pgen.1004005] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 10/22/2013] [Indexed: 11/18/2022] Open
Abstract
Interhomolog recombination plays a critical role in promoting proper meiotic chromosome segregation but a mechanistic understanding of this process is far from complete. In vegetative cells, Rad51 is a highly conserved recombinase that exhibits a preference for repairing double strand breaks (DSBs) using sister chromatids, in contrast to the conserved, meiosis-specific recombinase, Dmc1, which preferentially repairs programmed DSBs using homologs. Despite the different preferences for repair templates, both Rad51 and Dmc1 are required for interhomolog recombination during meiosis. This paradox has recently been explained by the finding that Rad51 protein, but not its strand exchange activity, promotes Dmc1 function in budding yeast. Rad51 activity is inhibited in dmc1Δ mutants, where the failure to repair meiotic DSBs triggers the meiotic recombination checkpoint, resulting in prophase arrest. The question remains whether inhibition of Rad51 activity is important during wild-type meiosis, or whether inactivation of Rad51 occurs only as a result of the absence of DMC1 or checkpoint activation. This work shows that strains in which mechanisms that down-regulate Rad51 activity are removed exhibit reduced numbers of interhomolog crossovers and noncrossovers. A hypomorphic mutant, dmc1-T159A, makes less stable presynaptic filaments but is still able to mediate strand exchange and interact with accessory factors. Combining dmc1-T159A with up-regulated Rad51 activity reduces interhomolog recombination and spore viability, while increasing intersister joint molecule formation. These results support the idea that down-regulation of Rad51 activity is important during meiosis to prevent Rad51 from competing with Dmc1 for repair of meiotic DSBs.
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Affiliation(s)
- Yan Liu
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - William A. Gaines
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Tracy Callender
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Valeria Busygina
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Ashwini Oke
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Jennifer C. Fung
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Nancy M. Hollingsworth
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
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19
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Rockmill B, Lefrançois P, Voelkel-Meiman K, Oke A, Roeder GS, Fung JC. High throughput sequencing reveals alterations in the recombination signatures with diminishing Spo11 activity. PLoS Genet 2013; 9:e1003932. [PMID: 24204324 PMCID: PMC3814317 DOI: 10.1371/journal.pgen.1003932] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 09/16/2013] [Indexed: 12/03/2022] Open
Abstract
Spo11 is the topoisomerase-like enzyme responsible for the induction of the meiosis-specific double strand breaks (DSBs), which initiates the recombination events responsible for proper chromosome segregation. Nineteen PCR-induced alleles of SPO11 were identified and characterized genetically and cytologically. Recombination, spore viability and synaptonemal complex (SC) formation were decreased to varying extents in these mutants. Arrest by ndt80 restored these events in two severe hypomorphic mutants, suggesting that ndt80-arrested nuclei are capable of extended DSB activity. While crossing-over, spore viability and synaptonemal complex (SC) formation defects correlated, the extent of such defects was not predictive of the level of heteroallelic gene conversions (prototrophs) exhibited by each mutant. High throughput sequencing of tetrads from spo11 hypomorphs revealed that gene conversion tracts associated with COs are significantly longer and gene conversion tracts unassociated with COs are significantly shorter than in wild type. By modeling the extent of these tract changes, we could account for the discrepancy in genetic measurements of prototrophy and crossover association. These findings provide an explanation for the unexpectedly low prototroph levels exhibited by spo11 hypomorphs and have important implications for genetic studies that assume an unbiased recovery of prototrophs, such as measurements of CO homeostasis. Our genetic and physical data support previous observations of DSB-limited meioses, in which COs are disproportionally maintained over NCOs (CO homeostasis). Most eukaryotes depend on the meiotic division to segregate each pair of chromosomes properly into their gametes. Chromosome segregation mistakes happening during meiosis are responsible for most miscarriages as well as many diseases such as Down's and Kleinfelter's syndromes in humans. Proper chromosome segregation during meiosis depends on efficient and regulated recombination events that link homologous chromosomes prior to the first meiotic division. These linkages are initiated at double-stranded breaks (DSBs) in chromosomal DNA by Spo11 and associated proteins. We isolated a valuable new set of SPO11 alleles in yeast with a wide range of Spo11 activity. Genetic analysis and high throughput sequencing of tetrads from these mutants has revealed unexpected features of meiotic recombination. First, Spo11 DSBs likely continue to form throughout a pachytene arrest in cells compromised for Spo11 activity. Second, the number of recombination initiation events in a given meiosis influences the repair outcome of those events. In addition, our results provide support for crossover homeostasis – a phenomenon in which crossovers are disproportionately maintained over other types of repair in the face of a decrease in DSBs.
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Affiliation(s)
- Beth Rockmill
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Philippe Lefrançois
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Karen Voelkel-Meiman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Ashwini Oke
- Department of Obstetrics, Gynecology and Reproductive Sciences and Center for Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - G. Shirleen Roeder
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Jennifer C. Fung
- Department of Obstetrics, Gynecology and Reproductive Sciences and Center for Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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20
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Rafelski SM, Viana MP, Zhang Y, Chan YHM, Thorn KS, Yam P, Fung JC, Li H, Costa LDF, Marshall WF. Mitochondrial network size scaling in budding yeast. Science 2012; 338:822-4. [PMID: 23139336 DOI: 10.1126/science.1225720] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Mitochondria must grow with the growing cell to ensure proper cellular physiology and inheritance upon division. We measured the physical size of mitochondrial networks in budding yeast and found that mitochondrial network size increased with increasing cell size and that this scaling relation occurred primarily in the bud. The mitochondria-to-cell size ratio continually decreased in aging mothers over successive generations. However, regardless of the mother's age or mitochondrial content, all buds attained the same average ratio. Thus, yeast populations achieve a stable scaling relation between mitochondrial content and cell size despite asymmetry in inheritance.
