We thank Dr. Roger Tsien for providing us with the miniSOG constructs. Dr. Xuejun Sun for help with the TEM. Lisa Lem, and Peter Shipple from the Cross Cancer Institute for supplying oxygen. Hilmar Strickfaden holds a postdoctoral fellowship by the Alberta Cancer foundation and was supported by the Bayrische Forschungsallianz. This work was supported by grants from the Canadian Institutes of Health Research and Alberta Cancer Foundation.

<ol>
	<li>Schermelleh, L., Heintzmann, R., Leonhardt, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+guide+to+super-resolution+fluorescence+microscopy.">A guide to super-resolution fluorescence microscopy.</a> The Journal of Cell Biology. 190, 165-175 (2010).</li><li>Bazett-Jones, D. P., Hendzel, M. J., Kruhlak, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stoichiometric+analysis+of+protein-+and+nucleic+acid-based+structures+in+the+cell+nucleus.">Stoichiometric analysis of protein- and nucleic acid-based structures in the cell nucleus.</a> Micron (Oxford, England: 1993). 30, 151-157 (1999).</li><li>Michael J Hendzel, F. M. B., Bazett-Jones, D. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+Visualization+of+a+Protein+Nuclear+Architecture.">Direct Visualization of a Protein Nuclear Architecture.</a> Molecular biology of the cell. 10, 2051 (1999).</li><li>Ottensmeyer, F. P., Andrew, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-resolution+microanalysis+of+biological+specimens+by+electron+energy+loss+spectroscopy+and+by+electron+spectroscopic+imaging.">High-resolution microanalysis of biological specimens by electron energy loss spectroscopy and by electron spectroscopic imaging.</a> Journal of ultrastructure research. 72, 336-348 (1980).</li><li>Leapman, R. D., Ornberg, R. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+electron+energy+loss+spectroscopy+in+biology.">Quantitative electron energy loss spectroscopy in biology.</a> Ultramicroscopy. 24, 251-268 (1988).</li><li>Simon, G. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electron+spectroscopic+imaging.">Electron spectroscopic imaging.</a> Ultrastructural pathology. 11, 705-710 (1987).</li><li>Egerton, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Electron Energy-Loss Spectroscopy in the Electron Microscope. , (2011).</li><li>Aronova, M. A., Kim, Y. C., Zhang, G., Leapman, R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantification+and+thickness+correction+of+EFTEM+phosphorus+maps.">Quantification and thickness correction of EFTEM phosphorus maps.</a> Ultramicroscopy. 107, 232-244 (2007).</li><li>Hopkins, C., Gibson, A., Stinchcombe, J., Futter, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chimeric+molecules+employing+horseradish+peroxidase+as+reporter+enzyme+for+protein+localization+in+the+electron+microscope.">Chimeric molecules employing horseradish peroxidase as reporter enzyme for protein localization in the electron microscope.</a> Methods in enzymology. 327, 35-45 (2000).</li><li>Shu, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Genetically+Encoded+Tag+for+Correlated+Light+and+Electron+Microscopy+of+Intact+Cells,+Tissues,+and+Organisms.">A Genetically Encoded Tag for Correlated Light and Electron Microscopy of Intact Cells, Tissues, and Organisms.</a> PLoS biology. 9, e1001041 (2011).</li><li>Gaietta, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multicolor+and+electron+microscopic+imaging+of+connexin+trafficking.">Multicolor and electron microscopic imaging of connexin trafficking.</a> Science (New York, NY). 296, 503-507 (2002).</li><li>Fernandez-Capetillo, O., Celeste, A., Nussenzweig, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Focusing+on+foci:+H2AX+and+the+recruitment+of+DNA-damage+response+factors.">Focusing on foci: H2AX and the recruitment of DNA-damage response factors.</a> Cell cycle (Georgetown, Tex). 2, 426-427 (2003).</li><li>Haaf, T., Golub, E. I., Reddy, G., Radding, C. M., Ward, D. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nuclear+foci+of+mammalian+Rad51+recombination+protein+in+somatic+cells+after+DNA+damage+and+its+localization+in+synaptonemal+complexes.">Nuclear foci of mammalian Rad51 recombination protein in somatic cells after DNA damage and its localization in synaptonemal complexes.</a> Proceedings of the National Academy of Sciences of the United States of America. 92, 2298-2302 (1995).</li><li>Maser, R. S., Monsen, K. J., Nelms, B. E., Petrini, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=hMre11+and+hRad50+nuclear+foci+are+induced+during+the+normal+cellular+response+to+DNA+double-strand+breaks.">hMre11 and hRad50 nuclear foci are induced during the normal cellular response to DNA double-strand breaks.</a> Molecular and Cellular Biology. 17, 6087-6096 (1997).</li><li>Bekker-Jensen, S., Mailand, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Assembly+and+function+of+DNA+double-strand+break+repair+foci+in+mammalian+cells.">Assembly and function of DNA double-strand break repair foci in mammalian cells.</a> DNA repair. 9, 1219-1228 (2010).</li><li>Chapman, J. R., Sossick, A. J., Boulton, S. J., Jackson, S. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=BRCA1-associated+exclusion+of+53BP1+from+DNA+damage+sites+underlies+temporal+control+of+DNA+repair.">BRCA1-associated exclusion of 53BP1 from DNA damage sites underlies temporal control of DNA repair.</a> Journal of cell science. 125, 3529-3534 (2012).</li><li>Dellaire, G., Kepkay, R., Bazett-Jones, D. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High+resolution+imaging+of+changes+in+the+structure+and+spatial+organization+of+chromatin,+gamma-H2A.X+and+the+MRN+complex+within+etoposide-induced+DNA+repair+foci.">High resolution imaging of changes in the structure and spatial organization of chromatin, gamma-H2A.X and the MRN complex within etoposide-induced DNA repair foci.</a> Cell cycle (Georgetown, Tex). 8, 3750-3769 (2009).</li><li>Kruhlak, M. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Changes+in+chromatin+structure+and+mobility+in+living+cells+at+sites+of+DNA+double-strand+breaks.">Changes in chromatin structure and mobility in living cells at sites of DNA double-strand breaks.</a> The Journal of Cell Biology. 172, 823-834 (2006).</li><li>Goodson, H. V., Dzurisin, J. S., Wadsworth, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Generation+of+stable+cell+lines+expressing+GFP-tubulin+and+photoactivatable-GFP-tubulin+and+characterization+of+clones.">Generation of stable cell lines expressing GFP-tubulin and photoactivatable-GFP-tubulin and characterization of clones.</a> Cold Spring Harbor protocols. 2010, (2010).</li><li>Zeyda, M., Borth, N., Kunert, R., Katinger, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optimization+of+sorting+conditions+for+the+selection+of+stable,+high-producing+mammalian+cell+lines.">Optimization of sorting conditions for the selection of stable, high-producing mammalian cell lines.</a> Biotechnology progress. 15, 953-957 (1999).</li><li>Dellaire, G., Nisman, R., Bazett-Jones, D. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Correlative+light+and+electron+spectroscopic+imaging+of+chromatin+in+situ.">Correlative light and electron spectroscopic imaging of chromatin in situ.</a> Methods in enzymology. , 375-456 (2004).</li><li>Campbell, S., Ismail, I. H., Young, L. C., Poirier, G. G., Hendzel, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Polycomb+repressive+complex+2+contributes+to+DNA+double-strand+break+repair.">Polycomb repressive complex 2 contributes to DNA double-strand break repair.</a> Cell cycle. 12, 2675-2683 (2013).</li><li>Mortusewicz, O., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recruitment+of+RNA+polymerase+II+cofactor+PC4+to+DNA+damage+sites.">Recruitment of RNA polymerase II cofactor PC4 to DNA damage sites.</a> J Cell Biol. 183, 769-776 (2008).</li><li>Bekker-Jensen, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spatial+organization+of+the+mammalian+genome+surveillance+machinery+in+response+to+DNA+strand+breaks.">Spatial organization of the mammalian genome surveillance machinery in response to DNA strand breaks.</a> The Journal of Cell Biology. 173, 195-206 (2006).</li><li>Ferrando-May, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Highlighting+the+DNA+damage+response+with+ultrashort+laser+pulses+in+the+near+infrared+and+kinetic+modeling.">Highlighting the DNA damage response with ultrashort laser pulses in the near infrared and kinetic modeling.</a> Frontiers in genetics. 4, 135 (2013).</li><li>Lukas, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=53BP1+nuclear+bodies+form+around+DNA+lesions+generated+by+mitotic+transmission+of+chromosomes+under+replication+stress.">53BP1 nuclear bodies form around DNA lesions generated by mitotic transmission of chromosomes under replication stress.</a> Nature. 13, 243-253 (2011).</li><li>Harrigan, J. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replication+stress+induces+53BP1-containing+OPT+domains+in+G1+cells.">Replication stress induces 53BP1-containing OPT domains in G1 cells.</a> The Journal of Cell Biology. 193, 97-108 (2011).</li><li>Aronova, M. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reprint+of+'Three-dimensional+elemental+mapping+of+phosphorus+by+quantitative+electron+spectroscopic+tomography+(QuEST).">Reprint of 'Three-dimensional elemental mapping of phosphorus by quantitative electron spectroscopic tomography (QuEST).</a> J. Struct. Biol. 161, 322-335 (2007).</li><li>Fussner, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Constitutive+heterochromatin+reorganization+during+somatic+cell+reprogramming.">Constitutive heterochromatin reorganization during somatic cell reprogramming.</a> The EMBO journal. 30, 1778-1789 (2011).</li><li>Kepkay, R., Attwood, K. M., Ziv, Y., Shiloh, Y., Dellaire, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=KAP1+depletion+increases+PML+nuclear+body+number+in+concert+with+ultrastructural+changes+in+chromatin.">KAP1 depletion increases PML nuclear body number in concert with ultrastructural changes in chromatin.</a> Cell cycle. 10, 308-322 (2011).</li></ol>

