This work was supported by the New College of Interdisciplinary Arts and Sciences at Arizona State University, Applied Maths NV, and by the National Science Foundation (ROA Supplement to Award No. MCB0604300). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

الحذر: بكتيريا مجهولة الهوية من أي بيئة قد تكون المسببة للأمراض ويجب التعامل معها بحذر باستخدام بروتوكولات المناسبة للسلامة الأحيائية. يجب إجراء عمل مع الثقافات الحية في مجلس الوزراء من الدرجة الثانية للسلامة الأحيائية باستخدام السلامة البيولوجية المستوى 2 (BSL-2) الإجراءات. مزيد من المعلومات حول 2 BSL-إجراءات متاحة في بعنوان دليل CDC / NIH، &quot;السلامة الأحيائية في الميكروبيولوجية الطبية الحيوية والمختبرات،&quot; صفحات 33-38. والوثيقة متاحة على الانترنت في <a href="http://www.cdc.gov/biosafety/publications/bmbl5/BMBL.pdf">http://www.cdc.gov/biosafety/publications/bmbl5/BMBL.pdf</a> . معدات الحماية الشخصية المناسبة (PPE)، بما في ذلك المختبر المعاطف / العباءات، ونظارات السلامة، والنتريل قفازات اللاتكس أو، يجب أن ترتديه. يجب اتباع الممارسات والاحتياطات القياسية الميكروبيولوجية، ويجب التخلص من النفايات biohazardous بشكل مناسب. تم عزل البكتيريا المستخدمة في هذه التظاهرة من Kartchner الكهوف،AZ، الولايات المتحدة الأمريكية، من أربع بيئات، بما في ذلك speleothem تجف، حجر التدفق، speleothem رطبة وبالتنقيط الهوابط (الجدول 1). تم تحديد جميع العزلات التي كتبها 16S rDNA التسلسل والاحتفاظ بها في -80 درجة مئوية في 25٪ الجلسرين-R 2 B المتوسطة. تم الانتهاء من جميع التجارب في RT. ملاحظة: نوصي باستخدام نفس العينة طريقة التحضير للحصول على الأطياف الشامل لبناء قاعدة البيانات والأطياف الشامل من المجاهيل. وقد تبين طريقة تحضير عينات سبق أن تؤثر على نوعية الطيف واستنساخ 3. باستخدام طريقة مختلفة وإعداد العينات قد يسبب تحديد غير صحيح من المجاهيل، القرار التصنيفية وخصوصا عندما العالي (على سبيل المثال، على مستوى السلالة) هو المطلوب. 1. ترسب على MALDI الهدف الحذر: عدة بروتوكولات للحصول على مستخلصات البروتين تتطلب استخدام الأحماض والمذيبات العضوية التي يجب أن تستخدم وفقا ارشدelines والمعلومات الواردة في ورقة بيانات سلامة المواد الخاصة بكل منها (MSDS). المناسبة PPE يجب أن ترتديه وسوف تختلف بناء على نوع وحجم المواد الكيميائية المستخدمة (على سبيل المثال، والمعاطف مختبر / العباءات، والقفازات، ونظارات السلامة، وحماية الجهاز التنفسي يجب أن تستخدم عند التعامل مع كميات كبيرة من السامة، والمذيبات القابلة للاشتعال، مثل الأسيتونتريل، والأحماض تآكل، مثل الأحماض الفورميك وtrifluoroacetic). <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> إيداع 1 ميكرولتر استخراج البروتين لا تحتوي على خلايا قابلة للحياة (تم الحصول عليها باستخدام المناسبة والبروتوكولات التي سبق وصفها 11-13) على الفولاذ المقاوم للصدأ لوحة الهدف MALDI واتركه حتى يجف. تراكب استخراج البروتين المجفف مع 1 ميكرولتر حل مصفوفة (α-cyano-4-هيدروكسي-السيناميك حل حامض)، واتركه حتى يجف. </li><li style=";text-align:right;direction:rtl"> لكل تكرار البيولوجي، بقعة عدد مناسب من مكررات الفنية (5 إلى 20 مكررات الفنية). هنا، بقعة 10 مكررات الفنية لكل تكرار البيولوجي و3 مكررات البيولوجية ثيحرث إعدادها. ملاحظة: نوصي باستخدام مصقول MALDI وحة الهدف الصلب عند استخدام استخراج البروتين طريقة تحضير العينة. باستخدام لوحات الهدف الصلب الأرض قد يسبب انتشار وخلط غير مقصود من عينات مختلفة خارج الآبار عينة الفردية. </li><li style=";text-align:right;direction:rtl"> إيداع 1 ميكرولتر مستوى calibrant على لوحة الهدف واتركه حتى يجف. تراكب مع 1 ميكرولتر حل المصفوفة واتركه حتى يجف. </li><li style=";text-align:right;direction:rtl"> إيداع 2 ميكرولتر حل مصفوفة على لوحة الهدف كعنصر تحكم السلبية. </li></ol> 2. قداس الأطياف اكتساب <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> استخدام مطياف الكتلة MALDI-TOF مجهزة ليزر النيتروجين (λ = 337 نانومتر) وتشغيلها باستخدام البرمجيات بروكر FlexControl. </li><li style=";text-align:right;direction:rtl"> جمع كل الطيف الشامل في الوضع الخطي الإيجابية التي كتبها تراكم 500 طلقات الليزر في 100 الزيادات النار. تعيين الجهد مصدر أيون 1 إلى 20 كيلو فولت. مصدر أيون 2 الجهد إلى 18.15 كيلو فولت. والجهد العدسة إلى 9.05 كيلو فولت. لاحظ أن هذه الثوابت هي صك SPECIالمرورية وقد تتطلب التعديل على الصكوك الأخرى للحصول على أفضل النتائج. </li><li style=";text-align:right;direction:rtl"> تعيين