ai_agent

<meta charset="utf8"></head><body>树木生态学研究中田间到实验室树木年轮数字化的协议

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</ol>

<table><tbody><tr><td>Core-microtome</td><td>WSL</td><td>https://www.wsl.ch/en/services-produkte/microtomes/</td><td>Microtome to cut micro sections from increment cores</td></tr><tr><td>Epson Expression 10000XL&amp;nbsp;</td><td>EPSON</td><td>https://epson.com/Support/Scanners/Expression-Series/Epson-Expression-10000XL---Graphic-Arts/s/SPT_E10000XL-GA</td><td>flatbed scanner</td></tr><tr><td>GSC holder</td><td>WSL</td><td>in-house</td><td>3D printed mount to fix cores for transport, preparation, analyses, and storage</td></tr><tr><td>Skippy image capturing system</td><td>WSL</td><td>https://www.wsl.ch/en/services-produkte/skippy/)&amp;nbsp;</td><td>Image capturing system developed at WSL equiped with a 61 MP camera (Sony Alpha 7R IV and Sony FE 90mm f/2.8 Macro lens)</td></tr></tbody></table>

a new workflow for sampling and digitizing increment cores

<meta charset="utf8"></head><body>作者聚焦:用于推进树木生态学和木材解剖学研究的创新设备开发

用于对增量岩芯进行采样和数字化的新工作流程 

Here we present a new workflow from taking increment cores in the field, storing and transporting them to the lab, to digitizing their tree rings for ...

a-new-workflow-for-sampling-and-digitizing-increment-cores

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Research

A New Workflow for Sampling and Digitizing Increment Cores

JoVE Journal

Environment

3.0K 次观看.  Swiss Federal Research Institute WSL. 通过开发新设备，我们打算突破树木年轮研究的界限。3D 建模软件和 3D 打印机的应用允许快速、廉价地开发新设备。其中之一是图像捕获系统 Skippy，它允许以高分辨率和短时间对增量航向的表面进行数字化。通常，在树木生态学、树木地貌学或树木气候学中取样时，我们会在偏远地区（如极高纬度地区）对树木进行取样，这些地区的条件、气?...

视频: 作者聚焦:用于推进树木生态学和木材解剖学研究的创新设备开发

A Technical Perspective in Modern Tree-ring Research - How to Overcome Dendroecological and Wood Anatomical Challenges

Dendroecological research uses information stored in tree rings to understand how single trees and even entire forest ecosystems responded to environmental changes and to finally reconstruct such changes. This is done by analyzing growth variations back in time and correlating various plant-specific parameters to (for example) temperature records. Integrating wood anatomical parameters in these analyses would strengthen reconstructions, even down to intra-annual resolution. We therefore present a protocol on how to sample, prepare, and analyze wooden specimen for common macroscopic analyses, but also for subsequent microscopic analyses. Furthermore we introduce a potential solution for analyzing digital images generated from common small and large specimens to support time-series analyses. The protocol presents the basic steps as they currently can be used. Beyond this, there is an ongoing need for the improvement of existing techniques, and development of new techniques, to record and quantify past and ongoing environmental processes. Traditional wood anatomical research needs to be expanded to include ecological information to this field of research. This would support dendro-scientists who intend to analyze new parameters and develop new methodologies to understand the short and long term effects of specific environmental factors on the anatomy of woody plants.

现代树木年轮研究的技术视角 - 如何克服树木生态学和木材解剖学挑战

Here we present a protocol outlining how to sample wooden specimens for the overall assessment of their growth structures. Macro- and microscopic preparation and visualization techniques necessary to generate well-replicated and highly resolved wood anatomical and dendroecological dataset, are described are described.

现代树轮研究技术的角度 - 如何克服Dendroecological和木解剖挑战

Dendroecological research uses information stored in tree rings to understand how single trees and even entire forest ecosystems responded to ...

科研

环境科学

Soil Lysimeter Excavation for Coupled Hydrological, Geochemical, and Microbiological Investigations

Studying co-evolution of hydrological and biogeochemical processes in the subsurface of natural landscapes can enhance the understanding of coupled Earth-system processes. Such knowledge is imperative in improving predictions of hydro-biogeochemical cycles, especially under climate change scenarios. We present an experimental method, designed to capture sub-surface heterogeneity of an initially homogeneous soil system. This method is based on destructive sampling of a soil lysimeter designed to simulate a small-scale hillslope. A weighing lysimeter of one cubic meter capacity was divided into sections (voxels) and was excavated layer-by-layer, with sub samples being collected from each voxel. The excavation procedure was aimed at detecting the incipient heterogeneity of the system by focusing on the spatial assessment of hydrological, geochemical, and microbiological properties of the soil. Representative results of a few physicochemical variables tested show the development of heterogeneity. Additional work to test interactions between hydrological, geochemical, and microbiological signatures is planned to interpret the observed patterns. Our study also demonstrates the possibility of carrying out similar excavations in order to observe and quantify different aspects of soil-development under varying environmental conditions and scale.

