我们感谢许多贡献者和用户的CT-FIRE和曲线对齐多年来，包括罗布诺瓦克博士， 卡罗琳·佩尔克博士、杰里米·布雷德费尔特博士、古内特·梅塔博士、安德鲁·莱希特博士、阿迪布·凯霍斯拉维博士、马特·康克林博士、杰恩·松鼠博士、保罗·普罗文扎诺博士、布伦达·奥格尔博士、帕特里夏·基利博士、约瑟夫·舒尔切夫斯基博士、苏珊娜·波尼克博士以及斯瓦蒂·阿南德和柯蒂斯·鲁登的其他技术贡献。这项工作得到了半导体研究公司、莫格里奇研究所的资助，国家卫生研究院向K.W.E.提供了R01CA19996、R01CA181385和U54CA210190。

作者没有什么可透露的。

此协议描述了使用 CT-FIRE 和曲线对齐进行纤维胶原蛋白量化，可应用于任何具有胶原纤维或其他线状或纤维状拉伸结构的图像，这些结构适合 CT-FIRE 或曲线对齐进行分析。例如，弹性蛋白或弹性纤维可以在此平台上以类似的方式进行处理。我们已经在计算产生的合成纤维21上测试了这两种工具。根据应用情况，用户应选择最适合其数据的分析模式。CT纤维分析模式可以直接使用CT?...

纤维胶原蛋白是突出的结构 ECM 成分。他们的组织变化影响组织功能，并可能与许多疾病的进展有关，从骨质疏松症1，心脏功能障碍2，伤口愈合3到不同类型的癌症，包括乳腺癌4，5，6，卵巢7，8，肾9，胰腺癌10。许多已建立的成像模式可用于可视化纤维胶原蛋白，如第二谐波一代显微镜11，污渍或染料与明亮的场或荧光显微镜或偏振光显微镜12，液晶基极化显微镜（LC-PolScope）13，电子显微镜14。随着纤维胶原蛋白组织的重要性越来越明显，而且这些方法的使用也越来越多，改进胶原纤维分析方法的需求也越来越大。
有许多努力来开发自动测量纤维状胶原蛋白的计算方法。免费提供的软件工具主要侧重于光纤对齐或方向的计算，采用第一个衍生或结构张力像素15，16，或傅立业基于转换的频谱分析图像磁贴17。所有这些工具都受到限制，例如手动步骤的要求、在嘈杂的背景中检测光纤边缘的不准确性或缺乏本地化特征特征。
与其他免费提供的开源免费软件工具相比，本协议中描述的方法使用CT——一种最佳、多尺度、定向的图像表示方法——去除纤维胶原蛋白图像中的噪声，增强或跟踪光纤边缘。有关位置和方向的信息可以直接从光纤提供，而不是使用间接像素或窗口信息来推断光纤组织的指标。这种基于CT的框架18、19、20、21可以在全球、ROI或光纤的基础上量化光纤组织，主要通过两个单独但相互关联的包，分别命名为"CT-FIRE"18、21和"曲线对齐"19、21。就软件的实现而言，在 CT-FIRE 中，多比例的 CT 系数可用于重建增强边缘和降低噪音的图像。然后，将单个光纤提取算法应用于 CT 重建图像中，以跟踪光纤以查找其代表性的中心点，将光纤分支从中心点延伸，并将光纤分支连接起来，形成光纤网络。在 Curve 对齐中，用户指定比例的 CT 系数可用于跟踪本地光纤方向，其中提取曲线小径的方向和位置并进行分组，以估计相应位置的光纤方向。由此产生的量化框架已经开发了十多年，在功能、用户界面和模块化等许多方面都取得了长足的发展。例如，此工具可以可视化局部光纤方向，并允许用户测量多达 30 个光纤功能，包括长度、角度、宽度和直度等单个光纤特性，以及密度和对齐等批量测量。此外，用户可以测量光纤角度相对于手动或自动分割的边界，例如，在基于图像的生物标志物发展在乳腺癌22和胰腺癌研究10发挥重要作用。此平台提供多个功能模块，包括用于投资回报率分析、自动边界创建和后处理的功能模块。投资回报率模块可用于注释不同形状的投资回报率，并进行相应的投资回报率分析。作为应用示例，自动边界创建模块可用于用第二谐波生成 （SHG） 图像注册血氧林和 eosin （H&E） 亮场图像，并从注册的 H&E 图像中生成肿瘤边界的图像掩膜。后处理模块可以帮助处理和集成来自单个图像的输出数据文件，以便进行可能的统计分析。
此量化平台不需要事先的编程或图像处理经验，可以处理包括数百或数千张图像在内的大型数据集，从而能够高效量化用于生物或生物医学应用的胶原蛋白组织。它已被包括我们在内的世界各地许多研究人员广泛应用于不同的研究领域。有四个主要出版物CT-FIRE和曲线对齐18，19，20，21，其中前三个已被引用272次（根据谷歌学者2020-05-04年）。对引用该平台（CT-FIRE 或曲线对齐）的出版物的审查表明，大约有 110 篇期刊论文直接用于分析，其中大约 35 篇出版物与我们的小组合作，其他出版物（约 75 篇）由其他组撰写。例如， 该平台用于以下研究:乳腺癌22，23，24，胰腺癌10，25，肾癌9，26，伤口愈合3，27，28，29，30，卵巢癌8，31，7，子宫韧带32，缺氧登丁3 3、基底细胞癌34例、缺氧肉瘤35例、软骨组织36例、心脏功能障碍37例、神经元38例、胶质母细胞瘤39例、淋巴收缩40例、纤维化41例、胃癌42例、微管癌43例、膀胱纤维化44例。图 1演示了 Curve 对齐的癌症成像应用，从 SHG 图像中查找乳腺癌19的肿瘤相关胶原蛋白特征。图 2描述了此平台的典型示意图工作流程。虽然这些工具已经审查技术18，19，21，和常规协议20对齐分析曲线对齐也可用，一个视觉协议，显示所有的基本功能可能是有用的。如本文所示，可视化协议将促进使用此平台的学习过程，并更有效地解决用户可能提出的问题和问题。

