From owner-recombination@net.bio.net Sun Jan 07 22:00:00 1996 Path: biosci!bcm.tmc.edu!news.msfc.nasa.gov!elroy.jpl.nasa.gov!lll-winken.llnl.gov!overload.lbl.gov!bks From: bks@s27w007.pswfs.gov (Bradley K. Sherman) Newsgroups: bionet.molbio.recombination,bionet.software Subject: Syd, a program to synthesize genome linkage data Date: 8 Jan 1996 22:03:39 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 35 Distribution: world Message-ID: <4cs4br$b1k@overload.lbl.gov> NNTP-Posting-Host: s27w007.pswfs.gov Xref: biosci bionet.molbio.recombination:84 bionet.software:14376 Software and details: http://s27w007.pswfs.gov/syd Syd simulates crossings in a 3 generation pedigree of 4 grandparents, 2 parents, 1-500 progeny. It outputs a data file which can be used as input --with some adjustments-- for standard linkage mapping programs. Here's the abstract prepared for Plant Genome IV: Syd simulates the genetics involved in a three-generation outbred pedigree with codominant alleles and produces a synthetic data file which can be analyzed with conventional linkage software. The simulation can be parameterized using a configuration file that allows control over chromosome number, population size, loci per chromosome, chiasmatic frequency, and allelic distribution in simulated crosses. The data can be produced with phase known or unknown. Multiple pedigrees of the same species can be created and the data sampled and resampled. Syd allows hypotheses about preparation of laboratory data for linkage analysis to be tested in a controlled manner. Consider this a ``beta'' release. Syd is written in C and has compiled and run under SunOS and AIX; it should work on other Unix-like systems. --bks -- Bradley K. Sherman | Institute of Forest Genetics bks@s27w007.pswfs.gov | P.O. Box 245 510-559-6437 FAX:510-559-6440 | Berkeley, CA 94701 USA Dendrome Project From owner-recombination@net.bio.net Mon Jan 08 22:00:00 1996 Path: biosci!news.Stanford.EDU!nntp-hub2.barrnet.net!newsfeed.internetmci.com!in1.uu.net!newsflash.concordia.ca!news.mcgill.ca!news From: Graham Dellaire Newsgroups: bionet.molbio.recombination Subject: Posting of Conference on Nuclear Structure-Gene Expression Date: 8 Jan 1996 23:01:32 GMT Organization: McGill University Lines: 230 Message-ID: <4cs7oc$n0s@sifon.cc.mcgill.ca> NNTP-Posting-Host: f-16.das.mcgill.ca X-Newsreader: SPRY News 3.03 (SPRY, Inc.) Revised 11/28/95 NUCLEAR STRUCTURE-GENE EXPRESSION INTERRELATIONSHIPS Organizers: Gary Stein, Gordon Hager and Ronald Berezney April 30-May 6, 1996; Bolton Valley, Vermont -------------------------------------------------------------------------- Application/Abstract Deadline: January 10, 1996 Nuclear Structure-Gene Expression Interrelationships Gifts provided by Pharmacia & Upjohn, Inc. Organizers: Gary Stein - University of Massachusetts Medical Center, Gordon Hager - National Institutes of Health and Ronald Berezney - SUNY-Buffalo April 30-May 6, 1996; Bolton Valley, Vermont Registration Deadline: February 29, 1996 ------------------------------------------------------------------------------- Tuesday 4/30 Registration Orientation OVERVIEW Speaker to be Announced Wednesday 5/1 Breakfast NUCLEAR STRUCTURE AND TRANSCRIPTIONAL CONTROL OF PROLIFERATION AND DIFFERENTIATION Gordon Hager*, National Institutes Health Gary Stein*, Univ Massachusetts Wolfgang Deppert, Heinrich-Pette-Inst fur Experimental Virologie and Immunogie, "Regulatory Interaction of p53 with Nuclear Targets" Coffee Break Donald Cleveland, Univ California-San Diego, "NuMA: A Nuclear Protein Required for Spindle Assembly during Mitosis" Craig Peterson, Univ Massachusetts Med Ctr, "The SWI/SNF Complex: A Chromatin Remodeling Machine" Jane Lian, Univ Massachusetts, "Features of Chromatin Remodelling Influencing Tissue-Specific Expression of the Osteocalcin Gene" Poster Set Up Posters Social Hour NUCLEOSOME-TRANSCRIPTION FACTOR INTERACTIONS: STRUCTURAL AND FUNCTIONAL ACTIVITIES IN VIVO AND IN VITRO Michael Grunstein*, Univ California-Los Angeles, "Histone Regulation of Transcription" Jerry Workman, Pennsylvania State Univ, "Transcription Factor-Induced Remodeling of Chromatin Structure" Coffee Break Robert Kingston, Massachusetts General Hosp, "Activator Function on Nucleosomal Templates" Speaker to be Announced Thursday 5/2 Breakfast THE VISUALIZATION, REGULATION AND FUNCTIONAL ACTIVITIES OF NUCLEAR DOMAINS Jeanne Lawrence*†Univ Massachusetts Med Sch Jeffrey Nickerson, Massachusetts Inst Technology, "Nuclear Architecture" Roel Van Driel, Univ Amsterdam, "Transcription Machinery: Nuclear Distribution" Coffee Break David Spector, Cold Spring Harbor Labs, "Nuclear Domains Involved in Trascription and Pre-mRNA Splicing" Andrew Belmont, Univ Illinois-Urbana, "Large Scale Chromatin Structure" Poster Set Up Posters Social Hour CONTRIBUTIONS OF NUCLEAR IMPORT, EXPORT AND TARGETING TO CELL CYCLE CONTROL Gunther Blobel*†Rockefeller Univ Arthur Pardee*, Dana Farber Cancer Inst, "Cell Cycle Dependent Protein Transport into the Nucleus" Thoru Pederson†The Worcester Foundation Ronald Laskey†Wellcome-CRC Inst Laura Davis, Duke Univ Med Ctr, "FG Nucleoporins Promote Translocation across the Nuclear Pore Complex" Coffee Break Ravi Dhar, National Institutes Health, "mRNA Trafficking and Cell Cycle Control in Schizosacccharomyces pombe" Pam Silver, Dana Farber Cancer Inst, "Co-regulation of Transport in and Out of the Nucleus" Douglass Forbes†Univ California-San Diego Friday 5/3 Breakfast GLOBAL ACTIVATION AND REPRESSION OF TRANSCRIPTION: CELL AND ANIMAL MODELS Ulrich Laemmli*†Univ Geneva Constanze Bonifer, Univ Freiburg, "Transcriptional Activation of Whole Genomic Loci-The Chicken Eysozyme Locus" Coffee Break Jurgen Bode, Gesellschaft Fur Biotechnologische Forschung, "Dentification and Structure of Transcriptionally Active Genomic Sites" Speaker to be Announced Poster Set Up WORKSHOP: CONTRIBUTIONS FROM YOUNG INVESTIGATORS Speakers to be selected from submitted abstracts Posters Social Hour NUCLEAR STRUCTURE AND GENOME REPLICATION Ronald Berezney*, SUNY-Buffalo Joyce Hamlin, Univ Virginia Sch Med, "Effects of Chromosomal Context on a Chromosomal Origin of Replication" Melvin DePamphilis, National Institutes of Health, "Origins of DNA Replication in Mammalian Chromosomes" Coffee Break David Knipe†Harvard Med Sch David Kaufman, Univ North Carolina-Chapel Hill, "Investigations of DNA Replicated Early in the S Phase" Saturday 5/4 Breakfast CONTROL OF CHROMATIN STRUCTURE AND NUCLEOSOME ORGANIZATION Ken Van Holde*, Oregon State Univ, "Linker Histones and Chromatin Fiber Structure" Gary Felsenfeld, National Institutes of Health, "Chromatin Structure and the Regulation of Transcription" James Davie, Univ Manitoba, "Histone Modifications and Nuclear Domains Involved in Transcription" Coffee Break Alan Wolffe, National Institutes Health, "Nucleosome Structure and Function" Barbara Sollner-Webb†Johns Hopkins University Poster Set Up WORKSHOP: STATE-OF-THE-ART EXPERIMENTAL APPROACHES Speakers to be announced Posters Social Hour NUCLEAR MATRIX AND CHROMATIN TRANSITIONS IN REGULATION OF GENE EXPRESSION Robert Goldman*, Northwestern Univ William Brinkley*, Baylor Coll Med, "Dynamics of Nuclear Matrix Proteins in the Cell Cycle" Kenneth Zaret, Brown Univ, "Potentiation and Activation of Developmentally Controlled Genes in Chromatin" Erin O'Shea, Univ California-San Francisco, "Phosphate Metabolism and Cell Cycle Control" Coffee Break William Gerrard†Univ Texas SW Med Ctr Andre J. Van Wijnen†Univ Massachusetts Sunday 5/5 Breakfast GENOME IMPRINTING Rudolph Grosschedl*, Univ California-San Francisco, "Role of MAR Sequences in Chromatin Accessibility and DNA Demethylation" Vicki Chandler, Univ Oregon, "Paramutation: An Allelic Interaction that leads to Heritable Changes in Transcription" Coffee Break Huntington Willard, Case Western Reserve Univ, "Epigenetic Regulation of X-Linked Gene Expression" NUCLEAR STRUCTURE IN DIAGNOSIS AND THERAPEUTICS Donald Coffey*†Johns Hopkins Hosp Speaker to be Announced Coffee Break Robert Getzenberg, Univ Pittsburgh, "Recent Studies in Cancer Associated Nuclear Matrix Protein: Rat Prostate and Human Bladder" Steven Ward, Robert W ood Johnson Med Sch SUMMARY AND PROSPECTS Sheldon Penman†Massachusetts Inst Technology Banquet Possible Entertainment Monday 5/6 Breakfast Departure * = Session Chairperson; †= Invited, not yet responded. ******************************************************** Graham Dellaire Snail Mail Div. of Experimental Medicine Institute du Cancer de Montreal Dept. of Medicine Louis Charles-Simard McGill University 1560 Sherbrooke Street E. e-mail:dellaire@odyssee.net Montreal, Quebec, Canada or B2XE@musicb.mcgill.ca ******************************************************** From owner-recombination@net.bio.net Tue Jan 09 22:00:00 1996 Path: biosci!rutgers!csn!carbon!night.primate.wisc.edu!sdd.hp.com!vixen.cso.uiuc.edu!newsfeed.internetmci.com!news.msfc.nasa.gov!sol.ctr.columbia.edu!news.columbia.edu!ciao.cc.columbia.edu!wl101 From: wl101@ciao.cc.columbia.edu (Wentian Li) Newsgroups: bionet.molbio.recombination Subject: larger female rec rate at centromere Date: 10 Jan 1996 21:37:34 GMT Organization: Columbia University Lines: 13 Message-ID: <4d1biu$5a3@apakabar.cc.columbia.edu> NNTP-Posting-Host: ciao.cc.columbia.edu the recombination rates for human female are usually larger than those of male AT CENTROMERE REGIONS (both by surveying the publications on genetic map and our unpublished results of linkage analysis on all 22 autosomal chromosomes). does anyone know why it is the case? what's the molecular basis for this observation? wli@linkage.cpmc.columbia.edu From owner-recombination@net.bio.net Tue Jan 09 22:00:00 1996 Path: biosci!agate!library.ucla.edu!info.ucla.edu!newsfeed.internetmci.com!in1.uu.net!newsflash.concordia.ca!news.mcgill.ca!news From: Graham Dellaire Newsgroups: bionet.molbio.recombination Subject: repost (McGill not receiving again!!!!) Conference announcement Nuclear Structure and Expression Date: 9 Jan 1996 19:25:40 GMT Organization: McGill University Computing Centre Lines: 230 Message-ID: <4cuffk$8n7@sifon.cc.mcgill.ca> NNTP-Posting-Host: e-14.das.mcgill.ca X-Newsreader: AIR News 3.X (SPRY, Inc.) Revised 11/28/95 NUCLEAR STRUCTURE-GENE EXPRESSION INTERRELATIONSHIPS Organizers: Gary Stein, Gordon Hager and Ronald Berezney April 30-May 6, 1996; Bolton Valley, Vermont -------------------------------------------------------------------------- Application/Abstract Deadline: January 10, 1996 Nuclear Structure-Gene Expression Interrelationships Gifts provided by Pharmacia & Upjohn, Inc. Organizers: Gary Stein - University of Massachusetts Medical Center, Gordon Hager - National Institutes of Health and Ronald Berezney - SUNY-Buffalo April 30-May 6, 1996; Bolton Valley, Vermont Registration Deadline: February 29, 1996 ------------------------------------------------------------------------------- Tuesday 4/30 Registration Orientation OVERVIEW Speaker to be Announced Wednesday 5/1 Breakfast NUCLEAR STRUCTURE AND TRANSCRIPTIONAL CONTROL OF PROLIFERATION AND DIFFERENTIATION Gordon Hager*, National Institutes Health Gary Stein*, Univ Massachusetts Wolfgang Deppert, Heinrich-Pette-Inst fur Experimental Virologie and Immunogie, "Regulatory Interaction of p53 with Nuclear Targets" Coffee Break Donald Cleveland, Univ California-San Diego, "NuMA: A Nuclear Protein Required for Spindle Assembly during Mitosis" Craig Peterson, Univ Massachusetts Med Ctr, "The SWI/SNF Complex: A Chromatin Remodeling Machine" Jane Lian, Univ Massachusetts, "Features of Chromatin Remodelling Influencing Tissue-Specific Expression of the Osteocalcin Gene" Poster Set Up Posters Social Hour NUCLEOSOME-TRANSCRIPTION FACTOR INTERACTIONS: STRUCTURAL AND FUNCTIONAL ACTIVITIES IN VIVO AND IN VITRO Michael Grunstein*, Univ California-Los Angeles, "Histone Regulation of Transcription" Jerry Workman, Pennsylvania State Univ, "Transcription Factor-Induced Remodeling of Chromatin Structure" Coffee Break Robert Kingston, Massachusetts General Hosp, "Activator Function on Nucleosomal Templates" Speaker to be Announced Thursday 5/2 Breakfast THE VISUALIZATION, REGULATION AND FUNCTIONAL ACTIVITIES OF NUCLEAR DOMAINS Jeanne Lawrence*†Univ Massachusetts Med Sch Jeffrey Nickerson, Massachusetts Inst Technology, "Nuclear Architecture" Roel Van Driel, Univ Amsterdam, "Transcription Machinery: