كتب بواسطة LeafJ JNM بينما كان في اجازة في مختبر الدكتور كاثرين بولارد في المعاهد جلادستون. وأيد هذا العمل من خلال منحة من مؤسسة العلوم الوطنية (عدد المنح IOS-0923752).

1. مصنع مواد لاحظ أن هذا البروتوكول يهدف للكشف عن نمو النبات استجابة تجنب الظل. هل يمكن أن تنمو النباتات تحت ظروف المفضلة لديك. <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> رش بذور thaliana ل arabidopsis على المياه غارقة أوراق الترشيح في 9 أطباق بتري الطول ومتجر (تطبق) منهم في 4 درجات مئوية لمدة أربعة أيام في الظلام. </li><li style=";text-align:right;direction:rtl"> نقل هذه أطباق بتري لظروف محاكاة أحد: 80-100 الإشعاع الضوئي μE بالموقع (PAR) والملحق الحمراء بعيدة لجلب R: FR نسبة إلى 1.86. استخدام الشروط يوم طويل (16 ساعة ضوء / 8 الظلام ساعة) ودرجة حرارة ثابتة من 22 ° C. احتضان في هذه الحالة لمدة ثلاثة أيام للسماح للبذور أن تنبت. </li><li style=";text-align:right;direction:rtl"> نقل البذور نبتت في التربة والحفاظ على النباتات تحت ظروف أحد على نطاق واسع التجارب، ونحن نوصي به إعداد صغيرة لوصفها كل النباتات باستخدام دمج البيانات في Microsoft Word مدير 2004 (أو أحدث) لجعل التسميات. </li><li style=";text-align:right;direction:rtl"> بعد أحد عشر يوما TRansfer إلى التربة، نقل نصف النباتات لحالة الظل: نفس الشمس ولكن مع الضوء الأحمر بعيدة تكميلية لتحقيق نسبة R / FR الى 0.52. </li><li style=";text-align:right;direction:rtl"> بعد اثني عشر يوما إضافية، والنباتات هي على استعداد للتصوير ورقة. في هذه المرحلة قد نضجت تماما وأقدم أوراق في حين يترك الأصغر مازالت تتوسع، بحيث يمكنك التقاط لقطة من التنمية. قد تحتاج إلى اختيار وقت آخر التنموية اعتمادا على احتياجاتك. </li></ol> 2. التقاط الصور ليف مشرح <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> إعداد ورقة الشفافية المسمى مع النمط الوراثي النباتي وحالة النمو مع خمسة إطارات مستطيلة. إطار واحد يتوافق مع الأوراق من مصنع واحد. يمكن استخدام Microsoft Excel لطباعة الشبكة بما يتفق مع التسميات. </li><li style=";text-align:right;direction:rtl"> تشريح أوراق النباتات القديمة 26 يوم. </li><li style=";text-align:right;direction:rtl"> مسح يترك في 600 نقطة في البوصة على الماسح الضوئي سرير مسطح. يجب وضع ملاحظة أن يترك من مصنع واحد عموديا ضمن إطار أسود في شطيرة من أوراق شفافة. تجنب لمس الأوراقإلى إطار نافذة سوداء والأوراق المتداخلة، والتي سوف تعطي أخطاء في الإجراءات التالية. </li></ol> 3. ورقة تحليل الصور بواسطة LeafJ <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> تحميل يماغيج سحب الملف إلى مجلد LeafJ.jar الإضافات من يماغيج. </li><li style=";text-align:right;direction:rtl"> فتح ملف صورة في 1.45s يماغيج أو 14 في وقت لاحق. </li><li style=";text-align:right;direction:rtl"> تقسيم الصورة إلى ثلاث قنوات اللون (الأحمر والأخضر والأزرق) من قبل &quot;صورة&gt; لون القنوات سبليت&gt;&quot; وتطبيق الحد الأدنى للصورة في القناة الزرقاء. </li><li style=";text-align:right;direction:rtl"> تحديد كافة الأوراق من مصنع واحد بواسطة أداة المستطيل (الشكل 1A). </li><li style=";text-align:right;direction:rtl"> حدد &quot;LeafJ&quot; من القائمة المساعد. </li><li style=";text-align:right;direction:rtl"> حدد المعلومات الشرح لهذا النبات من مربع الحوار الذي يظهر. يمكنكتحرير القيم الافتراضية التي تظهر هنا بالنقر على &quot;تحرير هذه الخيارات&quot;. </li><li style=";text-align:right;direction:rtl"> بعد تشغيل البرنامج المساعد وLeafJ قبل النقر فوق زر &quot;موافق&quot;، وتحرير خطوط تتبع من المنطقة من نافذة مدير مصلحة (ROI) (إذا لزم الأمر؛ 1B الشكل). A اللوحي التي تعمل باللمس (مثل آي باد) هو مفيد لهذا الإجراء. يمكن توصيل لاب توب بكمبيوتر وشاشة خارجية باستخدام البرمجيات الهواء العرض. </li><li style=";text-align:right;direction:rtl"> تصدير نتائج القياس والمعلومات المرتبطة بها (أسماء الملفات، والوقت المزهرة، تشريح من قبل، قياس، الخ) إلى Microsoft Excel أو برنامج ما يعادلها. </li></ol> 4. تحليل صورة ورقة خلية في يماغيج <ol style=";text-align:right;direction:rtl"><li style=";text-align:right;direction:rtl"> إصلاح تشريح يترك كما هو موضح في مرجع 15 بعد المسح (الخطوة 2). يمكن أن تظل ثابتة في أوراق FAA C ° 4 ل6 أشهر على الأقل. </li><li style=";text-align:right;direction:rtl"> مسح أوراق من خلال تغيير FAA مثبت على حل هيدرات الكلورال ويترك لاحتضان 1 ساعة 2 ~ المراقبة المجهرية قبل 15. </li><li style=";text-align:right;direction:rtl"> جبل يترك على ميلcroscope الشرائح مع trichomes مواجهة. باستخدام التكبير 40X على مجمع المجهر طبقة الصورة، ونسيج الورقة المتوسط ​​من وسط كل ورقة على جانبي الوريد الرئيسي، وتجنب الخلايا قرب trichomes أو الأوردة. </li><li style=";text-align:right;direction:rtl"> تتبع خلية ورقة تحدد بواسطة أداة يماغيج مدير ROI مع المعونة من قرص تعمل باللمس وقلم (كما هو موضح في الخطوة 3). خلية تحليل الصور يستخدم ميزات المدمج في ليماغيج ولكن لا يتطلب LeafJ. </li></ol>