The authors have nothing to disclose.

ESI يمكن أن تكون بمثابة أداة ممتازة لفحص حالات مختلفة من لونين وribonucleoproteins في النواة لأنه قادر على خريطة المناطق التي هي غنية في الفوسفور على وجه التحديد. وهو يعزز بشكل كبير من كمية التفاصيل التي يمكن الحصول عليها عن طريق المجهر الالكتروني وليس اعتمادا على الأساليب الم...

وعلى الرغم من التقدم الكبير في المجهر الضوئي خلال السنوات الأخيرة 1، خلية علماء الأحياء لا تزال تعاني من فجوة في القرار. هذا يحد من فهم العلاقات هيكل الوظائف في العمليات الخلوية الأساسية التي تنطوي على تفاعل منسق بين المجمعات الجزيئات (على سبيل المثال، في إعادة لونين، وإصلاح DNA، RNA النسخ والتكرار DNA). على الرغم من المجاهر الإلكترونية الإرسال (TEM) ق تقديم القرار المطلوب، فقد كان تحديا لتعريف هذه العمليات من الناحية الهيكلية بسبب عدم القدرة على تسمية بروتينات معينة في حين يجري أيضا قادرة على تحديد التركيب الكيميائي الحيوي للهياكل تصور. في غياب الأغشية الداخلية للمساعدة في التفريق الهياكل النووية، كانت نواة تحديا من نوع خاص. الإلكترون الطيفية التصوير (ESI) يحل بعض هذه القيود من خلال السماح للكشف في وقت واحد والتفريق بين DNA، RNA، والبروتوكول الاضافيهياكل النووية 2-5 عين المستندة إلى الإلكترون التصوير الطيفي: من أجل خريطة توزيعات عنصري في حساسية عالية ودقة في المجهر الإلكتروني، يمكن للمرء استخدام مطياف التصوير التي يختار الإلكترونات التي تشتتت inelastically من خلال التفاعل مع الإلكترونات قذيفة الداخلية عنصر في العينة 6. بسبب فقدان كميات عنصر معين من الطاقة نتيجة للتأين الذرات في العينة، وهذه الإلكترونات يمكن فصلها وتصور باستخدام مطياف التي يتم تركيبها على المجهر الالكتروني. وهكذا، تحليل الطيف من الإلكترونات التي تفاعلت مع العينة يكشف عن معلومات نوعية وكمية عن التركيب العنصري للعينة 7. تم العثور على الإلكترونات التي لا تفقد الطاقة عندما تمر العينة في &quot;عدم الخسارة الذروة&quot; من فقدان الطاقة الإلكترونالطيف. يرتبط وفرة من هذه الإلكترونات إلى الكتلة والكثافة وسمك العينة، وتتألف من الإلكترونات التي تمر من خلال عينة من دون الاصطدام مع العينة أو فقدان الطاقة أثناء مرورها من خلال العينة. يمكن أن تكون هذه المعلومات مفيدة لتقدير المطلق للأعداد ذرات عنصر معين موجود في العينة 8. منذ العينات البيولوجية تتكون في معظمها من العناصر الخفيفة التي تحرف سيئة الإلكترونات في شعاع حادثة TEM، وأساليب تلطيخ باستخدام أملاح المعادن الثقيلة يجب أن تطبق من أجل توليد التباين في العينة. عدم وجود خصوصية لمعظم هذه العوامل المتناقضة وعدم القدرة على تصور وصمة عار أكثر من حيث خصوصية ممكنة قد حد من قيمة المجهر الإلكتروني التقليدية في دراسة النواة. ESI له مزايا هامة على TEM التقليدية، وخاصة لدراسة هياكل نواة الخلية.فمن الممكن لاستغلال الطبيعة الفسفور الغني DNA- والمجمعات الجزيئات التي تحتوي على الحمض النووي الريبي للتمييز مجمعات البروتين النووي من المجمعات البروتين ولحل مجمعات البروتين النووي مختلفة على أساس كثافتها من الأحماض النووية. ولا يمكن تصوير المواد البيولوجية المتبقية على أساس وفرة من النيتروجين. رسم الخرائط فقط هذين العنصرين وتحليل توزيعها والوفرة النسبية داخل هياكل تشريحية مختلفة توفر لنا الكثير من المعلومات حول النواة. على سبيل المثال، فإنه من السهل تحديد لونين وريبوسوم في الخريطة تمثل وفرة الفوسفور. مساحة interchromatin والمجمعات المسام النووية، والهيئات النووية، من ناحية أخرى، يمكن أن يتم الكشف بسهولة في الخريطة النيتروجين الصورة. مصغرة النظام مولد الاوكسجين القميص (miniSOG) في حين ESI يمثل تقنية قوية لدراسة الموقع هيكل لونين في ليستغرقالصورة الاستفادة من نسب مميزة في التركيب العنصري بين الفوسفور والنيتروجين وتكوين عنصر لا يمكن في العادة يستخدم للتمييز بين مجموعات مختلفة من المجمعات البروتين. الأجسام المضادة المسمى مع جزيئات الذهب الصغيرة في نطاق نانومتر وقد استخدمت على نطاق واسع لرسم خريطة للموقع الجزيئات الفردية. منذ عادة يتم إرفاق الجسيمات الذهب إلى الضد الثانوية، وسوف تظهر ضمن محيط من حوالي 20 نانومتر حول حاتمة الكشف عنها بواسطة الأجسام المضادة الأولية. في عينات بعد التضمين، يمكن أن الأجسام المضادة كشف فقط الحواتم التي يتم كشفها على سطح الأجزاء. في حين أنه من الممكن أن يثبت وجود مستضد وربطها بنية تشريحية معينة من الخلايا، فإن المعلومات التي يتم الحصول عليها غير كاملة، حيث يتم حجب معظم الحواتم التي كتبها الراتنج. التقنيات التي تستخدم بروتوكولات مماثلة لتلك المستخدمة في مضان المجهري قبل التضمين، تسمح بالوصول إلى المستضدات في جميع أنحاءعمق الكامل للعينة لكن الخطوات permeabilization المطلوبة للسماح للأجسام المضادة لاختراق الخلية عادة ما تتطلب إزالة الأغشية الدهنية وإزالة المكونات التي لا