نطاق الكتلة إلى تهمة لتقييم الطيف الآلي من 2 إلى 20 كيلو دالتون لكل تهمة. استخدام خوارزمية الكشف الذروة النقطه الوسطى. تعيين دقة عتبة الحد الأدنى عند 100 دا. تعيين إشارة إلى نسبة الضوضاء (S: N) العتبة 2. تعيين عتبة كثافة الحد الأدنى عند 100. </li></ol> البناء 3. قاعدة البيانات <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> تصميم قاعدة البيانات <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> إنشاء قاعدة بيانات جديدة في BioNumerics 7.1 باستخدام &quot;معالج قاعدة بيانات جديد&quot;. </li><li style=";text-align:right;direction:rtl"> إنشاء نوع التجربة الطيف، على سبيل المثال، MALDI، وذلك باستخدام الأوامر في &quot;أنواع تجربة&quot; لوحة. </li><li style=";text-align:right;direction:rtl"> خلق مستويات استخدام &quot;قاعدة بيانات لوحة تصميم&quot;. إضافة مستويات جديدة باستخدام &quot;مستوى&gt; إضافة مستوى جديد ...&quot; الأمر في القائمة &quot;قاعدة بيانات&quot;. هنا، خلق &quot;الأنواع&quot; مستوى، مستوى &quot;تكرار البيولوجي&quot; &quot;و&quot; تكرار الفني &quot;مستوى، respectivاعل. </li></ol></li><li style=";text-align:right;direction:rtl"> استيراد وتجهيزها الخام أطياف الكتلة <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> تصدير الأطياف كتلة الخام كما ملفات .txt باستخدام FlexAnalysis بالضغط على &quot;تصدير&gt; الطيف الشامل&quot; الأوامر في القائمة &quot;ملف&quot;. </li><li style=";text-align:right;direction:rtl"> استيراد أطياف الكتلة الخام (ملفات .txt) في قاعدة البيانات في مستوى مكررات التقنية. </li><li style=";text-align:right;direction:rtl"> Preprocess أطياف الكتلة الخام. <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> استيراد وإعادة تشكيله (باستخدام خوارزمية المناسب من الدرجة الثانية). </li><li style=";text-align:right;direction:rtl"> إجراء الطرح الأساس (مع قرص المتداول مع حجم 50 نقطة). </li><li style=";text-align:right;direction:rtl"> حساب الضوضاء [المستمر المويجات تحول (CWT)]، على نحو سلس (كايزر النافذة مع حجم إطار 20 نقطة وبيتا من 10 نقطة)، وإجراء الطرح خط الأساس الثاني (المتداول القرص مع حجم 200 نقطة). </li><li style=";text-align:right;direction:rtl"> كشف قمم [CWT مع الحد الأدنى من إشارة إلى نسبة الضوضاء (S: N) من 10]. </li></ol></li><li style=";text-align:right;direction:rtl"> بعد تجهيزها، وتوفير أنماط مميزة من كل الطيف الشامل، مثل قوائم الذروة التي تحتوي الذروةالأحجام، وشدة الذروة، S: N، وما إلى ذلك، في قاعدة البيانات. </li></ol></li><li style=";text-align:right;direction:rtl"> خلق مركب أطياف الكتلة <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> خلق أطياف مركب من أطياف preprocessed باستخدام &quot;لخص ...&quot; الأمر في القائمة &quot;تحليل&quot;. اختيار &quot;تكرار البيولوجي&quot; كما المستوى المستهدف. </li><li style=";text-align:right;direction:rtl"> هنا، والجمع بين أطياف الشامل من 10 مكررات الفنية من نفس المستعمرة أن تسفر عن الطيف الكتلي مركب لتلك المستعمرة، مما أدى إلى ثلاثة أطياف الكتلة مركب لأنه وجد عزلة على مستوى &quot;تكرار البيولوجي&quot;. </li><li style=";text-align:right;direction:rtl"> هنا، تلخيص أطياف مركب من ثلاثة إلى إنشاء واحدة الطيف مركب لذلك عزل على مستوى &quot;الأنواع&quot;. ملاحظة: الطيف المركب هو متوسط ​​نقطة بنقطة من مكررات التقنية. يعيد مع تشابه (ارتباط بيرسون) لمتوسط ​​أقل من 95٪ (الإعداد الافتراضي) مستثناة من مركب. ويطلق على قمم على أطياف مركب فقط إذا كانت موجودة في 75٪ (الإعداد الافتراضي) من مكررات المدرجة. لمكررات البيولوجية، كانت هذه الإعدادات 90 و 60٪ على التوالي. </li></ol></li></ol> 4. تحليل قداس الطيف البيانات <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> حدد الإدخالات في قاعدة البيانات وإنشاء مقارنة بالضغط على &quot;إنشاء المقارنة الجديدة&quot; القيادة في &quot;مقارنات&quot; لوحة. </li><li style=";text-align:right;direction:rtl"> هنا، استخدم أطياف الشامل في &quot;تكرار الفني&quot; و / أو مستويات &quot;تكرار البيولوجي&quot; لإظهار المقارنات والتحليلات. </li><li style=";text-align:right;direction:rtl"> التحليل العنقودي القائم على التشابه والقياس متعدد الأبعاد (MDS) <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> إنشاء مجموعات مع الألوان. حدد البيولوجي أطياف الكتلة مركب ثلاثة وانقر على &quot;إنشاء مجموعة جديدة من اختيار&quot; الأمر في القائمة &quot;المجموعات&quot; لإنشاء مجموعة لعزل المقابل. تعيين اللون المستخدم تلقائيا لهذه الأطياف الشامل الثلاثة. </li><li style=";text-align:right;direction:rtl"> بدلا من ذلك، وتحديد ولايات الميدان مع الألوان المقابلة باستخدام الأوامر في &quot;إدخالات قاعدة بيانات &quot;لوحة مثل أن أي تجمع على أساس هذا المجال المحدد يستخدم نفس اللون محددة لهذه المجموعة. </li><li style=";text-align:right;direction:rtl"> أداء التحليل العنقودي. انقر على &quot;حساب التحليل العنقودي&quot; الأمر في القائمة &quot;تجميع&quot;. على مقارنة إعدادات صفحة 1، حدد &quot;ارتباط بيرسون&quot;، وترك غيرها من المعالم كما الافتراضي. في الصفحة 2، حدد &quot;UPGMA&quot;. ثم انقر فوق &quot;إنهاء&quot;. </li><li style=";text-align:right;direction:rtl"> الحصول على مؤامرة MDS باستخدام &quot;التحجيم متعدد الأبعاد ...&quot; الأمر في القائمة &quot;الإحصاء&quot;. </li></ol></li><li style=";text-align:right;direction:rtl"> مطابقة الذروة <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> انقر على نوع الطيف &quot;MALDI&quot; في &quot;تجارب&quot; لوحة. ثم حدد &quot;تخطيط&gt; مشاهدة الصورة&quot;. وتظهر الأطياف كما العصابات هلام. </li><li style=";text-align:right;direction:rtl"> أداء مطابقة ذروة باستخدام &quot;هل مطابقة ذروة&quot; الأمر في القائمة &quot;الأطياف&quot;. </li></ol></li><li style=";text-align:right;direction:rtl"> تحديد الطبقات الذروة <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> لتحليل المكون الرئيسي (PCA). تسليط الضوء على &quot;MALDI &quot;نوع التجربة في&quot; التجريبية &quot;لوحة واستخدام&quot; تحليل مكونات الرئيسية ... &quot;القيادة في&quot; القائمة الإحصائية &quot;لتنفيذ PCA. </li><li style=";text-align:right;direction:rtl"> أداء اتجاهين المجموعات. انقر على &quot;الاحصائيات&gt; التعدين ماتريكس&quot; ... في &quot;مقارنة&quot; نافذة. شدة القمم تتناسب مع الطبقات الذروة يتم تمثيل ألوان مختلفة (خريطة الحرارة). </li></ol></li></ol> 5. تحديد البكتيريا مع قاعدة البيانات المخصصة <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> تشابه طريقة المستندة إلى معامل <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> إنشاء المقارنة وتوليد dendrogram على أساس أطياف الشامل على مستوى &quot;تكرار الفني&quot; كما هو موضح في الخطوة 4.3.3. حفظ dendrogram للمقارنة التشابه. </li><li style=";text-align:right;direction:rtl"> تحديد الطيف الكتلي غير معروف، وانقر على &quot;تحليل&gt; تحديد الإدخالات المحددة&quot;. يظهر مربع الحوار تحديد الهوية. </li><li style=";text-align:right;direction:rtl"> حدد &quot;مقارنة على أساس&quot; نوع المصنف (أو classif المخزنةهيئة الإنصاف والمصالحة) وانقر على &quot;التالي&quot;. في الصفحة التالية، اختر dendrogram حفظها وعلى سبيل المقارنة المرجعية ومن ثم انقر فوق &quot;التالي&quot;. </li><li style=";text-align:right;direction:rtl"> اختيار &quot;التشابه الأساسي&quot; كطريقة تحديد ثم انقر فوق &quot;التالي&quot;. </li><li style=";text-align:right;direction:rtl"> اختيار &quot;التشابه الأقصى&quot;، كما طريقة التهديف. اكتب في قيم حدية مناسبة والقيم الفرق الحد الأدنى لكل معلمة ومن ثم انقر فوق &quot;التالي&quot;. </li><li style=";text-align:right;direction:rtl"> وبمجرد الانتهاء من الحسابات، يظهر إطار تحديد الهوية. في &quot;نتائج&quot; لوحة، يتم سرد أعضاء من قاعدة البيانات التي تطابق أفضل المجهول. </li><li style=";text-align:right;direction:rtl"> حفظ المشروع تحديد والتحقق من صحة الاستدلال باستخدام &quot;عبر التحقق من صحة التحليل&quot; القيادة في لوحة &quot;مشروع تحديد&quot;. </li></ol></li><li style=";text-align:right;direction:rtl"> محتمل طريقة القائم على العلامات البيولوجية <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> تحديد فئات الذروة. في الإطار &quot;مصفوفة تعدين&quot;، حدد مجموعات من قمم تقاسم الخصائص المشتركة وتحديد هذه القمم كما SPECIدروس المرورية الذروة (المؤشرات الحيوية المحتملة) باستخدام &quot;أطياف&gt; إدارة أنواع الطبقة الذروة ...&quot; في &quot;نافذة مقارنة&quot;. </li><li style=";text-align:right;direction:rtl"> هنا، وتحديد الطبقات الذروة محددة لعزل لجميع العزلات 15 لكل منهما. </li><li style=";text-align:right;direction:rtl"> حدد أطياف الشامل من المجاهيل وتطابق قمم هذه الأطياف إلى الطبقات الذروة محددة كما هو موضح سابقا. </li></ol></li></ol>