<ol>
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D., Magalhaes, P. J., Ram, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Image+Processing+with+ImageJ.">Image Processing with ImageJ.</a> Biophotonics International. 11, 36-42 (2004).</li><li>Horiguchi, G., Fujikura, U., Ferjani, A., Ishikawa, N., Tsukaya, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Large-scale+histological+analysis+of+leaf+mutants+using+two+simple+leaf+observation+methods:+identification+of+novel+genetic+pathways+governing+the+size+and+shape+of+leaves.">Large-scale histological analysis of leaf mutants using two simple leaf observation methods: identification of novel genetic pathways governing the size and shape of leaves.</a> Plant. J. 48, 638-644 (2006).</li><li>Horiguchi, G., Ferjani, A., Fujikura, U., Tsukaya, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Coordination+of+cell+proliferation+and+cell+expansion+in+the+control+of+leaf+size+in+Arabidopsis+thaliana.">Coordination of cell proliferation and cell expansion in the control of leaf size in Arabidopsis thaliana.</a> J. Plant. Res. 119, 37-42 (2006).</li><li>Pierik, R., de Wit, M., Voesenek, L. A. C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Growth-mediated+stress+escape:+convergence+of+signal+transduction+pathways+activated+upon+exposure+to+two+different+environmental+stresses.">Growth-mediated stress escape: convergence of signal transduction pathways activated upon exposure to two different environmental stresses.</a> New. Phytol. 189, 122-134 (2011).</li></ol>

الإعلان عن أي تضارب في المصالح.