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Affiliation(s)
- Susanne M Rafelski
- Department of Biochemistry and Biophysics, University of California-San Francisco (UCSF), San Francisco, CA, USA.
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21
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Anderson CM, Chen SY, Dimon MT, Oke A, DeRisi JL, Fung JC. ReCombine: a suite of programs for detection and analysis of meiotic recombination in whole-genome datasets. PLoS One 2011; 6:e25509. [PMID: 22046241 PMCID: PMC3201961 DOI: 10.1371/journal.pone.0025509] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 08/25/2011] [Indexed: 11/18/2022] Open
Abstract
In meiosis, the exchange of DNA between chromosomes by homologous recombination is a critical step that ensures proper chromosome segregation and increases genetic diversity. Products of recombination include reciprocal exchanges, known as crossovers, and non-reciprocal gene conversions or non-crossovers. The mechanisms underlying meiotic recombination remain elusive, largely because of the difficulty of analyzing large numbers of recombination events by traditional genetic methods. These traditional methods are increasingly being superseded by high-throughput techniques capable of surveying meiotic recombination on a genome-wide basis. Next-generation sequencing or microarray hybridization is used to genotype thousands of polymorphic markers in the progeny of hybrid yeast strains. New computational tools are needed to perform this genotyping and to find and analyze recombination events. We have developed a suite of programs, ReCombine, for using short sequence reads from next-generation sequencing experiments to genotype yeast meiotic progeny. Upon genotyping, the program CrossOver, a component of ReCombine, then detects recombination products and classifies them into categories based on the features found at each location and their distribution among the various chromatids. CrossOver is also capable of analyzing segregation data from microarray experiments or other sources. This package of programs is designed to allow even researchers without computational expertise to use high-throughput, whole-genome methods to study the molecular mechanisms of meiotic recombination.
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Affiliation(s)
- Carol M. Anderson
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Stacy Y. Chen
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Michelle T. Dimon
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- Biological and Medical Informatics Program, University of California San Francisco, San Francisco, California, United States of America
| | - Ashwini Oke
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- Howard Hughes Medical Institute, Bethesda, Maryland, United States of America
| | - Jennifer C. Fung
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Center for Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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22
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Abstract
Crossovers (COs) play an essential role in promoting successful chromosome segregation during meiosis. Crossing over generates chiasmata, which are physical bridges between homologs that provide the appropriate tension to properly align chromosomes on the meiosis I spindle. Homolog pairs that fail to cross over can result in meiosis I nondisjunction, leading to aneuploid gametes. Therefore, the number and distribution of crossovers are tightly regulated to ensure that each chromosome pair receives at least one CO. Here, we describe a DNA microarray-based method to map CO distribution genome-wide, on a cell-by-cell basis, allowing for rapid and accurate analysis of multiple aspects of CO control.
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Affiliation(s)
- Stacy Y Chen
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA 94143, USA.
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23
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Costanzo V, Chaudhuri J, Fung JC, Moran JV. Dealing with dangerous accidents: DNA double-strand breaks take centre stage. Symposium on Genome Instability and DNA Repair. EMBO Rep 2009; 10:837-42. [PMID: 19609319 PMCID: PMC2726687 DOI: 10.1038/embor.2009.173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 06/23/2009] [Indexed: 11/08/2022] Open
Affiliation(s)
- Vincenzo Costanzo
- Genome Stability, London Research Institute, South Mimms, Hertfordshire EN63LD, UK
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Jennifer C Fung
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, California 94158, USA
| | - John V Moran
- Howard Hughes Medical Institute, Departments of Human Genetics and Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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24
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Fung JC, Rockmill B, Odell M, Roeder GS. Imposition of crossover interference through the nonrandom distribution of synapsis initiation complexes. Cell 2004; 116:795-802. [PMID: 15035982 DOI: 10.1016/s0092-8674(04)00249-1] [Citation(s) in RCA: 178] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2003] [Revised: 01/21/2004] [Accepted: 01/27/2004] [Indexed: 10/26/2022]
Abstract
Meiotic crossovers (COs) are nonrandomly distributed along chromosomes such that two COs seldom occur close together, a phenomenon known as CO interference. We have used genetic and cytological methods to investigate interference mechanisms in budding yeast. Assembly of the synaptonemal complex (SC) initiates at a few sites along each chromosome, triggered by a complex of proteins (including Zip2 and Zip3) called the synapsis initiation complex (SIC). We found that SICs, like COs, display interference, supporting the hypothesis that COs occur at synapsis initiation sites. Unexpectedly, we found that SICs show interference in mutants in which CO interference is abolished; one explanation is that these same mutations eliminate the subset of COs that normally occur at SICs. Since SICs are assembled in advance of SC and they are properly positioned even in the absence of SC formation, these data clearly demonstrate an aspect of interference that is independent of synapsis.
