원자력 과학 및 공학의 호주 연구소의 지원 인정받고 있습니다. TCK는 AINSE 보너스받는했다. Epigenomic 의학 연구소는 국민 건강과 호주의 의료 연구위원회 (566559)에 의해 지원됩니다. LM은 멜버른 연구 (멜버른 대학)와 바이오 메디컬 이미징 CRC의 보조 장학금으로 지원됩니다. 모나 마이크로 이미징의 지원 (DRS 스티븐 코디 Iśka 카마 이클)이 작품 소중한했다. MMT는 국립 보건원에서 박사 올가 Sedelnikova에서 전문가 지원 및 조언 감사합니다.

조직 <ol><li> 최적의 절삭 온도 (-10 월) 4,583 화합물의 금형에 포함된 폐 조직, CM Leica 1,950 그라 이오 스탯을 사용하여 (5 μm의) sectioned되었으며 폴리 - L - 라이신 슬라이드에 장착. </li></ol> 냉동 샘플은 머독 아동 연구소에서 박사 사이먼 로이스 얻은되었습니다. 폐 조직은 치료 Balb / C 마우스에서 인간 천식 6 병적인 많은 기능을 보여줍니다 만성 알레르기기도 질환의 마우스 모델에서 얻은 것입니다. 동물 실험은 과학적 목적으로 실험 동물의 보호 및 사용에 대한 실천의 호주 강령을 준수 머독 아동 연구소의 동물 윤리위원회에 의해 명시된 지침과 규정에 따라 수행되었다. <ol start="2"><li> 제는 1 시간 동안 실온에서 건조 공기를 허용되었다. </li></ol> Immunofluorescence 염색법 <ol><li> 제 2 % (W / V) 인산의 paraformaldehyde 20 분 동안 호수 (PBS)를 버퍼로 고정되었습니다. </li><li> 섹션 15 분 각각에 대해 PBS에 두 세척과 equilibrated되었습니다. </li><li> 제 10 분마다 PBS에 세 세척 다음 20 분 70 % 에탄올 (-20 ° C로 냉각)과 치료를했다. </li></ol> 이 시점에서 슬라이드는 최대 2 주 4 ° C에서 밀폐 용기에 저장할 수 있습니다. <ol start="4"><li> 제 10 분마다 PBS로 세 번 씻어 후 갓 PBS는 0.5 % 트윈 - 20와 0.1 %를 포함하는 8 %의 BSA가 포함된 PBS에서 준비 100μL로 차단되었습니다 트리톤 실온에서 1 시간을위한 X - 100 (PBS - TT) . 모든 incubations은 humidified 얼룩 트러프에서 수행되었다. </li><li> 제 5 분간 PBS - TT와 세탁되었고 소수성 둘레는 자궁 펜으로 조직 주위에 표시되었다. </li><li> 초과 버퍼 밀고되었으며 기본 토끼 polyclonal 방지 γH2AX 항체 (PBS에 1 % BSA에 1:500 희석, Millipore)의 100μl은 상온에서 2 시간 보육에 대한 각 섹션에 추가되었습니다. 기본 항체와 배양 4에서 하룻밤을 수행할 수 있습니다 ° C. 자세한 증거를 들어, 그 γH2AX foci가 DSBs을 대표, DSB 복구 단백질을 인식 차 항체도 사용할 수 있습니다. 예를 들어, γH2AX 및 phospho - ATM의 공동 지방화는 일반적으로 사용되는 조합입니다. </li><li> 어둠 속에서 실온에서 1 시간, 섹션은 5 분마다 PBS - TT 두 번 씻어 및 보조 항체의 100μl (Invitrogen 알렉사 플루어 488 염소 안티 - 토끼 IgG가 1퍼센트 BSA에서 1:500 희석)와 incubated되었습니다 . (희석 항체가 절차를 통해 어둠에 보관했다). </li><li> 제 5 분마다 PBS - TT와 세 번 씻어 37시 30 분에 대한 0.5mg/mL RNAse ° C.와 incubated되었습니다 </li><li> counterstaining 및 장착 원자력은 propidium 요오드화물을 포함하는 제품 Vectashield 매체로 수행되었다. </li><li> 슬라이드는 매니큐어로 밀봉하고 ° C 어둠 속에서 분석하기 전에 4 박 저장되었습니다. </li></ol> 현미경 / 분석 <ol><li> (- 알렉사 플루어 488 염소 안티 - 토끼 IgG γH2AX)와 PI (543 NM) 레이저 자이스 혈구 LSM510 메타 공촛점 현미경은 표준 GFP를 사용하여 이미지를 획득하는 데 사용되었다. </li></ol> 이미지는 0.5 μm의의 스텝 크기와 Z - 시리즈 패턴에 인수했다. 분석하는 동안, 개인 비행기는 deconvoluted 및 foci의 중복을 최소화하기 위해 최대 예상 이미지를 생산 쌓인했다. 이전 입자 개수에 최대 예상 이미지를 만드는 방법은 얇은 섹션 (예 : 5μm)이 사용되며 배경 얼룩이 하찮은 것은 어디 있죠 상황에서만 사용해야합니다. 큰 배경 두꺼운 부분을 분석해야합니다 어디로 볼트와 Cordelieres (2006)에 의해 설명 같은 3D 개체 카운터와 같은 좀 더 복잡한 분석은 7 사용해야합니다. <ol start="2"><li> Metamorph (분자 디바이스, 미국)는 foci의 번호를 quantitate 합병 (빨간색과 초록색) 이미​​지를 만드는 데 사용되었다. </li></ol> Metamorph는 조직 섹션 foci가 높은 정확도 (눈으로) 수동으로 계산됩니다를 사용하여 일반적으로 때 foci 번호를 quantitate하는 데 사용할 수 있지만. 관심의 특정 세포 유형의 인스턴스 폐 상피 세포, quantitation에 대해 선택할 수 있습니다. 이것은 조직학 및 haematoxylin 및 eosin 스테인드 시리얼 섹션을 참조로 기반을 할 수 있습니다.