لدينا &quot;LeafJ&quot; البرنامج المساعد تمكن من قياس طول سويقات شبه تلقائيا، وزيادة الإنتاجية ما يقرب من 6 مرات خلال قياس دليل. طول سويقات هو مؤشر هام من SAS وأيضا معلما من ظواهر أخرى، مثل مقاومة الإغراق والنمو hyponastic 17. ولذلك قد يكون من المفيد هذا البرنامج المساعد لمجموع...

<html><table border="1" style=";text-align:right;direction:rtl"><tbody><tr><td> اسم كاشف </td><td> شركة </td><td> كتالوج رقم </td><td></td></tr><tr><td> الصمام بعيدة الضوء الأحمر </td><td> Orbitec </td><td> والعرف </td><td></td></tr><tr><td> شفافية </td><td> IKON </td><td> HSCA / 5 </td><td></td></tr><tr><td> الماسح الضوئي </td><td> EPSON </td><td> إبسون الكمال V700 PHOTO </td><td></td></tr><tr><td> الصورة J </td><td> NIH </td><td></td><td> <a href="http://rsbweb.nih.gov/ij/" target="_blank">http://rsbweb.nih.gov/ij/</a> </td></tr><tr><td> LeafJ </td><td> عرف </td><td></td><td> <a href="http://www.openwetware.org/wiki/Maloof_Lab" target="_blank">http://www.openwetware.org/wiki/Maloof_Lab</a> </td></tr><tr><td> عرض الجوية </td><td> Avatron برمجيات شركة </td><td></td><td>على بياض &quot;&gt; http://avatron.com/ </td></tr><tr><td> IPAD2 </td><td> شركة أبل </td><td></td><td> <a href="http://www.apple.com/" target="_blank">http://www.apple.com/</a> </td></tr></tbody></table>

leafj: an imagej plugin for semi-automated leaf shape measurement

عالية الإنتاجية phenotyping (phenomics) هو أداة قوية لربط الجينات لوظائفها (انظر 1 مشاركة الأمثلة الحديثة و2-4). يترك هي الجهاز الضوئي الأولية، وحجمها وشكلها تختلف تنمويا وبيئيا داخل المصنع. لهذه الأسباب دراسات مورفولوجية على ورقة تتطلب قياس معلمات متعددة من أوراق عديدة، والتي تتم من قبل أفضل شبه الآلي أدوات phenomics 5،6. الظل هو المظلة جديلة البيئية المهمة التي تؤثر على بنية النبات وتاريخ حياة؛ والتي تسمى مجتمعة مجموعة من الردود على تجنب متلازمة الظل (SAS) 7. بين استجابات SAS، الظل الناجمة استطالة سويقات ورقة والتغيرات في المنطقة هي شفرة مفيدة بشكل خاص حيث مؤشرات 8. حتى الآن، يمكن لبرامج الشكل ورقة (مثل SHAPE 9، الصفيحة 10، LeafAnalyzer 11، LEAFPROCESSOR 12) قياس الخطوط العريضة الأوراق وتصنيف الأشكال ورقةولكن لا يمكن إخراج طول سويقات. عدم وجود أنظمة قياس على نطاق واسع من أعناق الأوراق وتحول دون النهج phenomics للبحث SAS. في هذه الورقة، ونحن وصف البرنامج المساعد يماغيج وضعت حديثا، ودعا LeafJ، والتي يمكن قياس طول سويقات بسرعة والمعلمات رقة شفرة للل arabidopsis thaliana نموذج المصنع. لأوراق المطلوبة العرضية التي التصحيح اليدوي للحدود شفرة سويقات / نبات كنا قرص تعمل باللمس. علاوة على ذلك، شكل الخلية ورقة أرقام خلية ورقة من المحددات الهامة لحجم ورقة 13. منفصلة عن LeafJ نقدم أيضا على بروتوكول لاستخدام لوحة تعمل باللمس لقياس شكل الخلية والمساحة والحجم. لا يقتصر لدينا نظام قياس سمة ورقة لتجنب الظل والبحوث من شأنها أن تعجل من المسوخ phenotyping أوراق العديد من النباتات والفحص من قبل phenotyping ورقة.