<table>
	<tbody>
		<tr>
			<td>CT-FIRE</td>
			<td>Univerity of Wisconsin-Madison</td>
			<td>N/A</td>
			<td>open source software available from https://eliceirilab.org/software/ctfire/</td>
		</tr>
		<tr>
			<td>CurveAlign</td>
			<td>University of Wisconsin-Madison</td>
			<td>N/A</td>
			<td>open source software available from https://eliceirilab.org/software/curvealign/</td>
		</tr>
	</tbody>
</table>

quantifying fibrillar collagen organization with curvelet transform-based tools

纤维状胶原蛋白是突出的细胞外基质 （ECM） 成分，其拓扑变化已证明与乳腺癌、卵巢癌、肾脏癌和胰腺癌等多种疾病的进展有关。免费提供的光纤量化软件工具主要侧重于光纤对齐或方向的计算，它们受到手动步骤要求、嘈杂背景中光纤边缘检测不准确或缺乏本地化特征特征等限制。本文中描述的胶原纤维定量工具的特点是使用曲线变换 （CT） 启用的最佳多尺度图像表示。这种算法方法允许去除纤维胶原蛋白图像中的噪声，并增强光纤边缘，直接从光纤中提供位置和方向信息，而不是使用从其他工具获得的间接像素或窗口信息。此基于 CT 的框架包含两个单独但链接的包，名为"CT-FIRE"和"曲线对齐"，可在全球、感兴趣区域 （ROI） 或单个光纤基础上量化光纤组织。这个量化框架已经开发了十多年，现在已经发展成为一个全面和用户驱动的胶原蛋白量化平台。使用此平台，可以测量多达 30 种光纤功能，包括长度、角度、宽度和直度等单个纤维特性，以及密度和对齐度等批量测量。此外，用户可以测量光纤角度相对于手动或自动分割的边界。该平台还提供了多个附加模块，包括用于投资回报率分析、自动边界创建和后处理的模块。使用此平台不需要事先的编程或图像处理经验，它可以处理包括数百或数千张图像在内的大型数据集，从而能够高效量化用于生物或生物医学应用的胶原纤维组织。