Nuclear Distribution" Coffee Break David Spector, Cold Spring Harbor Labs, "Nuclear Domains Involved in Trascription and Pre-mRNA Splicing" Andrew Belmont, Univ Illinois-Urbana, "Large Scale Chromatin Structure" Poster Set Up Posters Social Hour CONTRIBUTIONS OF NUCLEAR IMPORT, EXPORT AND TARGETING TO CELL CYCLE CONTROL Gunther Blobel*†Rockefeller Univ Arthur Pardee*, Dana Farber Cancer Inst, "Cell Cycle Dependent Protein Transport into the Nucleus" Thoru Pederson†The Worcester Foundation Ronald Laskey†Wellcome-CRC Inst Laura Davis, Duke Univ Med Ctr, "FG Nucleoporins Promote Translocation across the Nuclear Pore Complex" Coffee Break Ravi Dhar, National Institutes Health, "mRNA Trafficking and Cell Cycle Control in Schizosacccharomyces pombe" Pam Silver, Dana Farber Cancer Inst, "Co-regulation of Transport in and Out of the Nucleus" Douglass Forbes†Univ California-San Diego Friday 5/3 Breakfast GLOBAL ACTIVATION AND REPRESSION OF TRANSCRIPTION: CELL AND ANIMAL MODELS Ulrich Laemmli*†Univ Geneva Constanze Bonifer, Univ Freiburg, "Transcriptional Activation of Whole Genomic Loci-The Chicken Eysozyme Locus" Coffee Break Jurgen Bode, Gesellschaft Fur Biotechnologische Forschung, "Dentification and Structure of Transcriptionally Active Genomic Sites" Speaker to be Announced Poster Set Up WORKSHOP: CONTRIBUTIONS FROM YOUNG INVESTIGATORS Speakers to be selected from submitted abstracts Posters Social Hour NUCLEAR STRUCTURE AND GENOME REPLICATION Ronald Berezney*, SUNY-Buffalo Joyce Hamlin, Univ Virginia Sch Med, "Effects of Chromosomal Context on a Chromosomal Origin of Replication" Melvin DePamphilis, National Institutes of Health, "Origins of DNA Replication in Mammalian Chromosomes" Coffee Break David Knipe†Harvard Med Sch David Kaufman, Univ North Carolina-Chapel Hill, "Investigations of DNA Replicated Early in the S Phase" Saturday 5/4 Breakfast CONTROL OF CHROMATIN STRUCTURE AND NUCLEOSOME ORGANIZATION Ken Van Holde*, Oregon State Univ, "Linker Histones and Chromatin Fiber Structure" Gary Felsenfeld, National Institutes of Health, "Chromatin Structure and the Regulation of Transcription" James Davie, Univ Manitoba, "Histone Modifications and Nuclear Domains Involved in Transcription" Coffee Break Alan Wolffe, National Institutes Health, "Nucleosome Structure and Function" Barbara Sollner-Webb†Johns Hopkins University Poster Set Up WORKSHOP: STATE-OF-THE-ART EXPERIMENTAL APPROACHES Speakers to be announced Posters Social Hour NUCLEAR MATRIX AND CHROMATIN TRANSITIONS IN REGULATION OF GENE EXPRESSION Robert Goldman*, Northwestern Univ William Brinkley*, Baylor Coll Med, "Dynamics of Nuclear Matrix Proteins in the Cell Cycle" Kenneth Zaret, Brown Univ, "Potentiation and Activation of Developmentally Controlled Genes in Chromatin" Erin O'Shea, Univ California-San Francisco, "Phosphate Metabolism and Cell Cycle Control" Coffee Break William Gerrard†Univ Texas SW Med Ctr Andre J. Van Wijnen†Univ Massachusetts Sunday 5/5 Breakfast GENOME IMPRINTING Rudolph Grosschedl*, Univ California-San Francisco, "Role of MAR Sequences in Chromatin Accessibility and DNA Demethylation" Vicki Chandler, Univ Oregon, "Paramutation: An Allelic Interaction that leads to Heritable Changes in Transcription" Coffee Break Huntington Willard, Case Western Reserve Univ, "Epigenetic Regulation of X-Linked Gene Expression" NUCLEAR STRUCTURE IN DIAGNOSIS AND THERAPEUTICS Donald Coffey*†Johns Hopkins Hosp Speaker to be Announced Coffee Break Robert Getzenberg, Univ Pittsburgh, "Recent Studies in Cancer Associated Nuclear Matrix Protein: Rat Prostate and Human Bladder" Steven Ward, Robert W ood Johnson Med Sch SUMMARY AND PROSPECTS Sheldon Penman†Massachusetts Inst Technology Banquet Possible Entertainment Monday 5/6 Breakfast Departure * = Session Chairperson; †= Invited, not yet responded. ******************************************************** Graham Dellaire Snail Mail Div. of Experimental Medicine Institute du Cancer de Montreal Dept. of Medicine Louis Charles-Simard McGill University 1560 Sherbrooke Street E. e-mail:dellaire@odyssee.net Montreal, Quebec, Canada or B2XE@musicb.mcgill.ca ******************************************************** From owner-recombination@net.bio.net Wed Jan 10 22:00:00 1996 Path: biosci!ATLAS.ODYSSEE.NET!dellaire From: dellaire@ATLAS.ODYSSEE.NET (Graham Dellaire) Newsgroups: bionet.molbio.recombination Subject: RE: larger female rec rate at centromere Date: 10 Jan 1996 19:31:43 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 61 Sender: daemon@net.bio.net Distribution: world Message-ID: <01BADFA9.E86C7900@pool23_9.odyssee.net> NNTP-Posting-Host: net.bio.net ---------- From: Wentian Li[SMTP:wl101@ciao.cc.columbia.edu] Sent: Wednesday, January 10, 1996 4:37 PM To: recom@net.bio.net Subject: larger female rec rate at centromere the recombination rates for human female are usually larger than those of male AT CENTROMERE REGIONS (both by surveying the publications on genetic map and our unpublished results of linkage analysis on all 22 autosomal chromosomes). does anyone know why it is the case? what's the molecular basis for this observation? wli@linkage.cpmc.columbia.edu I think this is still one of the great unknowns ... in molecular biology = but here is my best shot. One reason could be a difference of accessibility of the DNA for = recombination. One phenomenon called imprinting can affect many = different behaviours of a region of DNA (replication, transcription and = now even recombination (see Andras,Gyapay and Jami; Current Biology Sept = 1995 bol5 no9 pg 1030-1035)). Perhaps some sort of imprinting-like = mechanism could be involved in the different recombination frequencies = shown for chromosomal markers in males vs. females.) Further if this = mechanism involves something like imprinting perhaps methylation or some = other local change in chromatin is involved that alters the = accessibility of the DNA for recombination and thus alters the = frequencies seen between markers between male and female chromosomes.=20 To my knowledge there have been no studies that have conclusively shown = what the molecular basis of this phenomenon involves. Imprinting is = dependent on gamete sex rather than the sex of the diploid organism so = the above emphasis on the word "imprinting" should be dropped the real = emphasis is on the recombination frequencies (thus map distances) which = differ and this is most likely due a differential accessibility of the = DNA for the chromosomal markers on male and female chromosomes for = recombination. One can invoke all kinds of possible mediators of this = accessibility (Y specific factors perhaps) that could alter the = structure of DNA at the site of these markers directly or indirectly. = But until further research is done I think the question will remain open = for some time. RECOM Graham Dellaire McGill University=20 Experimental Medicine dellaire@odyssee.net =20 http://www.medcor.mcgill.ca/EXPMED/DOCS/recomfaq.html From owner-recombination@net.bio.net Thu Jan 11 22:00:00 1996 Path: biosci!rutgers!csn!carbon!night.primate.wisc.edu!sdd.hp.com!swrinde!newsfeed.internetmci.com!in2.uu.net!newsflash.concordia.ca!news.mcgill.ca!news From: Graham Dellaire Newsgroups: bionet.molbio.recombination Subject: Re:why the difference in Map Distances on Male or Female Chromosomes Date: 12 Jan 1996 14:30:01 GMT Organization: McGill University Lines: 66 Message-ID: <4d5r99$gdr@sifon.cc.mcgill.ca> NNTP-Posting-Host: g-02.das.mcgill.ca X-Newsreader: SPRY News 3.03 (SPRY, Inc.) >>the recombination rates for human female are >>usually larger than those of male AT CENTROMERE >>REGIONS (both by surveying the publications on >>genetic map and our unpublished results of linkage >>analysis on all 22 autosomal chromosomes). >> >>does anyone know why it is the case? what's the >>molecular basis for this observation? > > >I think this is still one of the great unknowns ... in molecular biology >but here is my best shot. > >One reason could be a difference of accessibility of the DNA for >recombination. One phenomenon called imprinting can affect many >different behaviours of a region of DNA (replication, transcription and >now even recombination (see Andras,Gyapay and Jami; Current Biology Sept >1995 bol5 no9 pg 1030-1035)). Perhaps some sort of imprinting-like >mechanism could be involved in the different recombination frequencies >shown for chromosomal markers in males vs. females.) Further if this >mechanism involves something like imprinting perhaps methylation or some >other local change in chromatin is involved that alters the >accessibility of the DNA for recombination and thus alters the >frequencies seen between markers between male and female chromosomes. > >To my knowledge there have been no studies that have conclusively shown >what the molecular basis of this phenomenon involves. Imprinting is >dependent on gamete sex rather than the sex of the diploid organism so >the above emphasis on the word "imprinting" should be dropped the real >emphasis is on the recombination frequencies (thus map distances) which >differ and this is most likely due a differential accessibility of the >DNA for the chromosomal markers on male and female chromosomes for >recombination. One can invoke all kinds of possible mediators of this >accessibility (Y specific factors perhaps) that could alter the >structure of DNA at the site of these markers directly or indirectly. >But until further research is done I think the question will remain open >for some time. > thanks for your posting. there are two observations from linkage analysis: (1) on average, more recombination in female than male (2) the locational effects, i.e., male tend to have higher recombination rate than female near telomere (not true for every chromosome), but female has higher rate than male at centromere (true for almost all chromosomes). is your suggestion related to (1) or (2)? wl101@columbia.edu >Dear Wentian I ment something more like 2. What I was saying is that the difference in map distances is based on a difference in recombination and this is a reflection of accessibility of that region of DNA... Interestingly markers near both Centromeres and Telomeres are less recombinogenic in general (hence why the markers are so far apart in that region) and the accessibility is reflected in the position effects seen for transcription of transgenes that are fortuitously integrated near these regions. Now as to the reason why....? I invoked a difference in chromosome structure at these regions. I wonder if anyone else any other ideas in this area From owner-recombination@net.bio.net Sat Jan 13 22:00:00 1996 Newsgroups: bionet.molbio.recombination Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!in1.uu.net!nih-csl!NewsWatcher!user From: lichten@helix.nih.gov (Michael Lichten) Subject: Re: larger female rec rate at centromere Message-ID: Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: 128.231.218.92 Organization: LB/DCBDC/NCI References: <4d1biu$5a3@apakabar.cc.columbia.edu> Date: Sun, 14 Jan 1996 20:55:38 GMT Lines: 44 In article <4d1biu$5a3@apakabar.cc.columbia.edu>, wl101@ciao.cc.columbia.edu (Wentian Li) wrote: > the recombination rates for human female are > usually larger than those of male AT CENTROMERE > REGIONS (both by surveying the publications on > genetic map and our unpublished results of linkage > analysis on all 22 autosomal chromosomes). > > does anyone know why it is the case? what's the > molecular basis for this observation? > > wli@linkage.cpmc.columbia.edu The observation of higher recombination frequencies around centromeres in females than in males (both mice and humans) is due to two factors. First, the genetic map is longer in females than in males overall (i.e. there are more total crossovers in female meiosis). Second, in both mice and in humans, crossovers in male meiosis tend to be telomeric or subtelomeric; this has been known from chiasmata studies for some time and is beginning to emerge from molecular marker studies as more telomeric markers are isolated. Alastair Goldman and I give a brief summary of the matter in Ann Rev Genet (1995) 29:423-444; a recent article (which I have not read yet) is Lawrie, Tease and Hulten (1995) Chromosoma 104:308. So the net effect is to have fewer centromeric crossovers in males, but this is really a matter of telomeric enrichment