1. صور ورقة عرض تقديرات سويقات ورقة شفرة الحدود، ونافذة قياسها واحدة من السمات الأكثر فائدة من الكشف الآلي هو LeafJ من الحدود شفرة / سويقات ورقة (الشكل 1). الخوارزمية LeafJ يعمل على النحو التالي: يتم استخدام المدمج في وظائف ParticleAnal...

Watch this Scientific Journal Video about LeafJ: An ImageJ Plugin for Semi-automated Leaf Shape Measurement at JoVE.com

LeafJ: An ImageJ Plugin for Semi-automated Leaf Shape Measurement

مظاهرة للطرق الرئيسية لارتفاع قياسات أوراق الإنتاجية. ويمكن استخدام هذه الأساليب لتسريع phenotyping أوراق النبات عند دراسة العديد من المسوخ أو النباتات فحص أوراق النمط الظاهري خلاف ذلك.

LeafJ: البرنامج المساعد ليماغيج نصف الآلي ورقة قياس الشكل

High throughput phenotyping (phenomics) is a powerful tool for linking genes to their functions (see review1 and recent examples2-4). Leaves are the ...

leafj-an-imagej-plugin-for-semi-automated-leaf-shape-measurement

Research

JoVE Journal

Biology

28.2K Views.  University of California Davis. مظاهرة للطرق الرئيسية لارتفاع قياسات أوراق الإنتاجية. ويمكن استخدام هذه الأساليب لتسريع phenotyping أوراق النبات عند دراسة العديد من المسوخ أو النباتات فحص أوراق النمط الظاهري خلاف ذلك.

Video: LeafJ: An ImageJ Plugin for Semi-automated Leaf Shape Measurement

Semi-automated Optical Heartbeat Analysis of Small Hearts

We have developed a method for analyzing high speed optical recordings from Drosophila, zebrafish and embryonic mouse hearts (Fink, et. al., 2009). Our Semi-automatic Optical Heartbeat Analysis (SOHA) uses a novel movement detection algorithm that is able to detect cardiac movements associated with individual contractile and relaxation events. The program provides a host of physiologically relevant readouts including systolic and diastolic intervals, heart rate, as well as qualitative and quantitative measures of heartbeat arrhythmicity. The program also calculates heart diameter measurements during both diastole and systole from which fractional shortening and fractional area changes are calculated. Output is provided as a digital file compatible with most spreadsheet programs. Measurements are made for every heartbeat in a record increasing the statistical power of the output. We demonstrate each of the steps where user input is required and show the application of our methodology to the analysis of heart function in all three genetically tractable heart models.

We have developed a Semi-automated Optical Heartbeat Analysis method (SOHA) for analyzing high speed optical recordings from Drosophila, zebrafish and embryonic mouse hearts. We demonstrate the application of our methodology to the analysis of heart function in fruit fly and embryonic mouse hearts.

شبه الآلي التحليل البصري نبضات القلوب الصغيرة

We have developed a method for analyzing high speed optical recordings from Drosophila, zebrafish and embryonic mouse hearts (Fink, et. al., 2009). Our ...