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R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Culture+conditions+and+sample+preparation+methods+affect+spectrum+quality+and+reproducibility+during+profiling+of+Staphylococcus+aureus+with+matrix-assisted+laser+desorption/ionization+time-of-flight+mass+spectrometry.">Culture conditions and sample preparation methods affect spectrum quality and reproducibility during profiling of Staphylococcus aureus with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.</a> Lett Appl Microbiol. 57 (2), 144-150 (2013).</li><li>Benagli, 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=A+rapid+MALDI-TOF+MS+identification+database+at+genospecies+level+for+clinical+and+environmental+Aeromonas+strains.">A rapid MALDI-TOF MS identification database at genospecies level for clinical and environmental Aeromonas strains.</a> Plos One. 7 (10), (2012).</li><li>Sauer, S., Kliem, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mass+spectrometry+tools+for+the+classification+and+identification+of+bacteria.">Mass spectrometry tools for the classification and identification of bacteria.</a> Nat Rev Microbiol. 8 (1), 74-82 (2010).</li><li>Bohme, K., 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=SpectraBank:+An+open+access+tool+for+rapid+microbial+identification+by+MALDI-TOF+MS+fingerprinting.">SpectraBank: An open access tool for rapid microbial identification by MALDI-TOF MS fingerprinting.</a> Electrophoresis. 33 (14), 2138-2142 (2012).</li><li>Walker, J., Fox, A. J., Edwards-Jones, V., Gordon, D. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intact+cell+mass+spectrometry+(ICMS)+used+to+type+methicillin-resistant+Staphylococcus+aureus:+media+effects+and+inter-laboratory+reproducibility.">Intact cell mass spectrometry (ICMS) used to type methicillin-resistant Staphylococcus aureus: media effects and inter-laboratory reproducibility.</a> J Microbiol Meth. 48 (2-3), 117-126 (2002).</li><li>Ruelle, V., El Moualij, B., Zorzi, W., Ledent, P., De Pauw, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+identification+of+environmental+bacterial+strains+by+matrix-assisted+laser+desorption/ionization+time-of-flight+mass+spectrometry.">Rapid identification of environmental bacterial strains by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.</a> Rapid Commun Mass Sp. 18 (18), 2013-2019 (2004).</li><li>Sedo, O., Sedlacek, I., Zdrahal, Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sample+Preparation+Methods+for+Maldi-MS+Profiling+of+Bacteria.">Sample Preparation Methods for Maldi-MS Profiling of Bacteria.</a> Mass Spectrom Rev. 30 (3), 417-434 (2011).</li><li>Swatkoski, S., Russell, S., Edwards, N., Fenselau, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+a+model+virus+using+residue-specific+chemical+cleavage+and+MALDI-TOF+mass+spectrometry.">Analysis of a model virus using residue-specific chemical cleavage and MALDI-TOF mass spectrometry.</a> Anal Chem. 79 (2), 654-658 (2007).</li><li>Freiwald, A., Sauer, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phylogenetic+classification+and+identification+of+bacteria+by+mass+spectrometry.">Phylogenetic classification and identification of bacteria by mass spectrometry.</a> Nat Protoc. 4 (5), 732-742 (2009).</li><li>Drevinek, M., Dresler, J., Klimentova, J., Pisa, L., Hubalek, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evaluation+of+sample+preparation+methods+for+MALDI-TOF+MS+identification+of+highly+dangerous+bacteria.">Evaluation of sample preparation methods for MALDI-TOF MS identification of highly dangerous bacteria.</a> Lett Appl Microbiol. 55 (1), 40-46 (2012).</li><li>Lasch, P., 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=MALDI-TOF+mass+spectrometry+compatible+inactivation+method+for+highly+pathogenic+microbial+cells+and+spores.">MALDI-TOF mass spectrometry compatible inactivation method for highly pathogenic microbial cells and spores.</a> Anal Chem. 80 (6), 2026-2034 (2008).</li><li>Usbeck, J. C., Kern, C. C., Vogel, R. F., Behr, J. <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+experimental+and+modelling+parameters+for+the+differentiation+of+beverage+spoiling+yeasts+by+Matrix-Assisted-Laser-Desorption/Ionization+Time-of-Flight+Mass+Spectrometry+(MALDI-TOF+MS)+in+response+to+varying+growth+conditions.">Optimization of experimental and modelling parameters for the differentiation of beverage spoiling yeasts by Matrix-Assisted-Laser-Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) in response to varying growth conditions.</a> Food Microbiol. 36 (2), 379-387 (2013).</li><li>Del Chierico, F., 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=MALDI-TOF+MS+proteomic+phenotyping+of+filamentous+and+other+fungi+from+clinical+origin.">MALDI-TOF MS proteomic phenotyping of filamentous and other fungi from clinical origin.</a> J Proteomics. 75 (11), 3314-3330 (2012).</li><li>Vitale, R., Roine, E., Bamford, D. H., Corcelli, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lipid+fingerprints+of+intact+viruses+by+MALDI-TOF/mass+spectrometry.">Lipid fingerprints of intact viruses by MALDI-TOF/mass spectrometry.</a> Bba-Mol Cell Biol L. 1831 (4), 872-879 (2013).</li><li>Zhang, L., Borror, C. M., Sandrin, T. 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+designed+experiments+approach+to+optimization+of+automated+data+acquisition+during+characterization+of+bacteria+with+MALDI-TOF+mass+spectrometry.">A designed experiments approach to optimization of automated data acquisition during characterization of bacteria with MALDI-TOF mass spectrometry.</a> Plos One. 9 (3), (2014).</li><li>Christner, M., Rohde, H., Wolters, M., Sobottka, I., Wegscheider, K., Aepfelbacher, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+identification+of+bacteria+from+positive+blood+culture+bottles+by+use+of+matrix-assisted+laser+desorption-ionization+time+of+flight+mass+spectrometry+fingerprinting.">Rapid identification of bacteria from positive blood culture bottles by use of matrix-assisted laser desorption-ionization time of flight mass spectrometry fingerprinting.</a> J ClinMicrobiol. 48 (5), 1584-1591 (2010).</li></ol>