يمكن إصلاحها من خلال الألدهيدات. وعلاوة على ذلك، تثبيتي ألدهيد المفضل للحفاظ التركيب الدقيق، غلوتارالدهيد، ويدمر عادة الحواتم، وبالتالي مطلوب امتصاص العرق عادة. هذا هو أقل فعالية في البروتين البروتين يشابك. عيب آخر من الأجسام المضادة التي وصفت مع جسيمات متناهية الصغر الذهب أن الذهب هو مادة الإلكترون كثيفة جدا أن يخلق تناقضا واضحا أن يمكن أن يحجب تفاصيل الهيكلية مثيرة للاهتمام من العينة، والتي على النقيض أضعف. ظهور البروتين الفلوري الأخضر (GFP) كما علامة البروتين أعرب حولت استخدام المجهر مضان الإجابة على الأسئلة في علم الأحياء الخلوي. علامات بروتين مع مجال الفلورسنت صغير يسمح رسم خرائط لتوزيعه في الجسم الحي </eم&gt; دون الحاجة إلى إجراءات permeabilization التي يمكن أن تغير هيكل. من أجل ترجمة مبدأ أنيقة من استخدام علامات البروتين لخريطة توزيع البروتين في خلية لالمجهر الإلكتروني، وبحاجة إلى نظام قادر على إنتاج وثيقة إشارة إلى بنية الفائدة وتوليد التباين في TEM. diaminobenzidine بلمرة وصمة التي كثيرا ما تستخدم في الأنسجة للكشف عن الأجسام المضادة ملزمة. وعادة ما يتم إيداع هذه وصمة عار باستخدام البيروكسيديز الفجل (HRP) مترافق إلى الضد الثانوية. على الرغم من أن رد فعل ينتج نتيجة موثوق بها، HRP غير نشطة تحفيزيا في العصارة الخلوية للخلايا 9. هذه المنتجات يمكن أن رد فعل HRP أيضا منتشر بعيدا من موقع جيل بحيث حلها هو أسوأ من طريقة nanogold 10. من أجل تجاوز هذه المشاكل، تم تطوير نظام فلاش / ReAsH 11. وهو يتألف من البروتينات الانصهار المؤتلف التي تمتلك عزر tetracysteine. هذا عزر يسمح ملزمة للوfluorophore biarsenic. عندما متحمس، ومضة المربوطة أو ReAsH قادر على توليد الأكسجين القميص شديدة التفاعل وdiaminobenzidine بالتالي photoconvert (DAB) إلى البوليمر الذي يترسب على الفور في موقع البروتينات الموسومة. يمكن أن تكون ملطخة البوليمر DAB مع رباعي أكسيد الأوزميوم، وهي كثيفة الإلكترون وبالتالي يمكن استخدامها لخريطة توزيع انصهار بروتين المؤتلف في TEM. في عام 2011، شو وآخرون 10 قدم نظام miniSOG، والذي يتألف من 106 الأمينية الصغيرة علامة الأحماض الانصهار مشتقة من بروتين فلافيني من نبات الأرابيدوبسيس هذا هو فلوري وقادرة على خلق العديد من المتطرفين الأكسجين القميص عندما متحمس مع 448 الضوء الأزرق نانومتر. تلك الجذور الأكسجين القميص يمكن أن تستخدم لالصور أكسدة diaminobenzidine لتشكيل البوليمرات في وبالقرب من سطح البروتين الموسومة، والتي هي أقرب بكثير من الأجسام المضادة المسمى immunogold 11. في حين أن نظام فلاش / ReAsH يتطلب يصل الفلوريةالكروم وdiaminobenzidine إلى خلايا قبل القيام photoconversion، ونظام miniSOG يتطلب سوى diaminobenzidine والضوء وبالإضافة إلى ذلك حوالي الفعال مرتين كما في البلمرة diaminobenzidine. هنا، يعمل miniSOG في تركيبة مع ESI من أجل رسم خريطة التركيب الدقيق للإصلاح الحمض النووي البؤر. إصلاح الحمض النووي بؤر (DRF) DNA دون اصلاح فواصل حبلا مزدوجة تشكل تهديدا خطيرا للخلية لأنها يمكن أن تؤدي إلى نقل المواقع وفقدان المعلومات الوراثية. وهذا بدوره يمكن أن يؤدي إلى الشيخوخة، والسرطان، وموت الخلايا. العديد من البروتينات التي تشارك في الحمض النووي المزدوج إصلاح كسر حبلا تتراكم في البؤر التي تجمع حول حبلا مزدوج DNA كسر 12-14. على الرغم من وظيفتها غير معروف، إلا أنها تمثل الموقع في النواة التي تحتوي على الحمض النووي المزدوج كسر حبلا وغير موقع من الحمض النووي حبلا مزدوجة إصلاح كسر. إصلاح الحمض النووي لجنة مسؤولي المنتدىوقد اتسمت ط (DRF) بواسطة المجهر مضان وأنها بمثابة المؤشرات الحيوية للتلف الحمض النووي 12،15. فهي نسبية كبيرة لحجم كسر مزدوج الجديلة واعتبرت متجانسة نسبيا حتى كشفت الدراسات الحديثة المجهر فائقة الدقة بعض الأدلة على التقسيم الفرعي للجزيئات في كل تركيز 16. من أجل فهم كيفية تنظيم هذه المواقع، لا بد من تصور كل من الهياكل البيولوجية الأساسية بالنسبة لبعضها البعض. لا يمكن أن يتحقق ذلك عن طريق الفحص المجهري مضان ولكن من الممكن من خلال المجهر الإلكتروني 17،18. هنا، يتم وصف أسلوب يجمع بين الإلكترون التصوير الطيفي مع أسلوب miniSOG لتوضيح إمكانات هذا النهج جنبا إلى جنب لاستكشاف التركيب الدقيق للDNA مزدوج الجديلة إصلاح كسر.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>35 mm glass bottom dishes</td>
			<td>MatTek</td>
			<td>P35G-1.5-14-C</td>
			<td></td>
		</tr>
		<tr>
			<td>Gridded 35 mm glass bottom dishes</td>
			<td>MatTek</td>
			<td>P35G-2-14-CGRD&#160;</td>
			<td>not made for immersion objectives</td>
		</tr>
		<tr>
			<td>LR White: acryl resin</td>
			<td>emsdiasum</td>
			<td>14381</td>
			<td></td>
		</tr>
		<tr>
			<td>LR White accelerator</td>
			<td>emsdiasum</td>
			<td>14385</td>