Measurement of Leaf Hydraulic Conductance and Stomatal Conductance and Their Responses to Irradiance and Dehydration Using the Evaporative Flux Method (EFM)

Water is a key resource, and the plant water transport system sets limits on maximum growth and drought tolerance. When plants open their stomata to achieve a high stomatal conductance (gs) to capture CO2 for photosynthesis, water is lost by transpiration1,2. Water evaporating from the airspaces is replaced from cell walls, in turn drawing water from the xylem of leaf veins, in turn drawing from xylem in the stems and roots. As water is pulled through the system, it experiences hydraulic resistance, creating tension throughout the system and a low leaf water potential (&Psi;leaf). The leaf itself is a critical bottleneck in the whole plant system, accounting for on average 30% of the plant hydraulic resistance3. Leaf hydraulic conductance (Kleaf = 1/ leaf hydraulic resistance) is the ratio of the water flow rate to the water potential gradient across the leaf, and summarizes the behavior of a complex system: water moves through the petiole and through several orders of veins, exits into the bundle sheath and passes through or around mesophyll cells before evaporating into the airspace and being transpired from the stomata. Kleaf is of strong interest as an important physiological trait to compare species, quantifying the effectiveness of the leaf structure and physiology for water transport, and a key variable to investigate for its relationship to variation in structure (e.g., in leaf venation architecture) and its impacts on photosynthetic gas exchange. Further, Kleaf responds strongly to the internal and external leaf environment3. Kleaf can increase dramatically with irradiance apparently due to changes in the expression and activation of aquaporins, the proteins involved in water transport through membranes4, and Kleaf declines strongly during drought, due to cavitation and/or collapse of xylem conduits, and/or loss of permeability in the extra-xylem tissues due to mesophyll and bundle sheath cell shrinkage or aquaporin deactivation5-10. Because Kleaf can constrain gs and photosynthetic rate across species in well watered conditions and during drought, and thus limit whole-plant performance they may possibly determine species distributions especially as droughts increase in frequency and severity11-14.
We present a simple method for simultaneous determination of Kleaf and gs on excised leaves. A transpiring leaf is connected by its petiole to tubing running to a water source on a balance. The loss of water from the balance is recorded to calculate the flow rate through the leaf. When steady state transpiration (E, mmol &bull; m-2 &bull; s-1) is reached, gs is determined by dividing by vapor pressure deficit, and Kleaf by dividing by the water potential driving force determined using a pressure chamber (Kleaf= E /- &Delta;&psi;leaf, MPa)15.
This method can be used to assess Kleaf responses to different irradiances and the vulnerability of Kleaf to dehydration14,16,17.

Measurement of Leaf Hydraulic Conductance and Stomatal Conductance and Their Responses to Irradiance and Dehydration Using the Evaporative Flux Method EFM

We describe a relatively rapid (30 min) and realistic method for simultaneously measurement of leaf hydraulic conductance (Kleaf) and stomatal conductance (gs) for transpiring excised leaves. The method can be modified to measure the light and dehydration responses of Kleaf and gs.

قياس المواصلة والمواصلة الهيدروليكية ليف الثغور وردودها على الإشعاع والجفاف باستخدام أسلوب التمويه التبخر (EFM)

Water is a key resource, and the plant water transport system sets limits on maximum growth and drought tolerance. When plants open their stomata to ...

RNA Secondary Structure Prediction Using High-throughput SHAPE

Understanding the function of RNA involved in biological processes requires a thorough knowledge of RNA structure. Toward this end, the methodology dubbed "high-throughput selective 2' hydroxyl acylation analyzed by primer extension", or SHAPE, allows prediction of RNA secondary structure with single nucleotide resolution. This approach utilizes chemical probing agents that preferentially acylate single stranded or flexible regions of RNA in aqueous solution. Sites of chemical modification are detected by reverse transcription of the modified RNA, and the products of this reaction are fractionated by automated capillary electrophoresis (CE). Since reverse transcriptase pauses at those RNA nucleotides modified by the SHAPE reagents, the resulting cDNA library indirectly maps those ribonucleotides that are single stranded in the context of the folded RNA. Using ShapeFinder software, the electropherograms produced by automated CE are processed and converted into nucleotide reactivity tables that are themselves converted into pseudo-energy constraints used in the RNAStructure (v5.3) prediction algorithm. The two-dimensional RNA structures obtained by combining SHAPE probing with in silico RNA secondary structure prediction have been found to be far more accurate than structures obtained using either method alone.