这些方法已成功地应用于许多研究。一些典型应用包括:1） Conklin 等人22 使用曲线对齐来计算肿瘤相关的胶原蛋白特征，并发现胶原纤维更频繁地垂直于原位导管癌 （DCIS） 病变中的导管周长:2） Drifka等人使用曲线 对齐中的CT-FIRE模式来量化胰腺导管腺癌和正常/慢性胰腺炎组织的频闪胶原对齐，发现与正常/慢性组织相比，癌组织中的对齐度有所提高:3） Alkmin<sup...

Watch this Scientific Journal Video about Quantifying Fibrillar Collagen Organization with Curvelet Transform-Based Tools at JoVE.com

Quantifying Fibrillar Collagen Organization with Curvelet Transform-Based Tools

在这里，我们提出了一个协议，使用基于曲线转换的开源 MATLAB 软件工具，用于量化正常组织和患病组织的细胞外基质中的纤维状胶原蛋白组织。此工具可应用于胶原纤维或其他类型的线状结构的图像。

使用基于曲线的转换工具量化纤维胶原蛋白组织

Fibrillar collagens are prominent extracellular matrix (ECM) components, and their topology changes have been shown to be associated with the progression ...

quantifying-fibrillar-collagen-organization-with-curvelet-transform

Research

JoVE Journal

Bioengineering

5.9K 次观看.  University of Wisconsin-Madison. 在这里，我们提出了一个协议，使用基于曲线转换的开源 MATLAB 软件工具，用于量化正常组织和患病组织的细胞外基质中的纤维状胶原蛋白组织。此工具可应用于胶原纤维或其他类型的线状结构的图像。

视频: Quantifying Fibrillar Collagen Organization with Curvelet Transform-Based Tools

Preparation of Complaint Matrices for Quantifying Cellular Contraction

The regulation of cellular adhesion to the extracellular matrix (ECM) is essential for cell migration and ECM remodeling. Focal adhesions are macromolecular assemblies that couple the contractile F-actin cytoskeleton to the ECM. This connection allows for the transmission of intracellular mechanical forces across the cell membrane to the underlying substrate. Recent work has shown the mechanical properties of the ECM regulate focal adhesion and F-actin morphology as well as numerous physiological processes, including cell differentiation, division, proliferation and migration. Thus, the use of cell culture substrates has become an increasingly prevalent method to precisely control and modulate ECM mechanical properties.
To quantify traction forces at focal adhesions in an adherent cell, compliant substrates are used in conjunction with high-resolution imaging and computational techniques in a method termed traction force microscopy (TFM). This technique relies on measurements of the local magnitude and direction of substrate deformations induced by cellular contraction. In combination with high-resolution fluorescence microscopy of fluorescently tagged proteins, it is possible to correlate cytoskeletal organization and remodeling with traction forces.
Here we present a detailed experimental protocol for the preparation of two-dimensional, compliant matrices for the purpose of creating a cell culture substrate with a well-characterized, tunable mechanical stiffness, which is suitable for measuring cellular contraction. These protocols include the fabrication of polyacrylamide hydrogels, coating of ECM proteins on such gels, plating cells on gels, and high-resolution confocal microscopy using a perfusion chamber. Additionally, we provide a representative sample of data demonstrating location and magnitude of cellular forces using cited TFM protocols.

In this video, we demonstrate the experimental techniques used to fabricate compliant, extracellular matrix (ECM) coated substrates suitable for cell culture, and which are amenable to traction force microscopy and observing effects of ECM stiffness on cell behavior.

投诉矩阵量化细胞收缩的准备工作

The regulation of cellular adhesion to the extracellular matrix (ECM) is essential for cell migration and ECM remodeling.  Focal adhesions are ...