rather than centromeric dimunition. As to why at telomeres? And why in males? I've been carrying the idea (which has probably been thought of before) that the reason has to do with the unique problem that males face (OK, one of the unique problems....), namely, ensuring a crossover in the pseudoautosomal region shared by the X and Y chromosomes. One way to do this would be to make all telomeres "hot" for recombination in males. It is interesting that in a couple of cases, translocations that bring telomeric sequences interstitial create male-specific recombination "hot spots". This problem is definitely not one of the great unknowns in molecular biology...it hasn't gotten to the stage where one can even HOPE to think in molecular terms.... -- Michael Lichten lichten@helix.nih.gov From owner-recombination@net.bio.net Sat Jan 13 22:00:00 1996 Path: biosci!ATLAS.ODYSSEE.NET!dellaire From: dellaire@ATLAS.ODYSSEE.NET (Graham Dellaire) Newsgroups: bionet.molbio.recombination Subject: RE: larger female rec rate at centromere Date: 14 Jan 1996 14:52:17 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 90 Sender: daemon@net.bio.net Distribution: world Message-ID: <01BAE2A7.7D343820@pool12_9.odyssee.net> NNTP-Posting-Host: net.bio.net ---------- From: Michael Lichten[SMTP:lichten@helix.nih.gov] Sent: Sunday, January 14, 1996 3:55 PM To: recom@net.bio.net Subject: Re: larger female rec rate at centromere In article <4d1biu$5a3@apakabar.cc.columbia.edu>, wl101@ciao.cc.columbia.edu (Wentian Li) wrote: >> the recombination rates for human female are >> usually larger than those of male AT CENTROMERE >> REGIONS (both by surveying the publications on >> genetic map and our unpublished results of linkage >> analysis on all 22 autosomal chromosomes). >>=20 >> does anyone know why it is the case? what's the >> molecular basis for this observation? >>=20 >> wli@linkage.cpmc.columbia.edu Previously Michael Lichten wrote..... >As to why at telomeres? And why in males? I've been carrying the idea >(which has probably been thought of before) that the reason has to do = with >the unique problem that males face (OK, one of the unique = problems....), >namely, ensuring a crossover in the pseudoautosomal region shared by = the X >and Y chromosomes. =20 >One way to do this would be to make all telomeres >"hot" for recombination in males. It is interesting that in a couple = of >cases, translocations that bring telomeric sequences interstitial = create >male-specific recombination "hot spots". -=20 Michael Lichten lichten@helix.nih.gov Than why have a pseudoautosomal region at all, if telomeres would = suffice?=20 For the male hot spots.... I would be interested in the reference for this point if it is handy. = Are they really male specific? What criteria did they use to deem them so? (i.e. was it only that the = cell line they used was male?) >This problem is definitely not one of the great unknowns in molecular >biology... That is your opinion I work in genome structure (laugh) and to me it is. = I would be interested in what you thought was a "great unknown"? ...and actually I think the "great uknowns of molecular biology" would = be a smashing start for a new thread..... How about it people! >it hasn't gotten to the stage where one can even HOPE to think >in molecular terms.... I agree whole heartedly Fact remains that explaining genome wide differences in recombination = frequencies between males and females is a "black box".=20 The article I sighted before in Current biology was the closest thing to = a "hint" I have seen. I think as we learn more about chromosome = structure we will get closer to filling the black box. Graham Dellaire dellaire@odyssee.net popa0206@po-box.mcgill.ca =20 From owner-recombination@net.bio.net Sat Jan 13 22:00:00 1996 Path: biosci!ATLAS.ODYSSEE.NET!dellaire From: dellaire@ATLAS.ODYSSEE.NET (Graham Dellaire) Newsgroups: bionet.molbio.recombination Subject: What are the Great Unknowns Of Molecular Biology? Date: 14 Jan 1996 15:20:26 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 28 Sender: daemon@net.bio.net Distribution: world Message-ID: <01BAE2AB.70288A60@pool12_9.odyssee.net> NNTP-Posting-Host: net.bio.net In recent posts we have had a suggestion for a great uknown in molecular = biology. It was "the difference in Recombination Rates between male and female = chromosomes" (i.e. by me (laugh)) Let's here some others ..... Of course these will all be the personal opinion of the writer and in no = way reflect the field consensus in general (where ever that may lie and = most likely it is polarized (laugh)). Although it is encouraged to talk about topics involving recombination = and DNA repair do not let this limit your contribution. =20 Graham Dellaire Discussion Leader=20 RECOM dellaire@odyssee.net popa0206@po-box.mcgil.ca From owner-recombination@net.bio.net Sat Jan 13 22:00:00 1996 Path: biosci!agate!news.ucdavis.edu!reqa-005.ucdavis.edu!user From: mezwick@ucdavis.edu (Michael E. Zwick) Newsgroups: bionet.molbio.recombination Subject: Re: larger female rec rate at centromere Date: 11 Jan 1996 16:38:08 GMT Organization: Center for Population Biology Lines: 23 Message-ID: References: <4d1biu$5a3@apakabar.cc.columbia.edu> NNTP-Posting-Host: reqa-005.ucdavis.edu In article <4d1biu$5a3@apakabar.cc.columbia.edu>, wl101@ciao.cc.columbia.edu (Wentian Li) wrote: > the recombination rates for human female are > usually larger than those of male AT CENTROMERE > REGIONS (both by surveying the publications on > genetic map and our unpublished results of linkage > analysis on all 22 autosomal chromosomes). > > does anyone know why it is the case? what's the > molecular basis for this observation? > > wli@linkage.cpmc.columbia.edu I am not intimately familiar with human data, but do have a couple of questions: 1) But, are rates of recombination equivalent in male and female humans? 2) Is there any evidence that the exchange events observed at centromeres are in fact the result of meiotic crossing over (i.e. form chiasmata) and not the result of DSB repair? Mike From owner-recombination@net.bio.net Sun Jan 14 22:00:00 1996 Path: biosci!ATLAS.ODYSSEE.NET!dellaire From: dellaire@ATLAS.ODYSSEE.NET (Graham Dellaire) Newsgroups: bionet.molbio.recombination Subject: RE: Why is DNA replication faster in Prokaryotes than in Eukaryotes Date: 14 Jan 1996 16:05:30 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 90 Sender: daemon@net.bio.net Distribution: world Message-ID: <01BAE2B1.B60FFDA0@ectopic.odyssee.net> NNTP-Posting-Host: net.bio.net To: biochrom@net.bio.net From: anon1@anon.penet.fi (anon1@anon.penet.fi) Subject: PLEASE HELP....re. rate of DNA replication... Date: Thu, 11 Jan 1996 16:43:17 GMT >for a biology paper,=20 >i need to solve the follwing question: >WHY IS DNA REPLICATION IN PROKARYOTES NEARLY 100 TIMES FASTER THAN >REPLICATION IN EUKARYOTES ? The numbers I have quote: E.coli at 500 nt/s and Human Fibroblast at 50 nt/s that would be 10X faster >i have wondered if it is because of (a) life span of pro vs eu >karyotes, (b) because of existence ofa nuclear membrane in eukaryotes, >where one is not found in prokaryotes... >if anyone can shed some light on this question, please reply by >posting or send email to: k.venkiteswaran@odyssey.on.ca Okay=20 Here are a few possibilities I could come up with. One, in E.coli you are not worrying about mutations that much. In fact = a high mutation rate is desirable if the bacterium is to adapt to = changing environments. The result is you can replicate your DNA faster = without worrying about a mutation occurring. In higher eukaryotes such = as mammals this is a big problem... mutations can kill the whole = organism if well placed (i.e. cancer). For yeast I don't think this is = as strong a point as they are unicellular and much like in bacteria = --high mutation rates are adaptive. The error rate in E.coli is consequently ~10-8 where as in human = Fibroblasts it is ~10-10 Two in E.coli you have very little packing of DNA compared to higher = eukaryotes. To start DNA replication you need to gain access to the DNA = and expose the template for the polymerase. For instance you have the = HU protein of bacteria compared to H1, H2A, H2B, H3 and H4 as well as = the HMG proteins in mammals. The bacterial genome is much less complex = so by simple logic to replicate DNA it is much easier to gain accesss to = DNA in bacteria then in a mammal and hence it is faster in bacteria. =20 Further as a point of interest In E.Coli you only have one origin of replication where as in mammalian = cells it is estimated there are between 10 to the 4 --10 to the 6 = possible origins. This may reflects both the difference in size and = complexity of the two genomes as well as the speed at which DNA is = replicated. Multiple initiations of replication could help increase the = time to replicate the genome if it is very large. E.Coli has 3 X10 to the 6 bp and in the human genome there are ~3X 10 to = the 9 or=20 1000X more DNA to replicate. =20 1000 X 10 (the difference in speed of DNA replication)=3D 10 000 or 10 = to the 4 hmmmm by a rough calculation it makes sense why you have ~10 to the 4 = origins in the human genome and only 1 in bacteria. --------------------------------- Lastly, To your suggestion of the nuclear membrane as a possible reason for = higher replication rates I think the membrane provides a way of = segregating transcription and translation first of all and may not = really have much to do with replication on a surface level. =20 Graham Dellaire dellaire@odyssee.net From owner-recombination@net.bio.net Mon Jan 15 22:00:00 1996 Path: biosci!rutgers!csn!carbon!night.primate.wisc.edu!sdd.hp.com!usc!elroy.jpl.nasa.gov!swrinde!newsfeed.internetmci.com!vixen.cso.uiuc.edu!news.ksu.ksu.edu!usenet From: "Beth A. Montelone" Newsgroups: bionet.molbio.recombination Subject: Re: What are the Great Unknowns Of Molecular Biology? Date: 16 Jan 1996 19:07:36 GMT Organization: Kansas State University Lines: 15 Message-ID: <4dgt1o$er0@newserv.ksu.ksu.edu> References: <01BAE2AB.70288A60@pool12_9.odyssee.net> NNTP-Posting-Host: 129.130.115.17 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) Okay, I'll play. 1) What is the basis of strand discrimination in mismatch repair in eukaryotes? 2) Does there exist a phenomenon of recombination competence in mitotic cells of eukaryotes? 3) Do transformation methods induce mutagenic or recombinogenic activities? That's a start. Other takers? Beth Montelone Kansas State University bethmont@ksu.ksu.edu From owner-recombination@net.bio.net Mon Jan 15 22:00:00 1996 Newsgroups: bionet.molbio.recombination Path: biosci!lhc.nlm.nih.gov!nih-csl!NewsWatcher!user From: lichten@helix.nih.gov (Michael Lichten) Subject: Re: larger female rec rate at centromere Message-ID: Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: 128.231.218.92 Organization: LB/DCBDC/NCI References: <01BAE2A7.7D343820@pool12_9.odyssee.net> Date: Tue, 16 Jan 1996 13:31:23 GMT Lines: 53 In article <01BAE2A7.7D343820@pool12_9.odyssee.net>, dellaire@ATLAS.ODYSSEE.NET (Graham Dellaire) wrote: > Than why have a pseudoautosomal region at all, if telomeres would = > suffice?