<ol>
	<li>Rogakou, E. P., Boon, C., Redon, C., Bonner, W. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Megabase+chromatin+domains+involved+in+DNA+double-strand+breaks+in+vivo.">Megabase chromatin domains involved in DNA double-strand breaks in vivo.</a> J. Cell Biol. 146, 905-916 (1999).</li><li>Bonner, W. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gamma+H2AX+and+cancer.">Gamma H2AX and cancer.</a> Nature Reviews Cancer. 8 (12), 957-967 (2008).</li><li>Dickey, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=H2AX:+functional+roles+and+potential+applications.">H2AX: functional roles and potential applications.</a> Chromosoma. 118 (6), 683-692 (2009).</li><li>Bhogal, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Late+residual+gamma-H2AX+foci+in+murine+skin+are+dose+responsive+and+predict+radiosensitivity+in+vivo.">Late residual gamma-H2AX foci in murine skin are dose responsive and predict radiosensitivity in vivo.</a> Radiat Res. 173 (1), 1-9 (2010).</li><li>Redon, C. E., Dickey, J. S., Bonner, W. M., Sedelnikova, O. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=gamma-H2AX+as+a+biomarker+of+DNA+damage+induced+by+ionizing+radiation+in+human+peripheral+blood+lymphocytes+and+artificial+skin.">gamma-H2AX as a biomarker of DNA damage induced by ionizing radiation in human peripheral blood lymphocytes and artificial skin.</a> Adv Space Res. 43 (8), 1171-1178 (2009).</li><li>Locke, N. R., Royce, S. G., Wainewright, J. S., Samuel, C. S., Tang, M. L., L, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+airway+remodeling+in+acute,+subacute,+and+chronic+models+of+allergic+airways+disease.">Comparison of airway remodeling in acute, subacute, and chronic models of allergic airways disease.</a> Am J Respir Cell Mol Biol. 36 (5), 625-632 (2007).</li><li>Bolte, S. &. a. m. p. ;. a. m. p., Cordelieres, F. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+guided+tour+into+subcellular+colocalization+analysis+in+light+microscopy.">A guided tour into subcellular colocalization analysis in light microscopy.</a> J Microsc. 224 (Pt 3), 213-232 (2006).</li></ol>

관심 없음 충돌 선언하지 않습니다.

우리가 치료 Balb / C 마우스에서와 만성 알레르기기도 질환의 마우스 모델에서 마우스 폐 조직을 사용하는이 예제의 목적을 위해. 우리는 치료 부분에 비해 손상된 폐에서 관찰 약간 높은 평균과 셀 당 foci의 숫자의 차이를 quantitated. 특히, quantitation는 각각의 치료 조직 및 만성 알레르기기도 질환의 조직에서 / 셀 당 6.5 foci 및 9.4 foci 당 / 셀 (항목 당 20의 세포 수동으로 계산) 지적했다. 그러나, 마우스 폐 모델 DSBs을 유발하는 것으로 알려져 예 : 나프탈렌에 대한 DSB - 유도 요원의 사용, 높은 foci 번호를 얻을 것입니다. 사실,이 프로토콜은 대부분의 조직에 이온화 방사선의 영향의 조사에 적합합니다, γH2AX foci 번호와 해상도 측면에서보다 눈에 띄는 결과는 이온화 방사선을 사용하는 경우 얻을 수 있습니다. 이곳은 X - 레이에 다음과 같은 노출이 빠르게 γH2AX foci 양식 및 foci 번호가 30-60분 2 사이의 최대에 도달 것이 알려져 있습니다. 따라서 1 시간 시간 포인트 (사후 조사)은 초기 DSB 형성과 DNA 복구를 모니터링하는 데 사용할 수있는 더 이상 시간 (일반적으로 최대 48 시간) 평가에 이상적입니다. 전체 조직에 γH2AX의 quantitation는 DSB 형성 및 수리를 모니터링하는 데 유용합니다. 이외 이온화 방사선의 맥락에서 그 유틸리티에서, 방법은 DSB가 - 유도하는 다양한 조직에서 화합물, 예를 들어 같은 doxorubicin과 같이 일반적으로 사용되는 anticancer anthracyclines가 DSBs를 일으키는 것으로 알려져 있습니다의 효능 평가에 적용할 수 있으며, 잠재적 모니터 반응 산소 종 - 중재 DSBs에 의해 특징 다양한 pathologies. 중요한 것은,이 프로토콜은 다른 마우스 조직에 적합합니다.