用于水文、地球化学和微生物耦合调查的土壤溶度计挖掘

This study presents an excavation method for investigating subsurface hydrological, geochemical, and microbiological heterogeneity of a soil lysimeter. The lysimeter simulates an artificial hillslope which was initially under homogeneous condition and had been subjected to approximately 5,000 mm of water over eight cycles of irrigation in an 18-month period.

土壤蒸渗仪开挖加之水文，地球化学和微生物调查

Studying co-evolution of hydrological and biogeochemical processes in the subsurface of natural landscapes can enhance the understanding of coupled ...

A Sectioning, Coring, and Image Processing Guide for High-Throughput Cortical Bone Sample Procurement and Analysis for Synchrotron Micro-CT

Bone is a dynamic and mechanically active tissue that changes in structure over the human lifespan. The products of the bone remodeling process have been studied substantially using traditional two-dimensional techniques. Recent advancements in X-ray imaging technology via desktop micro-computed tomography (&#181;CT) and synchrotron radiation micro-computed tomography (SR&#181;CT) have allowed for the acquisition of high-resolution three-dimensional (3D) scans of a larger field of view (FOV) than other 3D imaging techniques (e.g., SEM) providing a more complete picture of microscopic structures within human cortical bone. The specimen should be accurately centered within the FOV, however, to limit the appearance of streak artifacts known to impact data analysis. Previous studies have reported procurement of irregularly shaped rectilinear bone blocks that result in imaging artifacts due to uneven edges or image truncation. We have applied a geological sampling protocol (coring) to procure consistently sized cortical bone core specimens for SR&#181;CT experiments from the anterior aspect of human femora. This coring method is efficient and minimally destructive to tissue. It creates uniform cylindrical samples that decrease imaging artifacts by nature of being isometric during rotation and providing a uniform path length for X-ray beams throughout scanning. Image processing of X-ray tomographic data of cored and irregularly shaped samples confirms the potential of the technique to improve visualization and analysis of cortical bone microarchitecture. A goal of this protocol is to deliver a reliable and repeatable method for the extraction of cortical bone cores that is adaptable for various types of high-resolution bone imaging experiments. An overarching goal of the work is to create a standardized cortical bone procurement for SR&#181;CT that is affordable, consistent, and straightforward. This procedure may further be adapted by researchers in related fields who commonly evaluate hard composite materials such as in biological anthropology, geosciences, or material sciences.

用于同步辐射显微 CT 的高通量皮质骨样本获取和分析的切片、取芯和图像处理指南

We employed a geological (coring) sampling protocol to procure cortical bone specimens of uniform size for SR&#181;CT experiments from the anterior aspect of human femora. This method is minimally destructive, efficient, results in cylindrical specimens that minimize imaging artifacts from irregular sample shapes and improves microarchitectural visualization and analysis.

同步加速器微CT高通量皮质骨样品采购和分析的剖面、科林和图像处理指南

Bone is a dynamic and mechanically active tissue that changes in structure over the human lifespan. The products of the bone remodeling process have been ...

生物学

Advanced Workflow for Taking High-Quality Increment Cores - New Techniques and Devices

In dendroecological research, precise dating of each single growth ring is a basic requirement for all studies, focusing on ring-width variations only, chemical or isotope analyses, or wood anatomical studies. Independent of the sampling strategy for a certain study (e.g., climatology, geomorphology), the way samples are taken is crucial for their successful preparation and analyses.
Until recently, it was sufficient to use a (more or less) sharp increment corer to obtain core samples that could be sanded for further analyses. Since wood anatomical characteristics can be applied to long time series, the need to obtain high-quality increment cores has taken on a new meaning. Essentially, the corer needs to be sharp(ened) when used. When coring a tree by hand, there are some problems in handling the corer, resulting in the hidden occurrence of micro cracks along the entire core: When starting to drill by hand, the drill bit is strongly pressed against the bark and the outermost ring until the thread has fully entered the trunk. At the same time, the drill bit is moved up and down as well as sideward. Then, the corer is drilled all the way into the trunk; however, it is necessary to stop after each turn, change the grip, and turn again. All these movements, as well as the start/stop-coring, puts mechanical stress on the core. The resulting micro cracks make it impossible to create continuous micro sections, as they fall apart along all these cracks.
We present a protocol to overcome these obstacles by applying a new technique using a cordless drill to minimize these problems when coring a tree, as well as its effect on the preparation of long micro sections. This protocol includes the preparation of long micro sections, as well as a procedure to sharpen corers in the field.