=20 I correct myself. I meant to say telomeric or subtelomeric regions. The pseudoautosomal region is, for all intents and purposes, equivalent to a subtelomeric region. > > For the male hot spots.... > I would be interested in the reference for this point if it is handy. = > Are they really male specific? > What criteria did they use to deem them so? (i.e. was it only that the = > cell line they used was male?) We are talking about MEIOTIC recombination here. Pedigree analysis allows one to unambiguously distinguish recombination events that happen during male and female meiosis. Other evidence comes from the study of the locations of chiasma, which are the physical manifestation of crossovers in condensed pre-meiosis I chromosomes. Chiasma maps from males come from spermatocytes; from females come from oocytes. One can usually tell the difference between the two ;-). Also, Michael Zwick wrote: >I am not intimately familiar with human data, but do have a couple of >questions: > >1) But, are rates of recombination equivalent in male and female humans? > >2) Is there any evidence that the exchange events observed at centromeres >are in fact the result of meiotic crossing over (i.e. form chiasmata) and >not the result of DSB repair? We are talking here about meiotic recombination. Female genetic maps are, in total, less than twice the total male genetic map. The exchange events observed at centromeres are almost certainly crossovers. I would also like to point out that crossovers can be products of DSB repair....In saccharomyces, we have fairly solid evidence that most, if not all, meiotic recombination is initiated by DSBs....... Again, I don't want to toot my own horn too much, but Alastair Goldman and I did just finish a review on the subject of meiotic recombination hotspots, and I would be more than glad to either mail a copy to anyone who's interested (I have 200 copies taking up valuable room on my shelf) or attaching a copy of the file (Mac Word 5.1) to an email message. My email address is lichten@helix.nih.gov. -- Michael Lichten lichten@helix.nih.gov From owner-recombination@net.bio.net Tue Jan 16 22:00:00 1996 Path: biosci!rutgers!csn!carbon!night.primate.wisc.edu!sdd.hp.com!swrinde!newsfeed.internetmci.com!info.ucla.edu!library.ucla.edu!news.ucdavis.edu!reqb-092.ucdavis.edu!user From: mezwick@ucdavis.edu (Michael E. Zwick) Newsgroups: bionet.molbio.recombination Subject: Re: larger female rec rate at centromere Date: 17 Jan 1996 06:10:54 GMT Organization: Center for Population Biology Lines: 46 Message-ID: References: <01BAE2A7.7D343820@pool12_9.odyssee.net> NNTP-Posting-Host: reqb-092.ucdavis.edu In article , lichten@helix.nih.gov (Michael Lichten) wrote: > We are talking about MEIOTIC recombination here. Pedigree analysis allows > one to unambiguously distinguish recombination events that happen during > male and female meiosis. Other evidence comes from the study of the > locations of chiasma, which are the physical manifestation of crossovers > in condensed pre-meiosis I chromosomes. Chiasma maps from males come from > spermatocytes; from females come from oocytes. One can usually tell the > difference between the two ;-). But in reality, isn't what you deem a crossover event really is just the exchange of flanking markers? How that crossover event actually came about may not be clear. While you can certainly argue from the observed distribution and frequency of chiasmata that a large proportion or observed crossovers must be the result of meiotic crossing over, I don't think it is at all clear what proportion of events leading to the exchange of flanking markers occur outside the context of a chiasmate. The exchange events > observed at centromeres are almost certainly crossovers. I would also > like to point out that crossovers can be products of DSB repair....In > saccharomyces, we have fairly solid evidence that most, if not all, > meiotic recombination is initiated by DSBs....... Well, if by crossover you mean the exchange of flanking markers then I certainly agree. And I agree that DSBs can produce exchange of flanking markers - i.e. perhaps due to transposable elements, random DSBs etc. However, my point is there have to be some number of events which result in the exchange of flanking markers that are not the product of crossing over (with chiasmata). I don't think that the distribution of these events are well understood. Perhaps I am wrong - does anyone know of any data out there? Let me explain more clearly what I mean. For example, consider in Drosophila the data of Merriam and Frost 1964(I think Genetics), who conduct tetrad analysis (based on a maximum likelihood model from Weinstein 1936, Genetics) on nondisjunctional exceptions: They observed a large increase in nonexchange tetrads, double crossover tetrads and I think a small increase in triple crossover tetrads. There was a large decrease in single crossover tetrads. Now, if chiasmata are as important for proper chromosome segregation as the current view suggests, then it seems very unlikely to me that the crossovers (or exchanges of flanking markers) in this data set are the result of meiotic crossing over. What do you think? Mike From owner-recombination@net.bio.net Tue Jan 16 22:00:00 1996 Path: biosci!ATLAS.ODYSSEE.NET!dellaire From: dellaire@ATLAS.ODYSSEE.NET (Graham Dellaire) Newsgroups: bionet.molbio.recombination Subject: RE: What are the Great Unknowns Of Molecular Biology? Date: 16 Jan 1996 19:20:50 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 104 Sender: daemon@net.bio.net Distribution: world Message-ID: <01BAE45F.412B6920@pool12_15.odyssee.net> NNTP-Posting-Host: net.bio.net ---------- From: Beth A. Montelone[SMTP:bethmont@ksu.ksu.edu] Sent: Tuesday, January 16, 1996 2:07 PM To: recom@net.bio.net Subject: Re: What are the Great Unknowns Of Molecular Biology? Okay, I'll play. 1) What is the basis of strand discrimination in mismatch repair in = eukaryotes? I think the current view has something to do with the position of a nick = in the target strand near an area where a mismatch has occurred. This = nick then takes the place of the methylation system seen in prokaryotes = by distinguishing which strand is template and which is newly = replicated. 2) Does there exist a phenomenon of recombination competence in mitotic = cells of eukaryotes? Recombination competence? What do you mean? I have never heard of = this term? 3) Do transformation methods induce mutagenic or recombinogenic = activities? Hmmm this is a good question. I think that any DNA with free ends is = "recombinogenic" in itsself irregardless of the transfection method. If = a plasmid is linearized and transfected into cells the ends of the = molecule might look very much like a DSB and thus "integration" of DNA = into a genome may actually be a repair mechanism to deal with DSB that = doesn't always address the origin of the DNA. I think that if you look at the different transformation methods.... for = example just the basic trio of Electroporation; CaPO4 precipitation; and = DEAE-dextran you can see how transfection method can give you very = different outcomes.=20 Electroporation usually produces clones with single integrations and is = inefficient and usually hard to reproduce for transient assays. The DNA = is thought to enter the cell through pores in the cell membrane (and = nuclear membrane) induced by the current in the electroporation cuvet. = The DNA enters the nucleus most likely in an free form and may be = retained extra genomically for up to 36 hours (in some mammalian cell = lines); although in most cases the DNA is integrated into the genome = relatively quickly or is degraded. =20 Calcuim Phosphate and DEAE-dextran methods rely on phagocytosis of DNA = complexed with CaPO4 or DEAE-dextran. This means the DNA may be less = excessible than in electroporation and often the molecules when they do = integrate in to the genome are integrated as tandem repeats. = DEAE-dextran is usually is the best for transient expression protocols = or interplasmid recombination studies (i.e. transfection followd by Hirt = extraction and analysis of recombinants) even though it is nearly = impossible to produce stably transfected clones! This really perplexes = me!!! If you can have such effecient recombination between molecules = extra genomically (they are excessible to each other) then why don't = they interact with the genome? CaPO4 is good for transient expression assays (especially where = proportions of two plasmid transformed need to be maintained) and is = good for producing stable clones for many cell lines. The draw back is = that a large majority of your clones may contain multiple copies at one = locus orientated head to head and tail to tail. =20 Back to the Q?..... obviously electroporation is very disruptive and = many "stress" responses genes/proteins might concievably be affected = also I think the cell arrests in the cell cycle. If this occurs at say = S phase for instance while DNA is replicating this may be very = recombinogenic indeed as many regions of the genome may be opened up and = underwound (ie accessible), not to mention free dna ends that may be = left to initiate recombination (interestingly some synchronization = studies indicate that S phase and early G1 seem to be the most = productive time to electroporate for some cell types). =20 The point of comparing the three methods above was that each method = behaves different as to the recombinants you can produce. This would = infer to me, that the perturbation of the cell and the presentation of = the molecule (plasmid vector) to the nucleus for recombination may = follow different pathways. But again irrespective of the method, free = DNA ends in themselves are recombinogenic. =20 Graham Dellaire dellaire@odyssee.net That's a start. Other takers? Beth Montelone Kansas State University bethmont@ksu.ksu.edu From owner-recombination@net.bio.net Tue Jan 16 22:00:00 1996 Path: biosci!UABDPO.DPO.UAB.EDU!bch0016 From: bch0016@UABDPO.DPO.UAB.EDU (zheng gong) Newsgroups: bionet.molbio.recombination Subject: software for DNA recombination Date: 17 Jan 1996 09:33:52 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 10 Sender: daemon@net.bio.net Distribution: world Message-ID: <30FD4EC6.30AB@uabdpo.dpo.uab.edu> NNTP-Posting-Host: net.bio.net I don't know if this is right newgroup. I am searching for program which can be use to do molecular recombination. I hope it can do primer disign mutagenesis, restriction enzyme site search, drawing vector map, etc, just some common task. I already get demo copy of DNASIS, Oligo5 for window. But there are out of our budget, ($2000 for DNASIS, oligo5 for $1000). If you have use a better program, or cheaper program (like shareware), or have any recommands, Please give me a e-mail. Thank you for your attention. Zheng Gong From owner-recombination@net.bio.net Tue Jan 16 22:00:00 1996 Newsgroups: bionet.molbio.recombination Path: biosci!lhc.nlm.nih.gov!nih-csl!NewsWatcher!user From: lichten@helix.nih.gov (Michael Lichten) Subject: Abstract Message-ID: Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: 128.231.218.92 Organization: LB/DCBDC/NCI Date: Wed, 17 Jan 1996 13:52:50 GMT Lines: 30 I would like to post the following abstract: Lichten M, Goldman ASH 1995 Meiotic recombination hotspots Annu. Rev. Genetics. 29:423-444 Meiotic recombination occurs more frequently in some regions of the eukaryotic genome than in others, with variations of several orders of magnitude observed in frequencies of meiotic exchange per unit phusical distance. This article reviews what is known about meiotic recombination hotspots, loci or regions that display a greater than average frequency of meiotic exchange. Hotspots have been most intensively studied in Saccharomyces cerevisiae, which is a major focus of this article. Also reviewed is the current state of knowledge regarding hotspots in ofther fungi, in maize, in nematodes, in mice, and in humans. For reprints: Michael Lichten Building 37 Room 4D14 NIH 37 CONVENT DR MSC 4255 BETHESDA MD 20892-4255 USA lichten@helix.nih.gov I hope that others on this newsgroup will also post abstracts of their most recent/upcoming papers. -- Michael Lichten lichten@helix.nih.gov From owner-recombination@net.bio.net Tue Jan 16 22:00:00 1996 Newsgroups: bionet.molbio.recombination Path: biosci!rutgers!csn!carbon!night.primate.wisc.edu!sdd.hp.com!swrinde!newsfeed.internetmci.com!in1.uu.net!nih-csl!NewsWatcher!user From: lichten@helix.nih.gov (Michael Lichten) Subject: Re: larger female rec rate at centromere Message-ID: Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: 128.231.218.92 Organization: LB/DCBDC/NCI References: <01BAE2A7.7D343820@pool12_9.odyssee.net> Date: Wed, 17 Jan 1996 13:35:43 GMT Lines: 59 In article , mezwick@ucdavis.edu (Michael E. Zwick) wrote: > But in reality, isn't what you deem a crossover event really is just the > exchange of flanking markers? How that crossover event actually came > about may not be clear. While you can certainly argue from the observed > distribution and frequency of chiasmata that a large proportion or > observed crossovers must be the result of meiotic crossing over, I don't > think it is at all clear what proportion of events leading to the exchange > of flanking markers occur outside the context of a chiasmate. > Agreed. I think that the best guess, however, is just that chiasmata are what crossovers look like in the microscope. > > Well, if by crossover you mean the exchange of flanking markers then I > certainly agree. And I agree that DSBs can produce exchange of flanking > markers - i.e. perhaps due to transposable elements, random DSBs etc. > However, my point is there have to be some number of events which result > in the exchange of flanking markers that are not the product of crossing > over (with chiasmata). I don't think that the distribution of these > events are well understood. Perhaps I am wrong - does anyone know of any > data out there? I don't see how you can have EXCHANGE of flanking makers without a crossover. You can get a single recombinant with APPARENT flanking marker exchange by one-ended invasion followed by endo-duplication, or by a "half" crossover. In tetrad organisms these events would be detected as gene conversion of the entire distal portion of a chromosome. Such events are not detected in meiosis, although they are in mitotic recombination. > > Let me explain more clearly what I mean. For example, consider in > Drosophila the data of Merriam and Frost 1964(I think Genetics), who > conduct tetrad analysis (based on a maximum likelihood model from > Weinstein 1936, Genetics) on nondisjunctional exceptions: > > They observed a large increase in nonexchange tetrads, double crossover > tetrads and I think a small increase in triple crossover tetrads. There > was a large decrease in single crossover tetrads. Now, if chiasmata are > as important for proper chromosome segregation as the current view > suggests, then it seems very unlikely to me that the crossovers (or > exchanges of flanking markers) in this data set are the result of meiotic > crossing over. What do you think? I think I will have to read this paper. Could you dig up the reference? However, it's quite possible (and even likely) that although chiasmata are necessary for disjunction, they are not sufficient. For further discussion of this issue, I would refer to Hawley, Frazier and Rasooly, Separation anxiety: the etiology of nondisjunction in flies and people, Hum. Mol. Genet. 1994 3:1521-28. Recent discussions with Scott and others have left me with the conclusion that the primary cause of meiotic nondisjunction in human and fruit fly females is most likely aberrant kinetochore attachment or problems with sister chromatid cohesion or separation. PLEASE don't ask me to defend this assertion! It's more a gestalt than anything else. -- Michael Lichten lichten@helix.nih.gov From owner-recombination@net.bio.net Tue Jan 16 22:00:00 1996 Path: biosci!rutgers!csn!carbon!night.primate.wisc.edu!sdd.hp.com!swrinde!newsfeed.internetmci.com!vixen.cso.uiuc.edu!news.ksu.ksu.edu!usenet From: "Beth A. Montelone" Newsgroups: bionet.molbio.recombination Subject: Re: RE: What are the Great Unknowns Of Molecular Biology? Date: 17 Jan 1996 19:19:39 GMT Organization: Kansas State University Lines: 68 Message-ID: <4dji4b$isl@newserv.ksu.ksu.edu> References: <01BAE45F.412B6920@pool12_15.odyssee.net> NNTP-Posting-Host: 129.130.115.17 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.22 (Windows; I; 16bit) dellaire@ATLAS.ODYSSEE.NET (Graham Dellaire) wrote in response to my proposed questions: >1) What is the basis of strand discrimination in mismatch repair in = >eukaryotes? > >I think the current view has something to do with the position of a nick = >in the target strand near an area where a mismatch has occurred. This = >nick then takes the place of the methylation system seen in prokaryotes = >by distinguishing which strand is template and which is newly = >replicated. > Yes, this is the hypothesis and it's based on some old data from S. pnuemoniae (and on what happens in E. coli mutH mutants); really nothing is known about this in eukaryotes. Strathern et al. had an interesting article in Genetics this year (vol. 140, pp. 965-972) which suggested that DSB repair can be mutagenic in yeast and that this may be related to strand discrimination for mismatches created by recombination. >2) Does there exist a phenomenon of recombination competence in mitotic = >cells of >eukaryotes? > >Recombination competence? What do you mean? I have never heard of = >this term? This is mostly based on some fairly spotty yeast data which indicate that selection for cells which have recombined at one locus show higher than expected rates of recombination at unselected loci. One hypothesis is that a few cells in the population have become "recombinationally competent", perhaps as a result of spontaneous DNA damage and induction of a recombinational repair pathway??? >3) Do transformation methods induce mutagenic or recombinogenic = >activities? > >Hmmm this is a good question. I think that any DNA with free ends is = >"recombinogenic" in itsself irregardless of the transfection method. If = >a plasmid is linearized and transfected into cells the ends of the = >molecule might look very much like a DSB and thus "integration" of DNA = >into a genome may actually be a repair mechanism to deal with DSB that = >doesn't always address the origin of the DNA. > I agree and think that this is true.> (snipped stuff on damage induced by various methods of transfection) >Back to the Q?..... obviously electroporation is very disruptive and = >many "stress" responses genes/proteins might concievably be affected = >also I think the cell arrests in the cell cycle. (snip again) >The point of comparing the three methods above was that each method = >behaves different as to the recombinants you can produce. This would = >infer to me, that the perturbation of the cell and the presentation of = >the molecule (plasmid vector) to the nucleus for recombination may = >follow different pathways. But again irrespective of the method, free = >DNA ends in themselves are recombinogenic. =20 > Yes, but are other regions of the genome mutated and/or more likely to have recombined? (Ie. are "isogenic" strains produced by transformation really isogenic? We hope that they are!) Beth Montelone Kansas State University bethmont@ksu.ksu.edu From owner-recombination@net.bio.net Tue Jan 16 22:00:00 1996 Path: biosci!rutgers!csn!carbon!night.primate.wisc.edu!sdd.hp.com!swrinde!newsfeed.internetmci.com!info.ucla.edu!library.ucla.edu!news.ucdavis.edu!reqb-092.ucdavis.edu!user From: mezwick@ucdavis.edu (Michael E. Zwick) Newsgroups: bionet.molbio.recombination Subject: Re: What are the Great Unknowns Of Molecular Biology? Date: 17 Jan 1996 06:13:18 GMT Organization: Center for Population Biology Lines: 7 Message-ID: References: <01BAE2AB.70288A60@pool12_9.odyssee.net> <4dgt1o$er0@newserv.ksu.ksu.edu> NNTP-Posting-Host: reqb-092.ucdavis.edu I would suggest: 1. How are the locations of chiasmata regulated? 2. What is the molecular basis of interference? Mike From owner-recombination@net.bio.net Wed Jan 17 22:00:00 1996 Path: biosci!rutgers!nntp-xfer-1.csn.net!carbon!night.primate.wisc.edu!sdd.hp.com!swrinde!newsfeed.internetmci.com!info.ucla.edu!library.ucla.edu!news.ucdavis.edu!cpb-6.ucdavis.edu!user From: mezwick@ucdavis.edu (Michael E. Zwick) Newsgroups: bionet.molbio.recombination Subject: Re: larger female rec rate at centromere Date: Wed, 17 Jan 1996 11:32:10 -0800 Organization: University of California at Davis Lines: 8 Message-ID: References: <01BAE2A7.7D343820@pool12_9.odyssee.net> NNTP-Posting-Host: cpb-6.ucdavis.edu In article , lichten@helix.nih.gov (Michael Lichten) wrote: > I think I will have to read this paper. Could you dig up the reference? For those interested the reference is: Merriam and Frost, Genetics 49:109-122 January, 1964 From owner-recombination@net.bio.net Wed Jan 17 22:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.molbio.recombination Subject: BIOSCI miniFAQ, ver. 14-DEC-95 Date: 18 Jan 1996 02:00:53 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 199 Sender: daemon@net.bio.net Distribution: world Message-ID: <199601181000.CAA07100@net.bio.net> NNTP-Posting-Host: net.bio.net (LAST REVISION: 14-DEC-95) This BIOSCI "miniFAQ" is designed to answer the questions that come up the *most frequently*. The main BIOSCI FAQ (Frequently Asked Questions) is accessible on the World Wide Web at URL http://www.bio.net/. Contents: -------- 1) Using the WWW to access the BIOSCI/bionet newsgroups. 2) What to do about "spams," i.e., junk mail, ads, etc. 3) Examples of subscribing and unsubscribing to the mailing lists. 4) The BIOSCI user address and research interest directory. 1) Using the WWW to access the BIOSCI/bionet newsgroups. -------------------------------------------------------- As of 10 December 1995, all BIOSCI/bionet full newsgroups are accessible through the World Wide Web (WWW) at URL http://www.bio.net. One can read and reply publicly or privately to both recent postings and archived messages through one's Web browser if it is configured properly to send e-mail. Each newsgroup is equipped with its own WAIS index in addition to the master index for the entire set. The main BIOSCI home page also has access to the BIO-JOURNALS Table of Contents database WAIS index and the BIOSCI user address database described in another item further below. 2) What to do about "spams," i.e., junk mail, ads, etc. ------------------------------------------------------- BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups), mailing lists, and a hypermail archive at URL http://www.bio.net/. The same postings are distributed on all media (except for a small number of mailing-list-only groups at net.bio.net). Unfortunately it is becoming a despicable practice on the Internet (by a few people out to make a fast buck) to do automated mass postings to thousands of newsgroups and mailing lists. These attempts to grab free advertising are refered to as "spams" in the usual, somewhat boneheaded, net terminology. USENET is more susceptible to this practice, and many spams originate on the USENET groups and then are passed on to the mailing lists. However, spammers also get lists of mailing addresses and hit these too, so neither medium is immune. What should you do personally if you get junk mail? --------------------------------------------------- Just delete it and move on without reading it further. Filing a protest is becoming increasingly useless because spammers are often disguising the addresses where the messages are sent from. Unless you really understand Internet mail systems, your attempt at protest by sending replies to the message will often end up being sent to the address of an innocent person that the spammer is victimizing. What can BIOSCI/bionet do to protect its newsgroups? ---------------------------------------------------- The only solution currently available is to moderate the newsgroup. If this newsgroup is already moderated, then you are in good shape. Moderation protects the USENET distribution from about 95% of the spams that are being sent to date and protects the mailing lists completely. Moderation means, however, that someone has to take the time to review each message before it goes out. We have set up software here that simply allows the moderator to forward to an address at net.bio.net messages that (s)he wishes to have distributed. This takes no more time than that needed to read the message and pass it on, say about 1 min. per message. Most newsgroups currently have a discussion leader who is responsible for their newsgroup. The discussions leaders and their e-mail addresses are listed in the BIOSCI Information Sheet which is available on the Web at http://www.bio.net/. If a newsgroup is being hit with too many junk postings, please contact the discussion leader for that group and see if there is interest in moderating the group. Please do not assume that by simply posting a complaint to the newsgroup itself, anyone on the BIOSCI staff will act on your complaint. With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. Below we give an example utilizing the METHODS-AND-REAGENTS list at both of our two BIOSCI sites: Users in the Americas and Pacific Rim countries who use the BIOSCI ------------------------------------------------------------------ node at computer net.bio.net: ---------------------------- A) Determine the "listname" which is the <=8 character mail address ^^^^^^^^^^^^^ for the group. These can be found in the BIOSCI Info. Sheet. For the METHODS-AND-REAGENTS group the mailing address is methods@net.bio.net. The listname is the portion of the address to the left of the @ sign, i.e., "methods". The