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		<div>
		<table border="1">
		<thead>
		<tr>
		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
		</thead>
		<tbody>
		
<tr>
<td>Bovine Serum Albumin (BSA)</td>
<td>&nbsp;</td>
<td>Sigma-Aldrich</td>
<td>A7906</td>
<td>BSA (1%) is used to block any non-specific antibody binding. Primary and secondary antibodies are diluted in BSA.</td>
</tr>
<tr>
<td>PBS (without Ca2+ and Mg2+)</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>17-517Q</td>
<td>&nbsp;</td>
<tr>
<td>Optimal Cutting Temperature (OCT) Compound 4583</td>
<td>&nbsp;</td>
<td>Tissue-Tek</td>
<td>4583</td>
<td>&nbsp;</td>
<tr>
<td>Superfrost Plus</td>
<td>Polysine slides</td>
<td>Menzel-Gl&auml;ser, Germany</td>
<td>SF41296SP</td>
<td>Electrostatically attracts frozen tissue sections and reduces the need for additional coatings and adhesives.</td>
</tr>
<tr>
<td>Tween 20</td>
<td>Reagent</td>
<td>Calbiochem</td>
<td>655205</td>
<td>Tween 20 (0.5%), is a detergent to permeabilise cells</td>
</tr>
<tr>
<td>Triton X-100</td>
<td>Reagent</td>
<td>Sigma-Aldrich</td>
<td>T8787</td>
<td>Triton X-100 (0.1%) used to permeabilise cells.</td>
</tr>
<tr>
<td>Paraformaldehyde</td>
<td>Reagent</td>
<td>Sigma-Aldrich</td>
<td>158127</td>
<td>&nbsp;</td>
<tr>
<td>Anti-phospho-&gamma;H2AX (rabbit polyclonal antibody)</td>
<td>Primary Antibody</td>
<td>Upstate, USA</td>
<td>07-164</td>
<td>Dilution of primary antibody (1:500), in 1% BSA.</td>
</tr>
<tr>
<td>Alexa Fluor 488 goat anti-rabbit IgG (H+L)</td>
<td>Secondary Antibody</td>
<td>Invitrogen</td>
<td>A-11008</td>
<td>Dilution of secondary antibody (1:500), in 1% BSA.</td>
</tr>
<tr>
<td>Ethanol (70%)</td>
<td>&nbsp;</td>
<td>Thermo Fisher</td>
<td>BSPEL316</td>
<td>&nbsp;</td>
<tr>
<td>RNAse A</td>
<td>Reagent</td>
<td>Qiagen </td>
<td>19101</td>
<td>&nbsp;</td>
<tr>
<td>Vectashield PI</td>
<td>Reagent</td>
<td>Vector Laboratories</td>
<td>H-1300</td>
<td>A glycerol based mounting medium containing propidium iodide (a red nuclear stain).This medium must be used with an oil based lense that matches its refractive index. 
Note: DNA stain commonly used: 4,6-diamidino-2-phenylindole dihydrochloride (DAPI). Can only be used with microscopes with the appropriate excitation laser.</td>
</tr>
<tr>
<td>Mini PAP Pen</td>
<td>&nbsp;</td>
<td>Invitrogen, USA</td>
<td>008877</td>
<td>&nbsp;</td>
<tr>
<td>Coverslips (22x50mm)</td>
<td>&nbsp;</td>
<td>Menzel-Gl&auml;ser, Germany</td>
<td>CS2250100</td>
<td>&nbsp;</td>
<tr>
<td>Coplin Jar, glass</td>
<td>&nbsp;</td>
<td>Grale Scientific P/L</td>
<td>1771-OG</td>
<td>&nbsp;</td>
<tr>
<td>Staining Trough</td>
<td>&nbsp;</td>
<td>Grale Scientific P/L</td>
<td>V1991.99</td>
<td>&nbsp;</td>
<tr>
<td>Zeiss LSM 510 Meta Confocal</td>
<td>&nbsp;</td>
<td>Confocal Microscope</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>CM Leica 1950 Cryostat</td>
<td>&nbsp;</td>
<td>Leica Microsystems</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>Metamorph</td>
<td>Software for Imaging analysis</td>
<td>Molecular Devices, USA</td>
<td>&nbsp;</td>
<td>&nbsp;</td>		</tbody>
		</table>
		</div>