			<td></td>
		</tr>
		<tr>
			<td>3,3&#8242;-Diaminobenzidine tetrahydrochloride 10 mg tablets</td>
			<td>Sigma</td>
			<td>D5905</td>
			<td></td>
		</tr>
		<tr>
			<td>Slim Bar Grids 300 Mesh</td>
			<td>SPI</td>
			<td>1161123</td>
			<td></td>
		</tr>
		<tr>
			<td>Tungsten-Point Lab Pen</td>
			<td>emsdiasum</td>
			<td>41148</td>
			<td></td>
		</tr>
		<tr>
			<td>Osmium Tetroxide</td>
			<td>emsdiasum</td>
			<td>19100</td>
			<td></td>
		</tr>
		<tr>
			<td>Carbon Coater 208carbon</td>
			<td>Cressington</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Ultra microtome Leica EM UC6</td>
			<td>Leica</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Photoshop CS5</td>
			<td>Adobe</td>
			<td></td>
			<td>might even work with older versions</td>
		</tr>
		<tr>
			<td>Digital Micrograph V.2.30</td>
			<td>Gatan</td>
			<td></td>
			<td>might even work with older versions</td>
		</tr>
		<tr>
			<td>Hoechst 33342</td>
			<td>Sigma</td>
			<td>H-1399</td>
			<td></td>
		</tr>
		<tr>
			<td>Effectene</td>
			<td>Quiagen</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>MiniSOG-Constructs</td>
			<td>Tsien-Lab</td>
			<td></td>
			<td><a href="mailto:tsienlab@yahoo.com">tsienlab@yahoo.com</a></td>
		</tr>
		<tr>
			<td>MDC1 miniSOG mCherry</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>53BP1 miniSOG mCherry</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Rad52 miniSOG mCherry</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>cesium 137 radiation source &#34;MARK 1&#34;</td>
			<td>&#160;(J.L. Shepherd &#38; Associated)</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>ImageJ/FiJi</td>
			<td>open source</td>
			<td></td>
			<td>http://fiji.sc/Fiji</td>
		</tr>
		<tr>
			<td>2 ml Eppendorf tubes</td>
			<td>Fisherbrand</td>
			<td>05-408-146</td>
			<td></td>
		</tr>
		<tr>
			<td>Diamond Knife ultra 35&#176;</td>
			<td>Diatome</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Trimming Knife ultratrim</td>
			<td>Diatome</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium cacodylate trihydrate</td>
			<td>emsdiasum</td>
			<td>12300</td>
			<td>Caution Toxic!</td>
		</tr>
		<tr>
			<td>Glutaraldehyde EM Grade 8%</td>
			<td>emsdiasum</td>
			<td>16020</td>
			<td>Caution Toxic!</td>
		</tr>
		<tr>
			<td>Sodium phosphate dibasic</td>
			<td>emsdiasum</td>
			<td>21180</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium phosphate monobasic</td>
			<td>emsdiasum</td>
			<td>21190</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehyde</td>
			<td>emsdiasum</td>
			<td>19202</td>
			<td></td>
		</tr>
		<tr>
			<td>Osmium tetroxide 4% solution</td>
			<td>emsdiasum</td>
			<td>19150</td>
			<td></td>
		</tr>
		<tr>
			<td>Inverted Fluorescence Micoscope Axiovert 200M</td>
			<td>Zeiss</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrochloric Acid</td>
			<td>Fisherbrand</td>
			<td>A142-212</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Hydroxide Solution 10M</td>
			<td>Fluka</td>
			<td>72068</td>
			<td></td>
		</tr>
		<tr>
			<td>Oxygen</td>
			<td>Medigas</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>3-Amino-1,2,4-triazole</td>
			<td>Sigma</td>
			<td>A8056</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium cyanide</td>
			<td>Sigma</td>
			<td>207810</td>
			<td>Caution Toxic!</td>
		</tr>
		<tr>
			<td>Ethanol</td>
			<td>emsdiasum</td>
			<td>15058</td>
			<td>Caution Toxic!</td>
		</tr>
		<tr>
			<td>Razor blade Single Edge Carbon Steel</td>
			<td>emsdiasum</td>
			<td>71960</td>
			<td>Caution Sharp!</td>
		</tr>
		<tr>
			<td>DMEM</td>
			<td>Sigma</td>
			<td>D 5546</td>
			<td></td>
		</tr>
		<tr>
			<td>FBS</td>
			<td>lifetechnologies</td>
			<td>16000-044</td>
			<td></td>
		</tr>
		<tr>
			<td>G418</td>
			<td>lifetechnologies</td>
			<td>11811-023</td>
			<td></td>
		</tr>
		<tr>
			<td>DMSO</td>
			<td>Sigma</td>
			<td>D2650</td>
			<td></td>
		</tr>
		<tr>
			<td>Transmission Electron Microscope 200 kV</td>
			<td>JEOL</td>
			<td>2100</td>
			<td></td>
		</tr>
		<tr>
			<td>GIF Tridiem 863 Energy filter</td>
			<td>Gatan</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