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Affiliation(s)
- Jennifer C Fung
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
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25
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Abstract
BACKGROUND In budding yeast, Sgs1 is the sole member of the RecQ family of DNA helicases. Like the human Bloom syndrome helicase (BLM), Sgs1 functions during both vegetative growth and meiosis. The sgs1 null mutant sporulates poorly and displays reduced spore viability. RESULTS We have identified novel functions for Sgs1 in meiosis. Loss of Sgs1 increases the number of axial associations, which are connections between homologous chromosomes that serve as initiation sites for synaptonemal complex formation. In addition, mutation of SGS1 increases the number of synapsis initiation complexes and increases the rate of chromosome synapsis. Loss of Sgs1 also increases the number of meiotic crossovers without changing the frequency of gene conversion. The sgs1 defect in sporulation is due to checkpoint-induced arrest/delay at the pachytene stage of meiotic prophase. A non-null allele of SGS1 that specifically deletes the helicase domain is defective in the newly described meiotic functions of Sgs1, but wild-type for most vegetative functions and for spore formation. CONCLUSIONS We have shown that the helicase domain of Sgs1 serves as a negative regulator of meiotic interchromosomal interactions. The activity of the wild-type Sgs1 protein reduces the numbers of axial associations, synapsis initiation complexes, and crossovers, and decreases the rate of chromosome synapsis. Our data argue strongly that axial associations marked by synapsis initiation complexes correspond to sites of reciprocal exchange. We propose that the Sgs1 helicase prevents a subset of recombination intermediates from becoming crossovers, and this distinction is made at an early stage in meiotic prophase.
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Affiliation(s)
- Beth Rockmill
- Howard Hughes Medical Institute, Yale University, P.O. Box 208103, New Haven, 06520 CT, USA
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Malik NA, Fung JC. Anomalous burning rates of flamelets induced by self-similar multiple scale (fractal and spiral) initial fields. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 2000; 62:6636-47. [PMID: 11102001 DOI: 10.1103/physreve.62.6636] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2000] [Indexed: 11/07/2022]
Abstract
In contrast to the classical problem of a single idealized flamelet (which is described by a nonlinear reaction-diffusion equation of motion) which propagates at a constant burning rate, self-similar multiple scale fields, whether fractal or nonfractal, induce anomalous rates of burning determined by the space-filling properties of the initial field. We compare the regimes induced by (line-cuts through) three specific geometries with distinct space-filling characteristics: (1) an algebraic spiral which has capacity (box-counting dimension) D(k)>0, and fractal dimension H=0; (2) an exponential spiral which has D(k)=0 and H=0, and geometric ratio R>1; (3) a fractal Cantor dust which has D(k)=H>0. The (nondimensional) burning rate U(B) induced by all three geometries takes the general form U(B) approximately F(tau(-zeta)), where F is a function whose form depends on the specific geometry, zeta is an exponent that contains the space-filling characteristic of the geometry, and tau is a nondimensional time. (1) For the algebraic spiral, F(x)=1(x), and zeta=D(k); F is continuous. (2) For the exponential spiral, F(x)=ln(x), and zeta=1/(R-1); F is continuous. (3) For the fractal Cantor dust, F(u)(x)=1(x), and zeta=H (for the envelope); F itself is a step-like discontinuous function. Thus, as D(k)-->0, or as H-->0, or as R-->infinity, then zeta-->0 and U(B)-->const; and as D(k)-->1, or as H-->1, (space filling) then zeta-->1; and as R-->1 (space filling) then zeta-->infinity. Two numerical methods, a fundamental (Eulerian) solution to the equation of motion and a Lagrangian model for flamelet propagation, confirm these theoretical predictions. The Lagrangian model is based on the idealized flamelet as a "point" with finite flame thickness Delta(L), (which is determined by the two-flamelet collision process), propagating with a given flame speed U(L). The Lagrangian model allows simulations in parameter ranges not easily accessible by the fundamental method (such as the case for the fractal Cantor dust). Interestingly, the linear regime of scalar diffusion in an algebraic spiral field displays the same dependence on D(k) as in the present reaction-diffusion case. The nonlinear regime of advection-diffusion (Burger turbulence) shows a different dependence on D(k).
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Affiliation(s)
- NA Malik
- Department of Mechanical Engineering, Imperial College of Science, Technology, and Medicine, Exhibition Road, London SW7 2BX, England and Department of Mathematics, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
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Fung JC, Marshall WF, Dernburg A, Agard DA, Sedat JW. Homologous chromosome pairing in Drosophila melanogaster proceeds through multiple independent initiations. J Cell Biol 1998; 141:5-20. [PMID: 9531544 PMCID: PMC2132734 DOI: 10.1083/jcb.141.1.5] [Citation(s) in RCA: 173] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The dynamics by which homologous chromosomes pair is currently unknown. Here, we use fluorescence in situ hybridization in combination with three-dimensional optical microscopy to show that homologous pairing of the somatic chromosome arm 2L in Drosophila occurs by independent initiation of pairing at discrete loci rather than by a processive zippering of sites along the length of chromosome. By evaluating the pairing frequencies of 11 loci on chromosome arm 2L over several timepoints during Drosophila embryonic development, we show that all 11 loci are paired very early in Drosophila development, within 13 h after egg deposition. To elucidate whether such pairing occurs by directed or undirected motion, we analyzed the pairing kinetics of histone loci during nuclear cycle 14. By measuring changes of nuclear length and correlating these changes with progression of time during cycle 14, we were able to express the pairing frequency and distance between homologous loci as a function of time. Comparing the experimentally determined dynamics of pairing to simulations based on previously proposed models of pairing motion, we show that the observed pairing kinetics are most consistent with a constrained random walk model and not consistent with a directed motion model. Thus, we conclude that simple random contacts through diffusion could suffice to allow pairing of homologous sites.