用于获取高质量增量内核的高级工作流程 - 新技术和设备

Here, we present a protocol on how to avoid micro cracks in increment cores by applying a cordless drill with a torque multiplier to minimize problems when coring trees, as well as its effect on preparing long micro sections. This protocol also includes a procedure to sharpen corers in the field.

采用高质量增量核心的高级工作流程 - 新技术和设备

In dendroecological research, precise dating of each single growth ring is a basic requirement for all studies, focusing on ring-width variations only, ...

高通量树木年轮分析和密度估计

Tree Core Analysis with X-ray Computed Tomography

An X-ray computed tomography (CT) toolchain is presented to obtain tree-ring width (TRW), maximum latewood density (MXD), other density parameters, and quantitative wood anatomy (QWA) data without the need for labor-intensive surface treatment or any physical sample preparation. The focus here is on increment cores and scanning procedures at resolutions ranging from 60 &#181;m down to 4 &#181;m. Three scales are defined at which wood should be looked at: (i) inter-ring scale, (ii) ring scale, i.e., tree-ring analysis and densitometry scale, as well as (iii) anatomical scale, the latter approaching the conventional thin-section quality. Custom-designed sample holders for each of these scales enable high-throughput scanning of multiple increment cores. A series of software routines were specifically developed to efficiently treat three-dimensional X-ray CT images of the tree cores for TRW and densitometry. This work briefly explains the basic principles of CT, which are needed for a proper understanding of the protocol. The protocol is presented for some known species that are commonly used in dendrochronology. The combination of rough density estimates, TRW and MXD data, as well as quantitative anatomy data, allows us to broaden and deepen current analyses for climate reconstructions or tree response, as well as further develop the field of dendroecology/climatology and archeology.

作者聚焦:用于树芯分析的 X 射线 CT 工具链的进步

Here we show how to process tree cores with an X-ray computed tomography toolchain. Except for chemical extraction for some purposes, no further physical lab treatment is needed. The toolchain can be used for biomass estimations, for obtaining MXD/tree-ring width data as well as for obtaining quantitative wood anatomy data.

使用 X 射线计算机断层扫描进行树芯分析

An X-ray computed tomography (CT) toolchain is presented to obtain tree-ring width (TRW), maximum latewood density (MXD), other density parameters, and ...

Methods for Performing Crosses in Setaria viridis, a New Model System for the Grasses

Setaria viridis is an emerging model system for C4 grasses. It is closely related to the bioenergy feed stock switchgrass and the grain crop foxtail millet. Recently, the 510 Mb genome of foxtail millet, S. italica, has been sequenced 1,2 and a 25x coverage genome sequence of the weedy relative S. viridis is in progress. S. viridis has a number of characteristics that make it a potentially excellent model genetic system including a rapid generation time, small stature, simple growth requirements, prolific seed production 3 and developed systems for both transient and stable transformation 4. However, the genetics of S. viridis is largely unexplored, in part, due to the lack of detailed methods for performing crosses. To date, no standard protocol has been adopted that will permit rapid production of seeds from controlled crosses.
The protocol presented here is optimized for performing genetic crosses in S. viridis, accession A10.1. We have employed a simple heat treatment with warm water for emasculation after pruning the panicle to retain 20-30 florets and labeling of flowers to eliminate seeds resulting from newly developed flowers after emasculation. After testing a series of heat treatments at permissive temperatures and varying the duration of dipping, we have established an optimum temperature and time range of 48 &deg;C for 3-6 min. By using this method, a minimum of 15 crosses can be performed by a single worker per day and an average of 3-5 outcross progeny per panicle can be recovered. Therefore, an average of 45-75 outcross progeny can be produced by one person in a single day. Broad implementation of this technique will facilitate the development of recombinant inbred line populations of S. viridis X S. viridis or S. viridis X S. italica, mapping mutations through bulk segregant analysis and creating higher order mutants for genetic analysis.