visualization of minisog tagged dna repair proteins in combination with electron spectroscopic imaging (esi)

وكانت حدود لقرار بصري وتحدي تحديد السكان بروتين معين في المجهر الإلكتروني انتقال العقبات في علم الأحياء الخلوي. العديد من الظواهر لا يمكن تفسيره في المختبر تحليل نظم مبسطة وتحتاج المعلومات الهيكلية إضافية في الموقع، وخاصة في نطاق بين 1 نانومتر و 0.1 ميكرون، من أجل أن تكون مفهومة تماما. هنا، والتصوير الطيفي الإلكترون، وهي تقنية المجهر الإلكتروني النافذ الذي يسمح رسم الخرائط في وقت واحد لتوزيع البروتينات والأحماض النووية، وعلامة التعبير، miniSOG، يتم الجمع بين لدراسة بنية وتنظيم DNA مزدوج الجديلة إصلاح كسر البؤر.

ESI وبمقارنة الصور ESI للنواة (الشكل 1) مع الصور TEM التقليدية (على سبيل المثال، الشكل 7-1) يكشف عن زيادة كبيرة في البنى التشريحية التي يمكن تمييزها بسهولة. تظهر التلال لونين الأصفر وأنه من السهل جدا ...

Watch this Scientific Journal Video about Visualization of miniSOG Tagged DNA Repair Proteins in Combination with Electron Spectroscopic Imaging ESI at JoVE.com

Visualization of miniSOG Tagged DNA Repair Proteins in Combination with Electron Spectroscopic Imaging ESI

Electron spectroscopic imaging can image and distinguish nucleic acid from protein at nanometer resolution. It can be combined with the miniSOG system, which is able to specifically label tagged proteins in transmission electron microscopy samples. We illustrate the use of these technologies using double-strand break repair foci as an example.

تصور miniSOG معلم البروتينات إصلاح الحمض النووي في الجمع مع الكترون طيفية تصوير (ESI)

The limits to optical resolution and the challenge of identifying specific protein populations in transmission electron microscopy have been obstacles in ...

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Visualization of miniSOG Tagged DNA Repair Proteins in Combination with Electron Spectroscopic Imaging (ESI)

10.0K Views.  University of Alberta. Electron spectroscopic imaging can image and distinguish nucleic acid from protein at nanometer resolution. It can be combined with the miniSOG system, which is able to specifically label tagged proteins in transmission electron microscopy samples. We illustrate the use of these technologies using double-strand break repair foci as an example.