Authors Vranckx and Janssens are employees of Applied Maths NV, the manufacturer of data analysis software used in this video. Applied Maths NV provided select software modules highlighted in this video as well as a portion of the publication costs associated with this video.

وأظهرت هذه التظاهرة الإجراءات التفصيلية لتوصيف وتحديد البكتيريا باستخدام MALDI-TOF MS وقاعدة بيانات مخصصة. وبالمقارنة مع الأساليب الجزيئية التقليدية، على سبيل المثال، طرق بصمة 16S rDNA التسلسل، يستند إلى MS-MALDI-TOF تسهيل التعرف أكثر سرعة من البكتيريا متنوعة. بسبب قوة لها، ويس?...

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has been shown to be a rapid and reliable tool for identification of bacteria at the genus, species, and in some cases, strain levels1-4. MALDI-TOF MS ionizes biological molecules (typically proteins) that originate from cell surfaces, intracellular membranes, and ribosomes from bacterial whole cells or protein extracts1,5. The resulting peaks form characteristic patterns or &#8220;fingerprints&#8221; of the bacteria analyzed1. Identification of bacteria is based on these mass-to-charge &#8220;fingerprints&#8221;. 
Two of the most commonly used identification strategies are library-based and bioinformatics-based strategies1. Library-based approaches involve comparing the mass spectra of unknowns to previously collected mass spectra of known bacteria in databases/libraries for identification. Commercially available software, such as BioNumerics, Biotyper, and SARAMIS software packages, as well as open source software tools, such as SpectraBank6, are available to facilitate the comparison and quantification of similarity between mass spectra of unknowns and reference bacteria. Bioinformatics-based approaches usually rely on fully sequenced genomes of bacteria for identification. In contrast to library-based approaches which do not involve identification of the biological nature of particular peaks, bioinformatics-based approaches involve protein identification1. 
The majority of recent MALDI fingerprint-based studies have used library-based approaches to identify bacteria1. Library-based approaches require construction of databases and comparison of the similarity between mass spectra. Studies show that many experimental procedures, such as medium3,7, cultivation time8, sample preparation method3, and matrix used9, affect the mass spectra obtained. Furthermore, some closely-related species and strains generate spectra with only subtle differences. Thus, library-based approaches require rigorously standardized procedures to generate highly reproducible mass spectra between replicates. Minor variations in protocols may compromise the efficacy of identification, especially at the subspecies and strain levels1,3,10. However, neither manufacturer-provided reference databases nor reported custom databases include visually documented procedures for database construction and/or application of a data analysis pipeline. For this reason, the objective of this work was to develop, apply, and demonstrate a comprehensive and detailed procedure for library-based bacterial identification using MALDI-TOF MS. 
In this demonstration, mass spectra of 15 bacteria isolated from a karstic environment (Kartchner Cavern, AZ, USA) were collected and imported into software to construct a model database. Data processing and the analysis pipeline were detailed using the model database. Finally, mass spectra of blind-coded bacteria which were randomly selected from these 15 bacteria were collected again and compared to the reference spectra in the model database for identification. Results show that bacteria can be correctly identified either based on similarity coefficients or potential biomarkers/peak classes.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>&#945;-cyano-4-hydroxy-cinnamic acid</td>
			<td>ACROS Organics</td>
			<td align="right">163440050</td>
			<td>&#8805; 97%, CAS 28168-41-8</td>
		</tr>
		<tr>
			<td>MALDI calibration kit</td>
			<td>Aigma-Aldrich</td>
			<td>MSCAL1-1KT</td>
			<td>This kit also contains acetonitrile, trifluoroacetic acid , sinapinic acid, etc.</td>
		</tr>
		<tr>
			<td>MALDI target plate</td>
			<td>Bruker Daltonics</td>
			<td align="right">280800</td>
			<td>Polished Steel</td>
		</tr>
		<tr>
			<td>Bruker Microflex LRF MALDI-TOF mass spectrometer</td>
			<td>Bruker Daltonics</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Bruker FlexControl software</td>
			<td>Bruker Daltonics</td>
			<td></td>
			<td>version 3.0</td>
		</tr>
		<tr>
			<td>Bruker FlexAnalysis software</td>
			<td>Bruker Daltonics</td>
			<td></td>
			<td>version 3.0</td>
		</tr>
		<tr>
			<td>Bionumerics software</td>
			<td>Applied Maths</td>
			<td></td>
			<td>version 7.1</td>
		</tr>
	</tbody>
</table>

use of maldi-tof mass spectrometry and a custom database to characterize bacteria indigenous to a unique cave environment (kartchner caverns, az, usa)

MALDI-TOF mass spectrometry has been shown to be a rapid and reliable tool for identification of bacteria at the genus and species, and in some cases, strain levels. Commercially available and open source software tools have been developed to facilitate identification; however, no universal/standardized data analysis pipeline has been described in the literature. Here, we provide a comprehensive and detailed demonstration of bacterial identification procedures using a MALDI-TOF mass spectrometer. Mass spectra were collected from 15 diverse bacteria isolated from Kartchner Caverns, AZ, USA, and identified by 16S rDNA sequencing. Databases were constructed in BioNumerics 7.1. Follow-up analyses of mass spectra were performed, including cluster analyses, peak matching, and statistical analyses. Identification was performed using blind-coded samples randomly selected from these 15 bacteria. Two identification methods are presented: similarity coefficient-based and biomarker-based methods. Results show that both identification methods can identify the bacteria to the species level.

<html> قواعد البيانات التي شيدت في هذه المظاهرة كان أربعة مستويات، من أعلى إلى أدنى مستوى، بما في ذلك &quot;جميع المستويات&quot;، &quot;الأنواع&quot;، &quot;تكرار البيولوجي&quot; و &quot;تكرار الفني&quot;، على التوالي (الشكل 1A). وتضمن مستوى &quot;التقني تكرار&quot; جميع أطياف preprocessed من م?...

Watch this Scientific Journal Video about Use of MALDI-TOF Mass Spectrometry and a Custom Database to Characterize Bacteria Indigenous to a Unique Cave Environment Kartchner Caverns, AZ, USA at JoVE.c

Use of MALDI-TOF Mass Spectrometry and a Custom Database to Characterize Bacteria Indigenous to a Unique Cave Environment Kartchner Caverns, AZ, USA

This work details procedures for rapid identification of bacteria using MALDI-TOF MS. The identification procedures include spectrum acquisition, database construction, and follow up analyses. Two identification methods, similarity coefficient-based and biomarker-based methods, are presented.

استخدام MALDI-TOF الطيف الكتلي وقاعدة بيانات مخصصة لتوصيف البكتيريا الأصلية إلى فريد كهف البيئة (Kartchner الكهوف، AZ، ​​الولايات المتحدة الأمريكية)

MALDI-TOF mass spectrometry has been shown to be a rapid and reliable tool for identification of bacteria at the genus and species, and in some cases, ...

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Use of MALDI-TOF Mass Spectrometry and a Custom Database to Characterize Bacteria Indigenous to a Unique Cave Environment (Kartchner Caverns, AZ, USA)

13.9K Views.  Arizona State University. This work details procedures for rapid identification of bacteria using MALDI-TOF MS. The identification procedures include spectrum acquisition, database construction, and follow up analyses. Two identification methods, similarity coefficient-based and biomarker-based methods, are presented. 