科研

生物工程

Quantifying the Mechanical Properties of the Endothelial Glycocalyx with Atomic Force Microscopy

Our understanding of the interaction of leukocytes and the vessel wall during leukocyte capture is limited by an incomplete understanding of the mechanical properties of the endothelial surface layer. It is known that adhesion molecules on leukocytes are distributed non-uniformly relative to surface topography 3, that topography limits adhesive bond formation with other surfaces 9, and that physiological contact forces (&asymp; 5.0 &minus; 10.0 pN per microvillus) can compress the microvilli to as little as a third of their resting length, increasing the accessibility of molecules to the opposing surface 3, 7. We consider the endothelium as a two-layered structure, the relatively rigid cell body, plus the glycocalyx, a soft protective sugar coating on the luminal surface 6. It has been shown that the glycocalyx can act as a barrier to reduce adhesion of leukocytes to the endothelial surface 4. In this report we begin to address the deformability of endothelial surfaces to understand how the endothelial mechanical stiffness might affect bond formation. Endothelial cells grown in static culture do not express a robust glycocalyx, but cells grown under physiological flow conditions begin to approximate the glycocalyx observed in vivo 2. The modulus of the endothelial cell body has been measured using atomic force microscopy (AFM) to be approximately 5 to 20 kPa 5. The thickness and structure of the glycocalyx have been studied using electron microscopy 8, and the modulus of the glycocalyx has been approximated using indirect methods, but to our knowledge, there have been no published reports of a direct measurement of the glycocalyx modulus in living cells. In this study, we present indentation experiments made with a novel AFM probe on cells that have been cultured in conditions to maximize their glycocalyx expression to make direct measurements of the modulus and thickness of the endothelial glycocalyx.

The mechanical characteristics of endothelial glycocalyx were measured by indentation using micron sized spheres on AFM cantilevers. Endothelial cells were cultured in a custom chamber under physiological flow conditions to induce glycocalyx expression. Data were analyzed using a thin film model to determine the glycocalyx thickness and modulus.

量化的内皮细胞糖复合物的力学性能，用原子力显微镜

Our  understanding of the interaction of leukocytes and the vessel wall during  leukocyte capture is limited by an incomplete understanding of the ...

Observing and Quantifying Fibroblast-mediated Fibrin Gel Compaction

Cells embedded in collagen and fibrin gels attach and exert traction forces on the fibers of the gel. These forces can lead to local and global reorganization and realignment of the gel microstructure. This process proceeds in a complex manner that is dependent in part on the interplay between the location of the cells, the geometry of the gel, and the mechanical constraints on the gel. To better understand how these variables produce global fiber alignment patterns, we use time-lapse differential interference contrast (DIC) microscopy coupled with an environmentally controlled bioreactor to observe the compaction process between geometrically spaced explants (clusters of fibroblasts). The images are then analyzed with a custom image processing algorithm to obtain maps of the strain. The information obtained from this technique can be used to probe the mechanobiology of various cell-matrix interactions, which has important implications for understanding processes in wound healing, disease development, and tissue engineering applications.

Time-lapse microscopy and image processing techniques were used to observe and analyze fibroblast-mediated gel compaction and fibrin fiber realignment in an environmentally controlled bioreactor over a 48 hr&#160;period.

观察和量化纤维细胞介导的纤维素凝胶压实

Cells embedded in collagen and fibrin gels attach and exert traction forces on the fibers of the gel. These forces can lead to local and global ...

Imaging Denatured Collagen Strands In vivo and Ex vivo via Photo-triggered Hybridization of Caged Collagen Mimetic Peptides