High-throughput selective 2' hydroxyl acylation analyzed by primer extension (SHAPE) utilizes a novel chemical probing technology, reverse transcription, capillary electrophoresis and secondary structure prediction software to determine the structures of RNAs from several hundred to several thousand nucleotides at single nucleotide resolution.

RNA تنبؤ هيكل الثانوية باستخدام الشكل عالي الإنتاجية

Understanding the function of RNA involved in biological processes requires a thorough knowledge of RNA structure. Toward this end, the methodology dubbed ...

An Innovative Method for Exosome Quantification and Size Measurement

Although the biological importance of exosomes has recently gained an increasing amount of scientific and clinical attention, much is still unknown about their complex pathways, their bioavailability and their diverse functions in health and disease. Current work focuses on the presence and the behavior of exosomes (in vitro as well as in vivo) in the context of different human disorders, especially in the fields of oncology, gynecology and cardiology.
Unfortunately, neither a consensus regarding a gold standard for exosome isolation exists, nor is there an agreement on such a method for their quantitative analysis. As there are many methods for the purification of exosomes and also many possibilities for their quantitative and qualitative analysis, it is difficult to determine a combination of methods for the ideal approach. 
Here, we demonstrate nanoparticle tracking analysis (NTA), a semi-automated method for the characterization of exosomes after isolation from human plasma by ultracentrifugation. The presented results show that this approach for isolation, as well as the determination of the average number and size of exosomes, delivers reproducible and valid data, as confirmed by other methods, such as scanning electron microscopy (SEM).

A method for isolation of exosomes from whole blood and further analysis by nanoparticle tracking using a semi-automatic instrument is presented in this article. The presented technology provides an extremely sensitive method for visualizing and analyzing particles in liquid suspension.

طريقة مبتكرة لExosome الكمي وقياس الحجم

Although the biological importance of exosomes has recently gained an increasing amount of scientific and clinical attention, much is still unknown about ...

An Improved Method for Accurate and Rapid Measurement of Flight Performance in Drosophila

Drosophila has proven to be a useful model system for analysis of behavior, including flight. The initial flight tester involved dropping flies into an oil-coated graduated cylinder; landing height provided a measure of flight performance by assessing how far flies will fall before producing enough thrust to make contact with the wall of the cylinder. Here we describe an updated version of the flight tester with four major improvements. First, we added a &#34;drop tube&#34; to ensure that all flies enter the flight cylinder at a similar velocity between trials, eliminating variability between users. Second, we replaced the oil coating with removable plastic sheets coated in Tangle-Trap, an adhesive designed to capture live insects. Third, we use a longer cylinder to enable more accurate discrimination of flight ability. Fourth we use a digital camera and imaging software to automate the scoring of flight performance. These improvements allow for the rapid, quantitative assessment of flight behavior, useful for large datasets and large-scale genetic screens.

An Improved Method for Accurate and Rapid Measurement of Flight Performance in Drosophila

Here we describe a method for rapid and accurate measurement of flight performance in Drosophila, enabling high-throughput screening.

لتحسين طريقة لقياس دقة وسرعة الأداء في الطيران<em&gt; ذبابة الفاكهة</em

Drosophila has proven to be a useful model system for analysis of behavior, including flight. The initial flight tester involved dropping flies into an ...