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Affiliation(s)
- J C Fung
- Graduate Group in Biophysics, University of California, San Francisco, California 94143-0554, USA
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28
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Laurer JH, Hajduk DA, Fung JC, Sedat JW, Smith SD, Gruner SM, Agard DA, Spontak RJ. Microstructural Analysis of a Cubic Bicontinuous Morphology in a Neat SIS Triblock Copolymer. Macromolecules 1997. [DOI: 10.1021/ma970449l] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonathan H. Laurer
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27695, Department of Physics, Princeton University, Princeton, New Jersey 08544, Graduate Group in Biophysics, University of California, San Francisco, California 94143, Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239, and Howard Hughes Medical Institute, University of
| | - Damian A. Hajduk
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27695, Department of Physics, Princeton University, Princeton, New Jersey 08544, Graduate Group in Biophysics, University of California, San Francisco, California 94143, Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239, and Howard Hughes Medical Institute, University of
| | - Jennifer C. Fung
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27695, Department of Physics, Princeton University, Princeton, New Jersey 08544, Graduate Group in Biophysics, University of California, San Francisco, California 94143, Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239, and Howard Hughes Medical Institute, University of
| | - John W. Sedat
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27695, Department of Physics, Princeton University, Princeton, New Jersey 08544, Graduate Group in Biophysics, University of California, San Francisco, California 94143, Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239, and Howard Hughes Medical Institute, University of
| | - Steven D. Smith
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27695, Department of Physics, Princeton University, Princeton, New Jersey 08544, Graduate Group in Biophysics, University of California, San Francisco, California 94143, Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239, and Howard Hughes Medical Institute, University of
| | - Sol M. Gruner
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27695, Department of Physics, Princeton University, Princeton, New Jersey 08544, Graduate Group in Biophysics, University of California, San Francisco, California 94143, Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239, and Howard Hughes Medical Institute, University of
| | - David A. Agard
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27695, Department of Physics, Princeton University, Princeton, New Jersey 08544, Graduate Group in Biophysics, University of California, San Francisco, California 94143, Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239, and Howard Hughes Medical Institute, University of
| | - Richard J. Spontak
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27695, Department of Physics, Princeton University, Princeton, New Jersey 08544, Graduate Group in Biophysics, University of California, San Francisco, California 94143, Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239, and Howard Hughes Medical Institute, University of
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29
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Abstract
Recent advances in fluorescence in situ hybridization and three-dimensional microscopy have revealed a high degree of large-scale order in the nucleus, indicating that the position of each gene within the nucleus is not random. As with any other biological phenomenon, this large-scale organization must ultimately be specified by molecular interactions. Biochemical and molecular investigations have revealed a small set of local molecular-scale interactions that can be used together in a combinatorial fashion to establish a global large-scale nuclear architecture.
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Affiliation(s)
- W F Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, 94143, USA
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30
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Spontak RJ, Fung JC, Braunfeld MB, Sedat JW, Agard DA, Kane L, Smith SD, Satkowski MM, Ashraf A, Hajduk DA, Gruner SM. Phase Behavior of Ordered Diblock Copolymer Blends: Effect of Compositional Heterogeneity. Macromolecules 1996. [DOI: 10.1021/ma9515689] [Citation(s) in RCA: 121] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Richard J. Spontak
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, Graduate Group in Biophysics, University of California, San Francisco, California 94143, Department of Biochemistry and Biophysics and the Howard Hughes Medical Institute, University of California, San Francisco, California 94143, Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239, and Department of Physics, Princeton University, Princeton, New Jersey 08544
| | - Jennifer C. Fung
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, Graduate Group in Biophysics, University of California, San Francisco, California 94143, Department of Biochemistry and Biophysics and the Howard Hughes Medical Institute, University of California, San Francisco, California 94143, Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239, and Department of Physics, Princeton University, Princeton, New Jersey 08544
| | - Michael B. Braunfeld
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, Graduate Group in Biophysics, University of California, San Francisco, California 94143, Department of Biochemistry and Biophysics and the Howard Hughes Medical Institute, University of California, San Francisco, California 94143, Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239, and Department of Physics, Princeton University, Princeton, New Jersey 08544
| | - John W. Sedat
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, Graduate Group in Biophysics, University of California, San Francisco, California 94143, Department of Biochemistry and Biophysics and the Howard Hughes Medical Institute, University of California, San Francisco, California 94143, Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239, and Department of Physics, Princeton University, Princeton, New Jersey 08544
| | - David A. Agard
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, Graduate Group in Biophysics, University of California, San Francisco, California 94143, Department of Biochemistry and Biophysics and the Howard Hughes Medical Institute, University of California, San Francisco, California 94143, Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239, and Department of Physics, Princeton University, Princeton, New Jersey 08544