Video: Use of MALDI-TOF Mass Spectrometry and a Custom Database to Characterize Bacteria Indigenous to a Unique Cave Environment Kartchner Caverns, AZ, USA

MALDI Sample Preparation: the Ultra Thin Layer Method

This video demonstrates the preparation of an ultra-thin matrix/analyte layer for analyzing peptides and proteins by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) 1,2. The ultra-thin layer method involves the production of a substrate layer of matrix crystals (alpha-cyano-4-hydroxycinnamic acid) on the sample plate, which serves as a seeding ground for subsequent crystallization of a matrix/analyte mixture. Advantages of the ultra-thin layer method over other sample deposition approaches (e.g. dried droplet) are that it provides (i) greater tolerance to impurities such as salts and detergents, (ii) better resolution, and (iii) higher spatial uniformity. This method is especially useful for the accurate mass determination of proteins. The protocol was initially developed and optimized for the analysis of membrane proteins and used to successfully analyze ion channels, metabolite transporters, and receptors, containing between 2 and 12 transmembrane domains 2. Since the original publication, it has also shown to be equally useful for the analysis of soluble proteins. Indeed, we have used it for a large number of proteins having a wide range of properties, including those with molecular masses as high as 380 kDa 3. It is currently our method of choice for the molecular mass analysis of all proteins. The described procedure consistently produces high-quality spectra, and it is sensitive, robust, and easy to implement.

This video demonstrates the preparation of an ultra-thin matrix/analyte layer for analyzing peptides and proteins by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS).

MALDI تحضير العينة : الترا أسلوب طبقة رقيقة

This video demonstrates the preparation of an ultra-thin matrix/analyte layer for analyzing peptides and proteins by Matrix-Assisted Laser Desorption ...

Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry

There is a great need for quantitative assays in measuring proteins. Traditional sandwich immunoassays, largely considered the gold standard in quantitation, are associated with a high cost, long lead time, and are fraught with drawbacks (e.g. heterophilic antibodies, autoantibody interference, 'hook-effect').1 An alternative technique is affinity enrichment of peptides coupled with quantitative mass spectrometry, commonly referred to as SISCAPA (Stable Isotope Standards and Capture by Anti-Peptide Antibodies).2 In this technique, affinity enrichment of peptides with stable isotope dilution and detection by selected/multiple reaction monitoring mass spectrometry (SRM/MRM-MS) provides quantitative measurement of peptides as surrogates for their respective proteins. SRM/MRM-MS is well established for accurate quantitation of small molecules 3, 4 and more recently has been adapted to measure the concentrations of proteins in plasma and cell lysates.5-7 To achieve quantitation of proteins, these larger molecules are digested to component peptides using an enzyme such as trypsin. One or more selected peptides whose sequence is unique to the target protein in that species (i.e. "proteotypic" peptides) are then enriched from the sample using anti-peptide antibodies and measured as quantitative stoichiometric surrogates for protein concentration in the sample. Hence, coupled to stable isotope dilution (SID) methods (i.e. a spiked-in stable isotope labeled peptide standard), SRM/MRM can be used to measure concentrations of proteotypic peptides as surrogates for quantification of proteins in complex biological matrices. The assays have several advantages compared to traditional immunoassays. The reagents are relatively less expensive to generate, the specificity for the analyte is excellent, the assays can be highly multiplexed, enrichment can be performed from neat plasma (no depletion required), and the technique is amenable to a wide array of proteins or modifications of interest.8-13 In this video we demonstrate the basic protocol as adapted to a magnetic bead platform.

Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA) couples affinity enrichment of peptides with stable isotope dilution mass spectrometry (MRM-MS) to provide quantitative measurement of peptides as surrogates for their respective proteins. Here we describe the protocol using magnetic particles in a partially automated format.

الكمي من البروتينات عن طريق التخصيب الببتيد Immunoaffinity اقترن الطيف الكتلي

There is a great need for quantitative assays in measuring proteins. Traditional sandwich immunoassays, largely considered the gold standard in ...

Amide Hydrogen/Deuterium Exchange &amp; MALDI-TOF Mass Spectrometry Analysis of Pak2 Activation

Amide hydrogen/deuterium exchange (H/D exchange) coupled with mass spectrometry has been widely used to analyze the interface of protein-protein interactions, protein conformational changes, protein dynamics and protein-ligand interactions. H/D exchange on the backbone amide positions has been utilized to measure the deuteration rates of the micro-regions in a protein by mass spectrometry1,2,3. The resolution of this method depends on pepsin digestion of the deuterated protein of interest into peptides that normally range from 3-20 residues. Although the resolution of H/D exchange measured by mass spectrometry is lower than the single residue resolution measured by the Heteronuclear Single Quantum Coherence (HSQC) method of NMR, the mass spectrometry measurement in H/D exchange is not restricted by the size of the protein4. H/D exchange is carried out in an aqueous solution which maintains protein conformation. We provide a method that utilizes the MALDI-TOF for detection2, instead of a HPLC/ESI (electrospray ionization)-MS system5,6. The MALDI-TOF provides accurate mass intensity data for the peptides of the digested protein, in this case protein kinase Pak2 (also called &gamma;-Pak). Proteolysis of Pak 2 is carried out in an offline pepsin digestion. This alternative method, when the user does not have access to a HPLC and pepsin column connected to mass spectrometry, or when the pepsin column on HPLC does not result in an optimal digestion map, for example, the heavily disulfide-bonded secreted Phospholipase A2 (sPLA2). Utilizing this method, we successfully monitored changes in the deuteration level during activation of Pak2 by caspase 3 cleavage and autophosphorylation7,8,9.

MALDI-TOF mass spectrometry was successfully utilized to monitor the amide hydrogen/deuterium exchange in protein kinase Pak2 activation.

أميد الهيدروجينية / الديتريوم الطيف الكتلي تبادل و- TOF MALDI تحليل Pak2 التنشيط

Amide hydrogen/deuterium exchange (H/D exchange) coupled with mass spectrometry has been widely used to analyze the interface of protein-protein ...

A Fluorescence-based Exonuclease Assay to Characterize DmWRNexo, Orthologue of Human Progeroid WRN Exonuclease, and Its Application to Other Nucleases

WRN exonuclease is involved in resolving DNA damage that occurs either during DNA replication or following exposure to endogenous or exogenous genotoxins. It is likely to play a role in preventing accumulation of recombinogenic intermediates that would otherwise accumulate at transiently stalled replication forks, consistent with a hyper-recombinant phenotype of cells lacking WRN. In humans, the exonuclease domain comprises an N-terminal portion of a much larger protein that also possesses helicase activity, together with additional sites important for DNA and protein interaction. By contrast, in Drosophila, the exonuclease activity of WRN (DmWRNexo) is encoded by a distinct genetic locus from the presumptive helicase, allowing biochemical (and genetic) dissection of the role of the exonuclease activity in genome stability mechanisms. Here, we demonstrate a fluorescent method to determine WRN exonuclease activity using purified recombinant DmWRNexo and end-labeled fluorescent oligonucleotides. This system allows greater reproducibility than radioactive assays as the substrate oligonucleotides remain stable for months, and provides a safer and relatively rapid method for detailed analysis of nuclease activity, permitting determination of nuclease polarity, processivity, and substrate preferences.