Video: Visualization of miniSOG Tagged DNA Repair Proteins in Combination with Electron Spectroscopic Imaging ESI

Genetic Studies of Human DNA Repair Proteins Using Yeast as a Model System 

Understanding the roles of human DNA repair proteins in genetic pathways is a formidable challenge to many researchers. Genetic studies in mammalian systems have been limited due to the lack of readily available tools including defined mutant genetic cell lines, regulatory expression systems, and appropriate selectable markers. To circumvent these difficulties, model genetic systems in lower eukaryotes have become an attractive choice for the study of functionally conserved DNA repair proteins and pathways. We have developed a model yeast system to study the poorly defined genetic functions of the Werner syndrome helicase-nuclease (WRN) in nucleic acid metabolism. Cellular phenotypes associated with defined genetic mutant backgrounds can be investigated to clarify the cellular and molecular functions of WRN through its catalytic activities and protein interactions. The human WRN gene and associated variants, cloned into DNA plasmids for expression in yeast, can be placed under the control of a regulatory plasmid element. The expression construct can then be transformed into the appropriate yeast mutant background, and genetic function assayed by a variety of methodologies. Using this approach, we determined that WRN, like its related RecQ family members BLM and Sgs1, operates in a Top3-dependent pathway that is likely to be important for genomic stability. This is described in our recent publication [1] at <a href="http://www.impactaging.com">www.impactaging.com</a>. Detailed methods of specific assays for genetic complementation studies in yeast are provided in this paper.

Genetic Studies of Human DNA Repair Proteins Using Yeast as a Model System

Genetic studies in yeast can be employed to investigate the molecular and cellular functions of human genes in cellular DNA metabolism. Methods are described for the genetic characterization of the human WRN gene product defective in the premature aging disorder Werner syndrome in functionally conserved pathways using yeast as a tractable model system.

الدراسات الجينية البشرية البروتينات إصلاح الحمض النووي باستخدام خميرة كنظام النموذجي

Understanding the roles of human DNA repair proteins in genetic pathways is a formidable challenge to many researchers.  Genetic studies in mammalian ...

Imaging Mismatch Repair and Cellular Responses to DNA Damage in Bacillus subtilis

Both prokaryotes and eukaryotes respond to DNA damage through a complex set of physiological changes. Alterations in gene expression, the redistribution of existing proteins, and the assembly of new protein complexes can be stimulated by a variety of DNA lesions and mismatched DNA base pairs. Fluorescence microscopy has been used as a powerful experimental tool for visualizing and quantifying these and other responses to DNA lesions and to monitor DNA replication status within the complex subcellular architecture of a living cell. Translational fusions between fluorescent reporter proteins and components of the DNA replication and repair machinery have been used to determine the cues that target DNA repair proteins to their cognate lesions in vivo and to understand how these proteins are organized within bacterial cells. In addition, transcriptional and translational fusions linked to DNA damage inducible promoters have revealed which cells within a population have activated genotoxic stress responses. In this review, we provide a detailed protocol for using fluorescence microscopy to image the assembly of DNA repair and DNA replication complexes in single bacterial cells. In particular, this work focuses on imaging mismatch repair proteins, homologous recombination, DNA replication and an SOS-inducible protein in Bacillus subtilis. All of the procedures described here are easily amenable for imaging protein complexes in a variety of bacterial species.

Imaging Mismatch Repair and Cellular Responses to DNA Damage in Bacillus subtilis

A detailed protocol is described for imaging the real time formation of DNA repair complexes in Bacillus subtilis cells.

التصوير إصلاح عدم تطابق والردود الخليوي الى الحمض النووي من التلف في<emالعصوية الرقيقة></em

Both prokaryotes and eukaryotes respond to DNA damage through a complex set of physiological changes. Alterations in gene expression, the redistribution ...

Visualization of MG53-mediated Cell Membrane Repair Using in vivo and in vitro Systems

Repair of acute injury to the cell membrane is an elemental process of normal cellular physiology, and defective membrane repair has been linked to many degenerative human diseases. The recent discovery of MG53 as a key component of the membrane resealing machinery allows for a better molecular understanding of the basic biology of tissue repair, as well as for potential translational applications in regenerative medicine. Here we detail the experimental protocols for exploring the in vivo function of MG53 in repair of muscle injury using treadmill exercise protocols on mouse models, for testing the ex vivo membrane repair capacity by measuring dye entry into isolated muscle fibers, and for monitoring the dynamic process of MG53-mediated vesicle trafficking and cell membrane repair in cultured cells using live cell confocal microscopy.

Visualization of MG53-mediated Cell Membrane Repair Using in vivo and in vitro Systems

Described here are protocols used to visualize the dynamic process of MG53-mediated cell membrane repair in whole animals and at the cellular level. These methods can be applied to investigate the cell biology of plasma membrane resealing and regenerative medicine.

MG53 تصور بوساطة غشاء الخلية عن طريق إصلاح في الجسم الحي و في المختبر أنظمة

Repair of acute injury to the cell membrane is an elemental process of normal cellular physiology, and defective membrane repair has been linked to many ...