Collagen is a major structural component of the extracellular matrix that supports tissue formation and maintenance. Although collagen remodeling is an integral part of normal tissue renewal, excessive amount of remodeling activity is involved in tumors, arthritis, and many other pathological conditions. During collagen remodeling, the triple helical structure of collagen molecules is disrupted by proteases in the extracellular environment. In addition, collagens present in many histological tissue samples are partially denatured by the fixation and preservation processes. Therefore, these denatured collagen strands can serve as effective targets for biological imaging. We previously developed a caged collagen mimetic peptide (CMP) that can be photo-triggered to hybridize with denatured collagen strands by forming triple helical structure, which is unique to collagens. The overall goals of this procedure are i)&#160;to image denatured collagen strands resulting from normal remodeling activities in vivo, and ii) to visualize collagens in ex vivo tissue sections using the photo-triggered caged CMPs. To achieve effective hybridization and successful in vivo and ex vivo imaging, fluorescently labeled caged CMPs are either photo-activated immediately before intravenous injection, or are directly activated on tissue sections. Normal skeletal collagen remolding in nude mice and collagens in prefixed mouse cornea tissue sections are imaged in this procedure. The imaging method based on the CMP-collagen hybridization technology presented here could lead to deeper understanding of the tissue remodeling process, as well as allow development of new diagnostics for diseases associated with high collagen remodeling activity.

Imaging Denatured Collagen Strands In vivo and Ex vivo via Photo-triggered Hybridization of Caged Collagen Mimetic Peptides

This procedure demonstrates in vivo near IR fluorescence imaging of collagen remodeling activities in mice as well as ex vivo staining of collagens in tissue sections using caged collagen mimetic peptides that can be photo-triggered to hybridize with denatured collagen strands.

成像变性的胶原股<em&gt;在体内</em&gt;和<em&gt;体外</em&gt;通过光引发杂交笼胶原蛋白仿生肽

Collagen is a major structural component of the extracellular matrix that supports tissue formation and maintenance. Although collagen remodeling is an ...

Helical Organization of Blood Coagulation Factor VIII on Lipid Nanotubes

Cryo-electron microscopy (Cryo-EM)1 is a powerful approach to investigate the functional structure of proteins and complexes in a hydrated state and membrane environment2.
Coagulation Factor VIII (FVIII)3 is a multi-domain blood plasma glycoprotein. Defect or deficiency of FVIII is the cause for Hemophilia type A&#160;-&#160;a severe bleeding disorder. Upon proteolytic activation, FVIII binds to the serine protease Factor IXa on the negatively charged platelet membrane, which is critical for normal blood clotting4. Despite the pivotal role FVIII plays in coagulation, structural information for its membrane-bound state is incomplete5. Recombinant FVIII concentrate is the most effective drug against Hemophilia type A and commercially available FVIII can be expressed as human or porcine, both forming functional complexes with human Factor IXa6,7.
In this study we present a combination of Cryo-electron microscopy (Cryo-EM), lipid nanotechnology and structure analysis applied to resolve the membrane-bound structure of two highly homologous FVIII forms: human and porcine. The methodology developed in our laboratory to helically organize the two functional recombinant FVIII forms on negatively charged lipid nanotubes (LNT) is described.&#160;The representative results demonstrate that our approach is sufficiently sensitive to define the differences in the helical organization between the two highly homologous in sequence (86% sequence identity) proteins. Detailed protocols for the helical organization, Cryo-EM and electron tomography (ET) data acquisition are given. The two-dimensional (2D) and three-dimensional (3D) structure analysis applied to obtain the 3D reconstructions of human and porcine FVIII-LNT is discussed. The presented human and porcine FVIII-LNT structures show the potential of the proposed methodology to calculate the functional, membrane-bound organization of blood coagulation Factor VIII at high resolution.

We present a combination of Cryo-electron microscopy, lipid nanotechnology, and structure analysis applied to resolve the membrane-bound structure of two highly homologous FVIII forms: human and porcine. The methodology developed in our laboratory&#160;to helically organize the two functional recombinant FVIII forms on negatively charged lipid nanotubes (LNT) is described.

凝血因子VIII的脂质纳米管螺旋组织

Cryo-electron microscopy (Cryo-EM)1 is a powerful approach to investigate the functional structure of proteins and complexes in a hydrated state and ...