quantitation of &gamma;h2ax foci in tissue samples

DNA 이중 가닥 나누기 (DSBs)은 내생 (생리적 또는 병리) 프로세스 또는 외인성 요인, 특히 이온화 방사선 및 radiomimetic 화합물을 통해 발생할 수 특히 치명와 genotoxic 병변입니다. 세린 - 139 잔여물에서 H2A 히스톤 변형, H2AX,의 인산화는 높은 보존 C - 터미널 SQEY의 모티브에 γH2AX을 형성, DNA 이중 가닥의 휴식 시간에 초기 응답입니다<sup&gt; 1</sup&gt;. 이 인산화 이벤트는 phosphatidyl - inosito 3 키나제 (PI3K) 단백질의 가족 운동 실조증 telangiectasia 변이된 (ATM), DNA - 단백질 키나제 촉매 subunit와 ATM과 RAD3 관련하여 중재입니다 (ATR)<sup&gt; 2</sup&gt;. 전반적으로, 이산 핵 γH2AX foci의 형성에 DSB 유도 결과는 쉽게 감지하고 immunofluorescence 현미경에 의해 quantitated 수있는<sup&gt; 2</sup&gt;. 이 마커의 고유한 특이성과 감도, γH2AX foci 분석은 특히 방사선 생물학 및 핵 의학, 생명 의학 연구에 응용 프로그램의 다양한되었다 감안할 때. γH2AX foci의 quantitation는 가장 널리 이온화 방사선 유발 DSBs의 맥락에서 세포 배양 시스템에서 조사되었습니다. 외에도 세포 radiosensitivity에서 immunofluorescence 기반 assays도의 효능 방사선 - 수정 화합물을 평가하는 데 사용되었습니다. 특히 암, 또한, γH2AX 다양한 DSB - 유도 화합물의 효능을 검사하기위한 분자 마커로 사용되었으며, 최근에는 노화와 질병의 중요한 마커로 이동해되고있다<sup&gt; 3</sup&gt;. 또한, immunofluorescence 기반의 방법은 γH2AX foci 정장을 감지 및 quantitation 적응되었습니다<em&gt; 예 생체내</em&gt;과<em&gt; 생체내에</em<sup&gt; 4,5</sup&gt;. 여기서는 마우스 조직에서 γH2AX foci의 감지 및 quantitation에 대한 전형적인 immunofluorescence 방법을 보여줍니다.

Watch this Scientific Journal Video about Quantitation of ÃŽÂ³H2AX Foci in Tissue Samples at JoVE.com

Quantitation of &#947;H2AX Foci in Tissue Samples

γH2AX foci을 바탕으로 DNA 이중 가닥 나누기의 Quantitation는 조직 radiosensitivity 방사선 수정 화합물의 효과 평가를 위해, 특히 방사선 생물학에서 매우 중요한 도구가되었습니다. 여기 우리는 조직 샘플에서 γH2AX foci의 quantitation위한 immunofluorescence 분석의 사용을 보여줍니다.

조직 샘플에서 γH2AX Foci의 Quantitation

DNA double-strand breaks (DSBs) are particularly lethal and genotoxic lesions, that can arise either by endogenous (physiological or pathological) ...

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Nanyang Technological University

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JoVE Journal

Biology

Quantitation of &gamma;H2AX Foci in Tissue Samples

14.3K 조회수.  The Alfred Medical Research and Education Precinct. γH2AX foci을 바탕으로 DNA 이중 가닥 나누기의 Quantitation는 조직 radiosensitivity 방사선 수정 화합물의 효과 평가를 위해, 특히 방사선 생물학에서 매우 중요한 도구가되었습니다. 여기 우리는 조직 샘플에서 γH2AX foci의 quantitation위한 immunofluorescence 분석의 사용을 보여줍니다.