High-throughput Purification of Affinity-tagged Recombinant Proteins

X-ray crystallography is the method of choice for obtaining a detailed view of the structure of proteins. Such studies need to be complemented by further biochemical analyses to obtain detailed insights into structure/function relationships. Advances in oligonucleotide- and gene synthesis technology make large-scale mutagenesis strategies increasingly feasible, including the substitution of target residues by all 19 other amino acids. Gain- or loss-of-function phenotypes then allow systematic conclusions to be drawn, such as the contribution of particular residues to catalytic activity, protein stability and/or protein-protein interaction specificity.
In order to attribute the different phenotypes to the nature of the mutation - rather than to fluctuating experimental conditions - it is vital to purify and analyse the proteins in a controlled and reproducible manner. High-throughput strategies and the automation of manual protocols on robotic liquid-handling platforms have created opportunities to perform such complex molecular biological procedures with little human intervention and minimal error rates1-5.
Here, we present a general method for the purification of His-tagged recombinant proteins in a high-throughput manner. In a recent study, we applied this method to a detailed structure-function investigation of TFIIB, a component of the basal transcription machinery. TFIIB is indispensable for promoter-directed transcription in vitro and is essential for the recruitment of RNA polymerase into a preinitiation complex6-8. TFIIB contains a flexible linker domain that penetrates the active site cleft of RNA polymerase9-11. This linker domain confers two biochemically quantifiable activities on TFIIB, namely (i) the stimulation of the catalytic activity during the 'abortive' stage of transcript initiation, and (ii) an additional contribution to the specific recruitment of RNA polymerase into the preinitiation complex4,5,12 . We exploited the high-throughput purification method to generate single, double and triple substitution and deletions mutations within the TFIIB linker and to subsequently analyse them in functional assays for their stimulation effect on the catalytic activity of RNA polymerase4. Altogether, we generated, purified and analysed 381 mutants - a task which would have been time-consuming and laborious to perform manually. We produced and assayed the proteins in multiplicates which allowed us to appreciate any experimental variations and gave us a clear idea of the reproducibility of our results.
This method serves as a generic protocol for the purification of His-tagged proteins and has been successfully used to purify other recombinant proteins. It is currently optimised for the purification of 24 proteins but can be adapted to purify up to 96 proteins.

We describe a method for the affinity-tagged purification of recombinant proteins using liquid-handling robotics. This method is generally applicable to the small-scale purification of soluble His-tagged proteins in a high-throughput format.

عالية الإنتاجية تنقية تقارب الموسومة البروتينات المؤتلف

X-ray crystallography is the method of choice for obtaining a detailed view of the structure of proteins. Such studies need to be complemented by further ...

Visualization of ATP Synthase Dimers in Mitochondria by Electron Cryo-tomography

Electron cryo-tomography is a powerful tool in structural biology, capable of visualizing the three-dimensional structure of biological samples, such as cells, organelles, membrane vesicles, or viruses at molecular detail. To achieve this, the aqueous sample is rapidly vitrified in liquid ethane, which preserves it in a close-to-native, frozen-hydrated state. In the electron microscope, tilt series are recorded at liquid nitrogen temperature, from which 3D tomograms are reconstructed. The signal-to-noise ratio of the tomographic volume is inherently low. Recognizable, recurring features are enhanced by subtomogram averaging, by which individual subvolumes are cut out, aligned and averaged to reduce noise. In this way, 3D maps with a resolution of 2 nm or better can be obtained. A fit of available high-resolution structures to the 3D volume then produces atomic models of protein complexes in their native environment. Here we show how we use electron cryo-tomography to study the in situ organization of large membrane protein complexes in mitochondria. We find that ATP synthases are organized in rows of dimers along highly curved apices of the inner membrane cristae, whereas complex I is randomly distributed in the membrane regions on either side of the rows. By subtomogram averaging we obtained a structure of the mitochondrial ATP synthase dimer within the cristae membrane.

We present a protocol of how to collect and process electron cryo-tomograms of whole mitochondria. The technique provides detailed insights into the structure, function, and organization of large membrane protein complexes in native biological membranes.

التصور من ATP سينسيز Dimers في الميتوكوندريا بواسطة الكترون البرد المقطعي

Electron cryo-tomography is a powerful tool in structural biology, capable of visualizing the three-dimensional structure of biological samples, such as ...

Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons

The growing realization that both the temporal and spatial regulation of gene expression can have important consequences on cell function has led to the development of diverse techniques to visualize individual RNA transcripts in single living cells. One promising technique that has recently been described utilizes an oligonucleotide-based optical probe, ratiometric bimolecular beacon (RBMB), to detect RNA transcripts that were engineered to contain at least four tandem repeats of the RBMB target sequence in the 3&#8217;-untranslated region. RBMBs are specifically designed to emit a bright fluorescent signal upon hybridization to complementary RNA, but otherwise remain quenched. The use of a synthetic probe in this approach allows photostable, red-shifted, and highly emissive organic dyes to be used for imaging. Binding of multiple RBMBs to the engineered RNA transcripts results in discrete fluorescence spots when viewed under a wide-field fluorescent microscope. Consequently, the movement of individual RNA transcripts can be readily visualized in real-time by taking a time series of fluorescent images. Here we describe the preparation and purification of RBMBs, delivery into cells by microporation and live-cell imaging of single RNA transcripts.

Ratiometric bimolecular beacons (RBMBs) can be used to image single engineered RNA transcripts in living cells. Here, we describe the preparation and purification of RBMBs, delivery of RBMBs into cells by microporation and fluorescent imaging of single RNA transcripts in real-time.

التصوير في الوقت الحقيقي من واحدة المهندسة رنا النصوص في الخلايا الحية عن طريق Ratiometric ثنائي الجزيء منارات

The growing realization that both the temporal and spatial regulation of gene expression can have important consequences on cell function has led to the ...

Visualization of Surface-tethered Large DNA Molecules with a Fluorescent Protein DNA Binding Peptide

Large DNA molecules tethered on the functionalized glass surface have been utilized in polymer physics and biochemistry particularly for investigating interactions between DNA and its binding proteins. Here, we report a method that uses fluorescent microscopy for visualizing large DNA molecules tethered on the surface. First, glass coverslips are biotinylated and passivated by coating with biotinylated polyethylene glycol, which specifically binds biotinylated DNA via avidin protein linkers and significantly reduces undesirable binding from non-specific interactions of proteins or DNA molecules on the surface. Second, the DNA molecules are biotinylated by two different methods depending on their terminals. The blunt ended DNA is tagged with biotinylated dUTP at its 3' hydroxyl terminus, by terminal transferase, while the sticky ended DNA is hybridized with biotinylated complimentary oligonucleotides by DNA ligase. Finally, a microfluidic shear flow makes single DNA molecules stretch to their full contour lengths after being stained with fluorescent protein-DNA binding peptide (FP-DBP).

We present an approach for visualizing fluorescent protein DNA binding peptide (FP-DBP)-stained large DNA molecules tethered on the polyethylene glycol (PEG) and avidin-coated glass surface and stretched with microfluidic shear flows.