Semi-automated Imaging of Tissue-specific Fluorescence in Zebrafish Embryos

Zebrafish embryos are a powerful tool for large-scale screening of small molecules. Transgenic zebrafish that express fluorescent reporter proteins are frequently used to identify chemicals that modulate gene expression. Chemical screens that assay fluorescence in live zebrafish often rely on expensive, specialized equipment for high content screening. We describe a procedure using a standard epifluorescence microscope with a motorized stage to automatically image zebrafish embryos and detect tissue-specific fluorescence. Using transgenic zebrafish that report estrogen receptor activity via expression of GFP, we developed a semi-automated procedure to screen for estrogen receptor ligands that activate the reporter in a tissue-specific manner. In this video we describe procedures for arraying zebrafish embryos at 24-48 hours post fertilization (hpf) in a 96-well plate and adding small molecules that bind estrogen receptors. At 72-96 hpf, images of each well from the entire plate are automatically collected and manually inspected for tissue-specific fluorescence. This protocol demonstrates the ability to detect estrogens that activate receptors in heart valves but not in liver.

Described here is a protocol for semi-automated imaging of tissue-specific fluorescence in zebrafish embryos.

التصوير الآلي شبه الإسفار من الأنسجة محددة في الزرد الأجنة

Zebrafish embryos are a powerful tool for large-scale screening of small molecules. Transgenic zebrafish that express fluorescent reporter proteins are ...

Relating Stomatal Conductance to Leaf Functional Traits

Leaf functional traits are important because they reflect physiological functions, such as transpiration and carbon assimilation. In particular, morphological leaf traits have the potential to summarize plants strategies in terms of water use efficiency, growth pattern and nutrient use. The leaf economics spectrum (LES) is a recognized framework in functional plant ecology and reflects a gradient of increasing specific leaf area (SLA), leaf nitrogen, phosphorus and cation content, and decreasing leaf dry matter content (LDMC) and carbon nitrogen ratio (CN). The LES describes different strategies ranging from that of short-lived leaves with high photosynthetic capacity per leaf mass to long-lived leaves with low mass-based carbon assimilation rates. However, traits that are not included in the LES might provide additional information on the species&#39; physiology, such as those related to stomatal control. Protocols are presented for a wide range of leaf functional traits, including traits of the LES, but also traits that are independent of the LES. In particular, a new method is introduced that relates the plants&#8217; regulatory behavior in stomatal conductance to vapor pressure deficit. The resulting parameters of stomatal regulation can then be compared to the LES and other plant functional traits. The results show that functional leaf traits of the LES were also valid predictors for the parameters of stomatal regulation. For example, leaf carbon concentration was positively related to the vapor pressure deficit (vpd) at the point of inflection and the maximum of the conductance-vpd curve. However, traits that are not included in the LES added information in explaining parameters of stomatal control: the vpd at the point of inflection of the conductance-vpd curve was lower for species with higher stomatal density and higher stomatal index. Overall, stomata and vein traits were more powerful predictors for explaining stomatal regulation than traits used in the LES.

Unraveling how physiology and morphology are linked allows a deeper understanding of mechanistic functioning of plant leaves. We present both a procedure to derive parameters of stomatal regulation from stomatal conductance measurements and correlations with traditional functional leaf traits.

فيما الثغور المواصلة إلى ورقة الصفات الوظيفية

Leaf functional traits are important because they reflect physiological functions, such as transpiration and carbon assimilation. In particular, ...

Automated Quantification and Analysis of Cell Counting Procedures Using ImageJ Plugins

The National Institute of Health&#39;s ImageJ is a powerful, freely available image processing software suite. ImageJ has comprehensive particle analysis algorithms which can be used effectively to count various biological particles. When counting large numbers of cell samples, the hemocytometer presents a bottleneck with regards to time. Likewise, counting membranes from migration/invasion assays with the ImageJ plugin Cell Counter, although accurate, is exceptionally labor intensive, subjective, and infamous for causing wrist pain. To address this need, we developed two plugins within ImageJ for the sole task of automated hemocytometer (or known volume) and migration/invasion cell counting. Both plugins rely on the ability to acquire high quality micrographs with minimal background. They are easy to use and optimized for quick counting and analysis of large sample sizes with built-in analysis tools to help calibration of counts. By combining the core principles of Cell Counter with an automated counting algorithm and post-counting analysis, this greatly increases the ease with which migration assays can be processed without any loss of accuracy.