비디오: Quantitation of γH2AX Foci in Tissue Samples

Quantification of &gamma;H2AX Foci in Response to Ionising Radiation

DNA double-strand breaks (DSBs), which are induced by either endogenous metabolic processes or by exogenous sources, are one of the most critical DNA lesions with respect to survival and preservation of genomic integrity. An early response to the induction of DSBs is phosphorylation of the H2A histone variant, H2AX, at the serine-139 residue, in the highly conserved C-terminal SQEY motif, forming &gamma;H2AX1. Following induction of DSBs, H2AX is rapidly phosphorylated by the phosphatidyl-inosito 3-kinase (PIKK) family of proteins, ataxia telangiectasia mutated (ATM), DNA-protein kinase catalytic subunit and ATM and RAD3-related (ATR)2. Typically, only a few base-pairs (bp) are implicated in a DSB, however, there is significant signal amplification, given the importance of chromatin modifications in DNA damage signalling and repair. Phosphorylation of H2AX mediated predominantly by ATM spreads to adjacent areas of chromatin, affecting approximately 0.03% of total cellular H2AX per DSB2,3. This corresponds to phosphorylation of approximately 2000 H2AX molecules spanning ~2 Mbp regions of chromatin surrounding the site of the DSB and results in the formation of discrete &gamma;H2AX foci which can be easily visualized and quantitated by immunofluorescence microscopy2. The loss of &gamma;H2AX at DSB reflects repair, however, there is some controversy as to what defines complete repair of DSBs; it has been proposed that rejoining of both strands of DNA is adequate however, it has also been suggested that re-instatement of the original chromatin state of compaction is necessary4-8. The disappearence of &gamma;H2AX involves at least in part, dephosphorylation by phosphatases, phosphatase 2A and phosphatase 4C5,6. Further, removal of &gamma;H2AX by redistribution involving histone exchange with H2A.Z has been implicated7,8. Importantly, the quantitative analysis of &gamma;H2AX foci has led to a wide range of applications in medical and nuclear research. Here, we demonstrate the most commonly used immunofluorescence method for evaluation of initial DNA damage by detection and quantitation of &gamma;H2AX foci in &gamma;-irradiated adherent human keratinocytes9.

Quantification of &#947;H2AX Foci in Response to Ionising Radiation

Quantification of DNA double-strand streaks using &gamma;H2AX formation as a molecular marker has become an invaluable tool in radiation biology. Here we demonstrate the use of an immunofluorescence assay for quantification of &gamma;H2AX foci after exposure of cells to radiation.

Ionising 방사선에 대한 응답으로 γH2AX Foci의 부량

DNA double-strand breaks (DSBs), which are induced by either endogenous metabolic processes or by exogenous sources, are one of the most critical DNA ...

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생물학

NanoDrop Microvolume Quantitation of Nucleic Acids

Biomolecular assays are continually being developed that use progressively smaller amounts of material, often precluding the use of conventional cuvette-based instruments for nucleic acid quantitation for those that can perform microvolume quantitation.
The NanoDrop microvolume sample retention system (Thermo Scientific NanoDrop Products) functions by combining fiber optic technology and natural surface tension properties to capture and retain minute amounts of sample independent of traditional containment apparatus such as cuvettes or capillaries. Furthermore, the system employs shorter path lengths, which result in a broad range of nucleic acid concentration measurements, essentially eliminating the need to perform dilutions. Reducing the volume of sample required for spectroscopic analysis also facilitates the inclusion of additional quality control steps throughout many molecular workflows, increasing efficiency and ultimately leading to greater confidence in downstream results.
The need for high-sensitivity fluorescent analysis of limited mass has also emerged with recent experimental advances. Using the same microvolume sample retention technology, fluorescent measurements may be performed with 2 &mu;L of material, allowing fluorescent assays volume requirements to be significantly reduced. Such microreactions of 10 &mu;L or less are now possible using a dedicated microvolume fluorospectrometer.
Two microvolume nucleic acid quantitation protocols will be demonstrated that use integrated sample retention systems as practical alternatives to traditional cuvette-based protocols. First, a direct A260 absorbance method using a microvolume spectrophotometer is described. This is followed by a demonstration of a fluorescence-based method that enables reduced-volume fluorescence reactions with a microvolume fluorospectrometer. These novel techniques enable the assessment of nucleic acid concentrations ranging from 1 pg/ &mu;L to 15,000 ng/ &mu;L with minimal consumption of sample.

The use of NanoDrop microvolume systems as practical and efficient alternatives to traditional nucleic acid quantitation methodology is described through the demonstration of two microvolume nucleic acid quantitation protocols.

핵산의 NanoDrop Microvolume의 Quantitation

Biomolecular assays are continually being developed that use progressively smaller amounts of material, often precluding the use of conventional ...

Quantitative Comparison of cis-Regulatory Element (CRE) Activities in Transgenic Drosophila melanogaster

Gene expression patterns are specified by cis-regulatory element (CRE) sequences, which are also called enhancers or cis-regulatory modules. A typical CRE possesses an arrangement of binding sites for several transcription factor proteins that confer a regulatory logic specifying when, where, and at what level the regulated gene(s) is expressed. The full set of CREs within an animal genome encodes the organism&prime;s program for development1, and empirical as well as theoretical studies indicate that mutations in CREs played a prominent role in morphological evolution2-4. Moreover, human genome wide association studies indicate that genetic variation in CREs contribute substantially to phenotypic variation5,6. Thus, understanding regulatory logic and how mutations affect such logic is a central goal of genetics. 
Reporter transgenes provide a powerful method to study the in vivo function of CREs. Here a known or suspected CRE sequence is coupled to heterologous promoter and coding sequences for a reporter gene encoding an easily observable protein product. When a reporter transgene is inserted into a host organism, the CRE&prime;s activity becomes visible in the form of the encoded reporter protein. P-element mediated transgenesis in the fruit fly species Drosophila (D.) melanogaster7 has been used for decades to introduce reporter transgenes into this model organism, though the genomic placement of transgenes is random. Hence, reporter gene activity is strongly influenced by the local chromatin and gene environment, limiting CRE comparisons to being qualitative. In recent years, the phiC31 based integration system was adapted for use in D. melanogaster to insert transgenes into specific genome landing sites8-10. This capability has made the quantitative measurement of gene and, relevant here, CRE activity11-13 feasible. The production of transgenic fruit flies can be outsourced, including phiC31-based integration, eliminating the need to purchase expensive equipment and/or have proficiency at specialized transgene injection protocols. 
Here, we present a general protocol to quantitatively evaluate a CRE&prime;s activity, and show how this approach can be used to measure the effects of an introduced mutation on a CRE&prime;s activity and to compare the activities of orthologous CREs. Although the examples given are for a CRE active during fruit fly metamorphosis, the approach can be applied to other developmental stages, fruit fly species, or model organisms. Ultimately, a more widespread use of this approach to study CREs should advance an understanding of regulatory logic and how logic can vary and evolve.