listname is used with the "subscribe" and "unsubscribe" commands illustrated below. B) Mail all commands in the body of a mail message addressed to biosci-server@net.bio.net. Do NOT send commands to the newsgroup posting addresses! Leave the Subject: line blank, any text on it will be ignored. C) In the body of your message put one or more of the following commands with an "end" command on the last line, e.g., subscribe methods unsubscribe methods end Do NOT put your e-mail address or other text on these lines. The server only allows you to cancel your subscription if the address on your mail header matches the address on our mailing list. Please ask for help at biosci-help@net.bio.net if your address has changed, e.g., if you know you are on the list but the server tells you that you are not a member. Users in Europe, Africa, and Central Asia who use the BIOSCI node at -------------------------------------------------------------------- computer daresbury.ac.uk (also known as dl.ac.uk): ------------------------------------------------- To subscribe and unsubscribe to/from the BIOSCI lists, you need to specify the full USENET newsgroup name with "bionet-news." prepended. The USENET newsgroup names are listed in the BIOSCI Information sheet on the Web at http://www.bio.net/. For the METHODS-AND-REAGENTS list the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the appropriate commands are sub bionet-news.bionet.molbio.methds-reagnts unsub bionet-news.bionet.molbio.methds-reagnts These commands are included in a message addressed to mxt@dl.ac.uk, NOT to the newsgroup mailing addresses. As usual, include the text in the body of the message as text on the Subject: line is ignored. To unsubscribe from all the lists at the UK node, use unsub bionet-news Please note that if the address in the list is different than the one in your mail message header, you will not be able to unsubscribe by this method. If you have problems, please mail biosci@daresbury.ac.uk. 4) The BIOSCI user address and research interest directory. ----------------------------------------------------------- Please take this opportunity to add your name, address, and research interest information to the BIOSCI User Address Database if you have not already done so. You can fill out the address form directly through our Web page at URL http://www.bio.net/adrform.html. The address database is reindexed nightly for WWW access (the URL is http://www.bio.net/). If you are not directly on the Internet but can reach it by e-mail, please use our waismail server to access the user directory. waismail use is described above. You can also request a user address form by e-mail from biosci-help@net.bio.net. Please check your database entry from time-to-time to see if your address information is still up-to-date. Because of our limited personnel resources, we ask that you resubmit a *complete* form to revise your entry; we only replace complete entries and do not have resources to edit old forms. Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net From owner-recombination@net.bio.net Fri Jan 19 22:00:00 1996 Path: biosci!agate!usenet.kornet.nm.kr!news.kreonet.re.kr!news.dacom.co.kr!newsrelay.netins.net!delta.misha.net!news.ucdavis.edu!usenet From: Scott Hawley Newsgroups: bionet.molbio.recombination Subject: The sufficiency and necessity of recombination for homologous segregation Date: 18 Jan 1996 17:25:04 GMT Organization: UC Davis Lines: 85 Message-ID: <4dlvpg$9al@mark.ucdavis.edu> NNTP-Posting-Host: hawley-office.ucdavis.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) X-URL: news:bionet.molbio.recombination?ALL There are several lines of evidence supported the oft-cited 'rule' that "exchange is fully sufficient to ensure segregation". These are: 1. In higher organisms, exchange is fully sufficient to ensure the faithful segregation of those centromeres, even when it occurs between chromosomes with non-homologous centromeres. For example in an X,4 translocation heterozygote in Drosophila, exchange between the distal X bearing segment of the translocation and the normal X ensures the segrgation of those two elements, despite the fact that the translocation chromosome bears a 4th chromosomal centromere. On the other hand the other translocated element, which does bear the X centromere, usually does not recombine from the normal X and often segregates at random for the normal X. This also holds for X-ray induced ectopic meiotic exchanges. (The sufficiency of ectopic exchange to ensure segregation in yeast is rather less clear, at least to me; perhaps Dr. Lichten might like to enlighten all of us on this matter!!!) 2. In mutants that ablate the achiasmate segregation systems, such as the nod mutant in flies, exchange chromosomes nonetheless segregate properly. {There is, however a curious exception to even this rule: Although exchange chromosomes virtually segregate properly >99% of the time in nod oocytes, rare cases of nondisjunction of chiasmate bivalents are observed. In all of these cases so far studied (<20) the observed exchange is extremely distal. However before jumping to the conclusion that "oh then distal exchanges aren't sufficient, recall that the vast majority of such very distal exchanges in these nod females DO ensure segregation. Dean Dawson apparently has some similar data with respect to mini-chromosome recombination in yeast. Why some distal exchanges fail is unclear, we just know that they do). 3. In strong recombination defective mutations, nondisjunction is virtually always limited to achiasmate chromosomes, exchange chromosome segregate properly 4. The elegant and lovely studies by Nicklas that explain the mechanisms by which chiasmata ensure segregation But aren't there cases where exchange doesn't ensure segregation??? Yeah, well there a few and they are worth noting: 1. In mutants, such as nodDTW or ncd in flies, in which spidle assembly/stability/morphology/etc is greatly altered, exchange chromosomes nondisjoin at very high frequencies. Big surprise. But even in those cases, very proximal exchanges appear to be prophylactic (oops Compuserve just delete this message) to nondisjunction 2. Spontaneous nondisjunction in flies and humans. It is clear that a high fraction of 'simultaneous'nondisjunctions have undergone one or more exchanges. It is equally clear that the distribution of those exchanges among the population of simultaneous exchanges in flies and human appears to be abnormal. In the paper that michael lichten so generously cited in yesterdays post (thank you, michael), we considered two possible explanations for this phenomenon. First spontaneous nondisjunction may reflect the occurence of spindle anomalies similar to those induced by the mutants described in the preceding paragraph. Second, some of these 'exchanges' may not have resulted from meiotic exchanges at all but rather from repair-type events induced to repair DNA damage caused by transposon induced breakage. Indeed, Kara Koehler, a student in my lab, has some data that are strongly suggestive of a high level of transposon mobility in oocytes that undergo nondisjunction. Others have argued for a defect in sister chromatid cohesion leading to the nondisjuction of exchange chromosomes, and I think this is a very reasonable agument. I think the take home message for all of these observations is that exchanges are not really failing here, but rather the defect lies elsewhere in the segregational machinery creating a difficulty that exchange alone cannot resolve. Thus I think the only real exception to the rule here is that of the very distal exchanges referred to above. Perhaps all crossovers are sufficient, but some are more sufficient (under some conditions) than others. (N.B. We are actually trying to explore this possibility in what I think is an interesting way. The baby chromosome of flies, the 4th chromosome, NEVER undergoes exchange. PERHAPS this is because exchange wouldn't ensure segreagtion on this chromosome (maybe because all exchanges might be too distal on such a small chromosome). Anyway some years ago Paul Szauter showed that some recombination deficient mutations did allow a low level of exchange on chromosome 4. So consider the following case, we use such a muant to allow exchange on 4 n a nod background (ie a background in which the achiasmate sytem is dead0. Will such exchanges ensure segreation.One of the grad students, C.B. Boulton, is currently doing that experiment. It ought to be interesting, either way. ) From owner-recombination@net.bio.net Sun Jan 21 22:00:00 1996 Path: biosci!ATLAS.ODYSSEE.NET!dellaire From: dellaire@ATLAS.ODYSSEE.NET (Graham Dellaire) Newsgroups: bionet.molbio.recombination Subject: RE: The sufficiency and necessity of recombination for homologous segregation Date: 21 Jan 1996 19:56:27 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 52 Sender: daemon@net.bio.net Distribution: world Message-ID: <01BAE852.0FE5F140@pool23_13.odyssee.net> NNTP-Posting-Host: net.bio.net ---------- From: Scott Hawley[SMTP:shawley@netcom.com] Sent: Thursday, January 18, 1996 12:25 PM To: recom@net.bio.net Subject: The sufficiency and necessity of recombination for homologous = segregation Previously Scott Hawley wrote.... >There are several lines of evidence supported the oft-cited 'rule' that = >"exchange is fully sufficient to ensure segregation". These are: I read through your account of the evidence for this point and I was = wondering if any purely physical aspects of the segregation process have = been looked at yet. That is to say I always wondered if the exchange = and chiasmata formation were primarily providing a needed resistance to = the microtubules of the spindle apparatus. That non-disjunction may = arise out of the fact that without the resistance provided by = "untangling" the chiasmata, the normal movement of chromosomes to the = poles would be disrupted. I would also like to ask if anyone out there has looked at the possible = contribution of repetitive elements like the Alu's or Line-1 sequences = in the segregation of chromosomes. Work in Dr. Pierre Chartrand's lab = here in Montreal suggests that the degree of "homeology" between such = sequences is sufficient to produce homologous pairing (and in some cases = gene conversion) yet reciprocal exhange does not seem to occur readily. = That is that the resolution of these recombination events seems to be = affected by homeology (ie. fully homologous sequences are more likely to = undergo exchange). Thus unequal crossovers which could be a very real = possibility of exchange between Line elements on chromsomes may be = averted. SO ... perhaps these repetitive elements are involved in ensuring that a = critical number of recombination events are initiated (homology search = perhaps?) at meiosis (and thus ensure segregation) but without the = increased hazard or reciprocal exchange which might leading to unequal = crossover between homologs. Graham Dellaire McGill Experimental Medicine dellaire@odyssee.net popa0206@po-box.mcgill.ca From owner-recombination@net.bio.net Sun Jan 21 22:00:00 1996 Path: biosci!dc37a.nci.nih.gov!GOLDMANA From: GOLDMANA@dc37a.nci.nih.gov ("Goldman, Alastair") Newsgroups: bionet.molbio.recombination Subject: chiasmata (plural) and segregation Date: 22 Jan 1996 09:59:40 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 40 Sender: daemon@net.bio.net Distribution: world Message-ID: <3103D009@SMTP2.mm.hub.nih.gov> NNTP-Posting-Host: net.bio.net Scott Hawley wrote: >(The sufficiency of ectopic exchange to ensure segregation in yeast is >rather less clear, at least to me; perhaps Dr. Lichten might like to >enlighten all of us on this matter!!!) He may, but so would I.... Under the conditions we have looked at the segregation of chromosomes with an ectopic crossover, the segregation appears to be random, ie the two cross over chromosomes are as likely to go the same pole as they are to go to opposite poles. But - don't be mislead. This does not mean that the chiasma between heterologues is not playing a role in orientation/segregation. The 'conditions' in which we have looked do not distinguish between segregants from cells where there was either 1/ only and ectopic crossover on between heterologues or where there was 2/ both an ectopic exchange between heterologues and one or more allelic exchanges