This paper describes the quantification of hemocytometer and migration/invasion micrographs through two new open-source ImageJ plugins Cell Concentration Calculator and migration assay Counter. Furthermore, it describes image acquisition and calibration protocols as well as discusses in detail the input requirements of the plugins.

الآلي الكمي وتحليل إجراءات الفرز الخلية باستخدام يماغيج الإضافات

The National Institute of Health&#39;s ImageJ is a powerful, freely available image processing software suite. ImageJ has comprehensive particle analysis ...

Clock Scan Protocol for Image Analysis: ImageJ Plugins

The clock scan protocol for image analysis is an efficient tool to quantify the average pixel intensity within, at the border, and outside (background) a closed or segmented convex-shaped region of interest, leading to the generation of an averaged integral radial pixel-intensity profile. This protocol was originally developed in 2006, as a visual basic 6 script, but as such, it had limited distribution. To address this problem and to join similar recent efforts by others, we converted the original clock scan protocol code into two Java-based plugins compatible with NIH-sponsored and freely available image analysis programs like ImageJ or Fiji ImageJ. Furthermore, these plugins have several new functions, further expanding the range of capabilities of the original protocol, such as analysis of multiple regions of interest and image stacks. The latter feature of the program is especially useful in applications in which it is important to determine changes related to time and location. Thus, the clock scan analysis of stacks of biological images may potentially be applied to spreading of Na+ or Ca++ within a single cell, as well as to the analysis of spreading activity (e.g., Ca++ waves) in populations of synaptically-connected or gap junction-coupled cells. Here, we describe these new clock scan plugins and show some examples of their applications in image analysis.

This paper describes two novel ImageJ plugins for &#39;Clock Scan&#39; image analysis. These plugins expand the functionality of the original visual basic 6 program and, most importantly, make the program available to a large research community by bundling it with the ImageJ free image analysis software package.

بروتوكول المسح الضوئي على مدار الساعة لتحليل الصور: إيماجيج الإضافات

The clock scan protocol for image analysis is an efficient tool to quantify the average pixel intensity within, at the border, and outside (background) a ...

عزل شبه آلي للأنسجة الدهنية البيضاء للفأر

Semi-Automated Isolation of the Stromal Vascular Fraction from Murine White Adipose Tissue Using a Tissue Dissociator

The in vitro study of white, brown, and beige adipocyte differentiation enables the investigation of cell-autonomous functions of adipocytes and their mechanisms. Immortalized white preadipocyte cell lines are publicly available and widely used. However, the emergence of beige adipocytes in white adipose tissue in response to external cues is difficult to recapitulate to the full extent using publicly available white adipocyte cell lines. Isolation of the stromal vascular fraction (SVF) from murine adipose tissue is commonly executed to obtain primary preadipocytes and perform adipocyte differentiation. However, mincing and collagenase digestion of adipose tissue by hand can result in experimental variation and is prone to contamination. Here, we present a modified semi-automated protocol that utilizes a tissue dissociator for collagenase digestion to achieve easier isolation of the SVF, with the aim of reducing experimental variation, reducing contamination, and increasing reproducibility. The obtained preadipocytes and differentiated adipocytes can be used for functional and mechanistic analyses.

تسليط الضوء على المؤلف: عزل شبه آلي لجزء الأوعية الدموية اللحمية من الأنسجة الدهنية البيضاء الفئران باستخدام مفكك الأنسجة  

This protocol describes the semi-automated isolation of the stromal vascular fraction (SVF) from murine adipose tissue to obtain preadipocytes and achieve adipocyte differentiation in vitro. Using a tissue dissociator for collagenase digestion reduces experimental variation and increases reproducibility.

عزل شبه آلي للجزء الوعائي اللحمي من الأنسجة الدهنية البيضاء باستخدام مفكك الأنسجة

The in vitro study of white, brown, and beige adipocyte differentiation enables the investigation of cell-autonomous functions of adipocytes and their ...