Quantitative Comparison of cis-Regulatory Element CRE Activities in Transgenic Drosophila melanogaster

Phenotypic variation for traits can result from mutations in cis-regulatory element (CRE) sequences that control gene expression patterns. Methods derived for use in Drosophila melanogaster can quantitatively compare the levels of spatial and temporal patterns of gene expression mediated by modified or naturally occurring CRE variants.

의 양적 비교 CIS</em트렌스 제닉에서> - 규제 요소 (CRE) 활동 Drosophila melanogaster</em

Gene expression patterns are specified by cis-regulatory element (CRE) sequences, which are also called enhancers or cis-regulatory modules. A typical CRE ...

Do-It-Yourself Device for Recovery of Cryopreserved Samples Accidentally Dropped into Cryogenic Storage Tanks

Liquid nitrogen is colorless, odorless, extremely cold (-196 &deg;C) liquid kept under pressure. It is commonly used as a cryogenic fluid for long term storage of biological materials such as blood, cells and tissues 1,2. The cryogenic nature of liquid nitrogen, while ideal for sample preservation, can cause rapid freezing of live tissues on contact - known as 'cryogenic burn'2, which may lead to severe frostbite in persons closely involved in storage and retrieval of samples from Dewars. Additionally, as liquid nitrogen evaporates it reduces the oxygen concentration in the air and might cause asphyxia, especially in confined spaces2.
In laboratories, biological samples are often stored in cryovials or cryoboxes stacked in stainless steel racks within the Dewar tanks1. These storage racks are provided with a long shaft to prevent boxes from slipping out from the racks and into the bottom of Dewars during routine handling. All too often, however, boxes or vials with precious samples slip out and sink to the bottom of liquid nitrogen filled tank. In such cases, samples could be tediously retrieved after transferring the liquid nitrogen into a spare container or discarding it. The boxes and vials can then be relatively safely recovered from emptied Dewar. However, the cryogenic nature of liquid nitrogen and its expansion rate makes sunken sample retrieval hazardous. It is commonly recommended by Safety Offices that sample retrieval be never carried out by a single person. Another alternative is to use commercially available cool grabbers or tongs to pull out the vials3. However, limited visibility within the dark liquid filled Dewars poses a major limitation in their use.
In this article, we describe the construction of a Cryotolerant DIY retrieval device, which makes sample retrieval from Dewar containing cryogenic fluids both safe and easy.

Here we present a low cost, durable cryotolerant device for sample retrieval from Dewar tanks filled with liquid nitrogen. The ease of construction and modular design of the device makes the process of sample retrieval from cryogenic tanks safe and easy.

Cryopreserved 샘플 복구를 위해 손수 함 장치 실수로 극저온 저장 탱크 떨어졌고

Liquid nitrogen is colorless, odorless, extremely cold (-196 &deg;C) liquid kept under pressure. It is commonly used as a cryogenic fluid for long term ...

Method for Measuring the Activity of Deubiquitinating Enzymes in Cell Lines and Tissue Samples

The ubiquitin-proteasome system has recently been implicated in various pathologies including neurodegenerative diseases and cancer. In light of this, techniques for studying the regulatory mechanism of this system are essential to elucidating the cellular and molecular processes of the aforementioned diseases. The use of hemagglutinin derived ubiquitin probes outlined in this paper serves as a valuable tool for the study of this system. This paper details a method that enables the user to perform assays that give a direct visualization of deubiquitinating enzyme activity. Deubiquitinating enzymes control proteasomal degradation and share functional homology at their active sites, which allows the user to investigate the activity of multiple enzymes in one assay. Lysates are obtained through gentle mechanical cell disruption and incubated with active site directed probes. Functional enzymes are tagged with the probes while inactive enzymes remain unbound. By running this assay, the user obtains information on both the activity and potential expression of multiple deubiquitinating enzymes in a fast and easy manner. The current method is significantly more efficient than using individual antibodies for the predicted one hundred deubiquitinating enzymes in the human cell.