Exonucleases play critical roles in ensuring genome stability. Loss of WRN exonuclease function results in premature aging. Studying substrates and other requirements of the nuclease in vitro can help elucidate its role in vivo. Here we demonstrate a rapid and reproducible fluorescence-based assay to measure its nuclease activity.

WRN exonuclease is involved in resolving DNA damage that occurs either during DNA replication or following exposure to endogenous or exogenous genotoxins. ...

Capture Compound Mass Spectrometry - A Powerful Tool to Identify Novel c-di-GMP Effector Proteins

Considerable progress has been made during the last decade towards the identification and characterization of enzymes involved in the synthesis (diguanylate cyclases) and degradation (phosphodiesterases) of the second messenger c-di-GMP. In contrast, little information is available regarding the molecular mechanisms and cellular components through which this signaling molecule regulates a diverse range of cellular processes. Most of the known effector proteins belong to the PilZ family or are degenerated diguanylate cyclases or phosphodiesterases that have given up on catalysis and have adopted effector function. Thus, to better define the cellular c-di-GMP network in a wide range of bacteria experimental methods are required to identify and validate novel effectors for which reliable in silico predictions fail.
We have recently developed a novel Capture Compound Mass Spectrometry (CCMS) based technology as a powerful tool to biochemically identify and characterize c-di-GMP binding proteins. This technique has previously been reported to be applicable to a wide range of organisms1. Here we give a detailed description of the protocol that we utilize to probe such signaling components. As an example, we use Pseudomonas aeruginosa, an opportunistic pathogen in which c-di-GMP plays a critical role in virulence and biofilm control. CCMS identified 74% (38/51) of the known or predicted components of the c-di-GMP network. This study explains the CCMS procedure in detail, and establishes it as a powerful and versatile tool to identify novel components involved in small molecule signaling.

The ubiquitous second messenger c-di-GMP controls growth and behavior of many bacteria. We have developed a novel Capture Compound Mass Spectrometry based technology to biochemically identify and characterize c-di-GMP binding proteins in virtually any bacterial species.

التقاط الطيف الكتلي - أداة قوية لتحديد رواية ج-دي-GMP المستجيب البروتينات

Considerable progress has been made during the last decade towards the identification and characterization of enzymes involved in the synthesis ...

Using Digital Image Correlation to Characterize Local Strains on Vascular Tissue Specimens

Characterization of the mechanical behavior of biological and engineered soft tissues is a central component of fundamental biomedical research and product development. Stress-strain relationships are typically obtained from mechanical testing data to enable comparative assessment among samples and in some cases identification of constitutive mechanical properties. However, errors may be introduced through the use of average strain measures, as significant heterogeneity in the strain field may result from geometrical non-uniformity of the sample and stress concentrations induced by mounting/gripping of soft tissues within the test system. When strain field heterogeneity is significant, accurate assessment of the sample mechanical response requires measurement of local strains. This study demonstrates a novel biomechanical testing protocol for calculating local surface strains using a mechanical testing device coupled with a high resolution camera and a digital image correlation technique. A series of sample surface images are acquired and then analyzed to quantify the local surface strain of a vascular tissue specimen subjected to ramped uniaxial loading. This approach can improve accuracy in experimental vascular biomechanics and has potential for broader use among other native soft tissues, engineered soft tissues, and soft hydrogel/polymeric materials. In the video, we demonstrate how to set up the system components and perform a complete experiment on native vascular tissue.

We describe the use of digital image correlation to characterize the local surface strain field on vascular tissue samples subjected to uniaxial tensile testing. These measurements facilitate precise quantification of the sample mechanical response and the generation of constitutive stress-strain relations.

باستخدام ارتباط صورة رقمية لوصف سلالات المحلية على الأوعية الدموية عينات الأنسجة

Characterization of the mechanical behavior of biological and engineered soft tissues is a central component of fundamental biomedical research and ...

Identification of MyoD Interactome Using Tandem Affinity Purification Coupled to Mass Spectrometry

Skeletal muscle terminal differentiation starts with the commitment of pluripotent mesodermal precursor cells to myoblasts. These cells have still the ability to proliferate or they can differentiate and fuse into multinucleated myotubes, which maturate further to form myofibers. Skeletal muscle terminal differentiation is orchestrated by the coordinated action of various transcription factors, in particular the members of the Muscle Regulatory Factors or MRFs (MyoD, Myogenin, Myf5, and MRF4), also called the myogenic bHLH transcription factors family. These factors cooperate with chromatin-remodeling complexes within elaborate transcriptional regulatory network to achieve skeletal myogenesis. In this, MyoD is considered the master myogenic transcription factor in triggering muscle terminal differentiation. This notion is strengthened by the ability of MyoD to convert non-muscle cells into skeletal muscle cells. Here we describe an approach used to identify MyoD protein partners in an exhaustive manner in order to elucidate the different factors involved in skeletal muscle terminal differentiation. The long-term aim is to understand the epigenetic mechanisms involved in the regulation of skeletal muscle genes, i.e., MyoD targets. MyoD partners are identified by using Tandem Affinity Purification (TAP-Tag) from a heterologous system coupled to mass spectrometry (MS) characterization, followed by validation of the role of relevant partners during skeletal muscle terminal differentiation. Aberrant forms of myogenic factors, or their aberrant regulation, are associated with a number of muscle disorders: congenital myasthenia, myotonic dystrophy, rhabdomyosarcoma and defects in muscle regeneration. As such, myogenic factors provide a pool of potential therapeutic targets in muscle disorders, both with regard to mechanisms that cause disease itself and regenerative mechanisms that can improve disease treatment. Thus, the detailed understanding of the intermolecular interactions and the genetic programs controlled by the myogenic factors is essential for the rational design of efficient therapies.