在 Setaria viridis 中进行杂交的方法，一种新的草模型系统

We have developed a methodology for performing crosses in Setaria viridis (S. viridis). The method involves pruning the panicle prior to a hot water treatment to kill viable pollen. Crosses are performed following a well-controlled growth regime and typically result in the recovery of 1 to 7 cross-pollinated seed/s per panicle.

方法中进行杂交狗尾草，新模型体系的草

Setaria viridis is an emerging model system for C4 grasses. It is closely related to the bioenergy feed stock switchgrass and the grain crop foxtail ...

Soil Sampling and Isolation of Entomopathogenic Nematodes (Steinernematidae, Heterorhabditidae)

Entomopathogenic nematodes (a.k.a. EPN) represent a group of soil-inhabiting nematodes that parasitize a wide range of insects. These nematodes belong to two families: Steinernematidae and Heterorhabditidae. Until now, more than 70 species have been described in the Steinernematidae and there are about 20 species in the Heterorhabditidae. The nematodes have a mutualistic partnership with Enterobacteriaceae bacteria and together they act as a potent insecticidal complex that kills a wide range of insect species.
Herein, we focus on the most common techniques considered for collecting EPN from soil. The second part of this presentation focuses on the insect-baiting technique, a widely used approach for the isolation of EPN from soil samples, and the modified White trap technique which is used for the recovery of these nematodes from infected insects. These methods and techniques are key steps for the successful establishment of EPN cultures in the laboratory and also form the basis for other bioassays that consider these nematodes as model organisms for research in other biological disciplines. The techniques shown in this presentation correspond to those performed and/or designed by members of S. P. Stock laboratory as well as those described by various authors.

昆虫病原线虫 Steinernematidae、异线虫科 （Heterorhabditidae） 土壤取样与分离

Entomopathogenic nematodes are soil-inhabiting roundworms that parasitize a wide range of insects. We demonstrate sampling methods used for the isolation of these nematodes from the soil using two techniques: the insect baiting and the modified White trap, for the recovery of nematodes from soil samples and infected insect cadavers, respectively.

土壤采样及昆虫病原线虫的分离（Steine​​rnematidae，异小）

Entomopathogenic nematodes (a.k.a. EPN) represent a group of soil-inhabiting nematodes that parasitize a wide range of insects. These nematodes belong to ...

An Aquatic Microbial Metaproteomics Workflow: From Cells to Tryptic Peptides Suitable for Tandem Mass Spectrometry-based Analysis

Meta-omic technologies such as metagenomics, metatranscriptomics and metaproteomics can aid in the understanding of microbial community structure and metabolism. Although powerful, metagenomics alone can only elucidate functional potential. On the other hand, metaproteomics enables the description of the expressed in situ metabolism and function of a community. Here we describe a protocol for cell lysis, protein and DNA isolation, as well as peptide digestion and extraction from marine microbial cells collected on a cartridge filter unit (such as the Sterivex filter unit) and preserved in an RNA stabilization solution (like RNAlater). In mass spectrometry-based proteomics studies, the identification of peptides and proteins is performed by comparing peptide tandem mass spectra to a database of translated nucleotide sequences. Including the metagenome of a sample in the search database increases the number of peptides and proteins that can be identified from the mass spectra. Hence, in this protocol DNA is isolated from the same filter, which can be used subsequently for metagenomic analysis.

水生微生物宏蛋白质组学工作流程：从细胞到适用于基于串联质谱分析的胰蛋白酶肽

This protocol is for the extraction and concentration of protein and DNA from microbial biomass collected from seawater, followed by the generation of tryptic peptides suitable for tandem mass spectrometry-based proteomic analysis.

水生微生物Metaproteomics工作流程:从细胞对胰蛋白酶肽适合串联质谱为基础的分析

Meta-omic technologies such as metagenomics, metatranscriptomics and metaproteomics can aid in the understanding of microbial community structure and ...