The current protocol details a method for measuring the activity of functionally homologous deubiquitinating enzymes. Specialized probes covalently modify the enzyme and allow for detection. This method holds the potential to identify new therapeutic targets.

세포주 및 조직 샘플에서 Deubiquitinating 효소의 활성을 측정 방법

The ubiquitin-proteasome system has recently been implicated in various pathologies including neurodegenerative diseases and cancer. In light of this, ...

Quantitation of Endothelial Cell Adhesiveness In Vitro

One of the cardinal processes of inflammation is the infiltration of immune cells from the lumen of the blood vessel to the surrounding tissue. This occurs when endothelial cells, which line blood vessels, become adhesive to circulating immune cells such as monocytes. In vitro measurement of this adhesiveness has until now been done by quantifying the total number of monocytes that adhere to an endothelial layer either as a direct count or by indirect measurement of the fluorescence of adherent monocytes. While such measurements do indicate the average adhesiveness of the endothelial cell population, they are confounded by a number of factors, such as cell number, and do not reveal the proportion of endothelial cells that are actually adhesive. Here we describe and demonstrate a method which allows the enumeration of adhesive cells within a tested population of endothelial monolayer. Endothelial cells are grown on glass coverslips and following desired treatment are challenged with monocytes (that may be fluorescently labeled). After incubation, a rinsing procedure, involving multiple rounds of immersion and draining, the cells are fixed. Adhesive endothelial cells, which are surrounded by monocytes are readily identified and enumerated, giving an adhesion index that reveals the actual proportion of endothelial cells within the population that are adhesive.

Quantitation of Endothelial Cell Adhesiveness In Vitro

We report an in vitro method that allows the quantitation of the actual number of adhesive cells within an endothelial cell monolayer.

내피 세포 접착 정량<em&gt; 체외</em

One of the cardinal processes of inflammation is the infiltration of immune cells from the lumen of the blood vessel to the surrounding tissue. This ...

Quantitation of Protein Expression and Co-localization Using Multiplexed Immuno-histochemical Staining and Multispectral Imaging

Immunohistochemistry is a commonly used clinical and research lab detection technique for investigating protein expression and localization within tissues. Many semi-quantitative systems have been developed for scoring expression using immunohistochemistry, but inherent subjectivity limits reproducibility and accuracy of results. Furthermore, the investigation of spatially overlapping biomarkers such as nuclear transcription factors is difficult with current immunohistochemistry techniques. We have developed and optimized a system for simultaneous investigation of multiple proteins using high throughput methods of multiplexed immunohistochemistry and multispectral imaging. Multiplexed immunohistochemistry is performed by sequential application of primary antibodies with secondary antibodies conjugated to horseradish peroxidase or alkaline phosphatase. Different chromogens are used to detect each protein of interest. Stained slides are loaded into an automated slide scanner and a protocol is created for automated image acquisition. A spectral library is created by staining a set of slides with a single chromogen on each. A subset of representative stained images are imported into multispectral imaging software and an algorithm for distinguishing tissue type is created by defining tissue compartments on images. Subcellular compartments are segmented by using hematoxylin counterstain and adjusting the intrinsic algorithm. Thresholding is applied to determine positivity and protein co-localization. The final algorithm is then applied to the entire set of tissues. Resulting data allows the user to evaluate protein expression based on tissue type (ex. epithelia vs. stroma) and subcellular compartment (nucleus vs. cytoplasm vs. plasma membrane). Co-localization analysis allows for investigation of double-positive, double-negative, and single-positive cell types. Combining multispectral imaging with multiplexed immunohistochemistry and automated image acquisition is an objective, high-throughput method for investigation of biomarkers within tissues.

Immunohistochemistry is a powerful lab technique for evaluating protein localization and expression within tissues. Current semi-automated methods for quantitation introduce subjectivity and often create irreproducible results. Herein, we describe methods for multiplexed immunohistochemistry and objective quantitation of protein expression and co-localization using multispectral imaging.

멀티 플렉스 면역 조직 화학적 염색 및 멀티 스펙트럼 영상을 사용하여 단백질 발현 및 공동 현지화의 정량

Immunohistochemistry is a commonly used clinical and research lab detection technique for investigating protein expression and localization within ...

Hybrid-Cut: An Improved Sectioning Method for Recalcitrant Plant Tissue Samples

Maintaining plant section integrity is essential for studying detailed anatomical structures at the cellular, tissue, or even organ level. However, some plant cells have rigid cell walls, tough fibers and crystals (calcium oxalate, silica, etc.), and high water content that often disrupt tissue integrity during plant tissue sectioning.
This study establishes a simple Hybrid-Cut tissue sectioning method. This protocol modifies a paraffin-based sectioning technique and improves the integrity of tissue sections from different plants. Plant tissues were embedded in paraffin before sectioning in a cryostat at -16 &#176;C. Sectioning under low temperature hardened the paraffin blocks, reduced tearing and scratching, and improved tissue integrity significantly. This protocol was successfully applied to calcium oxalate-rich Phalaenopsis orchid tissues as well as recalcitrant tissues such as reproductive organs and leaves of rice, maize, and wheat. In addition, the high quality of tissue sections from Hybrid-Cut could be used in combination with in situ hybridization (ISH) to provide spatial expression patterns of genes of interest. In conclusion, this protocol is particularly useful for recalcitrant plant tissue containing high crystal or silica content. Good quality tissue sections enable morphological and other biological studies.