| | - Lisaleigh Kane
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, Graduate Group in Biophysics, University of California, San Francisco, California 94143, Department of Biochemistry and Biophysics and the Howard Hughes Medical Institute, University of California, San Francisco, California 94143, Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239, and Department of Physics, Princeton University, Princeton, New Jersey 08544
| | - Steven D. Smith
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, Graduate Group in Biophysics, University of California, San Francisco, California 94143, Department of Biochemistry and Biophysics and the Howard Hughes Medical Institute, University of California, San Francisco, California 94143, Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239, and Department of Physics, Princeton University, Princeton, New Jersey 08544
| | - Michael M. Satkowski
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, Graduate Group in Biophysics, University of California, San Francisco, California 94143, Department of Biochemistry and Biophysics and the Howard Hughes Medical Institute, University of California, San Francisco, California 94143, Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239, and Department of Physics, Princeton University, Princeton, New Jersey 08544
| | - Arman Ashraf
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, Graduate Group in Biophysics, University of California, San Francisco, California 94143, Department of Biochemistry and Biophysics and the Howard Hughes Medical Institute, University of California, San Francisco, California 94143, Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239, and Department of Physics, Princeton University, Princeton, New Jersey 08544
| | - Damian A. Hajduk
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, Graduate Group in Biophysics, University of California, San Francisco, California 94143, Department of Biochemistry and Biophysics and the Howard Hughes Medical Institute, University of California, San Francisco, California 94143, Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239, and Department of Physics, Princeton University, Princeton, New Jersey 08544
| | - Sol M. Gruner
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, Graduate Group in Biophysics, University of California, San Francisco, California 94143, Department of Biochemistry and Biophysics and the Howard Hughes Medical Institute, University of California, San Francisco, California 94143, Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239, and Department of Physics, Princeton University, Princeton, New Jersey 08544
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31
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Abstract
SUMMARY Position-effect variegation (PEV) describes the stochastic transcriptional silencing of a gene positioned adjacent to heterochromatin. Using FISH, we have tested whether variegated expression of the eye-color gene brown in Drosophila is influenced by its nuclear localization. In embryonic nuclei, a heterochromatic insertion at the brown locus is always spatially isolated from other heterochromatin. However, during larval development this insertion physically associates with other heterochromatic regions on the same chromosome in a stochastic manner. These observations indicate that the brown gene is silenced by specific contact with centromeric heterochromatin. Moreover, they provide direct evidence for long-range chromosome interactions and their impact on three-dimensional nuclear architecture, while providing a cohesive explanation for the phenomenon of PEV.
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Affiliation(s)
- A F Dernburg
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143-0554, USA
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32
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Spontak RJ, Fung JC, Braunfeld MB, Sedat JW, Agard DA, Ashraf A, Smith SD. Architecture-Induced Phase Immiscibility in a Diblock/Multiblock Copolymer Blend. Macromolecules 1996. [DOI: 10.1021/ma9515691] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Richard J. Spontak
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27695, Graduate Group in Biophysics and Department of Biophysics & Biochemistry and Howard Hughes Medical Institute, University of California, San Francisco, California 94143, and Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239
| | - Jennifer C. Fung
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27695, Graduate Group in Biophysics and Department of Biophysics & Biochemistry and Howard Hughes Medical Institute, University of California, San Francisco, California 94143, and Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239
| | - Michael B. Braunfeld
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27695, Graduate Group in Biophysics and Department of Biophysics & Biochemistry and Howard Hughes Medical Institute, University of California, San Francisco, California 94143, and Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239
| | - John W. Sedat
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27695, Graduate Group in Biophysics and Department of Biophysics & Biochemistry and Howard Hughes Medical Institute, University of California, San Francisco, California 94143, and Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239
| | - David A. Agard
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27695, Graduate Group in Biophysics and Department of Biophysics & Biochemistry and Howard Hughes Medical Institute, University of California, San Francisco, California 94143, and Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239
| | - Arman Ashraf
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27695, Graduate Group in Biophysics and Department of Biophysics & Biochemistry and Howard Hughes Medical Institute, University of California, San Francisco, California 94143, and Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239
| | - Steven D. Smith
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27695, Graduate Group in Biophysics and Department of Biophysics & Biochemistry and Howard Hughes Medical Institute, University of California, San Francisco, California 94143, and Corporate Research Division, The Procter & Gamble Company, Cincinnati, Ohio 45239
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33
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Abstract
Electron tomography is a powerful tool in elucidating the three-dimensional architecture of large biological complexes and subcellular organelles. Its use can be expanded through the simplification of the tomographic procedure by automation of its tasks. In this paper, we describe our EMACT/EMCAT system, which automates both tomographic data collection and reconstruction.