Electrospun Nanofiber Scaffolds with Gradations in Fiber Organization

The goal of this protocol is to report a simple method for generating nanofiber scaffolds with gradations in fiber organization and test their possible applications in controlling cell morphology/orientation. Nanofiber organization is controlled with a new fabrication apparatus that enables the gradual decrease of fiber organization in a scaffold. Changing the alignment of fibers is achieved through decreasing deposition time of random electrospun fibers on a uniaxially aligned fiber mat. By covering the collector with a moving barrier/mask, along the same axis as fiber deposition, the organizational structure is easily controlled. For tissue engineering purposes, adipose-derived stem cells can be seeded to these scaffolds. Stem cells undergo morphological changes as a result of their position on the varied organizational structure, and can potentially differentiate into different cell types depending on their locations. Additionally, the graded organization of fibers enhances the biomimicry of nanofiber scaffolds so they more closely resemble the natural orientations of collagen nanofibers at tendon-to-bone insertion site compared to traditional scaffolds. Through nanoencapsulation, the gradated fibers also afford the possibility to construct chemical gradients in fiber scaffolds, and thereby further strengthen their potential applications in fast screening of cell-materials interaction and interfacial tissue regeneration. This technique enables the production of continuous gradient scaffolds, but it also can potentially produce fibers in discrete steps by controlling the movement of the moving barrier/mask in a discrete fashion.

Here, we present a protocol to fabricate electrospun nanofiber scaffolds with gradated organization of fibers and explore their applications in regulating cell morphology/orientation. Gradients with regard to physical and chemical properties of the nanofiber scaffolds offer a wide variety of applications in the biomedical field.

静电纳米纤维支架与渐变的纤维组织

The goal of this protocol is to report a simple method for generating nanofiber scaffolds with gradations in fiber organization and test their possible ...

Engineering 3D Cellularized Collagen Gels for Vascular Tissue Regeneration

Synthetic materials are known to initiate clinical complications such as inflammation, stenosis, and infections when implanted as vascular substitutes. Collagen has been extensively used for a wide range of biomedical applications and is considered a valid alternative to synthetic materials due to its inherent biocompatibility (i.e., low antigenicity, inflammation, and cytotoxic responses). However, the limited mechanical properties and the related low hand-ability of collagen gels have hampered their use as scaffold materials for vascular tissue engineering. Therefore, the rationale behind this work was first to engineer cellularized collagen gels into a tubular-shaped geometry and second to enhance smooth muscle cells driven reorganization of collagen matrix to obtain tissues stiff enough to be handled.
The strategy described here is based on the direct assembling of collagen and smooth muscle cells (construct) in a 3D cylindrical geometry with the use of a molding technique. This process requires a maturation period, during which the constructs are cultured in a bioreactor under static conditions (without applied external dynamic mechanical constraints) for 1 or 2 weeks. The &#8220;static bioreactor&#8221; provides a monitored and controlled sterile environment (pH, temperature, gas exchange, nutrient supply and waste removal) to the constructs. During culture period, thickness measurements were performed to evaluate the cells-driven remodeling of the collagen matrix, and glucose consumption and lactate production rates were measured to monitor the cells metabolic activity. Finally, mechanical and viscoelastic properties were assessed for the resulting tubular constructs. To this end, specific protocols and a focused know-how (manipulation, gripping, working in hydrated environment, and so on) were developed to characterize the engineered tissues.

In this work, we present a technique for the rapid fabrication of living vascular tissues by direct culturing of collagen, smooth muscle cells and endothelial cells. In addition, a new protocol for the mechanical characterization of engineered vascular tissues is described.

工程三维细胞化胶原凝胶的血管组织再生

Synthetic materials are known to initiate clinical complications such as inflammation, stenosis, and infections when implanted as vascular substitutes. ...