This protocol describes a simple Hybrid-Cut tissue sectioning method that is useful for recalcitrant plant tissues. Good quality tissue sections enable anatomical studies and other biological studies including in situ hybridization (ISH).

하이브리드 컷 : 난 분해성 식물 조직 샘플에 대한 개선 단면 방법

Maintaining plant section integrity is essential for studying detailed anatomical structures at the cellular, tissue, or even organ level. However, some ...

Methods to Classify Cytoplasmic Foci as Mammalian Stress Granules

Cells are often challenged by sudden environmental changes. Stress Granules (SGs), cytoplasmic ribonucleoprotein complexes that form in cells exposed to stress conditions, are implicated in various aspects of cell metabolism and survival. SGs modulate cellular signaling pathways, post-transcriptional gene expression, and stress response programs. The formation of these mRNA-containing granules is directly connected to cellular translation. SG assembly is triggered by inhibited translation initiation, and SG disassembly is promoted by translation activation or by inhibited translation elongation. This relationship is further highlighted by SG composition. Core SG components are stalled translation pre-initiation complexes, mRNA, and selected RNA-binding Proteins (RBPs). The purpose of SG assembly is to conserve cellular energy by sequestering translationally stalled housekeeping mRNAs, allowing for the enhanced translation of stress-responsive proteins. In addition to the core constituents, such as stalled translation preinitiation complexes, SGs contain a plethora of other proteins and signaling molecules. Defects in SG formation can impair cellular adaptation to stress and can thus promote cell death. SGs and similar RNA-containing granules have been linked to a number of human diseases, including neurodegenerative disorders and cancer, leading to the recent interest in classifying and defining RNA granule subtypes. This protocol describes assays to characterize and quantify mammalian SGs.

Stress Granules (SGs) are nonmembranous cytoplasmic structures that form in cells exposed to a variety of stresses. SGs contain mRNAs, RNA-binding proteins, small ribosomal subunits, translation-related factors, and various cell signaling proteins. This protocol describes a workflow that uses several experimental approaches to detect, characterize, and quantify bona fide SGs.

포유류 스트레스 과립으로 세포질 초점을 분류하는 방법

Cells are often challenged by sudden environmental changes. Stress Granules (SGs), cytoplasmic ribonucleoprotein complexes that form in cells exposed to ...

Simultaneous Mapping and Quantitation of Ribonucleotides in Human Mitochondrial DNA

Established approaches to estimate the number of ribonucleotides present in a genome are limited to the quantitation of incorporated ribonucleotides using short synthetic DNA fragments or plasmids as templates and then extrapolating the results to the whole genome. Alternatively, the number of ribonucleotides present in a genome may be estimated using alkaline gels or Southern blots. More recent in vivo approaches employ Next-generation sequencing allowing genome-wide mapping of ribonucleotides, providing the position and identity of embedded ribonucleotides. However, they do not allow quantitation of the number of ribonucleotides which are incorporated into a genome. Here we describe how to simultaneously map and quantitate the number of ribonucleotides which are incorporated into human mitochondrial DNA in vivo by Next-generation sequencing. We use highly intact DNA and introduce sequence specific double strand breaks by digesting it with an endonuclease, subsequently hydrolyzing incorporated ribonucleotides with alkali. The generated ends are ligated with adapters and these ends are sequenced on a Next-generation sequencing machine. The absolute number of ribonucleotides can be calculated as the number of reads outside the recognition site per average number of reads at the recognition site for the sequence specific endonuclease. This protocol may also be utilized to map and quantitate free nicks in DNA and allows adaption to map other DNA lesions that can be processed to 5&#180;-OH ends or 5&#180;-phosphate ends. Furthermore, this method can be applied to any organism, given that a suitable reference genome is available. This protocol therefore provides an important tool to study DNA replication, 5&#180;-end processing, DNA damage, and DNA repair.

Here we describe a method amenable to simultaneously quantitate and genome-wide map ribonucleotides in highly intact DNA at single-nucleotide resolution, combining enzymatic cleavage of genomic DNA with its alkaline hydrolysis and subsequent 5&#180;-end sequencing.

동시 매핑 및 인간 미토 콘 드리 아 DNA에 Ribonucleotides의 정량

Established approaches to estimate the number of ribonucleotides present in a genome are limited to the quantitation of incorporated ribonucleotides using ...