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Affiliation(s)
- J C Fung
- Graduate Group in Biophysics, University of California at San Francisco 94143-0448, USA
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Moritz M, Braunfeld MB, Fung JC, Sedat JW, Alberts BM, Agard DA. Three-dimensional structural characterization of centrosomes from early Drosophila embryos. J Cell Biol 1995; 130:1149-59. [PMID: 7657699 PMCID: PMC2120545 DOI: 10.1083/jcb.130.5.1149] [Citation(s) in RCA: 175] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
An understanding of the mechanism and structure of microtubule (MT)-nucleating sites within the pericentriolar material (PCM) of the centrosome has been elusive. This is partly due to the difficulty in obtaining large quantities of centrosomes for analysis, as well as to the problem of attaining interpretable structural data with conventional EM techniques. We describe a protocol for isolating a large quantity of functional centrosomes from early Drosophila embryos. Using automated electron tomography, we have begun a three-dimensional structural characterization of these intact centrosomes with and without regrown MTs. Reconstructions of the centrosomes to approximately 6-8 nm resolution revealed no large structures at the minus ends of MTs, suggesting that if MT-nucleating material physically contacts the MTs, it must conform closely to the shape of the minus end. While many MTs originate near the centrioles, MT minus ends were found throughout the PCM, and even close to its outer boundary. The MTs criss-crossed the PCM, suggesting that nucleating sites are oriented in many different directions. Reconstructions of centrosomes without MTs suggest that there is a reorganization of the PCM upon MT regrowth; moreover, ring-like structures that have a similar diameter as MTs are apparent in the PCM of centrosomes without MTs, and may be MT-nucleating sites.
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Affiliation(s)
- M Moritz
- Department of Biochemistry & Biophysics, University of California at San Francisco 94143-0448, USA
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35
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Abstract
Eighty-three serum specimens from 24 patients infected with Candida albicans were examined for circulating Candida protein antigens with the Candida Detection System (CAND-TEC; Ramco Laboratories, Inc., Houston, Tex.). The medical records of each patient were reviewed for clinical evidence of Candida colonization or disease, predisposing factors for infection, underlying illness, the presence of a contaminated indwelling venous catheter, intravenous amphotericin B therapy, and outcome. Forty-nine serum specimens with antigen titers of 1:2 or less were obtained either from colonized patients or at a time when disseminated disease was not yet clinically suspected. Except for five specimens from two colonized patients, one with a contaminated arterial line, the other specimens with titers of 1:8 or greater (n = 14) were obtained from patients who had been clinically diagnosed and treated for disseminated candidiasis. Serum specimens with titers of 1:4 were often from patients with deep-seated candidal infection but were not uniformly diagnostic; in this situation additional specimens should be tested for Candida antigen titers. Only 1 of 24 serum specimens from patients with no evidence of C. albicans infection had a Candida protein antigen titer of 1:8. With a 1:8 or greater titer as a criterion for dissemination, the sensitivity of the CAND-TEC system was 71%, with a specificity of 98%. If the 1:8 titer for the colonized patient with a contaminated arterial line is not considered a false-positive result, the CAND-TEC sensitivity was 83%. The latex agglutination assay appears to be a useful, rapid, and noninvasive means of laboratory diagnosis of systemic candidiasis. The recovery of C. albicans from at least three body sites may also be a useful predictor of disseminated disease.
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Abstract
Two Streptococcus bovis isolates obtained from patients with endocarditis were found to be tolerant to penicillin and other cell wall active agents. By time-kill analysis, penicillin and streptomycin acted synergistically against these strains. The existence of tolerant S. bovis strains should be considered when initially choosing antibiotics for the treatment of serious S. bovis infections.
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Fung JC, Shanley J, Tilton RC. Comparison of the detection of herpes simplex virus in direct clinical specimens with herpes simplex virus-specific DNA probes and monoclonal antibodies. J Clin Microbiol 1985; 22:748-53. [PMID: 2997269 PMCID: PMC268519 DOI: 10.1128/jcm.22.5.748-753.1985] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A comparison of two commercially available kits for rapid herpes simplex virus (HSV) detection directly in patient specimens was performed. The immunofluorescence assay (IFA) utilized monoclonal antibodies to HSV, and the DNA probe assay utilized three HSV sequences cloned into pBR322. A sample of 243 specimens received in viral transport medium were inoculated into MRC-5 tissue cultures. The remainder of the specimen was centrifuged, and the cellular pellet was examined by IFA and DNA probes. One hundred and sixty-two (66.7%) specimens were considered satisfactory for IFA and DNA probe testing, based on a criterion of observing greater than or equal to 2 intact cells per high-power field. Of the 162 specimens, 35 (21.6%) yielded HSV by culture. By IFA, the sensitivity of detecting HSV culture-positive specimens was 77.1%; specificity was 100%, positive predictive value was 100%, and negative predictive value was 93.3%. DNA probe sensitivity was 71.4%; specificity was 90.6%; positive predictive value was 67.6%; and negative predictive value was 92%. Forty-four (27.2%) of the 162 specimens exhibited nonspecific cytoplasmic staining with the DNA probe. IFA and DNA probe assays can be completed in 2 to 3 h, whereas the average time to culture positivity in this series was 2.2 days. Rapid HSV diagnosis can aid in timely and appropriate patient management.
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38
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Fung JC, Tilton RC. TORCH serologies and specific IgM antibody determination in acquired and congenital infections. Ann Clin Lab Sci 1985; 15:204-11. [PMID: 2986514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Except for rubella testing, routine TORCH serology screens in prenatal care are of little use. Individual TORCH tests may, however, be useful based on the clinical presentation and history of the patient. The laboratory test of choice for diagnosing cytomegalovirus (CMV) and herpes simplex virus (HSV) infections is culture isolation for the virus. The presence for specific IgM antibodies in neonates is diagnostic of congenital infection. In adults, IgM antibody results should be interpreted along with the clinical findings and history of the patient. IgM antibodies may persist for months and even years and may be detected during reactivation of latent virus infections. Serum fractionation should always be performed in IgM antibody testing to avoid false positive results owing to rheumatoid factors and false negative results owing to competing levels of specific IgG antibodies. With a single serum specimen, specific IgM antibody detection may be helpful in differentiating between a recent versus past infection.