A Novel Tenorrhaphy Suture Technique with Tissue Engineered Collagen Graft to Repair Large Tendon Defects

Surgical management of large tendon defects with tendon grafts is challenging, as there are a finite number of sites where donors can be readily identified and used. Currently, this gap is filled with tendon auto-, allo-, xeno-, or artificial grafts, but clinical methods to secure them are not necessarily translatable to animals because of the scale. In order to evaluate new biomaterials or study a tendon graft made up of collagen type 1, we have developed a modified suture technique to help maintain the engineered tendon in alignment with the tendon ends. Mechanical properties of these grafts are inferior to the native tendon. To incorporate engineered tendon into clinically relevant models of loaded repair, a strategy was adopted to offload the tissue engineered tendon graft and allow for the maturation and integration of the engineered tendon in vivo until a mechanically sound neo-tendon was formed. We describe this technique using incorporation of the collagen type 1 tissue engineered tendon construct.

In this paper, we present an in vitro and in situ protocol to repair a tendon gap of up to 1.5 cm by filling it with engineered collagen graft. This was performed by developing a modified suture technique to take the mechanical load until the graft matures into the host tissue.

一种新型的腱绦缝合技术，采用组织工程胶原蛋白移植物修复大肌腱缺损

Surgical management of large tendon defects with tendon grafts is challenging, as there are a finite number of sites where donors can be readily ...

Quantifying Intermembrane Distances with Serial Image Dilations

A recently-described extracellular nanodomain, termed the perinexus, has been implicated in ephaptic coupling, which is an alternative mechanism for electrical conduction between cardiomyocytes. The current method for quantifying this space by manual segmentation is slow and has low spatial resolution.We developed an algorithm that uses serial image dilations of a binary outline to count the number of pixels between two opposing 2 dimensional edges.This algorithm requires fewer man hours and has a higher spatial resolution than the manual method while preserving the reproducibility of the manual process.In fact, experienced and novice investigators were able to recapitulate the results of a previous study with this new algorithm.The algorithm is limited by the human input needed to manually outline the perinexus and computational power mainly encumbered by a pre-existing pathfinding algorithm.However, the algorithm&#39;s high-throughput capabilities, high spatial resolution and reproducibility make it a versatile and robust measurement tool for use across a variety of applications requiring the measurement of the distance between any 2-dimensional (2D) edges.

The purpose of this algorithm is to continuously measure the distance between two 2-dimensional edges using serial image dilations and pathfinding. This algorithm can be applied to a variety of fields such as cardiac structural biology, vascular biology, and civil engineering.

用序列图像量化膜间隙距离伸缩

A recently-described extracellular nanodomain, termed the perinexus, has been implicated in ephaptic coupling, which is an alternative mechanism for ...

Biomimetic Replication of Root Surface Microstructure using Alteration of Soft Lithography

Biomimetics is the use of chemistry and material sciences to mimic biological systems, specifically biological structures, to better humankind. Recently, biomimetic surfaces mimicking the microstructure of leaf surface, were used to study the effects of leaf microstructure on leaf-environment interactions. However, no such tool exists for roots. We developed a tool allowing the synthetic mimicry of the root surface microstructure into an artificial surface. We relied on the soft lithography method, known for leaf surface microstructure replication, using a two-step process. The first step is the more challenging one as it involves the biological tissue. Here, we used a different polymer and curing strategy, relying on the strong, rigid, polyurethane, cured by UV for the root molding. This allowed us to achieve a reliable negative image of the root surface microstructure including the delicate, challenging features such as root hairs. We then used this negative image as a template to achieve the root surface microstructure replication using both the well-established polydimethyl siloxane (PDMS) as well as a cellulose derivative, ethyl cellulose, which represents a closer mimic of the root and which can also be degraded by cellulase enzymes secreted by microorganisms. This newly formed platform can be used to study the microstructural effects of the surface in root-microorganism interactions in a similar manner to what has previously been shown in leaves. Additionally, the system enables us to track the microorganism&#8217;s locations, relative to surface features, and in the future its activity, in the form of cellulase secretion.

Biomimetics has been previously used as a tool to study leaf-microorganism interactions. However, no such tool exists for roots. Here, we develop a protocol to form synthetic surfaces mimicking root surface microstructure for the study of root-environment interactions.

利用软光刻改变根面微结构的仿生复制

Biomimetics is the use of chemistry and material sciences to mimic biological systems, specifically biological structures, to better humankind. Recently, ...