between the two pairs of homologues involved in the ectopic exchange. Thus most of the time we are probably looking at the segregation of a first metaphase quadrivalent, which is a very different thing from two, independent, bivalents. This situation is analogous to a heterozygous reciprocal trnaslocation, in which case chiasmata effectively have to compete for influence over segregation, somebody has to loose in each meiosis, and this can lead to 'random' segregation (but doesn't allways). To answer the question directly we should set up markers/chromosomes to look at segregants which had no allelic exchanges between homologous pairs involved in an ectopic cross. (The problem is that in such cells the other two homologues would be univalent leading to some loss due to their non disjunction etc etc, but there maybe ways around this). In this case the heterologues would be held in a bivalent and I would be amazed if they did not disjoin efficiently. After all a chiasma, in a truelly chiasmate meiosis, is a chiasma - and the forces described by Ostergren (1951), demonstrated by Nicklas et al, require chromosomes to be connected not related. Ross et al (Genetics 142:79) show evidence that a crossover is required to promote disjunction of homologous mini chromosome IIIs. All for now. Alastair SH Goldman From owner-recombination@net.bio.net Sun Jan 21 22:00:00 1996 Path: biosci!MUSICA.MCGILL.CA!MDTY From: MDTY@MUSICA.MCGILL.CA (chow) Newsgroups: bionet.molbio.recombination Subject: RE: What are the Great Unknowns Of Molecular Biology? Date: 22 Jan 1996 05:54:58 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 99 Sender: daemon@net.bio.net Distribution: world Message-ID: <22JAN96.09580660.0292.MUSIC@MUSICA.MCGILL.CA> NNTP-Posting-Host: net.bio.net In article <01BAE45F.412B6920@pool12_15.odyssee.net> dellaire@ATLAS.ODYSSEE.NET > > >---------- > I do not have much comments on the first two items that Graham wrote, but I do have some for the third. In the article, Graham wrote: >3) Do transformation methods induce mutagenic or recombinogenic = >activities? > > >Hmmm this is a good question. I think that any DNA with free ends is = >"recombinogenic" in itsself irregardless of the transfection method. If = >a plasmid is linearized and transfected into cells the ends of the = >molecule might look very much like a DSB and thus "integration" of DNA = >into a genome may actually be a repair mechanism to deal with DSB that = >doesn't always address the origin of the DNA. > >I think that if you look at the different transformation methods.... for = >example just the basic trio of Electroporation; CaPO4 precipitation; and = >DEAE-dextran you can see how transfection method can give you very = >different outcomes.=20 > >Electroporation usually produces clones with single integrations and is = >inefficient and usually hard to reproduce for transient assays. The DNA = >is thought to enter the cell through pores in the cell membrane (and = >nuclear membrane) induced by the current in the electroporation cuvet. = >The DNA enters the nucleus most likely in an free form and may be = >retained extra genomically for up to 36 hours (in some mammalian cell = >lines); although in most cases the DNA is integrated into the genome = >relatively quickly or is degraded. =20 > >Calcuim Phosphate and DEAE-dextran methods rely on phagocytosis of DNA = >complexed with CaPO4 or DEAE-dextran. This means the DNA may be less = >excessible than in electroporation and often the molecules when they do = >integrate in to the genome are integrated as tandem repeats. = >DEAE-dextran is usually is the best for transient expression protocols = >or interplasmid recombination studies (i.e. transfection followd by Hirt = >extraction and analysis of recombinants) even though it is nearly = >impossible to produce stably transfected clones! This really perplexes = >me!!! If you can have such effecient recombination between molecules = >extra genomically (they are excessible to each other) then why don't = >they interact with the genome? > >CaPO4 is good for transient expression assays (especially where = >proportions of two plasmid transformed need to be maintained) and is = >good for producing stable clones for many cell lines. The draw back is = >that a large majority of your clones may contain multiple copies at one = >locus orientated head to head and tail to tail. =20 > >Back to the Q?..... obviously electroporation is very disruptive and = >many "stress" responses genes/proteins might concievably be affected = >also I think the cell arrests in the cell cycle. If this occurs at say = >S phase for instance while DNA is replicating this may be very = >recombinogenic indeed as many regions of the genome may be opened up and = >underwound (ie accessible), not to mention free dna ends that may be = >left to initiate recombination (interestingly some synchronization = >studies indicate that S phase and early G1 seem to be the most = >productive time to electroporate for some cell types). =20 > >The point of comparing the three methods above was that each method = >behaves different as to the recombinants you can produce. This would = >infer to me, that the perturbation of the cell and the presentation of = >the molecule (plasmid vector) to the nucleus for recombination may = >follow different pathways. But again irrespective of the method, free = >DNA ends in themselves are recombinogenic. =20 > Graham do bring up a point in transformation methods. But we can not assume that the path were the DNA is entering the cell are the same. If the DNA is exclusively remains in the cytosol and not entering the nuclei, do we expect stable transformation? whereas it may be recombinogenic between plasmids. The difference in results with the different methods may be a reflection of the mechanisms involved and we should not consider them the same only because the three transformation method all allows the entering of DNA into the cells. Any more suggestions? Terry Chow McGill University mdty@musica.mcgill.ca > > >Graham Dellaire >dellaire@odyssee.net > >That's a start. Other takers? > >Beth Montelone >Kansas State University >bethmont@ksu.ksu.edu > > > > > >. >. From owner-recombination@net.bio.net Mon Jan 22 22:00:00 1996 Path: biosci!rutgers!oitnews.harvard.edu!fas-news.harvard.edu!husc7.harvard.edu!echiu From: echiu@husc7.harvard.edu (Eugene Chiu) Newsgroups: bionet.molbio.recombination Subject: P1 Transduction Protocols Date: 23 Jan 1996 20:20:13 GMT Organization: Harvard University, Cambridge, MA Lines: 9 Message-ID: <4e3ftt$h4d@decaxp.harvard.edu> NNTP-Posting-Host: husc7.harvard.edu I am interested in introducing a mutated gene into a P1 phage and then to use P1 transduction to introduce the gene into the E. coli genome. Can anyone suggest a good introductory paper with a solid protocol in recent journals? Thanks in advance, Eugene echiu@fas.harvard.edu From owner-recombination@net.bio.net Tue Jan 23 22:00:00 1996 Path: biosci!rutgers!csn!ub!dsinc!netnews.upenn.edu!msunews!uwm.edu!vixen.cso.uiuc.edu!newsfeed.internetmci.com!info.ucla.edu!news.ucdavis.edu!usenet From: Scott Hawley Newsgroups: bionet.molbio.recombination Subject: Re: chiasmata (plural) and segregation Date: 23 Jan 1996 04:52:32 GMT Organization: UC Davis Lines: 13 Message-ID: <4e1pig$7lm@mark.ucdavis.edu> References: <3103D009@SMTP2.mm.hub.nih.gov> NNTP-Posting-Host: hawley-office.ucdavis.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: quoted-printable X-Mailer: Mozilla 1.1N (Macintosh; I; PPC) To: GOLDMANA@dc37a.nci.nih.gov X-URL: news:3103D009@SMTP2.mm.hub.nih.gov GOLDMANA@dc37a.nci.nih.gov ("Goldman, Alastair") wrote: To answer the question >directly we should set up markers/chromosomes to look at segregants which had >no allelic exchanges between homologous pairs involved in an ectopic cross. >(The problem is that in such cells the other two homologues would be >univalent leading to some loss due to their non disjunction etc etc, but >there maybe ways around this). In this case the heterologues would be held in >a bivalent and I would be amazed if they did not disjoin efficiently. So would I, Alastair, so would I. Still it is a lovely experiment nonetheless. Clearly such exchanges, at least when induced by X-Ra= ys, ensure segregation in flies... From owner-recombination@net.bio.net Wed Jan 24 22:00:00 1996 Path: biosci!ATLAS.ODYSSEE.NET!dellaire From: dellaire@ATLAS.ODYSSEE.NET (Graham Dellaire) Newsgroups: bionet.molbio.recombination Subject: Third announcement and change of URL : REPLICATION CONFERENCE Date: 25 Jan 1996 06:27:55 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 62 Sender: daemon@net.bio.net Distribution: world Message-ID: <01BAEB05.B685DD20@pool1_11.odyssee.net> NNTP-Posting-Host: net.bio.net THIRD ANNOUNCEMENT The Fourth McGill University Conference on Regulation of Eukaryotic DNA Replication St. Sauveur, Quebec, Canada October 1996. Organized by: Maria Zannis-Hadjopoulos and Gerald Price McGill Cancer Centre, Department of Oncology Faculty of Medicine and Faculty of Graduate Studies and Research McGill University http://blizzard.cc.mcgill.ca/MCO/dna.html The meeting will include plenary lecture sessions and poster sessions. TOPICS: * Eukaryotic Origins of DNA Replication * Nuclear and DNA Structure in DNA Replication * Modulation of Eukaryotic DNA Replication Preliminary Program The conference will be held at the Manoir Saint-Sauveur in the Laurentians. The first session will begin in the evening of October 17 and the final session will end in the early afternoon of October 20. Poster and oral presentations will take place on October 18 and 19. All participants are encouraged to present a poster on any of the topics that will be covered in the conference. Conference Location: The meeting will be held at the Laurentians' newest four-season conference resort hotel - a major luxury complex just about 45 minutes from Montreal, amid the dynamic beauty of the Laurentians. Saint-Sauveur-des-Monts, the Laurentians' most picturesque village, is the gateway village to the Laurentians. Transportation will be available from the airport to the conference site, and return. Registration materials and information regarding abstract submission will be sent in early 1996. *********Abstract deadline date: June 27, 1996.************ For More Information Please visit our Web Site http://blizzard.cc.mcgill.ca/MCO/dna.html From this site you can obtain: * A Preliminary Program * Further Information on Conference Location * A Reply Card to Obtain Registration Package From owner-recombination@net.bio.net Sat Jan 27 22:00:00 1996 Path: biosci!rutgers!csn!ub!dsinc!netnews.upenn.edu!msunews!uwm.edu!vixen.cso.uiuc.edu!howland.reston.ans.net!newsfeed.internetmci.com!in1.uu.net!utcsri!newsflash.concordia.ca!not-for-mail From: AMIN JAVANBAKHT Newsgroups: bionet.molbio.recombination Subject: Re: P1 Transduction Protocols Date: Sun, 28 Jan 1996 11:48:43 -0500 Organization: Concordia University, Montreal, Canada Lines: 18 Message-ID: References: <4e3ftt$h4d@decaxp.harvard.edu> NNTP-Posting-Host: alcor.concordia.ca Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII NNTP-Posting-User: ma_java In-Reply-To: <4e3ftt$h4d@decaxp.harvard.edu> On 23 Jan 1996, Eugene Chiu wrote: > I am interested in introducing a mutated gene into a P1 phage and then to > use P1 transduction to introduce the gene into the E. coli genome. Can > anyone suggest a good introductory paper with a solid protocol in recent > journals? > > Thanks in advance, > > Eugene > echiu@fas.harvard.edu > > you might want to look at the lab manual. short course in bacterial genetic author is Miller jeffery H. I think it's in page 263 . There is also refrences for original papers From owner-recombination@net.bio.net Mon Jan 29 22:00:00 1996 Path: biosci!rutgers!csn!carbon!night.primate.wisc.edu!sdd.hp.com!swrinde!howland.reston.ans.net!Germany.EU.net!Dortmund.Germany.EU.net!nntp.gmd.de!news.rwth-aachen.de!news.ruhr-uni-bochum.de!news.uni-stuttgart.de!news From: "Igor M. Kulic" Newsgroups: bionet.molbio.recombination Subject: Sticky Ends Problem in DNA-Computing Date: 30 Jan 1996 12:13:08 GMT Organization: UNI-Stuttgart Lines: 24 Message-ID: <4el20k$1h5g@info4.rus.uni-stuttgart.de> NNTP-Posting-Host: cip17.mathematik.uni-stuttgart.