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Fung JC, Clogston A, Swenson P, Kaplan M. Serologic diagnosis of toxoplasmosis with emphasis on the detection of Toxoplasma-specific immunoglobulin M antibodies. Am J Clin Pathol 1985; 83:196-9. [PMID: 3881928 DOI: 10.1093/ajcp/83.2.196] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Commercially available kits were used for the detection of Toxoplasma-specific IgM antibodies. False positive IgM results were observed in whole sera containing Toxoplasma-specific antibodies together with rheumatoid factor when tested by immunofluorescence (IFA). False negative IgM results occurred in whole sera containing competing levels of Toxoplasma-specific IgG antibodies, as indicated by the IFA:IgM-M ratio. False positive and false negative IgM results often occurred when whole sera were tested. These false reactions were eliminated by fractioning IgM from IgG using the Isolab's IgM Isolation System. All five sera in this study with an IFA titer to Toxoplasma of greater than or equal to 1:16,384 also contained Toxoplasma-specific IgM antibodies. This suggests that sera with high titers to Toxoplasma should be tested for Toxoplasma-specific IgM antibodies.
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40
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Fung JC, Kaplan MH, Hsieh HC, Stephens A, Tyburski MB, Tenenbaum MJ. Two coagulase-variant forms of Staphylococcus aureus isolated from blood cultures. J Clin Microbiol 1984; 20:115-7. [PMID: 6746882 PMCID: PMC271258 DOI: 10.1128/jcm.20.1.115-117.1984] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Two coagulase-variant forms of Staphylococcus aureus were isolated from blood cultures of a patient with infective endocarditis. The coagulase-positive isolate was hemolytic, whereas the coagulase-negative isolate was nonhemolytic. All other properties examined were identical in both strains. Since coagulase-negative S. aureus strains have been isolated from clinical specimens, laboratories should consider using a combination of other biological properties along with coagulase production for the identification of S. aureus.
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41
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Fung JC, McKinley G, Tyburski MB, Berman M, Goldstein J. Growth of coagulase-negative staphylococci on colistin-nalidixic acid agar and susceptibility to polymyxins. J Clin Microbiol 1984; 19:714-6. [PMID: 6330170 PMCID: PMC271164 DOI: 10.1128/jcm.19.5.714-716.1984] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Colistin-nalidixic acid agar, although recently recommended as a replacement for blood agar for primary plating of urine specimens ( Fung et al., J. Clin. Microbiol. 16:632-636, 1982), has also been reported to suppress the growth of some strains of staphylococci that are susceptible to colistin (polymyxin E). The susceptibility of 11 species of staphylococci to polymyxins was determined, and the ability of these species to grow on colistin-nalidixic acid agar was examined. Although the MICs for most of the strains tested were 8 micrograms/ml or less, only a few coagulase-negative staphylococci grew on or were inhibited by colistin-nalidixic acid agar. This descrepancy was explained by the antagonistic effects that medium components, such as physiological concentrations of magnesium and calcium and 5% sheep blood, had on the activity of polymyxin. Colistin-nalidixic acid agar is still recommended for routine urine processing; however, the poor growth of 13% of the Staphylococcus saprophyticus strains tested suggests that blood agar should be included in the primary plating battery of urine specimens obtained from female outpatients.
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Fung JC, Berman M, Fiorentino T. Capnocytophaga: a review of the literature. Am J Med Technol 1983; 49:589-91. [PMID: 6367464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Capnocytophaga species are normal mouth flora but can be opportunistic pathogens causing juvenile peridontitis and bacteremia in the compromised host. Indole-negative fusiforms isolated anaerobically or in the presence of increased CO2 can presumptively be identified as Capnocytophaga species.
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Wu TC, Fung JC. Evaluation of the usefulness of counterimmunoelectrophoresis for diagnosis of Clostridium difficile-associated colitis in clinical specimens. J Clin Microbiol 1983; 17:610-3. [PMID: 6853688 PMCID: PMC272702 DOI: 10.1128/jcm.17.4.610-613.1983] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Results of counterimmunoelectrophoresis (CIE) were compared with those of isolation of Clostridium difficile and assay for cytotoxicity in HeLa cells. On the basis of 471 stool specimens, CIE exhibited a sensitivity of 38% and a specificity of 88% as compared with the cytotoxin assay. The predictive value of a reactive CIE results is low (17%), whereas the predictive value of a nonreactive CIE result is significant (96%) and therefore warrants its use as a screening test. In addition, stool filtrates may nonspecifically precipitate with the C. difficile antitoxin in the CIE test. Such nonspecific reactions may be identified by simultaneous electrophoresis against nonimmune serum.
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Fung JC, Sun T, Kilius I, Gross S. Printcultures for postmortem microbiology. Ann Clin Lab Sci 1983; 13:83-6. [PMID: 6344746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A modified printculture method for postmortem bacteriology was compared to the traditional tissue homogenate inoculum method. The two methods were comparable in their recovery rate of bacterial isolates. However, printcultures is an easy and rapid method; thus, it is superior to the traditional technique for postmortem culture. Histologic examination of most postmortem lung specimens with no bacterial growth showed no evidence of pneumonia or bronchitis, suggesting that the lack of growth is a reliable indicator of no bacterial infection.