MyoD is a myogenic transcription factor with a strong capacity to induce myogenic transdifferentiation of many fully differentiated non-muscle cell lines. The epigenetic mechanisms involved in this transdifferentiation are largely unknown. Here we describe a double-affinity purification method followed by mass spectrometry to exhaustively characterize MyoD partners.

تحديد MyoD Interactome عن طريق جنبا الى جنب الانجذاب تنقية جانب لقياس الطيف الكتلي

Skeletal muscle terminal differentiation starts with the commitment of pluripotent mesodermal precursor cells to myoblasts. These cells have still the ...

Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis

Nucleosomes are the smallest structural unit of chromatin, composed of 147 base pairs of DNA wrapped around an octamer of histone proteins. Histone function is mediated by extensive post-translational modification by a myriad of nuclear proteins. These modifications are critical for nuclear integrity as they regulate chromatin structure and recruit enzymes involved in gene regulation, DNA repair and chromosome condensation. Even though a large part of the scientific community adopts antibody-based techniques to characterize histone PTM abundance, these approaches are low throughput and biased against hypermodified proteins, as the epitope might be obstructed by nearby modifications. This protocol describes the use of nano liquid chromatography (nLC) and mass spectrometry (MS) for accurate quantification of histone modifications. This method is designed to characterize a large variety of histone PTMs and the relative abundance of several histone variants within single analyses. In this protocol, histones are derivatized with propionic anhydride followed by digestion with trypsin to generate peptides of 5 - 20 aa in length. After digestion, the newly exposed N-termini of the histone peptides are derivatized to improve chromatographic retention during nLC-MS. This method allows for the relative quantification of histone PTMs spanning four orders of magnitude.

This protocol outlines a fully integrated workflow for characterizing histone post-translational modifications using mass spectrometry (MS). The workflow includes histone purification from cell cultures or tissues, histone derivatization and digestion, MS analysis using nano-flow liquid chromatography and instructions for data analysis. The protocol is designed for completion within 2 - 3 days.

سير العمل كاملا لتحليل هيستون التعديلات بعد متعدية عن طريق أسفل إلى أعلى الطيف الكتلي: من هيستون استخراج لتحليل البيانات

Nucleosomes are the smallest structural unit of chromatin, composed of 147 base pairs of DNA wrapped around an octamer of histone proteins. Histone ...

At-Risk Butterfly Captive Propagation Programs to Enhance Life History Knowledge and Effective Ex Situ Conservation Techniques

Improving knowledge of ex situ best practices for at-risk butterflies is important for generating successful conservation and recovery program outcomes. Research on such captive populations can also yield valuable data to address key information gaps about the behavior, life history, and ecology of the target taxa. We describe a protocol for captive propagation of the federally endangered Cyclargus thomasi bethunebakeri that can be used as a model for other at-risk butterfly ex situ programs, especially those in the family Lycaenidae. We further provide a simple and straightforward protocol for recording various life history metrics that can be useful for informing ex situ methodologies as well as adapted for laboratory studies of other lepidoptera.

Here, we present protocols for 1) the laboratory captive propagation of the federally endangered Miami blue butterfly (Cyclargus thomasi bethunebakeri), and 2) assessing basic life history information such as immature development time and number of larval stadia. Both methods can be adapted for use with other ex situ conservation programs.

برامج نشر الفراشات الأسيرة المعرضة للخطر لتعزيز معرفة تاريخ الحياة وتقنيات الحفظ الفعالة خارج الموقع

Improving knowledge of ex situ best practices for at-risk butterflies is important for generating successful conservation and recovery program outcomes. ...

Mass Spectrometry Analysis to Identify Ubiquitylation of EYFP-tagged CENP-A (EYFP-CENP-A)

Studying the structure and the dynamics of kinetochores and centromeres is important in understanding chromosomal instability (CIN) and cancer progression. How the chromosomal location and function of a centromere (i.e., centromere identity) are determined and participate in accurate chromosome segregation is a fundamental question. CENP-A is proposed to be the non-DNA indicator (epigenetic mark) of centromere identity, and CENP-A ubiquitylation is required for CENP-A deposition at the centromere, inherited through dimerization between cell division, and indispensable to cell viability.
Here we describe mass spectrometry analysis to identify ubiquitylation of EYFP-CENP-A K124R mutant suggesting that ubiquitylation at a different lysine is induced because of the EYFP tagging in the CENP-A K124R mutant protein. Lysine 306 (K306) ubiquitylation in EYFP-CENP-A K124R was successfully identified, which corresponds to lysine 56 (K56) in CENP-A through mass spectrometry analysis. A caveat is discussed in the use of GFP/EYFP or the tagging of high molecular weight protein as a tool to analyze the function of a protein. Current technical limit is also discussed for the detection of ubiquitylated bands, identification of site-specific ubiquitylation(s), and visualization of ubiquitylation in living cells or a specific single cell during the whole cell cycle.
The method of mass spectrometry analysis presented here can be applied to human CENP-A protein with different tags and other centromere-kinetochore proteins. These combinatory methods consisting of several assays/analyses could be recommended for researchers who are interested in identifying functional roles of ubiquitylation.

Mass Spectrometry Analysis to Identify Ubiquitylation of EYFP-tagged CENP-A EYFP-CENP-A

CENP-A ubiquitylation is an important requirement for CENP-A deposition at the centromere, inherited through dimerization between cell division, and indispensable to cell viability. Here we describe mass spectrometry analysis to identify ubiquitylation of EYFP-tagged CENP-A (EYFP-CENP-A) protein.

استخدام MALDI-TOF الطيف الكتلي وقاعدة بيانات مخصصة لتوصيف البكتيريا الأصلية إلى فريد كهف البيئة (Kartchner الكهوف، AZ، ​​الولايات المتحدة الأمريكية)

استخدام MALDI-TOF الطيف الكتلي وقاعدة بيانات مخصصة لتوصيف البكتيريا الأصلية إلى فريد كهف البيئة (Kartchner الكهوف، AZ، الولايات المتحدة الأمريكية)