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (X11; I; AIX 2) X-URL: news:bionet.molbio.recombination Dear Sirs/Madam I am working on a theoretical model of a "DNA-computer" and got two principal questions about practical feasebility which arose from my model: 1) How hard is it to create Oligos with sticky ends longer than just 4 bp.length (i.e. with a single stranded overhang longer than 4 nucleic assids)? 2) Is it still posible to link them efficiently with Ligase if the overhangs are longer than 4 ? In my model they needn't be significantly longer than 4 but should be at least 6 to 7 ! Than you in advance ! Igor M. Kulic (Mathematical Department ,Stuttgart, Germany) P.S: Are there biochemist in Germany with experimental experiences in DNA-recombination who are interessted in a interdisciplinary workshop on DNA-Computing ? If so ,please send me your coordinates and I'll also give you some links to DNA-computing resources on INTERNET ! From owner-recombination@net.bio.net Mon Jan 29 22:00:00 1996 Path: biosci!JULIET.UCS.INDIANA.EDU!JCLAY From: JCLAY@JULIET.UCS.INDIANA.EDU (JANE CLAY) Newsgroups: bionet.molbio.recombination Subject: Recombinant DNA courses at Indiana University Date: 30 Jan 1996 07:48:19 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 101 Sender: daemon@net.bio.net Distribution: world Message-ID: <199601301544.KAA10044@belize.ucs.indiana.edu> NNTP-Posting-Host: net.bio.net Indiana University Offers Recombinant DNA Laboratory Courses During the summer of 1996, Indiana University's Department of Biology, in cooperation with the I.U. Division of Continuing Studies, will offer two week-long laboratory courses focusing on the techniques and procedures used in recombinant DNA research and their application. Participants also have the opportunity to work with a DNA sample of their own research organism, if they choose. Both courses will be taught on the Indiana University campus in Bloomington. Recombinant DNA Technology The first course, "Recombinant DNA Technology," will introduce participants to procedures involved in recombinant DNA work and to the molecular aspects of genetic engineering. Most of the procedures that are taught to biology graduate students in the recombinant DNA section of a graduate techniques course at Indiana University will be covered. Participants can make arrangements to isolate genomic DNA from their own research organisms during the course. The following techniques will be included: *DNA and cloning vector manipulation *PCR technology *Preparation of recombinant DNA *Transformation of bacterial cells *Selection and assay of cloned and amplified fragments of "foreign" DNA *Transfer of DNA for probing (Southern blot) *Preparation of nonradioactive DNA probes "Recombinant DNA Technology" is designed for those with a basic understanding of the structure of DNA and elemental genetics and with a minimal understanding of enzymes and biochemistry. The course is scheduled for June 3-7, 1996. Registration deadline is May 17. Application of Recombinant DNA Technology: RFLP and Fingerprinting Analysis, RAPD Analysis, and DNA Sequencing This course will provide participants with the opportunity to learn about the materials and techniques used in recombinant DNA research. Participants may bring a DNA sample to sequence during the course. This course will emphasize the following techniques: *DNA sequencing using non-radioactive methods *DNA sequencing using automatic DNA sequencer *RAPD analysis of genomic DNA *Fingerprinting and RFLP analysis of genomic DNA *Electroporation of bacterial cells *Chemiluminescent detection of nucleic acids *Application of computers to DNA sequencing data analysis *Preparation of random fragment sequencing libraries and double-stranded DNA for sequencing *Use of bioneb cell and bipolymer disruption systems A basic understanding of the structure of DNA and elemental genetics is assumed for participants in this short course, as is a minimal understanding of enzymes and biochemistry. Previous experience with PCR or RFLP analysis and DNA sequencing is not a prerequisite, nor is completion of "Recombinant DNA Technology." This course is scheduled for June 10-14, 1996. Registration deadline is May 24. The instructor for both courses is Dr. Stefan J. Surzycki, associate professor of biology at Indiana University. Fees for these courses include all instruction, laboratory supplies, use of equipment, and lab manuals. For additional information, contact Jane Clay, Division of Continuing Studies, Owen Hall 204, Indiana University, Bloomington, IN 47405, phone (812) 855-6329. Internet: JClay@Indiana.edu Web: http://www.Indiana.edu/~scs/prof.html Jane Clay Associate Director Division of Continuing Studies Owen Hall 204 Indiana University Bloomington, IN 47405 Phone: 812-855-6329 Fax: 812-855-8997 email: JClay@Indiana.edu Jane Clay Associate Director Division of Continuing Studies Owen Hall 204 Indiana University Bloomington, IN 47405 Phone: 812-855-6329 Fax: 812-855-8997 email: JClay@Indiana.edu From owner-recombination@net.bio.net Mon Jan 29 22:00:00 1996 Path: biosci!ATLAS.ODYSSEE.NET!dellaire From: dellaire@ATLAS.ODYSSEE.NET (Graham Dellaire) Newsgroups: bionet.molbio.recombination Subject: REpost Re:Sticky Ends Problem in DNA-Computing Date: 30 Jan 1996 14:58:16 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 36 Sender: daemon@net.bio.net Distribution: world Message-ID: <01BAEF3A.BEDB61A0@pool21_13.odyssee.net> NNTP-Posting-Host: net.bio.net ---------- From: Igor M. Kulic[SMTP:kulicir@cip.mathematik.uni-stuttgart.de] Sent: Tuesday, January 30, 1996 7:13 AM To: recom@net.bio.net Subject: Sticky Ends Problem in DNA-Computing Dear Sirs/Madam I am working on a theoretical model of a "DNA-computer" and got two principal questions about practical feasebility which arose from my model: 1) How hard is it to create Oligos with sticky ends longer than just 4 bp.length (i.e. with a single stranded overhang longer than 4 nucleic assids)? 2) Is it still posible to link them efficiently with Ligase if the overhangs are longer than 4 ? In my model they needn't be significantly longer than 4 but should be at least 6 to 7 ! Than you in advance ! Igor M. Kulic (Mathematical Department ,Stuttgart, Germany) P.S: Are there biochemist in Germany with experimental experiences in DNA-recombination who are interessted in a interdisciplinary workshop on DNA-Computing ? If so ,please send me your coordinates and I'll also give you some links to DNA-computing resources on INTERNET ! From owner-recombination@net.bio.net Mon Jan 29 22:00:00 1996 Path: biosci!ATLAS.ODYSSEE.NET!dellaire From: dellaire@ATLAS.ODYSSEE.NET (Graham Dellaire) Newsgroups: bionet.molbio.recombination Subject: RE: Sticky Ends Problem in DNA-Computing Date: 30 Jan 1996 14:57:39 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 57 Sender: daemon@net.bio.net Distribution: world Message-ID: <01BAEF3A.43AA8420@pool21_13.odyssee.net> NNTP-Posting-Host: net.bio.net ---------- From: Igor M. Kulic[SMTP:kulicir@cip.mathematik.uni-stuttgart.de] Sent: Tuesday, January 30, 1996 7:13 AM To: recom@net.bio.net Subject: Sticky Ends Problem in DNA-Computing Dear Sirs/Madam I am working on a theoretical model of a "DNA-computer" and got two = principal questions about practical feasebility which arose from my model: =20 1) How hard is it to create Oligos with sticky ends longer than just = 4 bp.length (i.e. with a single stranded overhang longer than 4 nucleic = assids)? I don't think there should be any problem... if you are doing this in = vitro... in vivo I think that you might have sifnificant degredation of = the DNA before any end to end joining. I think the in vitro = limitation may be secondary structures in your single stranded region... = ie. things like stem loop structures etc. =20 As long as there are no repeats or palindromes in the sequence you = should be able to get larger than 4 bases pairs and 6 or 7 should be = achievable. =20 I assume you will have random overhangs (single stranded regions).... Creating them is easy enough too. You just produce the oligos as single = strands (Watson and Crick... or you can sythesize the other using = primers and pcr) and anneal them together by heating to 95 and then = cooling rapidly (liquid nitrogen). I hope this helps Igor. Discussion Leader=20 Recom Graham Dellaire McGill University Exp. Medicine dellaire@odyssee.net P.s. in the end I would appreciate it very much if you could post what = you finally decided on and later on still an abstract of what happened. = Thanks for trying RECOM. From owner-recombination@net.bio.net Wed Jan 31 22:00:00 1996 Path: biosci!cifn.unam.mx!edgar From: edgar@cifn.unam.mx (Edgar Valencia) Newsgroups: bionet.molbio.recombination Subject: Lox and Cre plasmid Date: 1 Feb 1996 13:43:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 18 Sender: daemon@net.bio.net Distribution: world Message-ID: NNTP-Posting-Host: net.bio.net Hi Netters I wish to know if anybody has a plasmid or could give me the references about a plasmid with the lox sites bordering a linker and about a plasmid with the cre recombinase from which y could activated cre and lost the fragment i had cloned beetween the lox Being a recombination group, I though this is the place where I should look for thanks in advance Edgar Valencia Morales Departamento de Genetica Molecular CIFN - UNAM MEXICO e-mail edgar@cifn.unam.mx From owner-recombination@net.bio.net Wed Jan 31 22:00:00 1996 Newsgroups: bionet.molbio.recombination Path: biosci!lhc.nlm.nih.gov!nih-csl!NewsWatcher!user From: lichten@helix.nih.gov (Michael Lichten) Subject: Re: The sufficiency and necessity of recombination for homologous segregation Message-ID: Sender: postman@alw.nih.gov (AMDS Postmaster) Nntp-Posting-Host: 128.231.218.92 Organization: LB/DCBDC/NCI References: <4dlvpg$9al@mark.ucdavis.edu> Date: Thu, 1 Feb 1996 13:42:32 GMT Lines: 50 In article <4dlvpg$9al@mark.ucdavis.edu>, Scott Hawley wrote: > ectopic meiotic exchanges. (The sufficiency of ectopic exchange to > ensure segregation in yeast is rather less clear, at least to me; > perhaps Dr. Lichten might like to enlighten all of us on this matter!!!) I wish that I could, but all I ever seem to do is endarken. Actually, Alastair Goldman has some indirect evidence that ectopic exchange does not significantly BIAS segregation. The observation is basically that you recover translocations at the expected frequency among ectopic recombinants. In the case most relevant here, ectopic recombination between interstitial inserts on heterologous chromosomes, he recovered balanced translocations at about the frequency expected if a) about half of ectopic gene convertants were resolved with an exchange and b) the ectopic exchange had no effect on disjunction. If an ectopic exchange had driven the disjunction of the two ectopically recombining chromosomes, then we should have almost never recovered balanced translocations. However, there is a bit of a fly in the ointment. Ectopic recombinants may be enriched for meiotic nondisjuntants, but these are certainly a minority population. I guess the best we can say is that ectopic exchange is not accompanied by OBLIGATE disjunction; perhaps the other exchange events that occur along the length of the two sets of bivalents override whatever signal ectopic exchange is providing. Experiments are in progress to create a situation where ectopic exchange is the ONLY event that happens. > are observed. In all of these cases so far studied (<20) the observed > exchange is extremely distal. However before jumping to the conclusion > that "oh then distal exchanges aren't sufficient, recall that the vast > majority of such very distal exchanges in these nod females DO ensure > segregation. Dean Dawson apparently has some similar data with respect > to mini-chromosome recombination in yeast. Why some distal exchanges > fail is unclear, we just know that they do). I think Dean's results should be out soon in PNAS (or so I hear). > Thus I think the only real exception to the rule here is that of the > very distal exchanges referred to above. Perhaps all crossovers are > sufficient, but some are more sufficient (under some conditions) than > others. But as you know, Scott, the distal-enrichment of crossover among human trisomies is true for chromosome 21 but not for other chromosomes. So it may not be as simple as we think.... -- Michael Lichten lichten@helix.nih.gov