التصور-المربوطة السطحية الكبيرة جزيئات الحمض النووي مع الحمض النووي البروتين الفلوري ملزم الببتيد

Large DNA molecules tethered on the functionalized glass surface have been utilized in polymer physics and biochemistry particularly for investigating ...

Visualization of DNA Compaction in Cyanobacteria by High-voltage Cryo-electron Tomography

This protocol describes how to visualize the transient DNA compaction in cyanobacteria. DNA compaction is a dramatic cytoplasmic event recently found to occur in some cyanobacteria before cell division. However, due to the large cell size and the transient character, it is difficult to investigate the structure in detail. To overcome the difficulties, first, DNA compaction is reproducibly produced in the cyanobacterium Synechococcus elongatus PCC 7942 by synchronous culture using 12 h each light/dark cycle. Second, DNA compaction is monitored by fluorescence microscopy and captured by rapid freezing. Third, the detailed structure of DNA compacted cells is visualized in three dimensions (3D) by high voltage cryo-electron tomography. This set of methods is widely applicable to investigate transient structures in bacteria, e.g. cell division, chromosome segregation, phage infection etc., which are monitored by fluorescence microscopy and directly visualized by cryo-electron tomography at appropriate time points.

This protocol describes how to visualize the transient DNA compaction in cyanobacteria. Synchronous cultivation, monitoring by fluorescence microscopy, rapid freezing, and high voltage cryo-electron tomography are used. A protocol for these methodologies is presented, and future applications and developments are discussed.

التصور للضغط الحمض النووي في البكتيريا الزرقاء بالتصوير المقطعي الفولت العالي Cryo-إلكترون

This protocol describes how to visualize the transient DNA compaction in cyanobacteria. DNA compaction is a dramatic cytoplasmic event recently found to ...

Visualization of DNA Repair Proteins Interaction by Immunofluorescence

Mammalian cells are constantly exposed to chemicals, radiations, and naturally occurring metabolic by-products, which create specific types of DNA insults. Genotoxic agents can damage the DNA backbone, break it, or modify the chemical nature of individual bases. Following DNA insult, DNA damage response (DDR) pathways are activated and proteins involved in the repair are recruited. A plethora of factors are involved in sensing the type of damage and activating the appropriate repair response. Failure to correctly activate and recruit DDR factors can lead to genomic instability, which underlies many human pathologies including cancer. Studies of DDR proteins can provide insights into genotoxic drug response and cellular mechanisms of drug resistance.
There are two major ways of visualizing&#160;proteins in vivo: direct observation, by tagging the protein of interest with a fluorescent protein and following it by live imaging, or indirect immunofluorescence on fixed samples. While visualization of fluorescently tagged proteins allows precise monitoring over time, direct tagging in N- or C-terminus can interfere with the protein localization or function. Observation of proteins in their unmodified, endogenous version is preferred. When DNA repair proteins are recruited to the DNA insult, their concentration increases locally and they form groups, or &#8220;foci&#8221;, that can be visualized by indirect immunofluorescence using specific antibodies.
Although detection of protein foci does not provide a definitive proof of direct interaction, co-localization of proteins in cells indicates that they regroup to the site of damage and can inform of the sequence of events required for complex formation. Careful analysis of foci spatial overlap in cells expressing wild type or mutant versions of a protein can provide precious clues on functional domains important for DNA repair function. Last, co-localization of proteins indicates possible direct interactions that can be verified by co-immunoprecipitation in cells, or direct pulldown using purified proteins.

Following DNA damage, human cells activate essential repair pathways to restore the integrity of their genome. Here, we describe the method of indirect immunofluorescence as a means to detect DNA repair proteins, analyze their spatial and temporal recruitment, and help interrogate protein-protein interaction at the sites of DNA damage.

التصور من الحمض النووي إصلاح البروتينات التفاعل من قبل immunofluorescence

Mammalian cells are constantly exposed to chemicals, radiations, and naturally occurring metabolic by-products, which create specific types of DNA ...

Photodiode-Based Optical Imaging for Recording Network Dynamics with Single-Neuron Resolution in Non-Transgenic Invertebrates

The development of transgenic invertebrate preparations in which the activity of specifiable sets of neurons can be recorded and manipulated with light represents a revolutionary advance for studies of the neural basis of behavior. However, a downside of this development is its tendency to focus investigators on a very small number of &#8220;designer&#8221; organisms (e.g., C. elegans and Drosophila), potentially negatively impacting the pursuit of comparative studies across many species, which is needed for identifying general principles of network function. The present article illustrates how optical recording with voltage-sensitive dyes in the brains of non-transgenic gastropod species can be used to rapidly (i.e., within the time course of single experiments) reveal features of the functional organization of their neural networks with single-cell resolution. We outline in detail the dissection, staining, and recording methods used by our laboratory to obtain action potential traces from dozens to ~150 neurons during behaviorally relevant motor programs in the CNS of multiple gastropod species, including one new to neuroscience &#8211; the nudibranch Berghia stephanieae. Imaging is performed with absorbance voltage-sensitive dyes and a 464-element photodiode array that samples at 1,600 frames/second, fast enough to capture all action potentials generated by the recorded neurons. Multiple several-minute recordings can be obtained per preparation with little to no signal bleaching or phototoxicity. The raw optical data collected through the methods described can subsequently be analyzed through a variety of illustrated methods. Our optical recording approach can be readily used to probe network activity in a variety of non-transgenic species, making it well suited for comparative studies of how brains generate behavior.

This protocol presents a method for imaging neuronal population activity with single-cell resolution in non-transgenic invertebrate species using absorbance voltage-sensitive dyes and a photodiode array. This approach enables a rapid workflow, wherein imaging and analysis can be pursued over the course of a single day.

التصوير البصري المستند إلى الصمامات الثنائية الضوئية لتسجيل ديناميكيات الشبكة بدقة أحادية الخلايا العصبية في اللافقاريات غير المعدلة وراثيا

The development of transgenic invertebrate preparations in which the activity of specifiable sets of neurons can be recorded and manipulated with light ...