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Abstract
It has been recommended that routine microbiological processing of urine specimens include quantitative plating onto blood agar medium along with a selective and differential agar such as MacConkey agar for gram-negative organisms. Few data have been published to justify this combination. To evaluate the validity of this recommendation 2,553 midstream, clean-voided urine samples were quantitatively plated onto blood agar, MacConkey agar, and colistin-nalidixic acid agar, which is a selective medium for gram-positive organisms. The amounts of growth on each of the three media were compared. Results indicated that the best medium combination was colistin-nalidixic acid agar and MacConkey agar. The use of colistin-nalidixic acid agar instead of blood agar increased the detection of significant growth of enterococci, lactobacilli, and Torulopsis glabrata.
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Abstract
Streptococcal group A, B, and C carbohydrates were analyzed by counterimmunoelectrophoresis, immunoelectrophoresis, and inhibition of immunoprecipitation. Extracts of streptococci group A or C were shown by counterimmunoelectrophoresis to contain both anodic and cathodic migrating components. In immunoelectrophoresis, group A and C substances formed a continuous precipitation line stretching from the anode to the cathode, suggesting a heterogeneous population of molecules with immunochemical identity. This identity was confirmed by inhibition of immunoprecipitation, in which both anodic and cathodic immunoprecipitates were inhibited by the same constituent sugars: group A-anti-A was inhibited by N-acetylglucosamine, and group C-anti-C was inhibited by N-acetylgalactosamine. Extracts of group B showed only anodic migration in counterimmunoelectrophoresis and a narrow, anodic arc in immunoelectrophoresis. The group B-anti-B reaction was inhibited by rhamnose. Carbohydrates of variant strains of group A streptococci were also analyzed by the same methods. The results suggest that the heterogeneity of group A carbohydrate may have resulted from attachment of various amounts of N-acetylglucosamine to the polyrhamnose backbone.
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Fung JC, Wicher K. Comparison of slide agglutination test (Phadebact) with counterimmunoelectrophoresis for detection of streptococcal group antigens. Am J Clin Pathol 1982; 77:608-10. [PMID: 7044102 DOI: 10.1093/ajcp/77.5.608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Sera from mice infected with group B streptococci and culture supernatants of group B, A, and C streptococci were examined for the presence of group-specific antigens by the Phadebact slide agglutination (PSA) test and counterimmunoelectrophoresis (CIE). The results were correlated with the number of organisms present in the blood or in vitro cultures. The PSA test was slightly more sensitive than CIE.
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Fung JC, Wicher K. Minimum number of bacteria needed for antigen detection by counterimmunoelectrophoresis: in vivo and in vitro studies. J Clin Microbiol 1981; 13:681-7. [PMID: 7014618 PMCID: PMC273859 DOI: 10.1128/jcm.13.4.681-687.1981] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Threshold concentrations of Streptococcus pneumoniae type 3, Haemophilus influenzae type b, and Streptococcus sp. group B type Ib required for positive counterimmunoelectrophoresis reactions were determined in vivo and in vitro. Animals were infected intraperitoneally with various concentrations of microorganisms: adult mice with S. pneumoniae, suckling rats with H. influenzae, and 3-week-old mice with Streptococcus sp. group B. At 24 h after infection a minimum blood concentration of 10(3) colony-forming units (CFU)/ml was needed for S. pneumoniae or H. influenzae before antigen was detected in the serum. A minimum concentration of 10(6) CFU/ml was needed for Streptococcus sp. group B at 10 h after infection. Larger threshold concentrations (10(4) CFU/ml for S. pneumoniae, 10(5) CFU/ml for H. influenzae, and 10(7) CFU/ml for Streptococcus) were required in broth-grown cultures before cell-free antigens could be demonstrated by counterimmunoelectrophoresis in the medium. Marked levels of antigen release by group B streptococci were observed as the cultures entered early stationary phase. This study provides evidence of a long-accepted, though poorly substantiated, hypothesis that a threshold concentration of microorganism is necessary before counterimmunoelectrophoresis reactions become positive. Counterimmunoelecrophoresis results for clinical specimens should be interpreted cautiously in light of this evidence.
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Fung JC, MacAlister TJ, Weigand RA, Rothfield LI. Morphogenesis of the bacterial division septum: identification of potential sites of division in lkyD mutants of Salmonella typhimurium. J Bacteriol 1980; 143:1019-24. [PMID: 7009540 PMCID: PMC294407 DOI: 10.1128/jb.143.2.1019-1024.1980] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
It previously has been shown that lkyD mutants of Salmonella typhimurium form large blebs of outer membrane over the septal and polar regions of dividing cells. To determine whether the outer membrane blebs are formed over potential sites of division even in the absence of septal ingrowth, lkyD strains were studied under conditions in which ingrowth of inner membrane and murein was prevented by inactivation of the envA gene product. In aseptate filaments of the LkyD EnvA strain, outer membrane blebs occurred with the usual frequency and were preferentially located over regions where new septa were formed when cell division was subsequently permitted to resume. The results indicate that the outer membrane blebs of the LkyD strain are markers for potential sites of cell division, implying that an alteration in association of outer membrane and murein exists in these sites before the initiation of septal ingrowth. This localized change in cell envelope organization is independent of the septation-inducing effects of the envA gene product.
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