Clean Sampling and Analysis of River and Estuarine Waters for Trace Metal Studies

Most of the trace metal concentrations in ambient waters obtained a few decades ago have been considered unreliable owing to the lack of contamination control. Developments of some techniques aiming to reduce trace metal contamination in the last couple of decades have resulted in concentrations reported now being orders of magnitude lower than those in the past. These low concentrations often necessitate preconcentration of water samples prior to instrumental analysis of samples. Since contamination can appear in all phases of trace metal analyses, including sample collection (and during preparation of sampling containers), storage and handling, pretreatments, and instrumental analysis, specific care needs to be taken in order to reduce contamination levels at all steps. The effort to develop and utilize "clean techniques" in trace metal studies allows scientists to investigate trace metal distributions and chemical and biological behavior in greater details. This advancement also provides the required accuracy and precision of trace metal data allowing for environmental conditions to be related to trace metal concentrations in aquatic environments.
This protocol that is presented here details needed materials for sample preparation, sample collection, sample pretreatment including preconcentration, and instrumental analysis. By reducing contamination throughout all phases mentioned above for trace metal analysis, much lower detection limits and thus accuracy can be achieved. The effectiveness of "clean techniques" is further demonstrated using low field blanks and good recoveries for standard reference material. The data quality that can be obtained thus enables the assessment of trace metal distributions and their relationships to environmental parameters.

对河流和河口水域进行清洁采样和分析，用于痕量金属研究

Special care using "clean techniques" is required to properly collect and process water samples for trace metal studies in aquatic environments. A protocol for sampling, processing, and analytical procedures with the aim of obtaining reliable environmental monitoring data and results with high sensitivity for detailed trace metal studies is presented.

清洁取样和痕量金属研究河和河口水域分析

Most of the trace metal concentrations in ambient waters obtained a few decades ago have been considered unreliable owing to the lack of contamination ...

Modification and Application of a Leaf Blower-vac for Field Sampling of Arthropods

Rice fields host a large diversity of arthropods, but investigating their population dynamics and interactions is challenging. Here we describe the modification and application of a leaf blower-vac for suction sampling of arthropod populations in rice. When used in combination with an enclosure, application of this sampling device provides absolute estimates of the populations of arthropods as numbers per standardized sampling area. The sampling efficiency depends critically on the sampling duration. In a mature rice crop, a two-minute sampling in an enclosure of 0.13 m2 yields more than 90% of the arthropod population. The device also allows sampling of arthropods dwelling on the water surface or the soil in rice paddies, but it is not suitable for sampling fast flying insects, such as predatory Odonata or larger hymenopterous parasitoids. The modified blower-vac is simple to construct, and cheaper and easier to handle than traditional suction sampling devices, such as D-vac. The low cost makes the modified blower-vac also accessible to researchers in developing countries.

鼓风机-真空吸尘器在节肢动物现场采样中的应用

Assessment of arthropod abundance in crops is critical for investigating population dynamics and species interactions. Here we describe the modification and application of a leaf blower-vac for suction sampling of arthropods in rice.

修改和叶鼓风机-VAC的节肢动物领域采样中的应用

Rice fields host a large diversity of arthropods, but investigating their population dynamics and interactions is challenging. Here we describe the ...

用于对增量岩芯进行采样和数字化的新工作流程

Transcript

Summary

Explore More Videos

现代树轮研究技术的角度 - 如何克服Dendroecological和木解剖挑战

土壤蒸渗仪开挖加之水文，地球化学和微生物调查

同步加速器微CT高通量皮质骨样品采购和分析的剖面、科林和图像处理指南

采用高质量增量核心的高级工作流程 - 新技术和设备

使用 X 射线计算机断层扫描进行树芯分析

方法中进行杂交狗尾草，新模型体系的草

土壤采样及昆虫病原线虫的分离（Steinernematidae，异小）

水生微生物Metaproteomics工作流程:从细胞对胰蛋白酶肽适合串联质谱为基础的分析

清洁取样和痕量金属研究河和河口水域分析

修改和叶鼓风机-VAC的节肢动物领域采样中的应用

用于对增量岩芯进行采样和数字化的新工作流程

Transcript

Summary

Explore More Videos

现代树轮研究技术的角度 - 如何克服Dendroecological和木解剖挑战

土壤蒸渗仪开挖加之水文，地球化学和微生物调查

同步加速器微CT高通量皮质骨样品采购和分析的剖面、科林和图像处理指南

采用高质量增量核心的高级工作流程 - 新技术和设备

使用 X 射线计算机断层扫描进行树芯分析

方法中进行杂交狗尾草，新模型体系的草

土壤采样及昆虫病原线虫的分离（Steine​​rnematidae，异小）

水生微生物Metaproteomics工作流程:从细胞对胰蛋白酶肽适合串联质谱为基础的分析

清洁取样和痕量金属研究河和河口水域分析

修改和叶鼓风机-VAC的节肢动物领域采样中的应用

土壤采样及昆虫病原线虫的分离（Steinernematidae，异小）